SNP MICROBIOLOGY The Commonsense Bug Workbook The Commonsense Bug Workbook A realistic & practical approach to the identification of difficult & medically important bacteria Source: The Commonsense Bug Workbook.doc Page: 1 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Table of Contents: Preface:............................................................................................................................................. 3 General: ............................................................................................................................................ 5 Identification Methods: ...................................................................................................................... 5 Characteristics: ............................................................................................................................... 10 Microscopic Appearance:................................................................................................................ 10 Culture Appearance: ....................................................................................................................... 11 Motility: ............................................................................................................................................ 11 Biochemical tests: ........................................................................................................................... 11 Growth Requirements of Value:...................................................................................................... 12 Safety Considerations:.................................................................................................................... 12 Identification of Listeria species ...................................................................................................... 13 Identification of Corynebacterium species and other non-sporing Gram positive rods .................. 16 Identification of the main clinically significant Corynebacterium species ....................................... 19 Identification of other Non-sporing Gram positive rods .................................................................. 21 Identification of Streptococcus species, Enterococcus species and similar organisms ................. 25 Identification of Staphylococcus species, Micrococcus species and Stomatococcus species....... 36 Identification of Non-sporing, Non-branching Anaerobes............................................................... 40 Identification of Anaerobic Cocci..................................................................................................... 49 Identification of Clostridium species ............................................................................................... 52 Identification of Anaerobic Gram positive non-sporing rods ........................................................... 56 Identification of Vibrio & related species ......................................................................................... 58 Identification of Campylobacter and related species ...................................................................... 63 Identification of Helicobacter species ............................................................................................. 66 Identification of Haemophilus species and the HACEK group of organisms.................................. 67 Identification of Pasteurella Species ............................................................................................... 72 Identification of Moraxella species and Morphologically similar species ........................................ 76 References...................................................................................................................................... 80 Source: The Commonsense Bug Workbook.doc Page: 2 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Preface: This workbook has been formulated from textbooks, journals and the testing of a large number of clinical isolates collected over many years. It is intended to be a guide only, a ‘hint’ book, and is best used in combination with relevant textbooks and bench method manuals. It is meant to be a useful tool for microbiology staff, which due to factors such as cost constraints, large workload, lack of expertise, lack of staff or geographical location, do not have the tools of a large reference to identify difficult organisms. The aim of this workbook is to provide a “commonsense” guide to the identification of unusual/difficult organisms encountered in the clinical microbiology laboratory. Identification of bacteria in the clinical microbiology laboratory is usually based on phenotypic characteristics. Experience with different specimen types, and knowledge of the bacteria involved in infections associated with these sites is valuable. “Brain Storming” amongst peers when encountered with a difficult organism is of great value, providing different ideas and solutions. Bacteria often vary in their reactions and morphology as stated in textbooks, even within a genus, e.g. with differing basic biochemical reactions such as oxidase. Until potentially dangerous organisms have been excluded, e.g. Brucella, all testing on unknown, unusual/difficult organisms should be performed in a biological safety cabinet (BSC). Questions that should be asked prior to identifying an organism in the clinical microbiology laboratory are: • Do I need to identify this organism? Ø Ø Is it clinically relevant or significant? Is it the cause of the disease? If the answer to these questions is ‘yes’ (ascertained by clinical aspects), then the next question is: • How far (to what level) do I identify an organism? Ø Clinical significance • clinical data • specimen site/type • isolation from multiple sites or specimens • culture purity and amount of growth • leucocyte response • presence or absence of normal regional flora. Ø Costs versus Clinical Relevance Ø Expertise and staffing levels Ø Available testing facilities (i.e. BSC, reagents and identification systems). Source: The Commonsense Bug Workbook.doc Page: 3 of 80 SNP MICROBIOLOGY • The Commonsense Bug Workbook Groups/organisms not included in this workbook: Ø Enterobacteriace There are many systems available for the identification of Enterobacteriace, which are easy to use, accurate and have a rapid turn-around time. Ensure, whichever system is used, that it is maintained and quality controlled as per manufacturers instruction, and that regular updates of the database are performed. The Enterobacteriace consists of a very large number of bacteria, which other than a few “weirdo’s” can be defined as: “Gram negative bacilli, that are facultative anaerobes, oxidase negative, catalase positive, grow on MacConkey agar, ferment glucose and reduce nitrate to nitrite*” *Nitrate negative species include some members of the genus Citrobacter, Panteoa (Enterobacter) agglomerans, Yersinia and Photorhabdus. Ø Legionella species Few laboratories culture for Legionella species. Identification is usually performed by a reference laboratory. Other pathology tests are used for detection i.e. urine antigen test, serology. Ø Bordetella species Culturing is being replaced by PCR. Ø Bacillus species Refer to separate texts eg Manual of Clinical Microbiology Ø Mycobacterium or Nocardia species Presumptive identification can and should be performed by most clinical laboratories. Definitive and species identification is usually performed by a reference laboratory. Source: The Commonsense Bug Workbook.doc Page: 4 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook General: Identification Methods: There are three main approaches to identification, particularly of unusual/difficult organisms. The ability to perform each method will vary between laboratories. 1. The first relies heavily on expertise, the “Guru Factor”. Likely identification is based on clinical data, growth on different media and under different atmospheric conditions. A small number of tests are then performed to support the identification. 2. The second is putting the organism through a large number of phenotypic tests such as those found in commercial systems. The choice of the identification system will vary in different laboratories and be dependent on the success in preliminary tests. The reaction data is examined and compared to test results or machine databases in order to provide identification. Knowledge of the organisms present in the identification system databases is critical. This dictates which system to use and also how to the interpret results. Commercial systems should always be used according to manufacturer’s instructions. 3. The third method is a detailed conventional approach. Primary fundamental tests such as Gram stain, oxidase and catalase tests are performed and results of these tests lead to secondary/tertiary tests being perform. As more tests are performed, the likely identity of an organism is revealed. This method is usually laborious, costly and slow as tests can only be performed when results of the previous tests are available. Setting up a barrage of tests blindly is impracticable. Although this method can be very effective and does not rely heavily on expertise, incorrect results at any point may force the investigation down the wrong path. The result is a wrong identification, and a waste of valuable time and resources. The best method is a combination of all three methods, resulting in a cost effective and efficient identification process, which is within the scope of the average clinical microbiology laboratory. Any identification result, irrespective of method or confidence, should always be supported by clinical details, antibiograms (when available), other laboratory results and textbook descriptions, to reduce the risk of misidentification. Note: • Always use a fresh restreak from nonselective media (where possible) for testing. • Always perform and examine purity restreak before accepting any identification. • Always use the recommended inoculum. • Incubate all tests under the correct conditions and for recommended testing times. • Run test controls particularly on infrequently used tests. Source: The Commonsense Bug Workbook.doc Page: 5 of 80 SNP MICROBIOLOGY Source: The Commonsense Bug Workbook.doc The Commonsense Bug Workbook Page: 6 of 80 SNP MICROBIOLOGY Source: The Commonsense Bug Workbook.doc The Commonsense Bug Workbook Page: 7 of 80 SNP MICROBIOLOGY Source: The Commonsense Bug Workbook.doc The Commonsense Bug Workbook Page: 8 of 80 SNP MICROBIOLOGY Source: The Commonsense Bug Workbook.doc The Commonsense Bug Workbook Page: 9 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Characteristics: When identifying bacteria, examine all available test results. In this workbook, certain characteristics have been selected for the purpose of identification. The first step is the performance of a few simple tests listed below, which will usually allow for primary provisional placement into a bacterial group: • • • • Morphology (Gram, wet preparation) Atmospheric requirement (growth in the presence/absence of oxygen) Growth performance of different agar types Catalase and oxidase tests Microscopic Appearance: Gram stain and/or wet preparation provide information on shape, arrangement, organism size and presence or absence of inclusions e.g. spores. The Gram stain also usually allows division into Gram positive or Gram negative groups. *Hint: • Perform from young cultures • From non-selective media • Away from antibiotics • From broth cultures when possible. Terms valuable in microscopic preparations: • Staining – even, irregular, bipolar, beaded, barred • Shape – coccoid, coccobacilli (short rods), long rods, filamentous, curve rods, spiral forms. • Motility – darting, wobbling, tumbling • Spores – spherical, oval, centered, sub terminal, terminal, cause bulging, presence outside cell. • Capsule – presence/absence • Size – length and width • Shape of sides and ends – pointed ends, parallel sides, bulging sides • Arrangement – singly, in pairs, chairs, tetrads, Chinese letter shapes • Irregular forms – variation in shape and size, branched, fusiform or swollen forms. • Pleomorphism – variation in shape e.g. filaments and coccobacilary forms. Source: The Commonsense Bug Workbook.doc Page: 10 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Culture Appearance: Colonies of a bacteria growing on specific media under certain specific conditions are described by size, shape, consistency and pigment production. This in many instances is critical, as it provides one of the primary steps in the identification process. Most good textbooks will provide you with further information and detailed characteristics. Presence/absence and type of haemolysis may also be very valuable in bacterial identification. Hint: When checking for pigment production observe both old and new cultures and look for pigment on swab after touching individual colonies. Motility: Many bacteria are observed to be motile and move from one position to another when suspended in fluid. True motility must not be confused with Brownian movement (vibration caused by molecular bombardment) or convection currents. Microscopic examination may indicate whether a motile organism has polar flagellae, shown by a darting, zigzag movement or peritrichate flagellae, which cause a less vigorous and more vibratory movement. Some bacteria may be motile at different temperatures e.g. motile at ambient temperature but not at 37ºC, or vice versa. Hint: To exclude Brownian motion, check for upstream swimming – phase microscopy is an advantage. A negative hanging drop or wet preparation may not mean the organism is non-motile Biochemical tests: Numerous biochemical tests may be used for the identification of bacteria. Some such as catalase and oxidase are rapid and easy to perform and may be used for preliminary differentiation purposes. The fermentation of glucose may also be used to distinguish between groups of organisms. • Catalase: Hydrogen peroxide is formed by some bacteria as an oxidative end product of the aerobic breakdown of sugars and, if allowed to accumulate, is highly toxic. The catalase enzyme breaks down hydrogen peroxide to water and gaseous oxygen. • Oxidase: The oxidase test is used to detect an intracellular cytochrome oxidase enzyme system. This system is usually present only in aerobic