molecular epidemiology of HCAI

types of strain typing

multi locus sequenec typing, pulsed field GE

HCAI outbreak can be determined when there is

same uncommon species - rarely seen, not commensal

phenotypic classification methods

bio, sero, phage typing and amic susceptibility

genotypic classifications

PFGE, MLST, WGS, variable number tandem repeat methods

WGS

sequence entire genome of sample

culture based how to

obtain sample, isolate, extract DNA, sequence DNA

microbial genetic variants

SNP, INDEL, variant

mutations can be

neutral, disadvantaheous (Weaker/dies), advantageous

nucleotide change outcomes

silencing of certain genes, reduction in viability of org, increased virulence, ab resistance

how do mutations/ variants arise

mistakes during DNA replication, exposure to mutagens, DNA recombination mobile genetic elements

can we infer phylogeny

based on genome sequences for patients bacterial isolates

e. faecium infections

intrinsic resistance to cephlosporins and aminoglycosides, acquired to glycopeptide (v)

how do vse become vre

when chromosome acquires van transposon, in aus vanB - encodes a ligase that modifies cell wall so vancomycin cant bind

vre transmission model a

patient arrives in hospital w vre already in gut - spreads to surrounding hospital env, patients contract from contaminated env

control for model a

screen patients for vre on arrival, isolate carriers, ensure staff follow appropriate protocol

expected outcomes on interventions for model a

reduction in newly colonised patient, natural attrition of colonised patients, progressivley eradicate vre from hospital

model b

vse carrier w vanb transposon present in other gut commensal, in hospital treated w v, vanb aquired from others under selection pressure, contaminate env w vre/ vanb locus

tn1549

carries vanb locus, can circularise itself and move independently - vse can spontaneoulsy aquire

clonal vs non clonal tranmission

c - same org replicates and spreads (A), nc - resistance element spreads between diff bac (b)