Microorganisms The agents most commonly seen in outpatient and hospital routine, with identification, growth media and conditions, intrinsic resistance and the reading pitfalls for each one. Search by name, infection site or mechanism — for example MRSA , urine or carbapenemase .
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All Gram-positive cocci Gram-positive bacilli Enterobacterales Non-fermenters Fastidious organisms Anaerobes Yeasts and fungi
57 microorganisms
Gram-positive cocci Staphylococcus aureus Gram-positive cocci in clusters
+ Identification Catalase-positive, coagulase-positive (tube or latex test) DNase-positive, ferments mannitol on mannitol salt agar Remains susceptible to novobiocin How it grows Blood agar: golden-yellow colonies, 1–3 mm, beta-hemolysis Mannitol salt agar (7.5% NaCl): yellow colonies with medium colour change 35–37 °C, aerobic incubation, 18–24 h Where it appears Skin and soft-tissue infection, abscesses, furunculosis (outpatient setting) Catheter-related bacteremia, endocarditis, osteomyelitis, pneumonia Intrinsic resistance Aztreonam, colistin and nalidixic acid have no activity against Gram-positive organisms (EUCAST Expected Resistant Phenotypes v1.2) Temocillin and the polymyxins should not be reported Bench alerts Cefoxitin is the surrogate marker for MRSA: if resistant, report resistance to all beta-lactams (except ceftaroline) Erythromycin R + clindamycin S requires a D-test for inducible MLSb resistance Disk diffusion for vancomycin is not valid — MIC testing must be used Interpret zones in antibiogram Gram-positive cocci Staphylococcus coagulase-negativos (S. epidermidis) Gram-positive cocci in clusters
+ Identification Catalase-positive, coagulase-negative S. epidermidis: novobiocin-susceptible, biofilm producer How it grows Blood agar: small, white, non-hemolytic colonies 35–37 °C, aerobic incubation, 18–48 h Where it appears Frequent blood culture contaminant (a single positive bottle) True infection on prosthetic material, long-term catheters and shunts Intrinsic resistance Aztreonam, colistin and nalidixic acid have no activity (intrinsic resistance in Gram-positive organisms) Bench alerts Only regard as clinically significant with ≥2 positive bottles or prosthetic material Methicillin resistance (cefoxitin-positive) is very common (>70% in the hospital setting) Interpret zones in antibiogram Gram-positive cocci Staphylococcus saprophyticus Gram-positive cocci in clusters
+ Identification Catalase-positive, coagulase-negative Resistant to novobiocin (5 µg disk) — defining feature How it grows Blood agar and CLED agar; white to slightly yellowish colonies, 35–37 °C/24 h Where it appears Cystitis in young, sexually active women, outpatient setting Intrinsic resistance Aztreonam, colistin and nalidixic acid have no activity Bench alerts May be clinically significant even at lower colony counts on urine culture Routine reporting of fosfomycin and nalidixic acid is not required — follow the standard urinary panel Interpret zones in antibiogram Gram-positive cocci Staphylococcus lugdunensis Gram-positive cocci in clusters
+ Identification Tube coagulase-negative, but clumping factor (latex test) frequently positive Ornithine decarboxylase and PYR positive How it grows Blood agar: colonies with mild hemolysis, characteristic odour, 24 h at 35 °C Where it appears Aggressive endocarditis, skin and prosthetic-device infection — behaves like S. aureus Intrinsic resistance Aztreonam, colistin and nalidixic acid have no activity Bench alerts Should never be dismissed as a contaminant Interpret oxacillin/cefoxitin using S. aureus criteria, not coagulase-negative staphylococci criteria Interpret zones in antibiogram Gram-positive cocci Streptococcus pyogenes (grupo A) Gram-positive cocci in chains
+ Identification Catalase-negative, PYR-positive Susceptible to bacitracin (0.04 U disk) Lancefield group A latex agglutination How it grows Sheep blood agar: small, translucent colonies with wide zones of beta-hemolysis 35–37 °C with 5% CO₂, 18–24 h Where it appears Pharyngotonsillitis, scarlet fever, erysipelas, necrotizing fasciitis Intrinsic resistance Aztreonam, colistin, aminoglycosides (low level) and sulfonamides have no clinical activity (EUCAST Expected Resistant Phenotypes v1.2) Bench alerts No confirmed penicillin resistance has ever been reported — report as susceptible without testing Test macrolides and clindamycin (with D-test) for penicillin-allergic patients Interpret zones in antibiogram Gram-positive cocci Streptococcus agalactiae (grupo B) Gram-positive cocci in chains
+ Identification Catalase-negative, CAMP test-positive, hippurate-positive Resistant to bacitracin, Lancefield group B latex-positive How it grows Blood agar: greyish colonies with a narrow zone of beta-hemolysis Selective Todd-Hewitt broth for antenatal screening; 35–37 °C, CO₂ Where it appears Vaginal/rectal colonization in pregnant women, early-onset neonatal sepsis, urinary tract infection Intrinsic resistance Aztreonam, colistin and low-level aminoglycosides have no activity Bench alerts Antenatal screening at 35–37 weeks requires enrichment broth In penicillin-allergic patients, test clindamycin with a D-test Interpret zones in antibiogram Gram-positive cocci Streptococcus pneumoniae Lancet-shaped Gram-positive diplococci