organisms, which are capable of utilizing oxygen as the final hydrogen acceptor. • Fermentation of glucose: Some aerobic organisms metabolise glucose oxidatively (i.e. oxygen is the ultimate hydrogen acceptor). Other organisms ferment glucose and the hydrogen acceptor is then another element such as sulphur. Source: The Commonsense Bug Workbook.doc Page: 11 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Growth Requirements of Value: • Atmosphere Ø Ø Ø Ø Ø Strict aerobes → grow only in the presence of O2 Strict anaerobes → grow only in the absence of O2 Facultative → organisms from aerobic and anaerobic Microaerophilic → grow best in reduced O2 atmosphere (addition of 5-10% CO2enhances growth) Capnophilic → organisms require CO2 for growth Hint: Use the same media, same inoculum and the same incubation times • Temperature Ø Ø Ø Psychrophilic → grow at ↓ temperatures Mesophiles → grow at temperatures between 10-45ºC (optimal 30-40ºC) Thermophiles → will not grow or grow poorly at 37ºC (optimal 40-60ºC) Hint: Most clinically significant organisms are mesophiles. • Nutrition Ø Ø Ø Ø The ability to grow on ordinary nutrient agar. Growth performance on blood or chocolate agar. Growth on MacConkey agar. Requirements for specific factors such as charcoal, X factor (haemin) or V factor (NAD), lipids. Safety Considerations: • Laboratory gowns recommendations. and gloves • Laboratory methods that give rise to infectious aerosols must be conducted in an appropriate biological safety cabinet particularly on unknown bacterial isolates. • Laboratories must comply with transport regulation of biological agents, if transportations of bacteria are required. Source: The Commonsense Bug Workbook.doc should be used as dictated by current Page: 12 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Listeria species Target Organisms • • • Listeria monocytogenes Listeria ivanovii Listeria seeligeri Taxonomy • There are currently seven species in the genus Listeria. Characteristics • Members of the genus are facultative anaerobes. • They are non-sporing, non-acid fast and do not possess a capsule. • Listeria species are motile by peritichous flagella when grown at < 30ºC and display a characteristic “tumbling” motility. Best viewed using phase microscopy. • They are catalase positive, oxidase negative and ferment carbohydrates. Microscopic appearance • Gram positive rods approximately 0.5 x 0.5-3µm with rounded ends, occurring singly or sometimes in pairs and may resemble “coryneforms’ or diplococci. • They are non-sporing, non-branching and non-capsulated Identification • Colonies on blood agar or Listeria selective agar are identified by colonial appearance, Gram stain, catalase production and tumbling motility at ambient temperature. . • All identification tests should ideally be performed from non-selective agar. • If confirmation of identification is required, isolates should be sent to a Reference Laboratory. Primary isolation media • Blood agar incubated in 5-10% CO2 at 35-37ºC for 16-48 hours. • Listeria selective agar incubated in air at 35-37 ºC for 40-48 hours Source: The Commonsense Bug Workbook.doc Page: 13 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Colonial appearance • All Listeria species produce non-pigmented colonies on blood agar, which have a characteristic ground glass appearance. • On Listeria selective agar, Listeria species appear as black colonies with a surrounding black zone produced by hydrolysis of the aesculin. • The appearance of L.monocytogenes, L.ivanovii, and L.seeligeri is described below. L.monocytogenes Blood agar: Colonies are 0.5-1.5mm in diameter, smooth, translucent and emulsifiable, with zones of hazy β-haemolysis. Colonies resemble Group B Streptococci. Non-haemolytic colonies occasionally occur L.ivanovii Blood agar: colonies are similar to L.monocytogenes but develop larger zones of complete haemolysis with outer zones of partial haemolysis. L.seeligeri Blood agar: zones of β-haemolysis are produced. Test Procedures • Motility test All Listeria species exhibit tumbling motility at ambient temperatures (<30ºC) but not at 37ºC • Commercial identification kit • Summary table of results Species Catalase Tumbling motility at <30ºC Tumbling motility at 37ºC L.monocytogenes + + - L.ivanovii + + - L.seeligeri + + - Source: The Commonsense Bug Workbook.doc Commercial identification kit Refer to manufacturer’s Instructions Refer to manufacturer’s Instructions Refer to manufacturer’s Instructions Page: 14 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Flowchart – Identification of Listeria species Clinical specimens Primary isolation plate (blood agar) Blood agar – non-pigmented translucent haemolytic colonies* Gram stain Gram positive rods Catalase Positive Negative Tumbling motility (Hanging drop, ambient temperature <30º Positive Negative All Listeria species Not Listeria species Not Listeria species Commercial identification kit If required, save pure isolate on a blood or nutrient agar slope for referral to a reference laboratory. *Non-haemolytic strains of L.monocytogenes occur occasionally Source: The Commonsense Bug Workbook.doc Page: 15 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Corynebacterium species and other non-sporing Gram positive rods Target Organisms: Corynebacterium species reported to have caused human infection: • • • • • • • • • • • • • • • Corynebacterium accolens Corynebacterium afermentans (two subspecies) Corynebacterium minutissimum Corynebacterium mucifaciens Corynebacterium propinquum Corynebacterium pseudodiphtheriticum Corynebacterium pseudotuberculosis Corynebacterium coyleae Corynebacterium diphtheriae Corynebacterium striatum Corynebacterium sundsvallense Corynebacterium thomssenii Corynebacterium ulcerans Corynebacterium jeikeium Corynebacterium lipophiloflavum • Corynebacterium macginleyi • Corynebacterium matruchotii • • • • • • • • • • • • Corynebacterium amycolatum Corynebacterium aquaticum Corynebacterium argentoratense Corynebacterium auris Corynebacterium confusum Corynebacterium riegelii Corynebacterium seminale Corynebacterium durum Corynebacterium falsenii Corynebacterium glucuronolyticum Corynebacterium imitans Corynebacterium urealyticum Note: Other Corynebacterium species may be clinically significant Species morphologically similar to Listeria and Corynebacterium species known to have caused human infection: • • • • • • • • Arcanobacterium species Aureobacterium species Bifidobacterium species Brevibacterium species Cellulomonas species Dermabacter hominis Erysipelothrix rhusiopathiae Lactobacillus species • • • • • • • Microbacterium species Mycobacterium species (MOTT) Oerskovia species Propionibacterium species Rhodococcus species Rothia dentocariosa Turicella otitidis Taxonomy • The organisms classified as non-sporing Gram-positive rods are very diverse not only morphologically, but also metabolically and structurally. Source: The Commonsense Bug Workbook.doc Page: 16 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Microscopic appearance • Gram-positive rods, microscopic appearance varies with the species. Identification • Colonies on blood agar are identified by colonial appearance, Gram stain, catalaseproduction and motility. • Identification is confirmed by further biochemical tests and/or referral to a Reference Laboratory. • All identification tests should ideally be performed from non-selective agar. Identification can be performed from Tween containing agar. Primary isolation media • Blood agar incubated in 5-10% CO2 at 35-37°C for 16-48h Colonial appearance Corynebacterium species Characteristics of growth on horse blood agar after aerobic incubation at 35-37°C for 16-48h in CO2 C.accolens White, dry colonies. 0.5-1mm after 24h. Sticks to agar C.afermentans subspecies afermentans Non-haemolytic, white. 1-2mm after 24h C.afermentans subspecies lipophilum Grey, glassy colonies C.amycolatum White/grey dry colonies. 1-1.5mm after 24h C.aquaticum Non-haemolytic, yellow convex colonies after 24h C.argentoratense Cream non-haemolytic colonies. 2mm after 24h C.auris Non-haemolytic dry colonies become prolonged incubation. 1-2mm after 48h C.confusum White glistening, convex creamy colonies. Up to 1.5mm after 48h C.coyleae White, slightly glistening, sticky colonies with entire edges after 24h in CO2 C.diphtheriae White, “Staph-like” colonies (may be Staph latex pos) C. durum Non-haemolytic, small convoluted beige colonies with irregular edges after 48h Source: The Commonsense Bug Workbook.doc yellow after Page: 17 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Corynebacterium species Characteristics of growth on blood agar after aerobic incubation at 35-37°C for 16-48h C. falsenii White glistening smooth colonies with entire edge. 2mm after 24h. Exhibit yellow pigment >72h C. glucuronolyticum Non-haemolytic white/yellow convex colonies. 1-1.5mm after 24h C. imitans White/grey, glistening, creamy colony with entire edge. 12mm after 24h C. jeikeium Non-haemolytic grey/white. Entire, low, convex. Good growth on blood agar at 42ºC, poor growth at 22ºC. Confluent on Tween containing media. C. kroppenstedtii Non-haemolytic, convex colonies C. lipophiloflavum Requires lipid for growth. Non-haemolytic <0.2mm on blood agar. With addition of Tween colonies are 1mm and yellow C. macginleyi Requires lipid for growth. Non-haemolytic, 1mm after 48h without lipid. With Tween red/beige colonies, 2-4mm C. matruchotii Flat colonies. Older cultures are circular, convex, rough and may be irregular C. minutissimum Shiny, moist, convex and circular. Entire edges. 1-1.5mm after 24h C. mucifaciens Yellow glistening, very mucoid colonies. 1-1.5mm after 24h in CO2 C. propinquum Non-haemolytic, matted surface. 1-2mm after 24h C. pseudodiphtheriticum White/cream butyrous colonies C. pseudotuberculosis White, dry, sometimes Mycobacterium colony. C. riegelii White, glistening, convex colonies. Entire edges. Up to 1.5mm after 48h C. seminale Non-haemolytic grey/beige non-mucoid colonies. Slight growth at 24h. Abundant growth at 48h C. striatum Non-haemolytic white, moist, smooth colonies. >2mm after 24h C. sundsvallense Non-haemolytic, buff/slightly yellow, opaque, shiny colonies. Adhere to the surface of the agar after 48-72h C. thomssenii Slightly glistens, smooth, convex colonies. Very small after 24h. Molar tooth-like after 96h. Adhere to surface of the agar non-pigmented, small, “cheesy”, smooth may look and like C. ulcerans C. urealyticum Non-haemolytic, white, smooth and convex. Pinpoint colonies after 48h in CO2. Grey/white colonies on CLED. Confluent growth on Tween containing media Source: The Commonsense Bug Workbook.doc Page: 18 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of the main clinically significant Corynebacterium species Target Organisms: C.diphtheriae C.ulcerans C.pseudodiphtheriticum C.pseudotuberculosis C.jeikeium C.urealyticum C.macginleyi • • • • • • • Corynebacterium species which are potentially toxigenic Corynebacterium diphtheriae var belfanti Corynebacterium diphtheriae var gravis Corynebacterium diphtheriae var intermedius Corynebacterium diphtheriae var mitis Corynebacterium pseudotuberculosis • • • • • • • • • • Corynebacterium ulcerans Corynebacterium pseudodiphtheriticum Corynebacterium ureolyticum Corynebacterium jeikeium Corynebacterium ulcerans Primary Separation: Table 1: (Non-lipid requiring) C.diphtheriae* C.ulcerans C.pseudodiphtheriticum C.pseudotuberculosis Nitrate +/+ v Urea + + + Glucose + + + Sucrose v *C.diphtheriae var belfanti is the only nitrate negative biotype. Table 2: (Lipid requiring) # C.jeikeium # C.urealyticum C.macginleyi Nitrate* + Urea* + - Glucose* + + Sucrose* + Resistant + + - *Hint: A heavy inoculum is required and a few drops of sterile serum or Tween 80 needs to be added to the CTA sugar tubes. # Resistant to most antibiotics except vancomycin. Confirmation using a commercial system e.g. API Coryne should be used on all provisionally identified clinically significant Corynebacterium isolates. To test for lipid requirement, restreak on media containing Tween 80. (Nalidixic acid Tween agar) is recommended. Source: The Commonsense Bug Workbook.doc The use of NAT Page: 19 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Primary screening of non-lipophilic Corynebacterium species * Further identification if regarded as significant, perform a commercial identification or refer to a reference laboratory. **Possible C.diphtheriae isolate, confirm using a commercial system ie API Coryne & forward to a reference laboratory for toxin testing. Consult Pathologist/Clinician urgently for clinical assessment of patient. Source: The Commonsense Bug Workbook.doc Page: 20 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of other Non-sporing Gram positive rods Other non-sporing Gram positive rods Characteristics of growth on blood agar after aerobic incubation at 35-37°C for 16-48h Arcanobacterium species β-haemolysis, which may not be present after 24h.Haemolysis of A. bernardiae is variable Aureobacterium species Non-haemolytic, yellow pigment Bifidobacterium species Colonies are low, greyish-brown, ovoid with a brown opaque centre and a translucent crenated edge Brevibacterium species Non-haemolytic, may turn yellow to green after 48h Cellulomonas species Non-haemolytic, yellow- or orange-pigmented Dermabacter hominis Non-haemolytic, small grey/white convex colonies Erysipelothrix rhusiopathiae At 48h 2 distinct colony types appear: a small smooth form, 0.3-1.5mm, transparent, convex and circular with entire edges. The large rough form is flatter, more opaque, with a matt surface and an irregular edge. Both exhibit α-haemolysis. Look like a viridans Streptococcus. Colonies are small and often α-haemolytic on blood after 48h. Sweet smell better growth anaerobically. Lactobacillus species Microbacterium species May produce a yellow or orange pigment Mycobacterium species (MOTT) Rough or smooth colonies. May produce yellow/orange pigment when grown either in the light or the dark. Oerskovia species Most strains produce a yellow pigment Propionibacterium species Small colonies after 48h, grow better anaerobically. Rhodococcus species Colonies may be rough, smooth or mucoid and may be pigmented, cream, beige, yellow, orange or red Rothia dentocariosa Non-haemolytic, creamy, dry, crumbly or mucoid Turicella otitidis Non-haemolytic, convex, whitish, creamy Test procedures • Catalase activity test (reactions vary). • Motility