Practice 08 Nomenclature and taxonomy [Kompatibilitási mód]

Practice 08 Nomenclature and taxonomy [Kompatibilitási mód]

2014.11.06.
Taxonomy
Nomenclature and taxonomy
The groups of pathogenic microbes
Eukarya
Protista
Kinetoplastida
Haemosporidea
Haemosporidia
Plasmodiaceae
Plasmodium
falciparum
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Species concept
Species definition
• Traditional – group of genetically closely related individuals
• In case of asexually reproducing creatures (as the majority of
microbes), the species is determined as a certain level of genetic
similarity.
• Genomospecies – genetically homogenous species
• Species complex – group of related genomospecies, which is
classified into the complex based on traditional methods
(biochemical activity, serological characteristics), but which are
genetically different (e.g. M. tuberculosis complex – M. tbc., M.
bovis, M. africanum és M. caprae)
• Sometimes taxa, which belong to one genomospecies genetically,
but differ pathogenetically, are calssified into different species, even
to different genera (Neisseria meningitidis and N. gonorrhoeae;
Escherichia coli and Shigella spp.)
Nomenclature
• Linné
• Genus
species
(subspecies)
(variant)
Staphylococcus cohnii ssp. cohnii
Salmonella enterica ssp. Enterica sv. Typhi
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Subspecies
Biovariants and serovariants
Isolate – individual microbes cultured from a single sample
Strain, clone – group of genetically related isolates
– DNA-DNA hybridization
– Sequences of conservative genes (rDNA, rpoB)
• Identification
– Still mostly based on the phenotype
– Biochemical tests
– Serological tests
• Taxonomic changes are slowly acknowledged and
accepted by medical microbiology; frequently an
outdated traditional name and classification is used
Phylogeny of living organisms
Escherichia coli
• Categories below species level:
• Criteria
• Archaea
(Crenarchaeot
a,
Euryarchaeot
a,
Nanoarchaeot
a,
Korachaeota)
• Eubacteria
• Eukarya
(Protista,
Chromista,
fungi,
plants,
animals)
• Viruses
(DNARNAviruses)
– Extremophil
es
– Methanogen
es
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Classification of bacteria
Human pathogenic eubacteria
• Gram positives
• Proteobacteria
– α-proteobacteria (Ehrlichia, Bartonella, Brucella, Rickettsia,
Rhizobium)
– β-proteobacteria (Neisseria, Burkholderia, Alcaligenes)
– γ-proteobacteria (Aeromonas, Enterobacteriaceae, Pseudomonas,
Vibrio)
– δ-proteobacteria
– ε-proteobacteria (Helicobacter, Campylobacter)
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Spirochaetes
Chlamydias
Bacteroidetes
Fusobacteria
Gram positive bacteria
• Gram positive cocci
– Staphylococci
– Streptococci
• Gram positive rods
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Bacillus
Listeria
Corynebacterium
Eubacterium
Clostridium
Actinomyces
Propionibacterium
Gardnerella
• Not based on taxonomic data
• Gram stain (based on cell wall structure), shape
– Gram positives (a phylogenetically homogeneous group)
– Gram negatives (a phylogenetically highly diverse group)
– Bacteria without cell wall
(Mycoplasmatales; phylogenetically related to Gram positives)
– Acid-fast bacteria (with acid fast cell wall)
(Mycobacteria; phylogenetically related to Gram positives)
– Bacteria not staining with Gram (others)
(Rickettsia, Chlamydia, spirochaetes; phylogenetically diverse)
• Based on oxigen requirement
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Obligate aerobic
Aerotolerant
Facultative anaerobic
Obligate anaerobic
Microaerophilic
Not stained by Gram
• Acid fast
– Mycobacterium
– Nocardia
• Cell-wall-less bacteria
– Mycoplasma
Gram positive cocci
• Staphylococcus
– Coagulase positive – S. aureus
– Coagulase negative – S. epidermidis, S. haemolyticus,
S. lugdunensis)
• Streptococcus
– Streptococcus – S. pyogenes, S. agalactiae, S.
pneumoniae, etc.
– Enterococcus – E. faecalis, E. faecium, etc.
– Peptostreptococcus (obligate anaerobic)
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Gram positive rods
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Aerobic/facultative anaerobic:
Bacillus – B. anthracis, B. cereus, B. subtilis
Listeria – L. monocytogenes
Corynebacterium – C. diphtheriae, C. jeikeium, etc.
Obligate anaerobic:
Eubacterium – E. lentum
Clostridium – C. tetani, C. botulinum, C. perfringens, etc.
Actinomyces – A. israeli, A. naeslundii, etc.
Propionibacterium – P. acnes
Gardnerella – G. vaginalis
Bacillus anthracis
Clostridium tetani
Corynebacterium diphtheriae
Actinomyces israelii
Acid-fast bacteria;
bacteria without a cell wall
• Acid-fast bacteria (phylogenetically related to
Actinomycetes)
• Mycobacterium – M. tuberculosis (complex), M. leprae, etc.