+ Identification Catalase-negative, alpha-hemolytic Susceptible to optochin (P disk), bile-soluble How it grows Blood agar with 5% CO₂: mucoid, umbilicate, alpha-hemolytic colonies 35 °C, 18–24 h; autolysis after 48 h Where it appears Community-acquired pneumonia, otitis media, sinusitis, meningitis Intrinsic resistance Aztreonam, colistin, aminoglycosides and sulfonamides have no activity Bench alerts Oxacillin 1 µg screening disk: a zone < 20 mm requires a penicillin MIC Interpretation of penicillin susceptibility depends on the infection site (meningeal vs. non-meningeal, per EUCAST breakpoint tables v15.0) Use Mueller-Hinton agar supplemented with blood, incubated in CO₂, for disk diffusion Interpret zones in antibiogram Gram-positive cocci Streptococcus do grupo viridans Gram-positive cocci in chains
+ Identification Catalase-negative, alpha-hemolytic, optochin-resistant, bile-insoluble Differentiation from pneumococcus is mandatory How it grows Blood agar, 35 °C with CO₂, 24–48 h; small alpha-hemolytic colonies Where it appears Subacute endocarditis, abscesses, bacteremia in neutropenic patients (mitis group) Intrinsic resistance Aztreonam, colistin and low-level aminoglycosides have no activity Bench alerts Penicillin resistance is not rare — always determine the MIC in suspected endocarditis Common as a single-bottle blood culture contaminant Interpret zones in antibiogram Gram-positive cocci Enterococcus faecalis Gram-positive cocci in pairs and short chains
+ Identification Catalase-negative, PYR-positive, bile-esculin-positive, grows in 6.5% NaCl Arabinose-negative (differentiates from E. faecium) How it grows Blood agar: grey colonies, gamma- or alpha-hemolytic Bile-esculin: blackening of the medium; 35 °C, 24–48 h Where it appears Urinary tract, intra-abdominal and endocarditis infections, hospital-acquired bacteremia Intrinsic resistance Cephalosporins (all generations) (EUCAST Expected Resistant Phenotypes v1.2) Low-level aminoglycosides — only high-level synergy testing is clinically useful Trimethoprim-sulfamethoxazole (may appear susceptible in vitro but is not clinically effective), clindamycin, aztreonam, polymyxins Bench alerts Never report a cephalosporin or SXT as susceptible In endocarditis, test high-level gentamicin/streptomycin for synergy Interpret zones in antibiogram Gram-positive cocci Enterococcus faecium Gram-positive cocci in short chains
+ Identification Catalase-negative, PYR-positive, bile-esculin-positive Arabinose-positive How it grows Blood agar and bile-esculin agar, 35 °C, 24–48 h Where it appears ICU bacteremia, surgical-site infection, intestinal colonization Intrinsic resistance Cephalosporins, low-level aminoglycosides, SXT, clindamycin, aztreonam, polymyxins (EUCAST Expected Resistant Phenotypes v1.2) Bench alerts Ampicillin resistance is the rule (commonly >80% in hospital isolates), unlike E. faecalis VRE: screen with vancomycin; confirm by MIC and notify infection control immediately Interpret zones in antibiogram Gram-positive bacilli Listeria monocytogenes Short Gram-positive bacilli, may resemble coccobacilli
+ Identification Catalase-positive, umbrella-shaped motility at 25 °C, CAMP-positive Esculin-positive How it grows Blood agar: small colonies with a narrow zone of beta-hemolysis Grows at 4 °C (cold enrichment) and at 35 °C Where it appears Meningitis in the elderly and immunosuppressed, gestational listeriosis, neonatal sepsis Intrinsic resistance Cephalosporins of all generations (EUCAST Expected Resistant Phenotypes v1.2) Fosfomycin (may appear susceptible in vitro but is not clinically effective) Bench alerts Do not mistake for a contaminant diphtheroid in CSF Treatment of choice is ampicillin; a cephalosporin should never be reported as an option Interpret zones in antibiogram Gram-positive bacilli Corynebacterium spp. (difteroides) Pleomorphic Gram-positive bacilli in palisade / Chinese-letter arrangement
+ Identification Catalase-positive, non-motile C. urealyticum: strongly urease-positive, slow growth How it grows Blood agar, 35 °C, 24–48 h; C. urealyticum may need 48–72 h C. diphtheriae: tellurite agar (black colonies) and Loeffler medium Where it appears A skin contaminant in most cases Clinically relevant with prosthetic material, catheters, alkaline urinary infection (C. urealyticum) and diphtheria Intrinsic resistance Fosfomycin in several species; polymyxins and aztreonam have no activity Bench alerts Only regard as significant in pure culture, sterile-site material, or on repeat isolation Vancomycin is the predictable option for multidrug-resistant strains Interpret zones in antibiogram Enterobacterales Escherichia coli Gram-negative bacilli
+ Identification Oxidase-negative, indole-positive, lactose-fermenting TSI A/A with gas; IMViC ++-- How it grows MacConkey agar: pink colonies (lactose-positive) EMB agar: green metallic sheen; CLED agar: yellow colonies 35–37 °C, aerobic incubation, 18–24 h Where it appears Leading cause of both outpatient and hospital-acquired urinary tract infection Bacteremia of urinary/abdominal source, peritonitis, diarrhea (diarrheagenic pathotypes) Intrinsic resistance Penicillin G, macrolides, clindamycin, glycopeptides, linezolid, daptomycin, fusidic acid (EUCAST Expected Resistant Phenotypes v1.2) Bench alerts ESBL: resistance to cefotaxime/ceftriaxone/ceftazidime — report cephalosporins as R and avoid their use Carbapenemase (KPC/NDM): a reduced meropenem zone requires confirmatory testing and notification to infection control Interpret zones in antibiogram Enterobacterales Klebsiella pneumoniae Encapsulated Gram-negative bacilli