test - performed at 37°C and <30°C for all organisms (reactions vary). • Commercial identification kit Source: The Commonsense Bug Workbook.doc Page: 21 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Characteristics Arcanobacterium species • Arcanobacterium pyogenes (formerly Corynebacterium or Actinomyces pyogenes) is a Gram-positive rod, which may show branching. Colonies on blood agar produce sharp zones of β-haemolysis after 48 hours incubation. A. pyogenes is facultatively anaerobic, non-motile, and catalase-negative. Differentiation between A. pyogenes and A.haemolyticum may prove difficult but they may be distinguished by fermentation of α-mannose, pyrazinamidase and gelatin tests. They are both mupirocin resistant. • Arcanobacterium haemolyticum (formerly Corynebacterium haemolyticum) is a Grampositive rod. Colonies on blood agar after 48 hours produce zones of β-haemolysis and are similar in appearance to A.pyogenes. A.haemolyticum is non-motile, facultatively anaerobic and, unlike Corynebacterium species, it is catalase-negative. • Arcanobacterium bernardiae formerly (Actinomyces bernardiae) exhibits variable haemolysis. Aureobacterium species • Aureobacterium species are Gram-positive, irregular, short rods and are catalasepositive. They are obligate aerobes, which produce acid from carbohydrates by oxidation rather than by fermentation. Strains may be vancomycin resistant and can be distinguished from C.aquaticum by casein and gelatin hydrolysis. Bifidobacterium species • Bifidobacterium species vary in shape and may be curved, clubbed or branched rods or occasionally coccoid, Gram-positive forms, 0.5-1.3 x 1.5-8µm. Cells often stain irregularly. Growth is anaerobic but some species can grow in air enriched with 10% CO2. Bifidobacterium species are non-sporing, non-acid fast and non-motile. Bifidobacterium species ferment carbohydrates and are catalase negative. Brevibacterium species • Brevibacterium species are Gram-positive rods, which that show a marked rod-coccus cycle. On fresh subculture, cells appear as bacilli but become coccal in older cultures. Colonies on blood agar are non-haemolytic and may turn a yellow to green colour after 48 hours incubation. Brevibacterium species are non-motile, aerobic, ureasenegative and catalase-positive. Cellulomonas species • Cellulomonas species produce yellow or orange-pigmented colonies. They are catalase-positive and some species are motile. Cellulomonas species differ from Oerskovia species as they lack hyphal growth. Source: The Commonsense Bug Workbook.doc Page: 22 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Dermabacter hominis • Dermabacter species are very short Gram-positive rods that may be mis-interpreted as cocci. Dermabacter hominis, currently the only member of the genus, is nonhaemolytic, non-motile and catalase-positive. Dermabacter species are fermentative and produce acid from glucose, lactose, sucrose and maltose. They hydrolyse aesculin and do not reduce nitrate or produce pyrazinamidase or DNase. Erysipelothrix rhusiopathiae • E.rhusiopathiae is a Gram-positive rod, which produces α-haemolysis on blood agar. It is facultatively anaerobic, non-motile and catalase-negative. Erysipelothrix species can be distinguished from Lactobacillus species by its ability to produce H2S in a triple sugar iron agar slant (may need ≥48hrs, a heavy inoculum is required). Gardnerella vaginalis • Gardnerella vaginalis is a pleomorphic, Gram-variable rod. It is facultatively anaerobic and non-motile. G.vaginalis is non-sporing, non-encapsulated and both oxidase and catalase-negative but hippurate positive. Lactobacillus species • Lactobacillus species are long Gram-positive rods. Colonies are small and often αhaemolytic on blood agar after 48 hours. They are facultatively anaerobic, rarely motile and catalase-negative. • Lactobacillus species is may not always be Vancomycin resistant. Microbacterium species • Microbacterium species are Gram-positive slender rods. They may produce a yellow or orange pigment. The optimum growth temperature is 30°C. Microbacterium species are aerobic and some species are motile. All species are catalase-positive. Mycobacterium species • Mycobacterium species other than Mycobacterium tuberculosis (MOTT) may be isolated on primary culture within 48 hours. Refer to the Reference Laboratory. Source: The Commonsense Bug Workbook.doc Page: 23 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Oerskovia species • Oerskovia species are Gram-positive branching rods. They form a mycelium, an extensively branching substrate hyphae that breaks up to form rod-shaped or coccoidrod elements. Most strains produce a yellow pigment. They are facultatively anaerobic, motile and catalase-positive. Propionibacterium species • Propionibacterium species are Gram-positive pleomorphic rods (short “Y” forms). Strains generally grow better anaerobically, particularly on primary isolation, producing small colonies after 48 hours. Propionibacterium species are facultatively anaerobic and are non-motile. They are catalase-positive except Propionibacterium propionicum (formerly known as Arachnia propionica), which is catalase negative. • The indole test for P.acnes, if not positive directly from colonies, is best performed on a broth culture (TSB), after overnight incubation. Hint: A sheen around colonies, is usually present due to propionic acid production. Rhodococcus species • Rhodococcus species usually stain Gram-positive and cells form as cocci or short rods which grow in length and may form an extensively branched vegetative mycelium which may fragment. They are usually partially acid-fast. Colonies may be rough, smooth or mucoid and are colourless, cream, beige, yellow, orange or red. Moisture and extended incubation enhances pigment production. Rothia dentocariosa • R. dentocariosa is a Gram-positive irregular rod and may show branching in young cultures. In older broth cultures cells may be coccoid, which distinguishes them from Actinomyces species. It grows well on simple media and colonies may be creamy, dry, crumbly or mucoid. Rothia species are facultatively anaerobic, non-motile, catalase positive and ferment carbohydrates. Turicella otitidis • This genus comprises a single species, Turicella otitidis. Microscopically it resembles a coryneform but has longer cells. It may be distinguished by colonial morphology from C.afermentans and C.auris. T.otitidis colonies are convex, whitish, creamy and non-haemolytic compared with the flat, grey-white and non haemolytic colonies of C.afermentans and the convex, dry, adherent, yellowish colonies of C.auris. T.otitidis is non-fermentative and occurs either alone or with Gram-negative rods. Strains exhibit a strong CAMP reaction and it is catalase-positive. T.otitidis may be misidentified, often as Corynebacterium species, by some commercial identification systems . Source: The Commonsense Bug Workbook.doc Page: 24 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Streptococcus species, Enterococcus species and similar organisms Target organisms • Streptococcus species reported to have caused human infection • Streptococci possessing Lancefield group antigens A-G Group A Streptococcus pyogenes (Streptococcus anginosus and Streptococcus constellatus may cross react with the Lancefield group A antigen Group B Streptococcus agalactiae Group C Streptococcus dysgalactiae subspecies equisimilis, Streptococcus equi subspecies equi, Streptococcus equi subspecies zooepidemicus (Streptococcus anginosus and Streptococcus the Lancefield group C antigen) Group D Enterococcus species (see below) Streptococcus bovis Streptococcus gallolyticus Group F Streptococcus anginosus Streptococcus constellatus Group G Group G streptococci (Streptococcus constellatus may cross react with the Lancefield group G antigen, Other streptococci Streptococcus pneumoniae Streptococcus suis Streptococcus anginosus/milleri group Streptococcus anginosus Streptococcus constellatus Streptococcus intermedius Streptococcus mutans group Streptococcus mutans Streptococcus sobrinus Streptococcus sanguis group Streptococcus cristatus Streptococcus gordonii Streptococcus snaguinis Streptococcus parasanguinis Streptococcus mitis group Streptococcus mitis Streptococcus oralis Streptococcus salivarius group Streptococcus salivarius Streptococcus vestibularis Nutritionally variant streptococci Abiotrophia adjacens Abiotrophia defective Abiotrophia elegans Source: The Commonsense Bug Workbook.doc Page: 25 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Enterococcus species reported to have caused human infections • • • • • • • • Enterococcus faecalis Enterococcus faecium Enterococcus casseliflavus Enterococcus dispar Enterococcus durans Enterococcus flavescens Enterococcus gallinarum Enterococcus raffinosus Other genera reported to have caused human infections • • • • • • Aerococcus species Gemella species Helcococcus species Lactococcus species Leuconostoc species Pediococcus species Microscopic appearance • Gram stain Ø Streptococcus, Enterococcus and Lactococcus species are Gram-positive, round or ovoid cells occurring in pairs, short or long chains or sometimes in clusters Ø Streptococcus pneumoniae are Gram-positive, lanceolate cells occurring in pairs, often with a visible capsule Ø Aerococcus, Pediococcus and Helcococcus species are Gram-positive cocci in clusters or tetrads Ø Gemella and Leuconostoc are Gram-positive cocci occurring in pairs, clusters and short chains (Gemella may be easily decolourised) Primary isolation media • Blood agar incubated in 5-10% CO2 at 35-37ºC for 16-48h • Staph/Strep agar incubated in air at 35-37ºC for 16-48h Source: The Commonsense Bug Workbook.doc Page: 26 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Flowchart: Identification of Streptococcus & Enterococcus Source: The Commonsense Bug Workbook.doc Page: 27 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Colonial appearance Organism “group” Haemolysis Characteristics of growth on blood agar after incubation at 35-37oC for 16-24h β-haemolytic Streptococci β Approximately 0.5mm, entire edged, may have a dry appearance, colonies may be difficult to pick off the plate “viridans” Streptococcus α or non Colonies are 0.5 - 1.0mm, entire edged Enterococcus species α,β or non Colonies are larger than those of streptococci, usually 1-2mm, with a wet appearance. Haemolysis is variable S. pneumoniae α Colonies are 1-2mm and may appear as “draughtsman” colonies. After anaerobic incubation colonies may be larger and mucoid “S. anginosus” α,β or non Colonies are small (≤ 0.5mm), haemolysis is variable. Some strains have a white “heaped” up colony NVS α or non Colonies are small (≤ 0.5mm), require pyridoxal for growth Aerococcus species α Resemble “viridans” Streptococci Gemella species α or non Resemble “viridans” Streptococci Helcococcus species non Colonies are 0.5 - 1.0mm, entire edged Lactococcus species α or non Resemble Enterococcus Leuconostoc species α or non Colonies are 0.5 - 1.0mm, entire edged Pediococcus species α or non Resemble “viridans” streptococci Source: The Commonsense Bug Workbook.doc Page: 28 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Summary of test results Possess Lancefield grouping antigen (Commercial kit) Optochin sensitivity Catalase Bile Aesculin hydrolysis PYR Group B, C, F and G + R - - - S. pneumoniae – S - - D Group D + R - + - Enterococci + R V + + S. bovis + R - + - Aerococcus species - R V V D Group A + R - - + S. anginosus group V R - V - “viridans” streptococci - V - Gemella species R W - + Helcococcus species R - - + Leuconostoc species R D D + - Pediococcus species CR R - V= variable, R=resistant , S=sensitive, CR=cross reacts, D=6-84% strains, W=weak positive reaction Characteristics Streptococcus pyogenes (Lancefield group A) • Streptococcus pyogenes is a Gram positive coccus occurring in chains. After 18-24h incubation at 35-37ºC on blood agar colonies are approximately 0.5mm, domed, with an entire edge. Some strains may produce mucoid colonies. Haemolysis is best observed by growing the culture under anaerobic conditions because the haemolysins are more stable in the absence of oxygen. • Lancefield group A streptococci will not grow on media containing bile. • Low concentration bacitracin susceptibility has been used for screening purposes but is unreliable. Resistance to benzyl penicillin has not been reported. • The pyrrolidonyl arylamidase (PYR-aminopeptidase) (PYR) test is positive for Group A streptococci and negative for most other groupable streptococci, although some human strains of groups C and G may be positive. Enterococcus are also PYR positive. • Minute colony forms of the S. anginosus group may cross react with Lancefield groups A C and G antibodies and may grow on media containing bile. Source: The Commonsense Bug Workbook.doc Page: 29 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Streptococcus agalactiae (Lancefield group B) • Streptococcus agalactiae are Gram positive coccus, occurring in chains. After 18-24h incubation at 35-37ºC, colonies tend to be slightly larger than other streptococci (approximately 1mm) and have a less distinct zone of β-haemolysis. Some strains may be non-haemolytic. • Lancefield group B Streptococci will grow on media containing bile. • Islam’s medium, to detect orange pigment production, may be useful for primary isolation and presumptive identification, but is not recommended in this workbook. Streptococcus dysgalactiae subspecies equisimilis (Lancefield grps A,C,G and L) Streptococcus equi subspecies zooepidemicus (Lancefield group C) and Lancefield group G Streptococcus • Microscopically these species are Gram positive cocci, occurring in chains. Large colony forms of Lancefield groups C and G Streptococcus (0.5mm) produce similar colonies to Group A Streptococcus. • Lancefield groups C and G streptococci will not grow on media containing bile. • Minute colony forms of the S.anginosus group (formerly the S.milleri group) can cross react with the Lancefield groups A C and G antibodies and may grow on media containing bile. Enterococcus species, Streptococcus bovis group (Lancefield group D) • The genus Enterococcus and organisms of the S.bovis group possess Lancefield group D antigen. Microscopically the organisms are Gram positive cocci, spherical or ovoid in shape (0.6-2.5µm), usually occurring in pairs or short chains in broth culture. After 18-24h incubation at 35-37ºC on blood