• Weakly acid-fast b. (phylogenetically related to
Actinomycetes)
• Nocardia – N. farcinica, etc. (presently changing taxonomy)
• (rare human pathogens – Rhodococcus)
• Cell-wall-less bacteria
• Mycoplasma – M. hominis, M. pneumoniae, etc.
• Ureaplasma – U. urealyticum
Gram negative bacteria
• Gram negative cocci
and coccobacilli
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Neisseria
Haemophilus
Moraxella
Acinetobacter
Pasteurella
Bordetella
Francisella
Brucella
Veilonella
• Gram negative rods
– Enterobacteriaceae
– Pseudomonas
– Aeromonas
– Anaerobic Gram negative
rods
– Streptobacillus
• Gram negative curved rods
– Vibrio
– Helicobacter
– Campylobacter
• Intracellular Gram negative
bacteria
• Spirillum
• Spirochaetes
Acid-fast stain (Ziehl-Neelsen)
M. tuberculosis
on LJ medium
Gram negative cocci and coccobacilli
• Neisseria – N. gonorrhoeae, N. meningitidis
(genetically a single species)
• Haemophilus – H. influenzae, H. ducreyi, etc.
• Moraxella – M. lacunata, M. (Branhamella) catarrhalis
• Acinetobacter – A. baumannii (complex), A. lwoffii, etc.
• Pasteurella – P. multocida, etc.
• Bordetella – B. pertussis, etc.
• Francisella – F. tularensis
• Brucella – B. melitensis, B. abortus, B. canis, B. suis
• Veilonella – V. parvula (obligate anaerobic)
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Gram negative rods
Neisseria gonorrhoeae
Francisella tularensis
• Enterobacteria
• Escherichia – E. coli
• Shigella (forms a single genomospecies together with E. coli)
– S. dysenteriae, S. flexneri, S. boydii, S. sonnei
• Salmonella – S. enterica, S. bongori
(complicated taxonomy based on serological properties)
• Klebsiella – K. pneumoniae, K. oxytoca
• Enterobacter – E. aerogenes, E. cloacae, etc.
• Citrobacter – C. freundii (complex), C. koseri, etc.
• Proteus – P. mirabilis, P. morganii, P. vulgaris
• Serratia – S. marcenscens, etc.
• many other genera, several may be opportunistic pathogens
Acinetobacter sp.
Gram negative rods
Gram negative curved rods
Pseudomonas (taxonomy has changed a lot, still debated)
Pseudomonas – P. aeruginosa, etc.
Stenotrophomonas – S. maltophilia
Burkholderia – B. cepacia (complex), B. mallei, B. pseudomallei, etc.
many other genera, several may be opportunistic pathogens
Aeromonas (taxonomy has changed a lot, still debated)
Aeromonas – taxonomically uncertain species, A. sobria, etc.
Plesiomonas – P. shigelloides
Obligate anaerobic (phylogenetically two unrelated large groups)
Bacteroides – B. fragilis, etc.
Prevotella – P. melaninogenica, etc.
Porphyromonas – P. gingivalis, etc.
Fusobacterium – F. nucleatum, F. necrophorum, etc.
(differs phylogenetically from the former three related groups)
• Streptobacillus – S. moniliformis (rat bite fever)
• Vibrio – V. cholerae, V. vulnificus, V.
parahaemolyticus, etc.
• Helicobacter – H. pylori
• Campylobacter – C. fetus, C. jejuni, C. coli, etc.
• Arcobacter – A. butzleri, etc.
Intracellular Gram negative bacteria
Spirillums and spirochaetes
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Chlamydia (ATP parasite)
Chlamydia – C. trachomatis
Chlamydophila – (formerly Chlamydia) C. psittaci, C. pneumoniae
many other genera, several were implicated in human disease
Rickettsia (NAD parasite)
Rickettsia – R. prowazeckii, R. slovaca, etc.
Orientia – (formerly Rickettsia) O. tsutsugamushi
Coxiella – C. burnettii
Ehrlichia
Ehrlichia – E. chafeensis, E. sennetsu, E. ewingi
Anaplasma – A. phagocytophylum
Bartonella (culturable in cell-free medium)
Bartonella – B. quintana, B. bacilliformis, B. henselae, etc.
Legionella (culturable) – L. pneumophila, L. micdadei, etc.
• Spirillum – S. minor
• Spirochaetes
• Treponema – T. pallidum ssp. pallidum, T. pertenue,
T. vincenti etc.
• Borrelia – B. recurrentis, B. burgdorferi, etc.
• Leptospira – L. icterohaemorrhagiae (complicated
taxonomy within
the genus)
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Borrelia hermsii - Giemsa
Treponema pallidum – dark-field
Leptospira sp. – silver imp.
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