+ Identification Oxidase-negative, non-motile, indole-negative, weakly urease-positive, VP-positive TSI A/A with abundant gas How it grows MacConkey agar: large, mucoid, pink colonies Hypervirulent strain: positive string test (> 5 mm) 35–37 °C, 18–24 h Where it appears Hospital-acquired pneumonia, UTI, bacteremia, surgical-site infection, liver abscess Intrinsic resistance Ampicillin and amoxicillin (chromosomal SHV beta-lactamase) Penicillin G, macrolides, clindamycin, glycopeptides, linezolid, daptomycin Bench alerts Never report ampicillin as susceptible The leading KPC producer in Brazil — a reduced meropenem zone is an outbreak warning ESBL production is frequent in the hospital setting Interpret zones in antibiogram Enterobacterales Klebsiella aerogenes (antiga Enterobacter aerogenes) Gram-negative bacilli
+ Identification Oxidase-negative, motile, ornithine-positive, lysine-positive, urease-negative TSI A/A with gas How it grows MacConkey agar: lactose-fermenting colonies, 35–37 °C, 24 h Where it appears Hospital-acquired respiratory, urinary and bloodstream infection Intrinsic resistance Ampicillin, amoxicillin-clavulanate, cefalotin and cefoxitin (chromosomal AmpC, EUCAST Expected Resistant Phenotypes v1.2) Bench alerts Inducible AmpC: a strain initially susceptible to ceftriaxone may become resistant during therapy Prefer cefepime or a carbapenem in severe infection Interpret zones in antibiogram Enterobacterales Enterobacter cloacae complex Gram-negative bacilli
+ Identification Oxidase-negative, motile, ornithine-positive, lysine-negative, VP-positive TSI A/A with gas How it grows MacConkey agar, lactose-positive, 35–37 °C, 18–24 h Where it appears Ventilator-associated pneumonia, hospital-acquired UTI, catheter-related infection Intrinsic resistance Ampicillin, amoxicillin-clavulanate, cefalotin, cefoxitin (chromosomal AmpC, EUCAST Expected Resistant Phenotypes v1.2) Bench alerts Risk of AmpC derepression under third-generation cephalosporin therapy Always report the natural resistance even when the zone appears susceptible Interpret zones in antibiogram Enterobacterales Serratia marcescens Gram-negative bacilli
+ Identification Oxidase-negative, DNase-positive, gelatinase-positive, lipase-positive Lactose-negative or late lactose fermenter; ONPG-positive How it grows May produce a red pigment (prodigiosin) at 25 °C MacConkey agar: colourless to pale-pink colonies; 35 °C, 24 h Where it appears Outbreaks in neonatal ICUs, pneumonia, catheter-associated UTI, bacteremia Intrinsic resistance Ampicillin, amoxicillin-clavulanate, cefalotin, cefoxitin (chromosomal AmpC) Colistin/polymyxin B and nitrofurantoin (EUCAST Expected Resistant Phenotypes v1.2) Bench alerts Never report a polymyxin as a therapeutic option Isolates clustered in time suggest a common source — notify infection control Interpret zones in antibiogram Enterobacterales Proteus mirabilis Gram-negative bacilli
+ Identification Oxidase-negative, strongly urease-positive, H₂S-positive on TSI (K/A H₂S+) Indole-negative (differentiates from P. vulgaris) How it grows Blood agar: swarming motility spreading as a veil across the plate MacConkey agar: lactose-negative, no swarming; 35 °C, 24 h Where it appears UTI, especially in catheterized patients; struvite stones from urine alkalinization Intrinsic resistance Colistin/polymyxin B (EUCAST Expected Resistant Phenotypes v1.2) Nitrofurantoin and tetracyclines (including tigecycline) Bench alerts Do not report nitrofurantoin on a urine culture with Proteus Imipenem breakpoints do not apply to this genus Swarming can mask another organism — use MacConkey agar to separate colonies Interpret zones in antibiogram Enterobacterales Morganella morganii Gram-negative bacilli
+ Identification Oxidase-negative, urease-positive, indole-positive, H₂S-negative, ornithine-positive How it grows MacConkey agar, lactose-negative, no swarming; 35 °C, 24 h Where it appears Complicated UTI, wound infection, bacteremia in hospitalized patients Intrinsic resistance Colistin/polymyxin B, nitrofurantoin, tetracyclines (EUCAST Expected Resistant Phenotypes v1.2) Ampicillin, amoxicillin-clavulanate, cefalotin, cefoxitin (chromosomal AmpC) Bench alerts Broad intrinsic-resistance profile — check before releasing the report Imipenem breakpoints do not apply Interpret zones in antibiogram Enterobacterales Providencia spp. Gram-negative bacilli
+ Identification Oxidase-negative, indole-positive, citrate-positive, ornithine-negative P. stuartii: variable urease activity How it grows MacConkey agar, lactose-negative; 35 °C, 24 h Where it appears UTI associated with prolonged catheterization and long-term care patients Intrinsic resistance Colistin/polymyxin B, nitrofurantoin, tetracyclines (EUCAST Expected Resistant Phenotypes v1.2) Ampicillin and first-generation cephalosporins Bench alerts Imipenem breakpoints do not apply Multidrug resistance is frequent Interpret zones in antibiogram Enterobacterales Citrobacter freundii Gram-negative bacilli
+ Identification Oxidase-negative, citrate-positive, H₂S-positive, indole-negative, lysine-negative May be confused with Salmonella on TSI How it grows MacConkey agar: late lactose fermentation; 35 °C, 24 h Where it appears UTI, wound infection, hospital-acquired bacteremia Intrinsic resistance Ampicillin, amoxicillin-clavulanate, cefalotin, cefoxitin (chromosomal AmpC, EUCAST Expected Resistant Phenotypes v1.2) Bench alerts Lysine-negative and ONPG-positive results separate it from Salmonella — confirm with serology on stool isolates Inducible AmpC: the same caution applies as for Enterobacter Interpret zones in antibiogram Enterobacterales Salmonella spp. Gram-negative bacilli