agar colonies are 1-2mm and may be α, β or non-haemolytic on horse blood agar. Most species will grow on nutrient agar at 45ºC. A few will grow at 50ºC, at pH 9.6 and in 6.5% NaCl. They can also survive 60ºC for 30 minutes. • Lancefield group D streptococci will grow on media containing bile and may be differentiated from other streptococci by rapid hydrolysis of aesculin in the presence of 40% bile. • Enterococcus species are also heat resistant (60oC/30mins) and PYR-positive which differentiates them from S.bovis and S.gallolyticus. • There are six species included in the S.bovis group: S. bovis, S.equinus, S.gallolyticus (formerly S.bovis biotype I), S.infantarius (formerly S.bovis biotype II), S.pasteurianus (formerly S.bovis biotype II/2) and S.lutetensis. • Microscopically these species are Gram-positive cocci, occurring in chains after 1824h incubation at 35-37ºC in CO2 or anaerobically. • Colonies are usually non-haemolytic on blood agar and 1-2mm in diameter. Source: The Commonsense Bug Workbook.doc Page: 30 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook • Members of the S.bovis group may be misidentified as Enterococcus species as many strains share the group D antigen. It is important to identify S.bovis group organisms from clinical material especially in cases of bacteraemia, as S.gallolyticus and S.pasteurianus are associated with chronic bowel disease particularly adenocarcinoma of the colon. S.bovis group may be differentiated from Enterococcus species by a negative reaction in both PYR and arginine tests, whereas Enterococcus is usually positive for both. • Enterococcus species are facultative anaerobes. Two species within the genus are motile, Enterococcus cassiflavus and Enterococcus gallinarum. Enterococcus are oxidase negative and ferment carbohydrates. Most species are catalase negative, but some strains produce a pseudocatalase. • Most Enterococcus possess the group D antigen although some strains may cross react with Lancefield group G antiserum. • E. faecalis are very rarely resistant to ampicillin. Streptococcus anginosus, Streptococcus constellatus, Streptococcus intermedius (formerly the Streptococcus milleri group) • Microscopically these species are Gram positive cocci, occurring in chains. Colonies on blood agar are small (≤0.5mm) and may exhibit α, β or no haemolysis after 16-24h at 35-37ºC. Incubation conditions may be of some value for the presumptive identification of the S.anginosus group as growth is enhanced by a low oxygen tension and raised CO2 levels. • Organisms of this group may possess the Lancefield group A, C, F or G antigen and in some instances may be ungroupable. S.intermedius is non-haemolytic and possesses no group antigen. S.constellatus may express group C, F or N and S.anginosus group A, C, F, G or N antigens. Streptococci in this group will grow on media containing bile although they are not salt tolerant. • Resistance to sulphonamides and bacitracin may be used as screening tests for organisms of the S.anginosus group. Streptococcus pneumoniae • Streptococcus pneumoniae are Gram positive typically lanceolate cells occurring in pairs, which may be capsular. Colonies are 1-2mm, α-haemolytic and may appear as ‘draughtsman' colonies due to autolysis of the organisms after incubation in 5-10% CO2 at 35-37oC for 16-24h. Under anaerobic conditions colonies may appear larger and more mucoid. • Pneumococci are usually sensitive to Optochin (ethylhydrocupreine hydrochloride), which enables rapid identification of the organism, but resistance may occur. Pneumococci are also soluble in bile salts solution. • Pneumococci may also be identified by serological methods. The ‘Quellung reaction' (capsular swelling) may be used microscopically to identify specific types of pneumococci. Commercial agglutination tests are also available for the rapid detection of pneumococcal antigen. Source: The Commonsense Bug Workbook.doc Page: 31 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Streptococcus suis • S.suis is β-haemolytic on horse blood agar, Optochin resistant and PYR-negative. They are commonly associated with the Lancefield groups R, S and T. S.suis I is associated with group S and S.suis II with group R. They do not grow in 6.5% NaCl broth. Some strains are able to grow in the presence of 40% bile and all are able to hydrolyse aesculin. Other streptococci (“viridans” streptococci) • These species are Gram-positive cocci occurring in chains, which are indistinguishable from β-haemolytic streptococci. Colonies are 0.5-1.0mm and may be α or non-haemolytic on blood agar after anaerobic incubation at 35-37ºC in CO2 for 16-24h. • Generally these streptococci would not require further identification, other than as α or non-haemolytic streptococcus, when isolated from sites where they are considered normal flora. Identification of streptococci in cases of suspected endocarditis has some value in the confirmation of the diagnosis and for epidemiological purposes. Some species of streptococci, eg Streptococcus sanguis and Streptococcus oralis (formerly mitior), may account for up to 80% of all streptococcal endocarditis cases. Nutritionally Variant Streptococci (NVS) • NVS have now been reclassified as Abiotrophia adiacens, Abiotrophia elegans and Abiotrophia defectiva. NVS require media supplemented with either pyridoxal or cysteine for growth. • NVS should be suspected when Gram positive cocci resembling streptococci are seen in positive blood cultures, which subsequently fail to grow on subculture. Repeat subculture of suspect broth should include a blood agar plate with a Staphylococcus aureus streak which is examined for satellitism of NVS around the staphylococcus. Alternatively, media may be supplemented with 10mg/L pyridoxal hydrochloride. Aerococcus species • Aerococci resemble “viridans” streptococci on culture but differ microscopically by characteristically occurring as tetrads or clusters, similar to staphylococci. Sometimes a weak catalase or pseudocatalase reaction is produced. Some strains of Aerococcus viridans are bile aesculin-positive and PYR-positive. Aerococcus urinae is bile aesculin-negative, PYR-negative. • In some commercial identification systems A.viridans may be mis-identified as Helcococcus kunzii. Gemella species • There are four species: Gemella haemolysans, Gemella morbillorum (formerly Streptococcus morbillorum), Gemella bergeriae and Gemella sanguinis. These bacteria easily decolourise on Gram staining, occurring as Gram negative cocci in pairs, tetrads, clusters or short chains. Gemella species are α or non-haemolytic on blood agar and resemble colonies of viridans streptococci. Source: The Commonsense Bug Workbook.doc Page: 32 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Helcococcus kunzii • Helcococcus kunzii, similar to Aerococcus species, has recently been described. H.kunzii produces tiny grey, slightly α-haemolytic colonies; growth is stimulated by the addition of serum or Tween 80 to the basal medium. • In some commercial identification systems A.viridans may be mis-identified as Helcococcus kunzii. Lactococcus species • Lactococcus species are physiologically similar to Enterococcus. They are α or nonhaemolytic, Gram positive cocci which occur singly, in pairs or chains. They are bile aesculin positive, but do not possess group D antigen. Leuconostoc species • Leuconostoc species are Gram positive lenticular cocci occurring in pairs and chains and are characteristically vancomycin resistant. They may be confused with the Enterococcus because most Leuconostoc species are bile aesculin positive and some cross-react with the group D antisera. Pediococcus species • Pediococcus species may resemble viridans streptococci on culture, but microscopically they are similar to staphylococci. They are Gram positive cocci appearing in pairs, clusters and tetrads and are vancomycin resistant. They may be confused with Enterococcus because they are bile aesculin-positive and cross-react with the Group D antisera. Source: The Commonsense Bug Workbook.doc Page: 33 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Flowchart: Non-β-haemolytic Gram positive cocci Non-beta-hemolytic catalase-negative gram-positive-cocci with “streptococcal” Gram stain (coccobacilli in pairs and chains) Vancomycin S R Leuconostoc LAP + Globicatella PYR + Streptococcus Lactococcus Satelliting behavior + Abiotrophia (formerly nutritionally variant streptococci) Enterococcus Lactococcus Enterococci grow at both 10 and 45oC. Lactococci grow at 10oC but not at 45oC. Streptococci may grow at 45oC but not at 10oC. Source: The Commonsense Bug Workbook.doc Page: 34 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Flowchart: Non-beta haemolytic, catalase negative Gram positive cocci with “Staphylococcal” Gram stain (cocci in clusters, tetrads, pairs) Non-beta-hemolytic catalase-negative Gram-positive cocci with “staphylococcal” Gramstain (cocci in clusters, tetrads, pairs)a PYR + Vancomycin LAP + R S Pedicoccus Esculin hydrolysis + - Stomatococcus Gemellab Stomatococcus Aerococcus urinae 6.5% NaCl 6.5% NaCl + + - Aerococcus urinae Stomatococcus - Aerococcus viridans (microaerophilic) Esculin hydrolysis Helcoccus (facultative) + - Helcoccus Gemellab Source: The Commonsense Bug Workbook.doc Page: 35 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Staphylococcus species, Micrococcus species and Stomatococcus species Target Organisms Staphylococcus species reported to have caused human infection • • Staphylococcus Staphylococcus aureus aureus • • • • • • • • • Staphylococcus Staphylococcus Staphylococcus Staphylococcus Staphylococcus Staphylococcus Staphylococcus Staphylococcus Staphylococcus epidermidis capitis capitis hominis hominis haemolyticus lugdunensis saccharolyticus warneri • • • • Staphylococcus Staphylococcus Staphylococcus saprophyticus cohnii cohnii • • • • • • Staphylococcus Staphylococcus Staphylococcus Staphylococcus Staphylococcus Staphylococcus caprae hyicus intermedius schleiferi schleiferi simulans subspecies aureus anaerobius capitis ureolyticus hominis novobiosepticus cohnii ureolyticus S.epidermidis group S. saprophyticus group coagulans schleiferi Other species reported to have caused human infection • • Micrococcus luteus Stomatococcus mucilaginosus Staphylococcus species Introduction • The staphylococci most frequently associated with human infection are S. aureus, S.epidermidis and S.saprophyticus. Other Staphylococcus species may also be associated with human infection. Taxonomy • More than thirty species of staphylococci have been recognised, most of which are found only in lower mammals. The coagulase positive staphylococci are S. aureus, S.intermedius, S.hyicus and S.schleiferi. The coagulase negative staphylococci (CNS) can be divided into six major groups but the species found on humans are located within two groups. Source: The Commonsense Bug Workbook.doc Page: 36 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Characteristics • Staphylococcus species are Gram positive, non-motile, non-sporing cocci occurring singly, in pairs and in irregular clusters, size may be variable. • Colonies are opaque and may be white or cream and are occasionally yellow or orange. The optimum growth temperature is 30-37°C. • They are facultative anaerobes and have a fermentative metabolism. • Staphylococcus species are usually catalase-positive and oxidase-negative. Nitrate is often reduced to nitrite. Some species are susceptible to lysis by lysostaphin but not by lysozyme and are usually able to grow in 10% sodium chloride. Some species produce extracellular toxins. Staphylococci may be identified by the production of deoxyribonuclease (Dnase) and/or a heat-stable DNase (thermostable nuclease). Coagulase-positive Staphylococcus species Staphylococcus aureus • Staphylococcus aureus is a primary pathogen, which may be associated with severe infection. It is important to distinguish it from the opportunistic coagulase negative Staphylococci. In routine laboratory practice, the production of coagulase is frequently used as the sole criterion to distinguish S.aureus from other Staphylococci; as other coagulase positive Staphylococci have been found only occasionally in human infection or carriage. The production of coagulase and thermostable nuclease by these staphylococci may lead to their misidentification as S.aureus. • S. aureus produces virulence factors such as protein A, capsular polysaccharides; α toxin and some strains produce toxic shock syndrome -1 toxin (TSST-1) or other toxins. Multiresistance to antibiotics may be associated with methicillin resistant strains. It is thermostable nuclease-positive. Staphylococcus aureus subspecies anaerobius • S.aureus subspecies anaerobius is rarely isolated from clinical specimens. It grows poorly aerobically and growth may be CO2 dependent. It is slide coagulase negative and thermonuclease negative. It may be catalase negative. Strains may be identified by better growth anaerobically and they may give a positive coagulase test result. However, because growth may be poor the coagulase result may be negative and suspected isolates should be referred to a Reference Laboratory. Other coagulase positive Staphylococcus species • S.hyicus may be coagulase-positive (11-89% of strains) and thermostable nucleasepositive. S.intermedius is coagulase-positive and thermostable nuclease-positive. S.schleiferi subspecies coagulans is coagulase-positive and thermostable nuclease positive, and S.schleiferi subspecies schleiferi is coagulase-negative and thermostable nuclease-positive. Source: The Commonsense Bug Workbook.doc Page: 37 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Coagulase negative Staphylococcus species • The CNS group are opportunistic pathogens, which lack many of the virulence factors associated with S.aureus. There are more than 30 species of CNS. S.epidermidis and S.saprophyticus are the species most often associated with infection but S.capitis, S.cohnii, S.haemolyticus, S.hominis, S.lugdenensis, S.schleiferi subspecies schleiferi, S.simulans and S.warneri have also been implicated. • Many of these species are also thermostable nuclease-negative. Multi-resistance is associated with some strains of S.epidermidis. It is thermostable nuclease-negative. S.haemolyticus is often multi-resistant and frequently demonstrates reduced susceptibility to teicoplanin. S.saprophyticus is novobiocin resistant. S.pasteuri can be phenotypically