Introduction
Items | Pathogens |
---|---|
Genome characteristics |
Escherichia coli and other Enterobacteriaceae |
Genomic approach |
Staphylococcus aureus and coagulase-negative staphylococci |
Typing and outbreak | Streptococci and enterococci |
Virulence |
Pseudomonas aeruginosa and Acinetobacter baumannii
|
Antimicrobial susceptibility |
Mycobacterium tuberculosis complex and other mycobacteria |
Chlamydia trachomatis
|
Escherichia coli and other Enterobacteriaceae
Genome characteristics
Genomic approach
Typing and outbreak
Virulence
Gene/genomic region/plasmid | Functional role | Comments |
---|---|---|
LEE PAI | Genomic island containing eae (encoding gene for an adhesin) as well as effectors and structural proteins associated with a type III secretion system | EPEC defining region |
pINV | Encodes for a type III secretion system and for effectors allowing intracellular survival | EIEC/Shigella defining plasmid |
est, elt
| Heat-stable (ST) and heat-labile (LT) enterotoxins | ETEC defining genes |
stx1, stx2
| Shiga toxins (verotoxins) 1 and 2 | EHEC defining genes |
aggR, aatA, aaiC
| Transcriptional regulator, transporter protein and secreted protein | Associated with EAEC phenotype |
Antimicrobial susceptibility
Staphylococcus aureus and coagulase-negative staphylococci
Genome characteristics
Genomic approach
Typing and outbreak
Virulence
Gene/genomic region/plasmid | Functional role | Comments |
---|---|---|
PVL locus (lukF-PV, lukS-PV) | Pore-forming toxin targeting polymorphonuclear leucocytes | Phage-encoded toxin associated with necrotising pneumonia or severe skin and soft tissue formation |
lukD/E, lukG/H
| Pore-forming toxins targeting polymorphonuclear leucocytes | Located on a pathogenicity island (LukDE), they act synergistically with PVL |
psm-mec locus | Cytolytic capacity, biofilm formation, methicillin resistance, cell spreading and expression of other virulence factors [70] | This locus may also be found in CoNS and could play a major role in CoNS sepsis [71] |
eta, etb, etd
| Exfoliative toxin A, B and D | Toxins involved in the pathogenesis of bullous impetigo and staphylococcal scaled-skin syndrome |
se(a-e), se(g-j), se(r-t), sel(k-q), sel(u-w), tsst-1
| Staphylococcal enterotoxins and enterotoxin-like toxins | Superantigens associated with S. aureus food poisoning and toxic shock syndrome |
Antimicrobial susceptibility
Streptococci and enterococci
Genome characteristics
Genomic approach
Typing and outbreak
Virulence
Gene/genomic region/plasmid | Functional role | Comments |
---|---|---|
hasA, hasB, hasC
| Hyaluronic acid capsule synthesis | Prevention of phagocytosis |
emm
| Antiphagocytic protein (M protein) | Sequence used for typing S. pyogenes isolates |
spyCEP
| Interleukin-8 protease | Inhibition of PMN leucocytes diapedesis |
sda1
| Streptodornase D (extracellular DNase) | Degradation of PMN DNA nets |
sagA, sagB, sagC, slo
| Streptolysin S and O | Lysis of red blood cells, epithelial cells, macrophages and PMN |
speA, speC, speH, speI, speJ, speL/M, ssa, SMEZ
| Superantigens | Involved in the pathogenesis of toxic shock syndrome or scarlet fever |
speB
| Cysteine protease | Tissue invasion and dissemination |
fbaA, sclA
| Adhesins |