+ Identification Oxidase-negative, lactose-negative, H₂S-positive, lysine-positive, indole-negative, urease-negative Serological confirmation with O and H antisera How it grows SS and Hektoen agar: colonies with a black centre; XLD agar: red colonies with a black centre Enrichment in selenite or tetrathionate broth; 35–37 °C, 24 h Where it appears Outpatient gastroenteritis, typhoid fever, bacteremia in immunosuppressed patients Intrinsic resistance Penicillin G, macrolides, clindamycin, glycopeptides, linezolid, daptomycin Bench alerts Aminoglycosides and first-/second-generation cephalosporins may appear susceptible in vitro but fail clinically — do not report Screen for reduced fluoroquinolone susceptibility with nalidixic acid/pefloxacin Notifiable disease in outbreak settings Interpret zones in antibiogram Enterobacterales Shigella spp. Gram-negative bacilli
+ Identification Oxidase-negative, non-motile, lactose-negative, H₂S-negative, lysine-negative, no gas production Serological confirmation by group (A–D) How it grows MacConkey/SS agar: colourless colonies; 35–37 °C, 24 h Where it appears Dysentery with mucus and blood, outpatient and daycare settings Intrinsic resistance Penicillin G, macrolides, clindamycin, glycopeptides, daptomycin Bench alerts Aminoglycosides and first-/second-generation cephalosporins should not be reported (clinical failure despite in vitro activity) Report outbreaks; SXT and ampicillin resistance rates are high in Brazil Interpret zones in antibiogram Non-fermenters Pseudomonas aeruginosa Slender Gram-negative bacilli
+ Identification Oxidase-positive, non-fermenter (TSI K/K), grows at 42 °C Pyocyanin (blue) and pyoverdine (green fluorescent) pigments; grape-like odour How it grows MacConkey agar: lactose-negative, flat colonies with an irregular edge and metallic sheen Selective cetrimide agar; 35–42 °C, 18–24 h Where it appears Ventilator-associated pneumonia, catheter-associated UTI, otitis externa, burn-wound infection and cystic fibrosis Intrinsic resistance Ampicillin, amoxicillin-clavulanate, first- and second-generation cephalosporins, cefotaxime and ceftriaxone (EUCAST Expected Resistant Phenotypes v1.2) Ertapenem, tetracyclines/tigecycline, SXT, chloramphenicol, nitrofurantoin Bench alerts Ertapenem is NEVER an option — do not report Under current BrCAST/EUCAST criteria, several combinations only carry the I and R categories (increased exposure) Resistance can emerge during therapy — repeat culture in cases of clinical failure Interpret zones in antibiogram Non-fermenters Acinetobacter baumannii complex Gram-negative coccobacilli, difficult to decolorize
+ Identification Oxidase-negative, catalase-positive, non-motile, non-fermenter Grows at 44 °C (A. baumannii) How it grows MacConkey agar: lactose-negative, mucoid, opaque colonies Blood agar, 35 °C, 24 h; survives for prolonged periods on dry surfaces Where it appears ICU pneumonia, catheter and wound infection, hospital outbreaks Intrinsic resistance Ertapenem, aztreonam, first- and second-generation cephalosporins (EUCAST Expected Resistant Phenotypes v1.2) Fosfomycin and nalidixic acid Bench alerts An XDR profile with carbapenem resistance is common in Brazil Environmental reservoir — reinforce cleaning protocols and notify infection control Ampicillin-sulbactam may retain activity through the sulbactam component Interpret zones in antibiogram Non-fermenters Stenotrophomonas maltophilia Gram-negative bacilli
+ Identification Oxidase-negative, DNase-positive, lysine-positive, motile Grows well on blood agar with a greyish-green pigment and ammoniacal odour How it grows MacConkey agar, lactose-negative; grows best at 30–35 °C, 24–48 h Where it appears Pneumonia in patients on carbapenem therapy, catheter infection, cystic fibrosis Intrinsic resistance ALL carbapenems (chromosomal L1 metallo-beta-lactamase, EUCAST Expected Resistant Phenotypes v1.2) Aminoglycosides, penicillins and most cephalosporins Bench alerts Never report meropenem/imipenem as susceptible, even with a large zone SXT is the reference option; alternatives are levofloxacin or minocycline Typically emerges after prolonged carbapenem use Interpret zones in antibiogram Non-fermenters Burkholderia cepacia complex Gram-negative bacilli
+ Identification Weakly oxidase-positive, lysine-positive, non-fermenter Selective BCSA/OFPBL agar How it grows Slow growth: 48–72 h at 35 °C; colonies may show a yellowish pigment Where it appears Pulmonary infection in cystic fibrosis, outbreaks from contaminated solutions Intrinsic resistance Colistin/polymyxin B, aminoglycosides, ampicillin and first-/second-generation cephalosporins (EUCAST Expected Resistant Phenotypes v1.2) Ertapenem Bench alerts Naturally polymyxin-resistant — a useful identification clue Isolation from serum/solutions suggests product contamination: investigate immediately Options: SXT, meropenem, ceftazidime, minocycline Interpret zones in antibiogram Fastidious organisms Haemophilus influenzae Small Gram-negative coccobacilli