distinguished from all of the other novobiocin-susceptible staphylococci except S.warneri, from which it can only be differentiated by genotyping. • S.saccharolyticus was previously known as Peptococcus saccharolyticus. Micrococcus species • Micrococcus species are strictly aerobic. Micrococcus luteus produces yellow colonies. Cells are large Gram positive cocci arranged in tetrads. Micrococci may be distinguished from staphylococci by a modified oxidase test. Staphylococcus species, with the exception of S.sciuri, S.lentus and S.vutulus are oxidase-negative and Micrococcus species are oxidase positive. Stomatococcus species • Stomatococcus species are weakly catalase-positive. Growth is facultatively anaerobic. The species associated with infection is S.mucilaginosus previously known a Micrococcus mucilaginosus or Staphylococcus salivarius. Source: The Commonsense Bug Workbook.doc Page: 38 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Presumptive identification of Staphylococcus species Source: The Commonsense Bug Workbook.doc Page: 39 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Non-sporing, Non-branching Anaerobes Introduction • This section describes the characterisation of non-sporing, non-branching anaerobic bacteria. Identification of this group of organisms to species level is difficult without the use of techniques such as gas-liquid chromatography (GLC) or PCR methods. Because of the large number of species, it is difficult to provide genus definitions and a single biochemical table to differentiate all species. In the routine laboratory, susceptibility to metronidazole is frequently regarded as sufficient indicator of an anaerobe being present in a clinical specimen. However, this approach is fundamentally flawed because if anaerobes are by definition sensitive to metronidazole, no metronidazole resistant anaerobes will ever be detected. An increasing number of metronidazole resistant Bacteroides fragilis are being recorded and these organisms will be missed by such an approach. Most clinical microbiology laboratories regard a report of “mixed anaerobes” as adequate in many instances . Taxonomy • Anaerobic Gram-negative rods The taxonomy of the anaerobic bacteria is in a state of continuous change with the addition of new species and reclassification of old species. An example occurs in the genus Bacteroides, most of the saccharolytic pigmented species are now included in the genus Prevotella and the asaccharolytic species have been assigned to the genus Porphyromonas. There are more than 20 genera of anaerobic Gram-negative rods. The commonest human isolates are Bacteroides, Fusobacterium, Porphyromonas and Prevotella. • Anaerobic Gram-negative cocci Three genera are included in the anaerobic Gram-negative cocci, but only one Veillonella - is found in clinical material. There are seven species of Veillonella, of which Veillonella parvula is the most commonly isolated species from human specimens. • Anaerobic Gram-positive cocci The classification of the anaerobic Gram-positive cocci is continually changing with the addition of new species and renaming old species. There are six genera of anaerobic Gram-positive cocci which may be isolated from humans. They are: Peptostreptococcus (12 species with three proposed new species), Peptococcus (one species), Atopobium (one species), Coprococcus (three species), Ruminococcus (10 species) and Sarcina (three species). The majority of human isolates are Peptostreptococcus species. • Anaerobic Gram-positive rods The only genus of non-sporing, non-branching anaerobic Gram-positive rods of clinical importance is Eubacterium. There are 25 members of the genus. The genus is currently ill-defined and further taxonomic work is likely to sub-divide it. Eubacterium lentum has been reclassified as Eggerthella. E.lenta and is the species most frequently associated with human infections. Note: Some clostridia do not produce spores in vitro (eg.C.perfringens and C.ramosum) Source: The Commonsense Bug Workbook.doc Page: 40 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Flowchart: Identification of Anaerobes Source: The Commonsense Bug Workbook.doc Page: 41 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Presumptive identification of Non-sporing, Non-branching Anaerobes Source: The Commonsense Bug Workbook.doc Page: 42 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Characteristics of anaerobic Gram-negative rods • Bacteroides species Bacteroides species are rod shaped of variable size. Many are pleomorphic and show terminal or central swellings, vacuoles or filaments. They are bile resistant and carbohydrates are fermented. Bacteroides fragilis is the most commonly isolated species and is often β-lactamase positive. • Fusobacterium species Fusobacterium species are rods which may be spindle-shaped (Fusobacterium nucleatum) or pleomorphic (Fusobacterium necrophorum) These two species are the most commonly isolated from human clinical material. F.necrophorum is a cause of serious infections (necrobacillosis or Lemierre’s disease) commonly diagnosed in young adults and it can be recognised by production of indole and lipase on egg yolk agar. Fusobacterium species grown on Fastidious Anaerobe Agar containing blood may fluoresce yellow green (chartreuse) when exposed to long wave (365 nm) ultraviolet light. This phenomenon is medium-dependent. • Porphyromonas species The genus Porphyromonas includes asaccharolytic, catalase-negative species of human and animal origin. They are short rods 0.5-0.8 x 1.0-3.0 µm. Bile sensitive. Most Porphyromonas species isolated from humans are catalase-negative whilst those from animals are catalase-positive. Porphyromonas species may fluoresce brick red when exposed to long wave (365 nm) ultraviolet light and may produce a pigment (buff to tan to black) when grown on blood containing media due to porphyrin production. This phenomenon is medium dependent & Bile sensitive • Prevotella species The genus Prevotella is composed of mainly saccharolytic, pigmented or nonpigmented species previously classified as Bacteroides. They are usually pleomorphic. Young cultures of Prevotella species may fluoresce brick red when exposed to long wave (365 nm) ultraviolet light and this may fade to a tan or black pigment when grown on blood containing media for extended periods. Characteristics of anaerobic Gram-negative cocci • Veillonella species Veillonella species are small asaccharolytic cocci, measuring only 0.5 µm in diameter. They are the only Gram-negative anaerobic cocci which are isolated from human clinical material and are rarely found in pure culture. Veillonella species also fluoresce red on exposure to ultraviolet light (365 nm), but this is medium dependent and may fade in a few minutes, on exposure to oxygen. Some species produce catalase. Source: The Commonsense Bug Workbook.doc Page: 43 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Characteristics of anaerobic Gram-positive rods • Eubacterium species Eubacterium species are irregularly sized rods 0.2-2.0 x 0.3-10.0 µm, varying in shape from coccoid to long rods. They may be arranged singly, in pairs or chains. They are not frequently encountered in clinical specimens. Eubacterium lentum (now reclassified as Eggerthella lenta) is the commonest species, usually occurring in mixed cultures. Characteristics of anaerobic Gram-positive cocci associated with human infection • Peptostreptococcus species Peptostreptococcus species vary in size from 0.3 to 2.0µm and can be arranged in chains, pairs, tetrads or clumps, although the majority are present either as clumps or chains. Some species are aerotolerant. Some species are asaccharolytic and others are strongly saccharolytic. • Peptococcus species The genus Peptococcus now contains only one species, Peptococcus niger. Typically, cells are 0.3 to 1.3µm in diameter arranged singly, in pairs or clumps and it grows very slowly. Black pigment is produced after five days incubation but is lost on subculture. Other Gram-positive cocci associated with human infection • • • Atopobium parvula Coprococcus species Ruminococcus species Principles of anaerobic identification • Colonies are usually isolated on fastidious anaerobe agar (or equivalent) or blood agar incubated anaerobically and may be characterised by colonial morphology, Gram’s stain reaction and are sensitive to metronidazole. Some species may require longer than 48 hours incubation to grow. Identification tends to be undertaken only in exceptional situations if clinically indicated. Further identification tests include fluorescence under long wave UV light (365 nm), pigment production, bile tolerance, glucose fermentation and lecithinase and lipase activity on egg yolk agar. Classification of many anaerobes to species or even genus level requires additional biochemical tests, metabolic end product analysis by GLC or molecular techniques. Identification may be undertaken using commercial kits. For reliable results it is important to ensure purity by subculture on non-selective agar before attempting identification. Source: The Commonsense Bug Workbook.doc Page: 44 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Anaerobic Gram negative rods Target Organisms Bacteroides fragilis group reported to have caused human infection • • • • • • • • • • B. fragilis B. caccae B. distasonis B. eggerthii B. merdae B. ovatus B. stercoralis B. thetaiotaomicron B. uniformis B. vulgatus Bacteroides species (taxonomic position uncertain) reported to have caused human infection • • • • • • • • B. capillosus B. coagulans B. forsythus B. putredinis B. pyogenes B. splanchnicus B. tectum B. ureolyticus Fusobacterium species reported to have caused human infection • • • • • • • • • • • • • • • • • • F. alocis F. gonidiafromis F. mortiferum F. naviforme F. necrogenes F. necrophorum F. necrophorum subspecies funduliforme F. necrophorum subspecies necrophorum F. nucleatum F. nucleatum subspecies fusiforme F. nucleatum subspecies nucleatum F. nucleatum subspecies polymorphum F. nucleatum subspecies vincentii F. periodonticum F. russii F. sulci F. ulcerans F. varium Porphyromonas species reported to have caused human infection • • • • P. asaccharolytica P. catoniae P. endodontalis P. gingivalis Source: The Commonsense Bug Workbook.doc Page: 45 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Other Gram-negative anaerobic rods associated with human infections • • • • • • • • • • • • • • Anaerobiospirillum species Anaerorhabdus species Bilophila species Catonella species Centipeda species Dialister species Hallella species Johnsonella species Leptotrichia species Mitsuokella species Oribaculum species Selenomonas species Succinivibrio species Sutterella wadsworthia Prevotella species reported to have caused human infection • • • • • • • • • • • • • • • P. bivia P. buccae P. corporis* P. dentalis P. denticola* P. disiens P. enoeca P. heparinolytica P. intermedia* P. loescheii* P. melaninogenica* P. nigrescens* P. oris P. tannerae* Pigmented species Other genera of Gram-negative rods reported to have caused human infection • • • • • • • • • • • • • • • • • • • • Anaerobiospirillum succiniproducens Anaerobiospirillum thomasii Anaerorhabdus furcosus Bilophila wadsworthia Catonella morbi Centipeda periodontii Dialister pneumosintes Hallella seregens Johnsonella ignava Leptotrichia buccalis Sneathia sanguinegens Mitsuokella multiacida Selenomonas artemidis Selenomonas dianae Selenomonas flueggei Selenomonas infelix Selenomonas noxia Selenomonas sputigena Succinivibrio dextrinosolvens Sutterella wadsworthia Other species may be associated with human disease Source: The Commonsense Bug Workbook.doc Page: 46 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Flowchart: Anaerobic Gram Negative Bacilli Anaerobic Gram negative bacilli Growth on BBE Yes - Growth (Bile tolerant) Positive + Black (Esculin Pos) 1. Va = R (Bacteroides fragilis group) K=R C=R No Black (Esculin Neg) 2. Va = R (Bacteroides group) K=R C = S/R No Growth (Bile sensitive) Negative Zone size > 10mm = Susceptible 3. Va = R K=S C=S Presumptive Fusobacterium Mortiferium/varium gp 1. Va=S K=R C=R Porphyromonas sp. (Pigmenters, most indole POS) 2. Va = R K = R/S C = R/S Pigment Bile sensitive Prevotella species No Pigment UREA Positive - B.ureolyticus (Pitting or flat or cols) 3. Va = R K=S C=S Commercial identification kit eg sterile site Negative Positive Spot Indole Fusobacterium nucleatum (pointed ends) Fusobacterium necrophorum (rounded ends,pleomorphic) Other Fusobacterium species Negative Commercial Identification Kit (if required - eg Sterile site) Source: The Commonsense Bug Workbook.doc Page: 47 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Microscopic appearance Gram stain • Bacteroides, Porphyromonas and Prevotella species are small, Gram-negative rods of variable length. • Fusobacterium species are Gram-negative rods, highly variable in length and width and may have pointed ends. F.nucleatum is a slim filamentous rod usually with pointed ends and is indole positive. F.necrophorum also produces indole and lipase on egg yolk agar. Primary isolation media • Fastidious anaerobe agar or equivalent, (with or without neomycin – (some organisms may be inhibited by neomycin) 40-48h incubation anaerobically at 35-37°C. Note: some species may require longer incubation. insert diagram from p 39 (Specimen inoculated on to appropriate media) of manual Colonial appearance Genus Characteristics of growth on blood anaerobe agar after incubation anaerobically at 35-37°C Bacteroides Colonies are 1-3 mm diameter, circular, low convex, smooth, semi-opaque grey and are often moist or even mucoid. Mostly non-haemolytic and resistant to an ox-bile disc. Fusobacterium Colonial appearance is variable, but most are 1-3mm diameter, with an irregular or dentate edge. They vary from translucent to granular and opaque, F.necrophorum may be beta-haemolytic. Porphyromonas 1.0 mm diameter after 48 h incubation, smooth, shiny and grey. Dark brown or black pigment develops after 3-7 days. Growth may be enhanced by “satellitism” around colonies of other organisms e.g. staphylococci Prevotella Colonies are similar to those of Bacteroides, except some species are pigmented (may be pale brown to black). Most pigmented species are haemolytic Colonial appearance varies with the other genera of Gram negative rods Identification of Commonly Isolated Fusobacterium Species Species Cellular Morphology