• Clinical science

Bacteria overview

Abstract

The nomenclature of bacteria is complex; human pathogenic bacteria are classified according to their form (cocci, bacilli, or coccobacilli) and Gram staining properties (gram‑positive, gram‑negative, and atypica). Further classification is based on metabolic activity (aerobic or anaerobic) and virulence factors (e.g., formation of coagulase or enterotoxins), among other traits. The most important human pathogenic bacteria are discussed in this learning card. An overview of the basics of bacteriology – including diagnosis and genetics – may be found in the learning card on general bacteriology.

Overview

The following tables provide an overview of the nomenclature of important human pathogenic bacteria, according to their form and Gram staining properties.

References:[1][2]

Gram-positive cocci

Staphylococcus

  • Catalase-positive
Important species Reservoir Characteristics and important virulence factors

Diseases

Antibiotic of choice
Staphylococcus aureus
  • Skin
  • Detectable in the nostrils in ∼ 30% of the healthy population
Staphylococcus epidermidis
  • Natural skin flora
  • Coagulase-negative
  • Novobiocin-sensitive
  • Does not ferment mannitol
  • Urease-positive
  • Biofilm formation

Staphylococcus saprophyticus

  • Natural (mucosal) skin flora

Streptococcus and enterococcus

Genus Important species Reservoir Characteristics and important virulence factors Diseases Antibiotic of choice
Streptococcus

Streptococcus pneumoniae (pneumococci)

  • Nasopharynx
Viridans streptococci
  • Usually present in the oral cavity

Streptococcus gallolyticus

  • Isolated in stool in up to 10% of the population (higher rates in patients with colorectal cancer)
Streptococcus pyogenes (Group A Streptococcus)
  • Humans are the sole host; nasopharynx
Streptococcus agalactiae (Group B Streptococcus)
  • Colonizes the human gastrointestinal and genital tracts
Peptostreptococcus Numerous peptostreptococcus species (e.g., P. anaerobius, P. magnus)
  • Part of the natural flora of mucocutaneous surfaces
  • Wound infections (soft tissue, bone)
  • Brain abscesses
  • Upper respiratory tract infections
  • Dental infections
  • Pelvic infections in women
Enterococcus

E. faecium and E. faecalis

“B for baby”: Group B streptococci primarily affect neonates.

References:[3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21]

Gram-negative cocci

Genus Important species Reservoir Characteristics and important virulence factors Diseases Antibiotic of choice
Neisseria
  • Neisseria meningitidis
  • Humans are the only hosts; nasopharynx
  • Aerobe
  • Bacterial growth on culture medium is usually challenging
    • Thayer-Martin Agar: selective medium that favors growth of Neisseria spp.
  • Microscopy: intracellular and extracellular location possible
  • Important virulence factors:
    • Capsular polysaccharides
      • Lipooligosaccharide (LOS) : serum levels correlate with severity of symptoms
    • IgA1 protease
    • Adhesins: pili and opacity proteins facilitate nasal colonization, which is a prerequisite for systemic infection
  • Maltose fermenter
  • Humans are the only hosts
Moraxella
  • Moraxella catarrhalis
  • Humans are the only hosts; nasopharynx
  • Microscopy: diplococci

References:[3][22][23][24][25][26][27][28][29]

Gram-positive bacilli

Genus

Important species

Reservoir

Characteristics and important virulence factors

Diseases

Antibiotic of choice

Clostridia (spore‑forming bacteria)

  • Natural gut flora of ∼ 5% of all adults
  • Part of the natural skin and gastrointestinal flora
  • Found in soil, worldwide
  • Found in soil, intestinal tracts of birds and fish, and agricultural products (e.g., vegetables)
  • Administration of a botulism antitoxin is the most important treatment measure. Antibiotics are of secondary importance.
Listeria
  • Most commonly found in unpasteurized milk products
Corynebacterium
  • Humans are the only hosts
Bacillus
  • Found in soil and mammals
  • Proliferate quickly in contaminated food; rice that is kept warm and/or reheated is a particularly good breeding ground.
  • There is no specific treatment against the enterotoxin available.
  • Antibiotic treatment is not indicated.

References:[30][31][3][32][33][34][35][36][37][38]

Gram-negative coccobacilli

Genus Important species Reservoir

Characteristics and important virulence factors

Diseases Antibiotic of choice
Haemophilus
  • Colonization of the nasopharynx is relatively common in young children.
  • Bacterial culture:
    • Hemophilic bacteria: isolation on chocolate agar
      • Requires factors X (hematin) and V (NAD), which are present in lysed red blood cells
    • May demonstrate satellitism in culture
  • Important virulence factors:
  • Humans are the only hosts
  • Bacterial culture: hemophilic bacteria
Brucella
  • Goats and sheep serve as hosts
  • Facultative intracellular
  • Cattle are the only hosts
Bordetella
  • Humans are the only hosts; particularly adults and adolescents

References:[39][40][41][42][43][44]

