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Bacteria overview

Last updated: August 26, 2021

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The nomenclature of bacteria is complex. Human pathogenic bacteria can be classified according to their characteristics: morphology (cocci, bacilli, coccobacilli, spiral, or presence of branching filaments), Gram-staining properties (Gram‑positive, Gram‑negative, and atypical), metabolic activity (aerobic, anaerobic, microaerophile, or facultative), or virulence factors (e.g., presence of capsule, pili, proteins, formation of coagulase, catalase or enterotoxins) among other traits. This article provides an overview of the most important human pathogenic bacteria. For an overview of the basics of bacteriology – including diagnosis and genetics – see “General bacteriology.”

The following table provides an overview of the nomenclature of important human pathogenic bacteria, according to their form and gram-staining properties. (See “Gram staining.”)

Pathogens with typical gram staining properties

Pathogens with atypical gram staining properties

Staphylococcus [1]

Overview of staphylococci
Pathogen Reservoir Bacterial culture Virulence factors and resistances


Antibiotic of choice
Coagulase positive staphylococcus (CoPS)
Staphylococcus aureus
Coagulase negative staphylococci (CoNS)
Staphylococcus epidermidis
  • Natural skin flora
Staphylococcus saprophyticus
  • Natural flora of the female genital tract and perineum
  • Grape‑like cluster arrangement
  • Novobiocin-resistant

NO StRESs: NOvobiocin sensitivity patterns, Saprophyticus (Resistant), Epidermidis (Sensitive)

Streptococcus [1]

Overview of streptococci
Pathogen Reservoir Bacterial culture Virulence factors and resistances Diseases Antibiotic of choice
Alpha-hemolysis (partial hemolysis)

Streptococcus pneumoniae (pneumococcus)

  • Nasopharynx

Viridans streptococci (e.g., S. mutans, S. mitis, and S. sanguinis)

Beta-hemolysis (complete hemolysis)
Streptococcus pyogenes (Group A Streptococcus) [4][5]
  • Nasopharynx
  • Humans are the sole host
Streptococcus agalactiae (Group B Streptococcus)
  • Gastrointestinal and genital tract
  • Capsule

Streptococcus gallolyticus [8]

Streptococcus anginosus [2][10]
  • Oropharynx, gastrointestinal, and genitourinary tract

B is for Babies: group B streptococci primarily affect neonates.

PaSsVORd: Pnemunoniae is Sensitive and Viridans is Optochin-Resistant.

BBRAS: Bacitracin sensitivity pattern of group B streptococci (Resistant) and for group A streptococci (Sensitive).

Sanguinis vessels lead to your heart: S. sanguinis can cause endocarditis.

Other gram positive cocci [1]

Overview of other gram positive cocci
Pathogen Reservoir Bacterial culture Diseases Antibiotic of choice
Peptostreptococcus (e.g., P. anaerobius, P. magnus)
  • Mucocutaneous surfaces
Enterococcus (e.g., E. faecium and E. faecalis) [11]

Bovis in the blood, cancer in the gut: S. bovis is associated with colon cancer.

Entero (intestine), faecalis (feces), strepto (twisted), and coccus (berry): the etymology of enterocci describes its characteristics.

Clostridia [1]



Bacterial culture

Virulence factors and resistances Diseases

Antibiotic of choice

Clostridioides difficile

Clostridium perfringens [12]

Clostridium tetani [14]

  • Soil worldwide

Clostridium botulinum

  • Soil
  • Intestinal tracts of birds and fish
  • Agricultural products (e.g., vegetables)
  • Only in case of secondary bacterial infection

Listeria, Corynebacteria, and Bacillus [1]

Overview of Listeria, Corynebacteria, and Bacilli



Bacterial culture

Virulence factors and resistances Diseases

Antibiotic of choice

Listeria monocytogenes

  • Unpasteurized milk products
  • Cold deli meats
  • Transplacental transmission/vaginal transmission during birth

Corynebacterium diphtheriae

  • Respiratory tract
  • Humans are the only hosts
  • Club-shaped rods in angular arrangements
  • Facultative anaerobe
  • Stainable using Neisser stain: detection of characteristic metachromatic granules (red and blue)
  • Positive Elek test for toxin
  • Black colonies on cystine-tellurite agar
  • Löffler medium: metachromatic granules

Bacillus anthracis

  • Soil
  • Mammals
  • Aerobe
  • Bamboo stick-shaped
  • Colonies show a halo of projections (Medusa head)

Bacillus cereus

  • Contaminated food (particularly rice that is kept warm and/or reheated)
  • Not indicated, only supportive care

Neisseria and Moraxella [1][15]

Overview of Neisseriae and Moraxella
Pathogen Reservoir Bacterial culture Virulence factors and resistances Diseases Antibiotic of choice

Neisseria meningitidis (meningococcus)

  • Nasopharynx
  • Humans are the only hosts (most commonly affects individuals living in close vicinity to one another, e.g., college students or soldiers).
  • Diplococcus
  • Facultative intracellular
  • Aerobe
  • Bacterial growth on culture medium is usually challenging
  • Selective medium: Thayer-Martin agar
  • Maltose and glucose fermenter
Neisseria gonorrhoeae (gonococcus)
  • Genital tract
  • Humans are the only hosts
Moraxella catarrhalis [16]
  • Nasopharynx
  • Humans are the only hosts

MeninGococci: Maltose + Glucose production and Gonococci: Glucose production.