Indole Bile Growth Lipase Esculin hydrolysis F.nucleatum Slender, pointed ends + - - - F.mortiforum Bizarre,round bodies - + - + F.necrophorum Large, pleomorphic + -/+ + - V + - - F.varium Hint: Do not heat fix Gram of F.necrophorum, as bizarre shape morphology may not be seen. Greening of agar on oxygen exposure commonly occurs. This due to H2O2 production. Source: The Commonsense Bug Workbook.doc Page: 48 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Anaerobic Cocci Target Organisms Peptostreptococcus species reported to have caused human infection • • • • • • • • • • • • • • P. anaerobius P. asaccharolyticus P. hydrogenalis P. harei P. indolicus P. ivorii P. lacrimalis P. lactolyticus P. magnus P. micros P. octavius P. prevotii P. tetradius P. vaginalis Peptococcus species reported to have caused human infection • P. niger Other genera of Gram-positive cocci reported to have caused human infection • • • • • • • • • Atopobium parvulum Ruminococcus hansenii Ruminococcus productus Sarcina albus Sarcina pasteurii Sarcina ventriculi Coprococcus eutactus Coprococcus comes Coprococcus catus Veillonella species reported to have caused human infection • • • V. parvula V. atypica V. dispar Other species may be associated with human disease Microscopic appearance Gram stain • Peptostreptococcus and Peptococcus are Gram-positive cocci arranged in chains, pairs, tetrads or clumps. Veillonella are small Gram-negative cocci arranged in clumps. Primary isolation media • Fastidious anaerobe agar or equivalent (with or without neomycin) 40-48h incubation anaerobically at 35-37°C. Note: some species may require longer incubation. Source: The Commonsense Bug Workbook.doc Page: 49 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Flowchart: Anaerobic Cocci Source: The Commonsense Bug Workbook.doc Page: 50 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Colonial appearance Genus Characteristics of growth on fastidious anaerobe agar after incubation anaerobically at 35-37°C Peptostreptococcus magnus Small colonies (<1.0mm), often with variation in size and colour. Colonies may be convex and whitish and flatter and translucent on the same plate. Peptostreptococcus anaerobius Colonies 1-2mm in diameter, grey with slightly raised off-white centres, sensitive to SPS (liquoid) disc. Peptostreptococcus asaccharolyticus Colonies 1-2mm in diameter, glistening, low convex usually whitish to lemon-yellow. Peptostreptococcus micros Small colonies (<1.0mm), typically white (but sometimes grey), glistening and domed, sometimes surrounded by a yellow-brown halo up to 2mm wide. Peptococcus species Small colonies (<1.0mm), raised, grey, becoming dark brown/black. Veillonella species Small colonies (<1.0mm) after 48 hours incubation. May fluoresce red under long wavelength UV light (365nm). Colonial appearance varies with the other genera Source: The Commonsense Bug Workbook.doc Page: 51 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Clostridium species Target Organisms Clostridium species reported to have caused human disease Commonly isolated Rarely isolated Very rarely isolated • C.perfringens • C.novyii type A • C.tetani • C.septicum • C.sordellii • C.histolyticum • C.tertium • C.fallax • C.difficile • C.clostridioforme • C.botulinum Commonly isolated usually “non-pathogenic” clostridia • C.sporogenes • C.ramosum • C.innocuum • C.paraputrificum • C.cadaveris Primary isolation media • Agar containing blood incubated anaerobically at 35-37oC for 40-48h Microscopic appearance Gram stain • Gram-positive rods, which may possess a single endospore. Some species may be Gram-variable Spore stain • Used to determine the shape and position of the spore (phase contrast microscopy is an alternative option) • Gram stain is usually adequate to observe spores. Source: The Commonsense Bug Workbook.doc Page: 52 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Colonial appearance • Colonial appearance varies with species. Organism Classic Colony & Gram Morphology on Blood agar incubation at 35ºC for 48 hrs C.sporogenes Large (2-6mm), irregularly circular, raised yellowish grey centre and a “medusa head” periphery β-haemolytic and adhere to agar lipase positive C.sphenoides Small (1-2mm), non-haemolytic, circular with an entire margin Usually Gram negative, straight with tapered ends Spores oval & subterminal & swell the cell Sporing only occurs after ≥48hrs & involves only small number of cells. Indole positive Large, smooth convex colonies, but may be rough with an irregular edge. Usually have a double zone of haemolysis Spores rarely seen in vivo, when present are large oval, central or subterminal and distend the cell Lecithinase positive Grey-white, convex, circular colonies with crenated edge, which may spread. Many are β-haemolytic. Spores easily, oval, subterminal, often occur as free spores, and swell the cell slightly. Spores have a thick exosporium. Lecithinase positive, indole positive, urease positive. Spreading growth with a narrow zone of β-haemolysis, may spread over entire plate. Gram positive in young cultures, but Gram negative in old cultures Regularly combination of both Spores oval subterminal and distend the cell with no exosporium. 2-4mm, circular with slightly irregular margins May look like alpha streptococcus under aerobic conditions with no spores Spores are large, oval and terminal and greatly distend the cell. Large colonies, irregular margins and tend to swarm on moist media Gram positive in young cultures but become Gram negative after >24hrs incubation. Spores round and terminal and distend cell. “spoon” shaped. Often indole positive. C.perfringens C.sordellii C.septicum C.tertium C.tetani Source: The Commonsense Bug Workbook.doc Page: 53 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Clostridium Species Guidance Clinical specimens Primary isolation plate (blood containing agar incubated anaerobically) Β, or non-haemolytic colonies which may spread Gram stain Gram positive rods, which may have a single endospore (some species may appear Gram-negative) Further identification Identify further if clinically indicated Refer to Identification of Commonly Isolated Clostridia table Note: it is important to ensure the culture is pure, as the fine spreading growth of some Clostridium species may mask contamination organisms. Clostridium septicum Clostridium sordelli Clostridium perfringens Clostridium tertium Clostridium sphenoides Clostridium tetani Clostridium sporogenes Source: The Commonsense Bug Workbook.doc Page: 54 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Commonly Isolated Clostridia Species Spores* Egg Yolk Agar Lecthinase Lipase Aerobic Growth Indole Production Urease Comments C.bifermentans OS + - - + - Spores don’t swell or are free. C.perfringens** OS + - - - - No spores, non-motile, double zone haemolysis, box car shaped. C.septicum OSD - - - - - Swarms on plate. C.sordelli OSF + - - + + Spores swell & are free. Colonies are rhizoid shaped. C.sporogenes** OSD - + - - - Spores easily – may be only spores. OS - - - - - Horse stable smell. RS/TD - - - + - Few spores, pointed ends, usually stain Gram negative. OTD - - + - - Stains Gram positive in young cultures & Gram negative in old cultures. Aerotolerant, swarms. C.tetani RT - - - +/- - Tennis racket shape, may swarm C.clostridioforme OS - - - -/+ - Usually Gram negative. C.histolyticum OS - - +/- - - C.difficile C.sphenoides C.tertium** * O = oval R = round F = free D = distends cell S = subterminal T = terminal **Hints: Clostridium tertium - doesn’t spore aerobically Clostridium perfringens – haemolysis double zone enhanced by cold Clostridium sporogenes – ‘weird’ lipase reaction -> less ‘oily’ Source: The Commonsense Bug Workbook.doc Page: 55 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Anaerobic Gram positive non-sporing rods Target organisms Gram positive non-sporing rods reported to have caused human infection • • • • Bifidobacterium species Eubacterium lentum Propionibacterium species Actinomyces species Other species may be associated with human disease Microscopic appearance • Gram stain Irregular sized Gram positive non-branching rods, may be arranged singly, in pairs or chains. Primary isolation media • Fastidious anaerobe agar or equivalent (with or without neomycin), 40-48hr incubation anaerobically at 35-37ºC. For Actinomyces species use Actinomyces selective agar. Note: some species may require longer incubation. Colonial appearance • Colonies of Eubacterium species are 0.5-2mm diameter, circular, convex and translucent or slightly opaque, usually sensitive to 5µg metronidazole disc. Preliminary tests • N/A Source: The Commonsense Bug Workbook.doc Page: 56 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Presumptive Identification of Anaerobic Gram positive non-sporing rods Clinical specimen Primary isolation plate: Fastidious Anaerobe agar or equivalent with or without neomycin or metronidazole and naladixic acid for Actinomyces species. Gram stain Gram positive rod Metronidazole 5ug disc senstivity* Sensitive May have spore Large colony Fast growing Large rods Clostridium Resistant No spore Small colony Slow growing Small coccobacilli Actinomyces Propionibacterium Bifidobacterium Lactobacillus Further identification Identify further if clinically indicated Commercial identification kit *Rarely, some strains of Clostridium species may be resistant to metronidazole Source: The Commonsense Bug Workbook.doc Page: 57 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Vibrio & related species Target Organisms Vibrio species reported to have caused human disease • • • • • • • • • • • • • Vibrio alginolyticus Vibrio carchariae Vibrio cholerae Vibrio cincinnatiensis Vibrio damsela Vibrio fluvialis Vibrio furnissii Vibrio hollisae Vibrio metschnikovii Vibrio mimicus Vibrio parahaemolyticus Vibrio vulnificus Vibrio furnissii Any species of Vibrio may be found in faeces after the ingestion of seafood or water that contains them. Insert vibio flowchart MICROSCOPIC APPEARANCE Gram stain • Gram negative rods characteristically curved or comma.-shaped. This characteristic appearance is not always observed when the organism is Gram stained from solid media, and rarely from TCBS agar. Primary isolation media • • Blood agar incubated in air at 35-37ºC for 18-24hr TCBS agar incubated in air at 35-37ºC for 18-24hr Source: The Commonsense Bug Workbook.doc Page: 58 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Flowchart: Identification of Vibrio species Clinical Specimen Primary isolation plate (Blood agar or TCBS) Blood agar – colonies 2-3mm in diameter (some colonies haemolytic) TCBS – yellow/green 2-3 mm diameter colonies Gram stain (Characteristically curved or comma-shaped Gram-negative rods) Oxidase (from non-selective media) Positive Negative Vibrio string test Possible V.metschnikovii (check biochemistry before discarding*) Negative Positive ?Aeromonas species ?Shewanella species ?Plesiomonas species ?Vibrio species Commercial identification kit (may require NaCl supplementation) Vibrio species - confirm using salt tolerance test - Serological aggs eg V.cholerae 01,0139 Aeromonas species Shewanella species *V.metschnikovii produces yellow colonies on TCBS. Oxidase negative isolates with a different morphological appearance may be discarded Source: The Commonsense Bug Workbook.doc Page: 59 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Colonial Appearance • On blood agar colonies are 2-3mm in diameter. Some strains may be haemolytic. • After 18-24 hours incubation colonies on TCBS are at least 2mm in diameter and yellow for sucrose fermenters and green for non-sucrose fermenters. • Cultures should be examined quickly after removal from the incubator as the yellow colouration of the colonies may revert to a green colour when left at room temperature. • Organisms other than Vibrio species grow on TCBS. Organism V.cholerae V.alginolyticus V.cincinnatiensis V.damsela V.carchariae V.fluvialis V.furnissii V.hollisae V.parahaemolyticus V.metschnikovii V.vulnificus V.mimicus Aeromonas species Pseudomonas species Proteus species Enterococcus species Shewanella species Colour of colonies on TCBS yellow yellow yellow green yellow/green yellow yellow green green yellow green green yellow blue/green* yellow/green* yellow blue/green *The colonies are smaller than those produced by Vibrio species. Test procedures Oxidase Vibrio species are oxidase positive (oxidase tests may give false negative results on media containing carbohydrates – subculture to nutrient or blood agar before testing). Sensitivity to pteridine 0129 Most Vibrio species are sensitive with 150 µg but species differ with 10 µg discs (some strains of V.cholerae 01 and 0139 may be resistant to both disc contents) Vibrio String Test Vibrio species are positive, as are many other closely related organisms including Shewanella & Plesiomonas species. Aermonas species are negative. Serology Commercial identification kit These tests may require supplementation with NaCl. Refer to the manufacturer’s instructions. Source: The Commonsense Bug Workbook.doc Page: 60 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Interpretation & Reporting of Results • Presumptive identification may be made If appropriate growth characteristics, colonial appearance, Gram stain of the culture and oxidase results are demonstrated. • Confirmation of identification may be made Following 0129 sensitivity testing and/or Vibrio string testing, serology and commercial identification kit results. • To medical microbiologist Inform the medical microbiologist of all positive cultures from normally sterile sites, of all presumptive and confirmed Vibrio species that are known to be pathogenic or potentially pathogenic, and all isolates in outbreak situations. Inform the medical microbiologist if the request card bears information which suggests infection with V.cholerae or V.parahaemolyitcus, according to local protocols e.g. • • • • Severe water diarrhea Suspected cholera History of foreign travel, Suspected food poisoning (especially cases involving consumption of seafood). The medical microbiologist should also be informed of presumptive or confirmed Vibrio species in association with” • • • • • • Wound infection or (necrotizing) myofascitis Septicaemia history of foreign travel History of foreign travel Contact with (brackish) water, fishing/eating fish or seafood (suggestive of infection with V.vulnificus, V.damsela or Aeromonas