+ Identification Requires factor X (hemin) and factor V (NAD) — X, V and XV disk test Satellitism around S. aureus on blood agar How it grows Chocolate agar with 5% CO₂, 35 °C, 24 h; translucent, greyish colonies Does not grow on plain sheep blood agar Where it appears Otitis media, sinusitis, COPD exacerbation, pneumonia, meningitis (unvaccinated patients) Intrinsic resistance Glycopeptides, clindamycin, linezolid, daptomycin, penicillin G (EUCAST Expected Resistant Phenotypes v1.2) Bench alerts Disk diffusion on Mueller-Hinton Fastidious (MH-F) agar with CO₂ Beta-lactamase-positive: ampicillin R — confirm directly with a nitrocefin test BLNAR: resistance via PBP alteration even in the absence of beta-lactamase Interpret zones in antibiogram Fastidious organisms Neisseria gonorrhoeae Intracellular Gram-negative diplococci
+ Identification Oxidase-positive, catalase-positive Ferments only glucose (not maltose, which differentiates it from meningococcus) How it grows Thayer-Martin/Martin-Lewis medium, 35–37 °C with 5% CO₂, 24–48 h Highly sensitive to cold and desiccation — plate immediately Where it appears Urethritis, cervicitis, pelvic inflammatory disease, neonatal conjunctivitis Intrinsic resistance Vancomycin, clindamycin, linezolid, daptomycin, trimethoprim Bench alerts A direct Gram stain of male urethral discharge already has high diagnostic value Ciprofloxacin and penicillin resistance rates are high — empirical treatment is ceftriaxone Inadequate transport is the main cause of a false-negative culture Interpret zones in antibiogram Fastidious organisms Neisseria meningitidis Gram-negative diplococci, often intracellular in CSF
+ Identification Oxidase-positive; ferments both glucose and maltose Serogrouping by latex agglutination (A, B, C, W, Y) How it grows Blood and chocolate agar, 35 °C with CO₂, 18–24 h CSF samples should not be refrigerated Where it appears Meningitis and meningococcemia — a clinical and public health emergency Intrinsic resistance Vancomycin, clindamycin, linezolid, trimethoprim Bench alerts Immediate mandatory notification and contact prophylaxis Handle inside a class II biological safety cabinet Disk diffusion on MH-F agar; test penicillin by MIC Interpret zones in antibiogram Fastidious organisms Moraxella catarrhalis Gram-negative diplococci
+ Identification Oxidase-positive, DNase-positive, does not ferment sugars Colony can be pushed intact across the plate with a loop (hockey-puck sign) How it grows Blood and chocolate agar, 35 °C, 24 h; dry, opaque colonies Where it appears Otitis media, sinusitis, COPD exacerbation Intrinsic resistance Trimethoprim, clindamycin, vancomycin, linezolid Bench alerts Nearly 100% produce a BRO beta-lactamase — ampicillin/amoxicillin alone will fail Amoxicillin-clavulanate, a macrolide, or an oral cephalosporin are the treatment options Interpret zones in antibiogram Fastidious organisms Campylobacter jejuni Curved Gram-negative bacilli, seagull-wing shaped
+ Identification Oxidase-positive, catalase-positive, hippurate-positive (C. jejuni) Corkscrew-like motility on wet-mount microscopy How it grows Skirrow/Campy agar, microaerophilic atmosphere (5% O₂, 10% CO₂), 42 °C, 48–72 h Where it appears Acute inflammatory diarrhea in outpatients; associated with Guillain-Barré syndrome Intrinsic resistance Trimethoprim, sulfonamides, cephalosporins, aztreonam, vancomycin Bench alerts Without a microaerophilic atmosphere and 42 °C incubation it will not grow — leads to a false-negative culture Azithromycin is first-line; fluoroquinolone resistance rates are high Interpret zones in antibiogram Anaerobes Bacteroides fragilis Pleomorphic Gram-negative bacilli
+ Identification Strict anaerobe, grows in 20% bile, resistant to kanamycin, vancomycin and colistin Catalase-positive (uncommon among anaerobes) How it grows Bacteroides Bile Esculin (BBE) agar: dark colonies with a brown-black halo Anaerobic jar or chamber, 35 °C, 48–72 h Where it appears Intra-abdominal abscess, peritonitis, polymicrobial soft-tissue infection Intrinsic resistance Aminoglycosides, aztreonam, older quinolones, colistin, vancomycin Bench alerts Produces beta-lactamase: penicillin and ampicillin alone will fail Metronidazole, piperacillin-tazobactam and carbapenems are the predictable options The specimen must be sent in anaerobic transport medium, without air exposure Interpret zones in antibiogram Anaerobes Clostridioides difficile Spore-forming Gram-positive bacilli
+ Identification Strict anaerobe, subterminal spore Routine diagnosis by GDH plus toxin A/B testing, with confirmatory PCR How it grows CCFA agar (cycloserine-cefoxitin-fructose): yellow colonies with a horse-manure odour and fluorescence Anaerobic incubation, 35 °C, 48 h Where it appears Antibiotic-associated diarrhea and pseudomembranous colitis in hospitalized patients Intrinsic resistance Cephalosporins, aztreonam, aminoglycosides Bench alerts Do not test formed stools or repeat testing for test-of-cure An isolated culture without toxin does not define disease Contact precautions and soap-and-water hand hygiene (alcohol does not inactivate the spore) Interpret zones in antibiogram Yeasts and fungi Candida albicans Gram-positive yeasts with pseudohyphae
+ Identification Germ tube-positive within 2–3 h at 37 °C Chlamydoconidia on cornmeal agar with Tween 80 CHROMagar: green colonies How it grows Sabouraud dextrose agar with chloramphenicol, 25–30 °C or 35 °C, 24–48 h White, creamy, smooth colonies Where it appears Oral and vulvovaginal candidiasis (outpatient), catheter-related candidemia, candiduria Intrinsic resistance No antibacterial has activity; echinocandins and azoles are the relevant drug classes Bench alerts Candidemia requires catheter removal/exchange Fluconazole is usually active, unlike some other Candida species Interpret zones in antibiogram Yeasts and fungi Candida não-albicans (glabrata, krusei, parapsilosis, tropicalis, auris) Gram-positive yeasts