Overview of gram negative coccobacilli [1]
Pathogen Reservoir

Bacterial culture

Virulence factors and resistances Diseases Antibiotic of choice

Haemophilus influenzae

  • Nasopharynx (particularly in young children)
  • Aerosol transmission

Haemophilus ducreyi

  • Humans are the only hosts
Brucella Brucella melitensis
  • Goats and sheep serve as hosts
Brucella abortus
  • Unpasteurized dairy
  • Cattle are the only hosts

Bordetella pertussis

  • Humans are the only hosts (particularly adults and adolescents)

Pasteurella multocida

  • Oropharynx of animals (especially dogs and cats)
  • Cellulitis (secondary to dog and cat bites)
  • Respiratory tract infections
Acinetobacter baumanni [23]
  • Outer membrane protein A (OmpA): biofilm formation and immunomodulation [24]

Influenza virus causes the flu whereas H. influenzae causes epiglottitis and meningitis.
Bordetella pertussis grows on Bordet-Gengou agar.

Enterobacteriaceae [1]

Escherichia coli [25]

Overview of E. coli
Pathogen Reservoir Characteristics Important virulence factors Diseases Antibiotic of choice

EPEC (enteropathogenic E. coli)

  • Natural gut flora
  • Usually in children
  • Adherence to intestinal epithelium destruction of microvilli (inhibits absorption)
  • No toxin is produced
ETEC (enterotoxin E. coli)
  • Fecal contaminated food and water
EIEC (enteroinvasive E. coli)
  • Natural gut flora
EAEC (enteroaggregative E. coli)
  • Fecal contaminated food and water
  • Aggregation ("stacked-brick" pattern) with one another and adherence to intestinal mucosa inflammation watery (possibly bloody) diarrhea [26]
EHEC (enterohemorrhagic E. coli)
  • Undercooked meat, raw leafy vegetables
UPEC (uropathogenic E. coli)
  • Natural gut flora
  • Most common cause of UTIs [28]
NMEC (neonatal meningitis-causing E. coli) [29]
  • Common cause of neonatal bacterial meningitis in industrialized countries

Light as Air: (heat-Labile toxin upregulates ↑ cAMP and Adenylate cyclase), Stable as Granit: (heat-Stable toxin: upregulates ↑ cGMP and Guanylate cyclase).

Other Enterobacteriaceae

Overview of other Enterobacteriaceae
Pathogen Reservoir Characteristics Virulence factors and resistances Diseases Antibiotic of choice

Yersinia pestis [30]

  • Facultative intracellular
  • Bipolar staining (“closed safety pin” appearance)

Yersinia enterocolitica, Yersinia pseudotuberculosis [31]

Shigella: S. dysenteriae, S. flexneri, S. boydii, S. sonnei (in order of decreasing severity) [33]

  • Spread from cell to cell → invasion of M cells (MALT)
  • Resistant to gastric acid low infectious dose required [34]
  • Fastidious: stool samples require prompt testing
  • Slow/absent lactose fermentation
  • Immune response primarily via PMN infiltration

Salmonella enterica serotype Enteritidis, and Salmonella enterica serotype Typhimurium

  • Humans, animals, animal products (e.g., reptiles, poultry, pets, eggs) serve as hosts
  • Obligate pathogen
  • High infectious dose required → not resistant against gastric acid
  • Hematogenous dissemination is possible
  • Immune response primarily via PMN infiltration
  • Produces H2S
  • No lactose fermentation
  • Facultative intracellular

Salmonella enterica serotype Typhi, and Salmonella enterica serotype Paratyphi

Klebsiella pneumoniae

Klebsiella granulomatis [37]

  • Genital tract (endemic in tropical and subtropical developing countries)

Proteus (Proteus vulgaris; Proteus mirabilis)

  • Swarming motility on agar
  • Produces H2S

Mac and Cheese: MacConkey agar is used for lactose fermentors (Cheese).
PADDOCK: Aspiration Pneumonia, lung/liver Abscess, Diabetics, Drug resistance, alcOhOlics, Currant jelly, Klebsiella are most common features of Klebsiella infection.

Other gram negative bacilli [1]

Overview of other gram negative bacilli
Pathogen Reservoir Characteristics Virulence factors and resistances Diseases Antibiotic of choice

Helicobacter pylori [38]

  • Humans are the predominant hosts
  • Urease: ammonia formation increases the pH and enables survival in the acidic environment of the gut.