hydrophila sensu lato) Alcoholism, substance abuse, immunodeficiency Other serious medical conditions such as cancer, or persons receiving treatment for cancer which induces neutropenia and/or mucositis. Source: The Commonsense Bug Workbook.doc Page: 61 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook % Positive V. V. V. V. V. V V. V. V. V. V. V cholerae mimicus metschnikovii cincinnatiensis hollisae .damsela fluvialis furnissii alginolyticus parahaemolyticus vulnificus .carchariae 0% NaCl 100 100 0 0 0 0 0 0 0 0 0 0 1% NaCl 100 100 100 100 99 100 99 99 99 100 99 100 6% NaCl 53 49 78 100 83 95 96 100 100 99 65 100 8% NaCl 1 0 44 62 0 0 71 78 94 80 0 0 10% NaC 0 0 4 0 0 0 4 0 69 2 0 0 12% NaCl 0 0 0 0 0 0 0 0 17 1 0 0 Test Growth in nutrient broth with: Reference: Manual of Clinical Microbiology Sixth Ed. Page 470. Shewanella algae Shewanella putrefaciens 0% NaCl - + 1% NaCl + - 42ºC Growth - + Source: The Commonsense Bug Workbook.doc Page: 62 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Campylobacter and related species Taxonomy • The family Campylobacteraceae (proposed in 1991) includes two colony related genera, Campylobacter and Arcobacter. The genus Campylobacter contains 14 species. TARGET ORGANISMS Campylobacter species reported to have caused human gastrointestinal infection • • • • Campylobacter jejuni Campylobacter coli Campylobacter lari Campylobacter upsaliensis Campylobacter species reported to have caused human extraintestinal infection • • • Campylobacter fetus Campylobacter hyointestinalis Campylobacter sputorum Campylobacter species reported to have caused human dental infection • • • Campylobacter consisus Campylobacter curvus Campylobacter rectus Characteristics • Members of the family Campylobacteraceae are curved, S-shaped or spiral Gram negative rods: coccal forms may be seen under sub-optimal conditions. • On selective agar the colonies are grey/white or creamy grey and moist in appearance. They are motile, Microaerophilic (optimum 5-10% oxygen) and oxidase positive. • Campylobacter species do not ferment or oxidise carbohydrates. A well recognized problem associated with identification of Campylobacter species is the lack of effective discriminating tests. • The species most commonly associated with diarrheal disease in humans are thermophilic i.e. they will grow at 42-43ºC and 37ºC but not at 25ºC. Source: The Commonsense Bug Workbook.doc Page: 63 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Principles of Identification • Preliminary identification of Campylobacter species from primary culture is by colonial appearance, Gram stain, growth in oxygen and oxidase test. • Species differentiation is difficult due to the lack of discriminating tests available in most routine microbiology laboratories. Primary isolation media • Blood agar or fastidious anaerobe agar incubated microaerobically or anaerobically at 42ºC, for at least 40-48 hours. • Blood cultures may be incubated at 37ºC as there is unlikely to be competing flora in these samples • Charcoal cefoperazone deoxycholate agar (CCDA) incubated microaerobically at 42ºC for 40-48 hours • Cultures may be incubated for a further 24 hours, if required • Some species may be inhibited by the antibiotics contained within the medium Source: The Commonsense Bug Workbook.doc Page: 64 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Differential characteristics of clinically relevant Campylobacter, Helicobacter, and Arcobacter species Genus & species C.coliº C.concisus C.curvus* C.fetus subsp fetus C.hyointestinalis C.jejuni C.jejuni subsp doylei C.lari C.rectus* C.sputorum C.upsaliensis H.cinaedi H.fennelliae H.pylori^ # A.butzleri # A.cryaerophilus Growth at 25°C 42°C + +/+ + + + + -/+ + +/-*** +/+ Slight + + + -/+ + - Hippurate Hydrolysis Catalase H2S in Triple Sugar Iron Agar Indoxyl Acetate Hydrolysis Nitrate to Nitrite + + - + + + + +/- or weak + + -/+ -/weak + + + + -/weak + +/- + + + + + - + + + + + + -/+ + + + + + + + + + + + + + + +/+ + Susceptible to 30µg disc Cephalothin Nalidixic acid +** ND + + + +** + + ND + + -/+ + + +/+ + + + +/+/- +, most strains positive; -, most strains negative; +/-, variable (more often positive); -/+, variable (more often negative); ND, test not done. * Anaerobic, not microaerobic. ^Strong and rapid positive urease # Aerotolerant, not microaerobic; except for a few strains, A.cryaeophilus cannot grow on MacConkey agar, whereas A.butzleri grows on MacConkey agar. **Isolates of quinolone resistant are becoming increasing more common. ***Hippurate negative strains exist. ºShould be reported as Campylobacter species as hippurate negative C.jejuni strains exist. Source: The Commonsense Bug Workbook.doc Page: 65 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Helicobacter species Target Organisms Helicobacter species reported to have caused human infection • • • • • • Helicobacter pylori Helicobacter cinaedi Helicobacter fennelliae Helicobacter canis Helicobacter pullorum Helicobacter heilmannii (non-culturable) Principles of Identification • Colonies from primary isolation plates are identified by colonial morphology, Gram stain and biochemical test. • Isolates may be referred to the Reference laboratory for confirmation of identification and typing. Microscopy • Gram negative curved or comma-shaped rods. Spiral or helical shapes are less evident. Older cultures may produce coccoid forms. Primary Isolation Media • Chocolate agar incubated in 5% oxygen with 5-10% CO2 at 35-37ºC for up to 7 days. Incubation for up to 10 days may be required post treatment. H.pylori is small (1mm) and translucent grey, may be slightly haemolytic. • H.pylori selective agar incubated in 5% oxygen with 5-10% CO2 at 35-37ºC for up to 7 days. Incubation for up to 10 days may be required post treatment. H.pylori are small (1-2mm) and convex on primary isolation. Test Procedures Organism Oxidase Urease Nitrate Growth at 42ºC Catalase H.pylori H.cinaedi H.fennelliae H.canis H.pullorum + + + + + + - + + + + + + + + + Source: The Commonsense Bug Workbook.doc Page: 66 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Haemophilus species and the HACEK group of organisms Introduction This section describes the identification of Haemophilus species and other members of theHACEK group (Haemophilus species, Actinobacillus actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens and Kingella species). Target Organisms HACEK group reported to have caused human infection • • • • • • Haemophilus influenzae Haemophilus aphrophilus Haemophilus ducreyi Haemophilus parainfluenzae Haemophilus paraphrophilus Haemophilus segnis Other species may be associated with human disease • • • • Actinobacillus actinomycetemcomitans Cardiobacterium hominis Kingella kingae Eikenella corrodens Characteristics of Haemophilus species • Haemophilus are Gram negative spherical, oval or rod-shaped cells less than 1µm in width, variable in length with marked pleomorphism and sometimes forming filaments. Small, round, convex, colonies, which may be iridescent, develop in 24 hours on chocolate blood agar. Iridescence is seen with capsulated strains. • All species require preformed growth factors present in blood, particularly X factor (protoporphyrin IX or protoheme) and/or V factor [nicotinamide adenine dinucleotide (NAD) or NAD phosphate (NADP)]. On blood agar H.influenzae exhibits satellitism around colonies of haemolytic S.aureus (a source of V factor). Haemophilus aphrophilus and Haemophilus paraphrophilus require CO2 for primary isolation. Carbohydrates are catabolised with the production of acid. A few species produce gas. The optimum growth temperature is 35-37ºC. They are facultatively anaerobic and non-motile. Nitrates are reduced to nitrites. • The optimum temperature for growth of Haemophilus ducreyi is 33-34ºC but growth is very slow and may be improved by the addition of Isovitalex to the culture medium. Some strains require CO2 for primary isolation. Source: The Commonsense Bug Workbook.doc Page: 67 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Characteristics of the HACEK group of organisms (For identification of Haemophilus species in the HACEK group see above_. • A systematic approach is used to differentiate the HACEK group of clinically encountered morphologically similar, aerobic and facultatively anaerobic Gram negative rods mainly associated with endocarditis and infections from normally sterile sites. These organisms are oropharyngeal/respiratory tract commensals. The identification is considered together with the clinical details and the isolates may be identified further if clinically indicated. • Actinobacillus actinomycetemcomitans A.actinomycetemcomitans is a Gram negative coccobacillus or a short rod 0.3-0.5 x 0.5-1.5 µm, which may exhibit irregular staining. A.actinomycetemcomitans is mostly bacillary but cocci are interspersed. Occasional longer forms up to 6 µm may occur. Cells are arranged singly, in pairs, or more rarely, in chains. Small amounts of extracellular slime may be produced. A.actinomycetemcomitans does not require X or V factors. After 24 hours incubation, colonies on blood or chocolate agar may be less than 0.5 mm and enlarge to 1mm after several days’ incubation. These colonies on blood or chocolate agar may be firm, adherent, star-shaped, sometimes with rough surfaces and pitting and may be difficult to remove from the agar surface. If extracellular slime is produced, cultures may be sticky on primary isolation. Surface cultures have low viability and may die within 5-7 days. It grows best under microaerophilic conditions with added CO2 and is facultatively anaerobic. The optimal growth temperature is 37ºC. Cells are nonmotile and urease is not produced. • Cardiobacterium hominis The genus Cardiobacterium contains only one species, Cardiobacterium hominis. Cells are pleomorphic or straight rods 0.5-0.75 µm in diameter and 1-3 µm in length with rounded ends, and long filaments may occur. Cells are arranged singly, in pairs, in short chains and in rosette clusters. They are Gram negative, but parts of the cell may stain Gram positive. Growth on blood agar is poor. C.hominis does not require X or V factors. Very small colonies are produced unless incubated in a humid aerobic or anaerobic atmosphere with 5% CO2. After incubation for two days, colonies are 1 mm in diameter, smooth, opaque and butyrous and some strains may pit the agar. C.hominis is facultatively anaerobic, but CO2 may be required by some strains on primary isolation. The optimum growth temperature is 30-37ºC. It is non-motile, oxidase positive and catalase and urease negative. • Eikenella corrodens The genus Eikenella contains only one species, Eikenella corrodens. Cells are straight, unbranched, non-sporing, slender Gram negative rods 0.3-0.4 x 1.5-4 µm in length. Colonies may be very small on blood agar after overnight incubation or may not be visible for several days. The colonies have moist, clear centres surrounded by flat, and sometimes spreading, growth. Pitting of the medium may occur and yellow colouration may be seen in older cultures due to cell density. There may be colonial variation and spreading growth may vary between colonies of the same isolate. E.corrodens is non-haemolytic but a slight greening may occur around the colonies. Haemin is usually required for aerobic growth and rare strains remain X-dependent after further subculture. The optimum growth temperature is 35-37ºC. Source: The Commonsense Bug Workbook.doc Page: 68 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook E.corrodens is non-motile, but twitching motility may be produced on some media. Strains are facultatively anaerobic, oxidase positive, catalase negative, urease negative and capnophilic. It may be confused with Bacteroides ureolyticus, which also exhibits pitting or corroding, but unlike E.corrodens is an obligate anaerobe and urease positive. • Kingella species The genus Kingella comprises two species, Kingella kingae and Kingella dentrificans. Kingella indologenes has been transferred to a new genus and classified as Suttonella indologenes. Kingella species are straight rods, 1.0 µm in length with rounded or square ends. They occur in pairs and sometimes short chains. Endospores are not formed. Cells are Gram negative but tend to resist decolourisation. Two types of colonies occur on blood agar, a spreading, corroding type and a smooth, convex type. It does not require X or V factors. Growth is aerobic or facultatively anaerobic. The optimum growth temperature is 33-37ºC. Kingella species are non-motile, oxidase positive, catalase negative and urease negative. Glucose and other carbohydrates are fermented with the production of acid but not gas. Kingella species may grow on Neisseria selective agar and therefore maybe misidentified as pathogenic Neisseria species. They can be differentiated from Moraxella and Neisseria species by a catalase test. Most Kingella species are catalase negative: Moraxella and most Neisseria species (except Neisseria elongate) are catalase positive. Primary isolation media • Chocolate agar incubated in 5-10% CO2 at 35-37ºC for 16-48 hrs Blood agar incubated in 5-10% CO2 at 35-37ºC for 16-48 hrs H.ducreyi selective agar incubated in 5-10% CO2 at 33-34ºC for 5 days Colonial appearance • Haemophilus species are small, round, convex colonies, which may be iridescent and develop after 24 hours incubation on chocolate agar. Satellitism of H.influenzae may be seen around colonies of S.aureus on blood agar. • Colonial morphology of other HACEK organisms varies with species and isolation media (see introduction and below) Source: The Commonsense Bug Workbook.doc Page: 69 of 80 SNP MICROBIOLOGY HACEK group organisms The Commonsense Bug Workbook Characteristics of growth on blood agar after aerobic incubation at 35-37ºC for 16-48 hrs For descriptions of Haemophilus species see Haemophilus species A.actinomycetemcomitans Will not grow in air but grows in air + CO2. Minute colonies at 24 hrs, 1 mm at 48 hrs. Firm, adherent, star-shaped colonies with rough surface and which may produce pitting of the agar. Some strains may be sticky. Non-haemolytic. C.hominis Some strains will not grow without added CO2. Colonies smooth, convex and opaque. 