Study Design - Clinical Significance Flashcards
Biofilm producing organisms
P. aeruginosa and its small colony variants
Acinetobacter
S. aureus - dry surface biofilms
CPE
Colonisation >40% of ICU sinks -> tends to regrow quicly
In one study 90% of surfaces samples harboured DSBs -> detection not recovered by swabbing and less suceptible to physical and chemical disinfection and sterilisation
Comment on growing threat of antibiotic resistance in general
One of the top global public health and development threats
Estimated that AMR was dorectly responsible for 1.27 million global deaths and contributed to 4.95 million deaths in 2019
Expected to contribute to 50 million deaths by 2050
Comment on the growing threat of antimicrobial resistance, give specific tats
Third generation cephalosporin resistance in 42% of E. coli
Methicillin resistance in 35% of S. aureus
1 in 5 E. Coli UTIs show reduced susceptibility to standard antibiotics e.g. amipicillin, co-trimoxazole and fluoroquinolones
K. pneumonia reliance on last resort antibiotics rising
anticipated x2 surge in resistance to last resort antibiotics by 2035
Resistance in Pseudomonas aeruginosa, mechanism ,detection etc
Fluoroquinolone resistance trhough efflux pumps, mutations in DNA gyrase and outer membrane changes
gyrA and parC genes
Resistance in Klebsiella pneumonia, mechanisms and targets
resistance against beta lactams
beta-lactamase production, porin loss and efflux pumps
produces KPC - klebsiella pneumoniae carbapenemase and alters porins
What resistant organisms are crossing into the community
MRSA
CPEs -> MDR R>3 antibiotic classes
HCAI crossing into the community
Talk about resistance emerging in community pathogens
Resistance in traditionally community pathogens such as:
- S. pneumoniae
- N. gonothoea
- Shigella
- TB -> XDR
Clinical significance of MRSA
Resistance and potential for cross-infection
Community acquired MRSA arround since the 1990s - displays less cross-resistance but retains virulence of mssa - often linked to production of panton-valentine leukocidin (PVL toxin)
Livestock associated MRSa also an emerging threat
Used to have high levels of MRSA but numbers have reduced
Outbreaks of CA reported in schools, sports teams and other community groups
Peaked at 42% in 2006 but now as low as 9.7% in 2023
Target for MRSA and the significance of this
mecA/mecC gene
This leads to production of an altered penicillin-binding protein known as PBP2a
This has a reduced affinity for methicillin and other B-lactams, resulting in high-level resistance to these antibiotics
MecA is part of the staphylococcal chromosomal cassette mec (SCCmec), a larger mobile genetic element, allowing spread
Vancomycin resistant MRSA has been reported since 1990s but this hasnt been seen in ireland - vanA
How do we screen for MRSA?
Screen using chromagar
Samples such as nasal, groin, auxilaa
Confirmation using commercial real-time PCR detection systems e.g. geneXpert
What tests do we use to detect MRSA?
MIC for cefoxitin, >4mg/L = methicillin resistant
Disk diffusion 30ug cefoxitin, zone <22mm =resistant
MASTalex Latex agglutination to detect PBP2a -> will detect MecA and not MecC
Genotypically using PCR for MecA or MecC
Clinical significance of VRE
Resistance to vanc and now other antimicrobials including quinolones, high level aminoglycosides (30-60%), macrolides, tetracyclines, linezolid, - virtually all
VRE spreads efficiently, persisting in hospital environments and colonizes many individuals but few develop infections
Has both intrinsic and mutational resistance
VRE decreased from 38.6% in 2019 to 21.4% in 2023, lowest level but still high - were above eu average of 16.8% though
Rates are increasing across europe
B-lactam resistance in VREs
penicillin binding protein 5 production - which has low affinity for beta lactams
intinsic, chromosally encoded, low-level resistance or
Mutational - high level resistance
Rare in E. faecalis but common in E. faecium
Glycopeptide resistance in VRE
Glycopeptides such as vancomycin bind to DalaDala preventing cross linking of peptidoglycan
VREs acquire vanA or vanB gene clusers which alter the target site of vancomycin and thus reduce its binding affinity - loss of H bond required for vanc binding
VanA confers high-level resistance to both vanc and teicoplanin while vanB are typically susceptible to teicoplanin
These genes are often located on mobile genetic elements, thus facilitating horizontal gene transfer among enterococci and other GPs
Linezolid resistance in VRE
Linezolid was introduced in 2000 as a last resort antibiotic
Linezolid inhibits bacterial protein synthesis by binding to the 23S rRNA of the 50s ribosomal subunit
VRE has a point mutation, G2576T, in the 23S rRNA mutations which alters the linezolid binding site reducing its affinity for the ribosome
How do we screen for VRE
Rectal swabs
chromaogenic agar
Confirm with real time PCR either directly from sample or a colony
How do we test for VRE in the lab
MIC - agar dilution, broth microdilution, gradient MIC
-> high level van resist = Van A >64m/L
-> low level van resist = Van B, MIC = 4
Disk diffusion - vancomycin 5ug disk
-> <12 mm = resistant
-> fuzzy zone edges and/or colonies reported as resistant
VITEK/automation nont recommended
Confirm genotypically using PCR for VanA or vanB
Strep pneumoniae resistance, clinical significance
Historically S. pneumoniae was suceptible to penicillin
Resistance appeared in the 1970s
From 1997 weve had abou 20% resitance
Considerable increase in incidence of invasive isolates
- significance increasing trend in AMR over lat 5 years
In 2023 17.5% of all invasive strains were Penicilin nonwild type representing a decrease form 23.6% in 2022
Strep pneumoniae, resistance mechanism
Mediated by alterations in PBPs especially PBP2x, PBP2b or PBP1a
Resistance arises from mutations or horizontal acquisition of altered PBP genes via transformation from related bacterial species - results in reduced binding affinity for penicillin and other beta-lactam antibiotics
Most PNSP and Pen-I strains remain susc to broad spectrum B-lactams but Pen-HLR strains are often co-resistant to macrolides, cephalosporins and quinolones
Many strains exhibit MDR, defined as resistance to three or more antibiotic classes -> MDR is often associated with mobile genetic elements including transposons
How do we test for Penicillin resistance in the lab
PNSP strains with reduced susceptiblity to penicillin -> will have MICs above those of wildtype >0.06 mg/L
Screen using 1 ug Oxacilin -> disk diffusion -> if oxacillin susceptible then penicillin susceptible
Confirm oxacillin non suscpetibles by performing penicillin and cefotaxime MIC
Clinical significance of TB
8.6 million cases and 1.4 million deaths a year
high levels in southern africa
etc
Detection of tuberculosis
Resistance in TB
Clinical significance of VTEC
Shiga toxin causes diarrhoea, haemorrhagic colitis, HUS
Detection of VEC
Stx1 or Stx2