Legionella pneumophila

  • Natural aquatic habitats
  • Transmitted by water aerosols (e.g., air conditioning systems)

Campylobacter jejuni

  • Poultry, unpasteurized milk (natural gut flora in birds)
  • Contact with infected persons or infected animals (e.g., pigs, dogs, cats)

Pseudomonas aeruginosa [41][42]

  • Water and humid conditions (e.g., hot tubs, contaminated contact lens solution)
Burkholderia cepacia
  • Aquatic environments
  • Aerobic

Vibrio cholerae [45]

  • Contaminated water
  • Uncooked seafood (e.g., raw shellfish)
Vibrio vulnificus [46]
  • Contaminated water
  • Raw or undercooked seafood (e.g., raw shellfish, fish intestines)
  • Wounds infected by contaminated water or seafood
Vibrio parahaemolyticus [47]
  • Contaminated water
  • Raw or undercooked seafood (e.g., mussels)

Fusobacteriaceae [48]

  • Anaerobic produce CO2 and H2 in tissue
  • Bile-resistant
  • Foul smelling

Bacteroides (e.g., Bacteroides fragilis)

  • Up to 40% of fecal flora [49]

Bartonella henselae [50]

  • Cats are asymptomatic carriers

Bartonella quintana [51]

Eikenella corrodens [53][54]

Pseudomonas produces PEEPP: Phospholipase C, Exotoxin A, Endotoxin, Pyoverdin, and Pyocyanin are P. aeruginosa virulence factors.

CAMPFIRE: Carbapenems, Aminoglycosides, Monobactams, Polymyxins, Fluoroquinolones, thIRd and fourth-generation cephalosporins, Extended-spectrum penicillins are the drugs used to treat P. aeruginosa infections.

Overview of Actinomyces and Nocardiae [1]
Pathogen Reservoir Characteristics Virulence factors and resistances Diseases Antibiotic of choice

Actinomyces israelii [56]

Nocardia asteroides and Nocardia brasiliensis [57]

  • Soil worldwide

They are NOw ACTually gone with the SNAP of a finger: To treat NOcardia and ACTinomyces useSulfonamides, Nocardia, Actinomyces, and Penicillin.

Mycobacterium, Mycoplasmataceae (Mycoplasma), and Gardnerella [1]

Overview of Mycobacteria, Mycoplasma, and Gardnerella
Pathogen Reservoir Characteristics Virulence factors and resistances Diseases Antibiotic of choice

Mycobacterium tuberculosis

  • Humans

Mycobacterium leprae [59]

  • Humans and armadillos

Nontuberculous mycobacteria M. kansasii, M. ulcerans

M. avium-intracellulare
  • Ubiquitous
M. marinum
M. scrofulaceum

Mycoplasma pneumoniae

  • Humans are the only host

Ureaplasma urealyticum

  • Normal urogenital flora
  • Urocystitis
Gardnerella vaginalis [62][63][64][65]


Overview of Spirochetes
Pathogen Reservoir Characteristics Diseases Antibiotic of choice

Treponema pallidum

  • Humans

Treponema vincentii

Borrelia burgdorferi

Borrelia recurrentis

Leptospira interrogans, Leptospira kirschneri

  • Animal urine in water (e.g., rats, cattle, sheep, and goats)
  • Very thin wall
  • Hook-shaped ends

SPecial for SPirochetes and SPecial BLT sandwich: Spirochetes are Borrelia, Leptospira, and Treponema .

Borrelia is the Biggest of all the Spirochetes.

Overview of obligate intracellular bacteria
Pathogen Reservoir Characteristics Virulence factors and resistances Diseases Antibiotic of choice

Chlamydia trachomatis

  • Humans are the only host

Chlamydophila psittaci

  • Parrots and other birds
  • Aerosol transmission

Chlamydophila pneumoniae

  • Humans are the only host
  • Aerosol transmission

Rickettsia rickettsii

Rickettsia prowazekii

  • Human to human (body louse)

Rickettsia typhi

Coxiella burnetii

  • Cattle, sheep, and goats
  • Aerosol transmission

Ehrlichia chaffeensis, Ehrlichia ewingii [67][68]

Anaplasma phagocytophilum [68][69][70][71]

When it's Rainy and Chilly outside, Cozy up and Eat Apple pie: Rickettsia, Chlamydia, Coxiella, Ehrlichia, Anaplasma are obligate intracellular bacteria.

Diagnostic associations of bacteria
Bacteria Diagnostic hint Clinical scenario
Actinomyces israelii
  • Patient with odontogenic infection develops an oral/facial abscess.
Borrelia burgdorferi
Clostridium perfringens
Clostridium tetani
  • Drumstick shaped
  • Patient punctures their sole with a dirty nail and develops trismus.
Klebsiella pneumoniae
  • Mucoid colonies
Pasteurella multocida
  • A patient that owns 3 cats present with signs of cellulitis.
Legionella pneumophila
  • Patient presents with productive cough, nausea, and confusion after a cruise trip.
Haemophilus influenzae
  • An unvaccinated child presents with high fever, drooling, and muffled voice.
  • Patient with a history of severe abdominal trauma develops fulminant sepsis.
Encapsulated bacteria
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