Gram-negative bacilli

Enterobacteriaceae

  • All enterobacteria express enterobacterial common antigen (ECA).
  • Possess an intrinsic resistance against bile salts, which allows the bacteria to proliferate in the gastrointestinal tract
Genus Species/serotype Reservoir Characteristics and important virulence factors Diseases Antibiotic of choice
Yersinia
  • Primarily rodents
  • Contaminated pork and milk products
Shigella
  • Humans are the only host
  • Obligate pathogen
  • Important virulence factor: shiga toxin
  • Fastidious: Stool samples require prompt testing.
Salmonella
  • Humans and animals serve as hosts
  • Obligate pathogen
  • Humans are the only hosts
  • Obligate pathogen
Klebsiella
  • Human genital tract (endemic in tropical and subtropical developing countries)

Escherichia coli (E. coli)

  • Part of the natural gut flora
  • Important virulence factor: produce an enterotoxin that is structurally similar to the cholera toxin
  • ETEC for Travelers
  • Important virulence factor: K1 capsular polysaccharide protects from phagocytosis
Proteus

Further gram‑negative bacilli

Genus Important species Reservoir Characteristics and important virulence factors Diseases Antibiotic of choice
Helicobacter
  • Humans are the predominant hosts
  • Type B gastritis

Legionella

  • Natural aquatic habitats
  • Facultative intracellular
  • Aerobic
  • Waterborne bacteria; often symbiotic with amebae

Campylobacter

  • Component of the gut flora in birds. Transmission often occurs via contaminated poultry.
Pseudomonas
  • Common in the environment; grows in water and humid conditions, e.g., hot tubs, contaminated contact lens solution
  • Lophotrichous flagella
  • Aerobic
  • Special macroscopic characteristics
    • A typical blue‑green pus may form in infection
    • Sweet odor, if grown in culture
  • Produces exotoxin A, which inhibits protein synthesis by inactivating elongation factor 2
  • Produces phospholipase C, which degrades cell membranes
  • Produces pyoverdin and pyocyanin
Burkholderia
  • Aquatic environments
  • Aerobic
Vibrio
  • Humans and contaminated water
  • Straight or curved, polar flagella
  • Facultative anaerobe
  • Produces cholera toxin (enterotoxin) consisting of two subunits:
    • The B unit binds to the intestinal epithelium.
    • The toxic A unit is cleaved and channeled into the cell.
Fusobacteriaceae
  • Numerous
  • Humans; oral cavity
  • Anaerobic
  • In some cases, formation of a capsule
  • Bile-resistant
  • Injury to the skin or mucous membranes can lead to the formation of foul‑smelling abscess or even peritonitis and sepsis
Bacteroides
  • Numerous
  • Account for 90% of all fecal flora
  • Responsible for the typical odor of stool
Bartonella
  • Cats are asymptomatic carriers
  • Humans (the louse is usually the vector)
  • Nonhuman vertebrates
  • Facultative intracellular
  • Flagellate

References:[45][46][47][48][49][50][51][52][53][54][55][56][57][58][59][60][61][62][63][64]

Branching filamentous bacteria

Genus Species Reservoir Characteristics and important virulence factors Diseases Antibiotic of choice
Actinomyces
  • Natural bacteria of the oral cavity and the intestine
High-dose penicillin G; alternatively tetracycline or erythromycin
Nocardia
  • Ubiquitous in soil worldwide
  • Aerobe
  • Weakly acid-fast staining

References:[65][66][67][68][69]

Atypical gram‑staining bacteria

Mycobacterium and mycoplasmataceae

Important species Reservoir Characteristics and important virulence factors Diseases Antibiotic of choice
Mycobacterium
  • Humans
  • Humans and armadillos
  • Ubiquitous
  • Microscopy: acid-fast bacilli
  • PCR confirms
  • Generation time: varies among the subtypes; faster than other mycobacteria
Mycoplasmataceae (Mycoplasma)
  • Humans are the only hosts
  • Microaerophile
  • Incomplete cell wall
  • Bacterial culture is time consuming (2–3 weeks) and the bacteria are fastidious → Serological diagnosis is required in most cases.
  • May be part of the normal flora
  • Urocystitis

Spirochetes

Genus Important species Reservoir Characteristics and important virulence factors Diseases Antibiotic of choice
Treponema
  • Humans
  • Bacterial growth in culture is not possible.
  • Darkfield microscopy and serology are primarily used for detection.
Borrelia
Leptospira
  • Animals (e.g., rats, cattle, sheep, and goats) are the natural hosts; incidental transmission to humans through direct contact to animals, or indirectly through contact with contaminated water or soil
  • Aerobic
  • Darkfield microscopy or silver-stain are primarily used for detection.

References:[2][70][71][72][73][74][75]

Obligate intracellular bacteria

Genus Species Reservoir Characteristics and important virulence factors Diseases Antibiotic of choice

Chlamydiaceae (Chlamydia)

  • Humans are the only hosts
  • Gram-negative
  • Culture: difficult; requires tissue medium
  • Various pathogenic serotypes with different organ associations (see table in chlamydia infections)
  • Birds are the typical hosts
  • Microscopy: visible as inclusion bodies
  • Culture: difficult and dangerous (highly infectious)
  • Humans are the only known hosts
  • Microscopy: visible as inclusion bodies
  • Culture: difficult; requires tissue culture
Rickettsia
  • Arthropods (transmission to humans via ticks or mites)
  • Weakly gram-negative bacteria
Coxiella
  • Cattle, sheep, and goats are the typical hosts
  • Gram-negative bacteria
  • Ability to survive in very harsh environments

References:[76][77][78][79][80][81]