ESBL E coli genome sequencing

Background: The prevalence of extended-spectrum beta-lactamase (ESBL)-producing isolates reported by the principal Central Australian referral centre has increased from 7% in 2013 to 21% in 2020. We aimed to describe the demographics, clinical and molecular epidemiology of ESBL Escherichia coli bloodstream infections in Central Australia. Methods: We retrospectively identified all ESBL-producing E. coli bloodstream isolates from January 2018 to December 2020. Demographic and clinical information was extracted by chart review. Whole-genome sequencing was performed for multi-locus sequence typing, antibiotic resistance genes, and phylogenetic relationships. Results: We identified 42 non-duplicate episodes of ESBL E. coli bloodstream infection. Median age was 55 years (IQR 47-63), 76% (32/42) were female, 93% (39/42) were Aboriginal, and half came from a remote community (outside Alice Springs). Infections were predominantly of urinary source (67%, 28/42). In the 12 months prior, 68% (26/38) of identified patients had been hospitalized and 71% (30/42) had been prescribed antibiotics (including outpatient and community prescribing). Piperacillin-tazobactam susceptibility was maintained in 93% of isolates, with all isolates susceptible to meropenem. Co-resistance to non-beta-lactam antibiotics was common: 31% (13/42) were non-susceptible to gentamicin, 62% (26/42) to trimethoprim/sulfamethoxazole, and 67% (28/42) to ciprofloxacin. For sequenced E. coli isolates, 44% (16/36) were sequence type 131 (ST131). Median acquired antibiotic resistance genes for each isolate was 13 (IQR 11-14) and 97% (35/36) carried a blaCTX-M gene (14,15,or 27). Four isolates carried an OXA-1 gene. Only non-ST131 isolates carried AmpC and acquired quinolone resistance genes. There was some evidence of clustering of closely related strains, but no evidence of community or healthcare admission overlap. Conclusions: ESBL rates are rapidly rising in Central Australia. Central Australia represents a conducive environment for antibiotic resistance to occur, with overcrowding and a low socioeconomic population, high healthcare exposure and high antibiotic use. Future research is required to explore carriage rates of ESBL-producing E. coli in Central Australia, and to better understand transmission dynamics in this unique setting.