+ Identification Germ tube-negative; identify by CHROMagar, carbohydrate assimilation panel, or MALDI-TOF C. glabrata: small yeast, without pseudohyphae How it grows Sabouraud agar, 30–35 °C, 24–72 h; C. auris grows well at 42 °C Where it appears Hospital-acquired candidemia, catheter infection, fungal UTI; C. parapsilosis linked to catheters and parenteral nutrition Intrinsic resistance C. krusei: intrinsically resistant to fluconazole C. glabrata: susceptible-dose-dependent response to azoles C. parapsilosis: intrinsically higher MICs to echinocandins (FKS polymorphism) C. auris: multidrug resistance is frequent Bench alerts Always identify to species level — the therapeutic choice depends on it C. auris requires contact precautions and notification to infection control Interpret zones in antibiogram Yeasts and fungi Cryptococcus neoformans Encapsulated yeasts
+ Identification India ink stain: capsular halo visible in CSF Urease-positive, phenoloxidase-positive (Niger seed/birdseed agar: brown colony) Cryptococcal antigen (latex/LFA) in CSF and serum How it grows Sabouraud agar without cycloheximide, 30–35 °C, 48–72 h; mucoid, creamy colonies Where it appears Meningitis in people living with HIV and other immunosuppressed patients; pulmonary cryptococcoma Intrinsic resistance Echinocandins have no activity — never use caspofungin Bench alerts Never report an echinocandin as an option Treatment is amphotericin B plus flucytosine, followed by fluconazole CSF opening pressure measurement is part of management Interpret zones in antibiogram Gram-positive cocci Streptococcus dysgalactiae (grupos C e G) Gram-positive cocci in chains
+ Identification Beta-hemolytic, catalase-negative Lancefield latex agglutination positive for group C or G Large colonies (> 0.5 mm), distinct from Streptococcus anginosus group How it grows Blood agar, 35–37 °C, 5% CO2, 18–24 h; wide zones of beta-hemolysis Where it appears Cellulitis, erysipelas, soft-tissue infection in diabetic patients Bacteremia, septic arthritis and pharyngitis in adults Intrinsic resistance Never report susceptibility to aminoglycosides alone No confirmed penicillin resistance has been described — an R result requires repeat testing Bench alerts Penicillin remains the drug of choice; test clindamycin with a D-test Differentiate from the anginosus group (small colonies, caramel-like odour) Interpret zones in antibiogram Gram-positive cocci Streptococcus gallolyticus (antigo S. bovis) Gram-positive cocci in short chains
+ Identification Lancefield group D-positive, bile-esculin-positive, does not grow in 6.5% NaCl (differs from Enterococcus) PYR-negative How it grows Blood agar, 35–37 °C, CO2; alpha- or non-hemolytic colonies Where it appears Endocarditis and bacteremia associated with colonic neoplasia Hepatobiliary infection Intrinsic resistance Low activity of aminoglycosides used alone Bench alerts Isolation in blood culture warrants flagging colonoscopy investigation Do not confuse with Enterococcus: the 6.5% NaCl test is the differentiator Interpret zones in antibiogram Gram-positive cocci Aerococcus urinae Gram-positive cocci in tetrads
+ Identification Catalase-negative, alpha-hemolytic, PYR-negative, LAP-positive Frequently mistaken for viridans streptococci or Enterococcus How it grows Blood agar and CLED agar, 35–37 °C, CO2, 24–48 h; small alpha-hemolytic colonies Where it appears UTI in the elderly and men with outflow obstruction; urosepsis and endocarditis Intrinsic resistance Resistant to trimethoprim-sulfamethoxazole in vivo despite an apparent in vitro zone Bench alerts Do not dismiss as a contaminant in a monomicrobial urine culture with pyuria MALDI-TOF resolves identification Interpret zones in antibiogram Gram-positive cocci Micrococcus / Kocuria spp. Gram-positive cocci in tetrads and packets
+ Identification Catalase-positive, coagulase-negative, modified oxidase-positive (Micrococcus) Resistant to bacitracin 0.04 U and susceptible to furazolidone — the opposite pattern to Staphylococcus How it grows Blood agar, 35 °C, 24–48 h; dry, yellow or pink colonies Where it appears Normal skin flora; rarely catheter, prosthetic, and dialysis-related peritonitis infections Intrinsic resistance No disk-diffusion breakpoints in BrCAST/EUCAST — do not interpret as if it were Staphylococcus Bench alerts Most often a single-bottle blood culture contaminant Only regard as significant with multiple positive bottles and a compatible clinical picture Interpret zones in antibiogram Gram-positive bacilli Bacillus cereus Large, spore-forming Gram-positive bacilli
+ Identification Catalase-positive, motile, beta-hemolytic, lecithinase-positive Resistant to penicillin; differs from B. anthracis (non-motile, non-hemolytic) How it grows Blood agar and MYP agar, 35 °C, 24 h; large, matte colonies with irregular edges Where it appears Food poisoning (rice-associated), post-traumatic eye infection Catheter-related bacteremia in neutropenic patients Intrinsic resistance Constitutive beta-lactamase: penicillins and cephalosporins should not be reported Bench alerts Vancomycin is the empirical option for invasive infection A single positive blood culture bottle is usually environmental contamination Interpret zones in antibiogram Gram-positive bacilli Nocardia spp. Filamentous, branching Gram-positive bacilli