1-2 mm at 48 hrs. Slight alpha-haemolysis E.corrodens Colonies very small, moist, clear centres surrounded by flat growth. Pitting may occur. Spreading is rare and usually confined to a very small area around the colony. Non-haemolytic. Colonies 0.5-1 mm after 48 hrs. Requires 5-10% CO2. K.kingae Two types of colony: a spreading, corroding type and a smooth, convex type. Small zone of ß-haemolysis. Cells are often capsulate, producing mucoid colonies. Does not require 5-10% CO2. K.denitrificans Non-haemolytic. Two types of colony: a spreading, corroding type and a smooth, convex type Microscopic appearance • Gram stain: Haemophilus species are small coccobacilli or longer rod-shaped Gram negative cells, variable in length with marked pleomorphism and sometimes forming filaments. Other HACEK organisms produce spherical, oval or rod-shaped Gram negative cells which may be variable in length with marked pleomorphism or filament formation. Test procedures • Growth requirement for X and V factors or porphyrin synthesis test • Serotyping capsular H.influenzae strains with commercial type-specific antisera • Commercial identification kit Presumptive identification may be made • If appropriate growth characteristics, colonial appearance, Gram stain of the culture, oxidase and tributyrin test results are demonstrated Source: The Commonsense Bug Workbook.doc Page: 70 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Confirmation of identification may be made • Following commercial identification kit or other biochemical test results. Summary of X and V test results X factor V factor X + V factor Porphyrin No growth No growth Growth Negative H.haemolyticus No growth No growth Growth Negative H.parainfluenzae No growth Growth Growth Positive Growth Growth Growth Positive (weak) H.paraphrophilus No growth Growth Growth Negative H.segnis No growth Growth Growth Negative a H.influenzae b H.aphrophilus a H.influenzae biovar aegyptius is indistinguishable from H.influenzae biotype III in normal laboratory tests b ß-haemolytic on horse blood agar Source: The Commonsense Bug Workbook.doc Page: 71 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Pasteurella Species Introduction • This section describes the procedure for the identification of Pasteurella species and distinguishes these from morphologically similar species. Taxonomy • Currently some 20 species are included in the genus Pasteurella. Not all of these are true members. DNA-DNA hybridization indicates that some of the species are more closely related to the genus Actinobacillus. • Pasteurella multocida is the type species of the genus. Characteristics of Pasteurella species • Pasteurella species are spherical, ovoid or rod-shaped cells 0.3-1.0 µm in diameter and 1.0-2.0 µm in length. Cells are Gram negative, and occur singly, or in pairs or short chains. Bipolar staining may be seen. Capsules may be present. Pasteurella species are non-motile, and are facultatively anaerobic. • Pasteurella species have both an oxidative and fermentative metabolisms. The optimum growth temperature is 37ºC. Glucose and other carbohydrates are catabolised with the production of acid but no gas. Most species are catalase positive and oxidase positive; nitrates are reduced to nitrites by almost all species. • Colonies of Pasteurella species are usually grey and viscous, with a strong mucinous odour. Rough, irregular colonies may also occur. Freshly isolated strains of Pasteurella haemolytica produce clear zones of ß-haemolysis on blood agar – this organism is a cause of mastitis and septicaemia in some peridomestic animals, but is very rarely the cause of human infection. • Pasteurella and Actinobacillus species are so similar, that no single phenotypic feature reliable distinguishes between the two genera. In clinical practice, however, an organism with characteristics corresponding to the genus Pasteurella is highly likely to be so, if recovered from clinical specimens in association with a bite from a cat or dog. • The genus Actinobacillus now includes Actinobacillus ureae – formerly Pasteurella ureae. A.ureae is thought to be a commensal or opportunist pathogen of human beings, and is principally reported in connection with disease of the respiratory tract (e.g. cases of pneumonia, lung abscess). Occasionally, invasive infections (septicaemia, meningitis) are also reported. • As the name suggest, A.ureae is urease positive. Most species of Pasteurella are urease negative (including P.multocida). Thus, a Pasteurella – like organism, urease positive, recovered in association with human respiratory tract disease, is likely to be A.ureae. • Phenotypically, Pasteurella species may resemble Haemophilus species – but Pasteurella species will not regularly exhibit satellitism around colonies of Staphylococcus species, nor are they regularly auxotropic for X or V factors; growth is not especially enhanced by use of chocolatised blood agar. Source: The Commonsense Bug Workbook.doc Page: 72 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification • Colonies on blood agar are identified by colonial morphology, Gram stain, and oxidase test and catalase production. Additional tests are needed for confirmation and/or isolates should be referred to the Reference laboratory. Target Organisms Pasteurella species reported to have caused human infection • • • • • • • • • • • P.aerogenes P.bettyae P.canis P.dagmatis P.gallinarum P.haemolytica (Biotype A) P.multocida subspecies gallicida P.multocida subspecies multocida P.multocida subspecies septica P.pneumotropica P.stomatis Microscopic Appearance • Gram stain Spherical, ovoid or rod-shaped Gram negative cells which occur singly or in pairs or short chains. Bipolar staining is common. Capsules may be present. Primary Isolation • Blood agar 16-48 hrs incubation in 5-10% CO2 at 35-37ºC Colonial Appearance • Colonies are grey and viscous but rough irregular colonies occur frequently. Freshly isolated strains of P.haemolytica produce clear zones of ß-haemolysis on blood agar. Identification Oxidase test – Positive (almost always) Catalase test – Positive Sensitivity to penicillin – Sensitive Commercial identification kit Source: The Commonsense Bug Workbook.doc Page: 73 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Flowchart: Identification of Pasteurella species – summary Clinical specimens Primary isolation plate (blood agar) Pasteurella species are grey, viscous, rough, irregular, non-haemolytic colonies on blood agar P.haemolytica are beta-haemolytic on blood agar Gram stain Gram negative rods or cocco-bacilli Oxidase* Positive Possible Pasteurella species Negative Not Pasteurella species** Catalase* Positive Possible Pasteurella species Negative Not Pasteurella species*** Sensitivity to Penicillin Sensitive Possible Pasteurella species Resistant Not Pasteurella species Commercial identification kit *All oxidase and catalase reactions may be weak **P.bettyae is oxidase negative ***P.haemolytica Biotype T is catalase negative Source: The Commonsense Bug Workbook.doc Page: 74 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Results & Reporting Presumptive identification may be made: If appropriate growth characteristics, colonial appearance, Gram stain of the culture, oxidase and catalase test results are demonstrated Confirmation of identification may be made: Following use of a commercial kit and/or referral to a Reference laboratory To medical microbiologist The medical microbiologist should be informed of presumptive or confirmed Pasteurella species when the request bears relevant information e.g. • • • • • • Animal bite Wound infection or septic arthritis Septicaemia Meningeoencephalitis Pneumonia, empyema thoracis or lung abscess History of farming or veterinary work Source: The Commonsense Bug Workbook.doc Page: 75 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Moraxella species and Morphologically similar species Introduction • This section describes the identification of Moraxella species and those species which are morphologically similar. Target Organisms Moraxella species and morphologically similar organisms reported to have caused human infection • • • • • • • • • • M.atlantae M.catarrhalis M.lacunata M.nonliquefaciens M.osloensis K.denitrificans K.kingae O.urethralis P.immobilis P.phenylpyruvicus Taxonomy • The genera Moraxella (including the former Branhamella), Acinetobacter and Psychrobacter currently belong to the family Moraxellaceae; the classification is still under review. The genus Oligella includes the previous Moraxella urethralis and CDC group M-4 now both classified as Oligella ureolytica. Kingella kingae (formally referred to as Moraxella kingii or Moraxella new species I) has been placed in the genus Kingella. Kingella denitrificans, previously designated CDC group TM-1 has also been placed in this genus. Psychrobacter phenylpyruvicus (formally Moraxella phenylpyruvica) is phenotypically similar to Moraxella lincolnii and M.osloensis. P.phenylpyruvicus is urease positive. Brucella species can be misidentified as P.phenylpyruvicus in some commercial identification kits. Microscopic Appearance • Gram stain Gram negative with a tendency to resist decolourisation Moraxella subgenus Moraxella Rods often coccobacilli. Usually occur in pairs or short chains with one plane of division Moraxella subgenus Branhamella Cocci occur singly or in pairs with adjacent sides flattened, sometimes forming tetrads Kingella species Plump rods or coccobacilli occurring in pairs or chains Oligella species Small rods or coccobacilli, often occurring in pairs. Cells lack the typical plumpness of Moraxella species. Psychrobacter phenylpyruvicus Rods, often coccobacilli. Usually occur in planes with one plane of division. Microscopy can differentiate Brucella species (very small coccobacilli) from P.phenylpyruvicus Source: The Commonsense Bug Workbook.doc Page: 76 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Characteristics of Moraxella species • Genus Moraxella Moraxella species are Gram negative and cells may be capsulated. They are nonmotile and aerobic, but some strains may grow weakly under anaerobic conditions. Most species except Moraxella osloensis are nutritionally fastidious. The optimum growth temperature is 33-35ºC. Moraxella species are usually catalase positive, oxidase positive and do not produce acid from carbohydrates. Colonies of Moraxella lacunata and Moraxella nonliquefaciens are small on blood agar. Some strains of M.lacunata are haemolytic. Moraxella catarrhalis is the most frequently isolated species of Moraxella and can be differentiated form Neisseria species by the tributyrin test: M.catarrhalis is positive and Neisseria species are negative. However, as the tributyrin test is positive for Moraxella species other than M.catarrhalis, it cannot be used to differentiate among the Moraxellae. Ninety percent of M.catarrhalis are ßlactamase positive. The genus is divided into Moraxella subgenus Moraxella that includes all the rod shaped species, and Moraxella subgenus Branhamella which contains the cocci. • Moraxella subgenus Moraxella Rods are often very short and plump, approaching a coccus shape 1.0-1.5 x 1.5-2.5 µm. Cells usually occur in pairs or short chains with one plane of division. Pleomorphism is enhanced by lack of oxygen and by incubation at temperatures above the optimum. The medically important species are Moraxella atlantae, M.lacunata, M.nonliquefaciens and M.osloensis. • Moraxella subgenus Branhamella Cocci 0.6-1.0 µm in diameter occur singly or in pairs with adjacent sides flattened and sometimes from tetrads. There is one medically important species M.catarrhalis. Identification • Colonies isolated on chocolate or blood agar plates are identified by colonial morphology, Gram stain and oxidase reaction. Further biochemical identification may be performed. If required, isolates may be referred to the Reference laboratory for confirmation and further identification. Primary isolation media • Blood or chocolate agar 16-48 hrs incubation in 5-10% CO2 at 35-37ºC Source: The Commonsense Bug Workbook.doc Page: 77 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Identification of Moraxella species and morphologically similar species Clinical specimens Primary isolation plate Moraxella species are white or buff, convex colonies on blood agar Kingella species are smooth entire convex or spreading colonies 0.5-1 mm in diameter. K.kingae is haemolytic Oligella species are small, white opaque and non-haemolytic Psychrobacter species are non-pigmented smooth opaque colonies Gram stain Gram negative rods or coccobacilli Oxidase Positive Possible Moraxella species or P.phenylpyruvicus Negative Possible Acinetobacter species Tributyrin Negative Neisseria species Positive Moraxella species If clinically indicated If clinically indicated Commercial identification kit* or other identification *Note: Commercial kits may misidentify Brucella species as P.phenylpyruvicus Source: The Commonsense Bug Workbook.doc Page: 78 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook Colonial appearance • Moraxella subgenus Moraxella Smooth, flat, uniform, buff colonies 1-2mm in diameter Colonies of M.lacunata, M.atlantae and M.nonliquefaciens are small on blood agar. M.lacunata and M.atlantae also pit the agar. Some strains of M.lacunata are haemolytic. • Moraxella subgenus Branhamella Smooth, round, uniform, grey/brown colonies 1 mm in diameter • Kingella species Two types of colonies occur on blood agar, a smooth entire convex type or a spreading colony. Colonies are small 0.5-1 mm in diameter after 48 hrs. Kingella kingae produce distinct zones of beta-haemolysis. • Oligella species Colonies are small after 24 hrs incubation. They are white, opaque, entire and nonhaemolytic. • Psychrobacter phenylpyruvicus Requires incubation at 20-25ºC. Colonies of P.phenylpyruvicus are small on blood agar. Growth is enhanced by bile salts to form non-pigmented, smooth, opaque colonies. Identification • Oxidase test – positive • Tributyrin test - positive • Commercial identification kit – Additional biochemical / other tests Source: The Commonsense Bug Workbook.doc Page: 79 of 80 SNP MICROBIOLOGY The Commonsense Bug Workbook References • Bergey’s Manual of Systematic Bacteriology, Volume 2. • Identification of Unusual Pathogenic Gram-Negative Aerobic and Facultatively Anaerobic Bacteria, Second Edition. • Manual of Clinical Microbiology, 7 Edition. • Manual of Clinical Microbiology, 8 Edition. • Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3 Edition. • British National Standard Methods – Bacteriology 2006. th th rd Source: The Commonsense Bug Workbook.doc Page: 80 of 80
© Copyright 2024