Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2022

FIXATION OF ANTIMICROBIAL RESISTANCE GENES IN BACTERIAL CHROMOSOMES (82393)

Alicia Fajardo-Lubian 1 2 , Sally Partridge 1 2 3 , Elena Martinez 4 , Jenny Draper 4 , Jon Iredell 1 2 3
  1. Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
  2. Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW, Australia
  3. Centre for Infectious Diseases and Microbiology, Westmead Hospital, WSLHD, Westmead, NSW, Australia
  4. Centre for Infectious Diseases and Microbiology, Laboratory Services, NSW Health Pathology, Westmead, NSW, Australia

Aim. To define the extent of chromosomal AMR gene carriage in Gram-negative bacteria in Australia.

Background. Antimicrobial resistance (AMR) genes in Gram-negative organisms commonly disseminate on plasmids, but critical AMR genes are increasingly reported on bacterial chromosomes [1,2,3]. If this leads to a permanent change in multiple species, restricting antibiotic use (the primary policy setting globally) will be powerless to reverse the threat of AMR.

Methods. Whole genome sequencing was performed by the Microbial Genomics Reference Laboratory (Westmead Hospital) using the Illumina NextSeq™ 500 platform. Data were analyzed using a modification of the Nullarbor bioinformatic pipeline [4], followed by a custom AMR-specific pipeline. Ambiguities, potential multiple gene copies/variants and gene location (plasmid or chromosomal) were checked manually by mapping reads to references using Geneious. Bandage was used for visualization of the connections between assembled contigs [5].

Results. Our analysis of short-read WGS data for 2019 and 2020 isolates from the Gram-negative Sepsis Outcome Program (Australian Group on Antimicrobial Resistance) revealed that the most prevalent AMR genes conferring resistance to widely-used extended-spectrum β-lactam antibiotics (ESBL, blaCTX-M genes) are mostly found on the chromosome in some major pandemic lineages of Escherichia coli (Table 1), the most predominant pathogen isolated from sepsis episodes in Australia (55.5% and 55.8% in 2019 and 2020, respectively).

Table 1. Prevalence of chromosomal ESBL in most common E. coli sequence types (STs) in Australia.

E. coli

ESBL gene

Chromosomal location (%)

ST12

blaCTX-M-14 / blaCTX-M-15

100% (6/6)

ST38

blaCTX-M-14

100% (16/16)

ST131-FimH30

blaCTX-M-14

87% (7/8)

ST131-FimH30x

blaCTX-M-15

*23% (17/72)

ST131-FimH41

blaCTX-M-27 / blaCTX-M-15

*80% (44/55)

*For some isolates, location of ESBL genes could not be determined.

Conclusion. Some global epidemic bacterial strains might be permanently incorporating AMR genes into their core genome. The chromosomal fixation of AMR genes will have enormous implications for antibiotic use policies as the view that less antibiotic use will allow AMR to vanish might not be valid in the near future.

 

 

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