+ Identification Partially acid-fast (positive with modified Kinyoun stain) Catalase-positive, strict aerobe; species identification by MALDI-TOF or sequencing How it grows Grows slowly (3–14 days) on blood agar, Sabouraud agar and BCYE agar Dry, adherent colonies with an earthy odour; notify the laboratory to extend incubation Where it appears Pneumonia in immunosuppressed patients, brain abscess, cutaneous mycetoma Intrinsic resistance Susceptibility pattern varies by species — do not presume; send to a reference laboratory Bench alerts Trimethoprim-sulfamethoxazole is the backbone of treatment Respiratory isolation in an immunosuppressed patient warrants CNS investigation Interpret zones in antibiogram Enterobacterales Proteus vulgaris / Proteus penneri Gram-negative bacilli
+ Identification Urease-positive, H2S-positive, phenylalanine deaminase-positive Indole-positive (differs from P. mirabilis, which is indole-negative) How it grows Blood agar with swarming; MacConkey agar lactose-negative, 35–37 °C, 24 h Where it appears Complicated UTI, wound infection and struvite stones Intrinsic resistance Chromosomal beta-lactamase: ampicillin, amoxicillin-clavulanate and cefuroxime should not be reported Resistant to colistin, tigecycline, nitrofurantoin and tetracyclines (EUCAST Expected Resistant Phenotypes v1.2) Bench alerts Swarming can obscure another colony on the plate — subculture to isolate Never report colistin as an option Interpret zones in antibiogram Enterobacterales Hafnia alvei Gram-negative bacilli
+ Identification Lysine and ornithine decarboxylase-positive, indole-negative, H2S-negative Biochemical reactions are more pronounced at 25 °C than at 37 °C How it grows MacConkey agar, lactose-negative, 35–37 °C, 24 h Where it appears Opportunistic infection: UTI, wound, bacteremia in hospitalized patients Intrinsic resistance Inducible AmpC: ampicillin, amoxicillin-clavulanate and first-/second-generation cephalosporins should not be reported Bench alerts Risk of AmpC derepression during third-generation cephalosporin therapy The biochemical profile can be confused with Salmonella — confirm with serology Interpret zones in antibiogram Enterobacterales Yersinia enterocolitica Gram-negative, coccobacillary rods
+ Identification Urease-positive, oxidase-negative, motile at 25 °C and non-motile at 37 °C CIN agar: bull's-eye colonies (red centre) How it grows Grows well at 25–28 °C; CIN agar for 48 h on targeted stool culture Where it appears Enteritis, mesenteric adenitis mimicking appendicitis, post-transfusion bacteremia Intrinsic resistance Chromosomal beta-lactamases A and B: ampicillin, amoxicillin-clavulanate and first-generation cephalosporins should not be reported Bench alerts Only isolated if CIN medium and 25 °C incubation are specifically requested Ask about recent pork consumption and blood transfusion Interpret zones in antibiogram Non-fermenters Pseudomonas putida / fluorescens Non-fermenting Gram-negative bacilli
+ Identification Oxidase-positive, fluorescein-positive, pyocyanin-negative Does not grow at 42 °C (differs from P. aeruginosa) How it grows MacConkey agar, lactose-negative; blood agar 30–35 °C, 24–48 h Where it appears Contamination of solutions and catheters; bacteremia related to blood-product transfusion Intrinsic resistance Natural resistance to ampicillin, first- and second-generation cephalosporins and trimethoprim-sulfamethoxazole, similar to other environmental Pseudomonas spp. Bench alerts No dedicated BrCAST/EUCAST breakpoints: use PK/PD criteria and annotate the report Repeated isolates suggest an environmental source — investigate water and solutions Interpret zones in antibiogram Non-fermenters Achromobacter xylosoxidans Non-fermenting Gram-negative bacilli
+ Identification Oxidase-positive, motile by peritrichous flagella, oxidizes xylose Confirmation by MALDI-TOF How it grows MacConkey agar-positive, blood agar 35 °C, 24–48 h; greyish colonies Where it appears Colonization in cystic fibrosis, catheter-related bacteremia, post-surgical infection Intrinsic resistance Resistant to aztreonam, first- and second-generation cephalosporins and aminoglycosides Bench alerts Piperacillin-tazobactam, meropenem and trimethoprim-sulfamethoxazole are the usual options Do not extrapolate Pseudomonas breakpoints Interpret zones in antibiogram Non-fermenters Elizabethkingia meningoseptica Slender, non-fermenting Gram-negative bacilli
+ Identification Oxidase-positive, indole-positive (weak; use Kovacs reagent on pure culture), some isolates fail to grow on MacConkey agar Colonies with a pale-yellow pigment How it grows Blood agar 35 °C, 24–48 h; grows best at 30 °C Where it appears Neonatal meningitis, ICU bacteremia, ventilator-associated pneumonia Intrinsic resistance Chromosomal metallo-beta-lactamase and extended-spectrum beta-lactamase: carbapenems, cephalosporins, aztreonam and colistin have no activity Bench alerts Carbapenem resistance is intrinsic, not acquired — do not report as an epidemiological finding Vancomycin, rifampicin, minocycline and fluoroquinolones are the usual alternatives Interpret zones in antibiogram Fastidious organisms Gardnerella vaginalis Gram-variable coccobacilli
+ Identification Clue cells on wet mount and Gram stain (Nugent score) Beta-hemolytic on human blood bilayer (HBT) agar, catalase- and oxidase-negative How it grows HBT agar, 35–37 °C, 5% CO2, 48 h; pinpoint colonies Where it appears Bacterial vaginosis; occasional UTI and puerperal infection Intrinsic resistance No disk-diffusion breakpoints — routine susceptibility testing is not performed Bench alerts Diagnosis rests on the Nugent score, not culture Treatment is metronidazole or clindamycin; an isolated positive culture is not an indication to treat Interpret zones in antibiogram Fastidious organisms Grupo HACEK (Haemophilus/Aggregatibacter, Kingella, Eikenella) Fastidious Gram-negative coccobacilli
+ Identification Slow, CO2-dependent growth; variable oxidase reaction Eikenella pits the agar and has a bleach-like odour How it grows Chocolate agar, 35–37 °C, 5% CO2, up to 5 days — do not discard blood cultures early Where it appears Subacute native-valve endocarditis, oral abscess, human-bite infection Intrinsic resistance Eikenella is resistant to clindamycin and aminoglycosides Bench alerts Culture-negative endocarditis blood cultures require prolonged incubation Ceftriaxone is the backbone of treatment Interpret zones in antibiogram Anaerobes Prevotella / Fusobacterium spp. Anaerobic Gram-negative bacilli
+ Identification Prevotella: black pigment on laked blood agar, brick-red fluorescence under UV light Fusobacterium: fusiform bacilli with tapered ends How it grows Brucella/laked blood agar with hemin and vitamin K, anaerobic incubation, 48–72 h Where it appears Periodontal abscess, aspiration pneumonia, chronic sinusitis Fusobacterium necrophorum: Lemierre's syndrome Intrinsic resistance Resistant to aminoglycosides, aztreonam and trimethoprim-sulfamethoxazole Bench alerts Increasing beta-lactamase production: report amoxicillin-clavulanate or metronidazole Collection in an air-free syringe or anaerobic transport medium is essential Interpret zones in antibiogram Anaerobes Peptostreptococcus / cocos Gram-positivos anaeróbios Anaerobic Gram-positive cocci
+ Identification Growth only under anaerobic conditions, catalase-negative Identification by MALDI-TOF from an isolated colony How it grows Supplemented Brucella agar, anaerobic incubation, 48–96 h; small white colonies Where it appears Polymicrobial abscesses, pelvic infection, diabetic foot, empyema Intrinsic resistance Resistant to aminoglycosides and aztreonam Bench alerts Almost always part of mixed flora — the report should read 'anaerobic Gram-positive cocci' Penicillin, amoxicillin-clavulanate and metronidazole are the options Interpret zones in antibiogram Anaerobes Clostridium perfringens Large, straight Gram-positive bacilli, spores rarely seen
+ Identification Double zone of hemolysis on blood agar, lecithinase-positive (Nagler reaction), non-motile How it grows Anaerobic incubation, 35–37 °C; rapid growth, 18–24 h Where it appears Gas gangrene, anaerobic cellulitis, food poisoning, hemolytic bacteremia Intrinsic resistance Resistant to aztreonam and aminoglycosides Bench alerts A large Gram-positive bacillus with double hemolysis from a wound is a surgical emergency — notify immediately Penicillin plus clindamycin is the classic regimen Interpret zones in antibiogram Yeasts and fungi Candida auris Small yeasts, without obvious pseudohyphae
+ Identification Germ tube-negative; CHROMagar Candida Plus shows a pale colony with a blue halo Identification requires MALDI-TOF with an updated database — biochemical systems misidentify it as C. haemulonii How it grows Grows at 42 °C and in high salinity; Sabouraud agar 35–37 °C, 24–48 h Where it appears Candidemia and skin/axillary colonization in the ICU; hospital outbreaks Intrinsic resistance Fluconazole resistance is frequent; a subset of isolates is resistant to amphotericin B and echinocandins Bench alerts Mandatory notification and immediate contact precautions Always perform antifungal susceptibility testing and notify infection control Interpret zones in antibiogram Yeasts and fungi Trichosporon asahii Yeasts with arthroconidia
+ Identification Urease-positive, arthroconidia and blastoconidia seen on microculture May cause a false-positive cryptococcal antigen and galactomannan test How it grows Sabouraud agar 30–35 °C, 48–72 h; dry, cerebriform colonies Where it appears Fungemia in neutropenic patients, catheter infection, white piedra Intrinsic resistance Resistant to echinocandins; amphotericin B has limited activity Bench alerts Voriconazole is the drug of choice Never report caspofungin as susceptible Interpret zones in antibiogram Yeasts and fungi Aspergillus fumigatus Septate, hyaline filamentous fungus
+ Identification Septate hyaline hyphae with acute-angle (45°) branching Conidiophore with a columnar vesicle and uniseriate phialides; grey-green colony How it grows Sabouraud agar without cycloheximide; grows at 48 °C, 48–72 h Where it appears Invasive pulmonary aspergillosis, aspergilloma, sinusitis and otomycosis Intrinsic resistance Resistant to fluconazole; echinocandin monotherapy has only fungistatic, not fungicidal, activity Bench alerts Voriconazole is first-line; consider azole resistance in cases of treatment failure Isolation from a respiratory sample in an immunosuppressed patient should be reported alongside galactomannan results Interpret zones in antibiogram Want the essential agar guide? Sign up to receive the PDF covering the lab's main agars: composition, purpose, colony appearance and incubation conditions.
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