RESULTS:

In Aotearoa New Zealand urinary tract infections in humans are commonly caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. This group of antimicrobial-resistant bacteria are often multidrug resistant. However there is limited information on ESBL-producing E. coli found in the environment and their link with human clinical isolates. In this study we examined the genetic relationship between environmental and human clinical ESBL-producing E. coli and isolates collected in parallel within the same area over 14 months. Environmental samples were collected from treated effluent stormwater and multiple locations along an Aotearoa New Zealand river. Treated effluent stormwater and river water sourced downstream of the treated effluent outlet were the main samples that were positive for ESBL-producing E. coli (7/14 samples 50.0%; 3/6 samples 50%; and 15/28 samples 54% respectively). Whole-genome sequence comparison was carried out on 307 human clinical and 45 environmental ESBL-producing E. coli isolates. Sequence type 131 was dominant for both clinical (147/307 47.9%) and environmental isolates (11/45 24.4%). Only one ESBL gene was detected in each isolate. Among the clinical isolates the most prevalent ESBL genes were bla CTX-M-27 (134/307 43.6%) and bla CTX-M-15 (134/307 43.6%). Among the environmental isolates bla CTX-M-15 (28/45 62.2%) was the most prevalent gene. A core SNP analysis of these isolates suggested that some strains were shared between humans and the local river. These results highlight the importance of understanding different transmission pathways for the spread of ESBL-producing E. coli.

Introduction. Dairy calves particularly pre-weaned calves have been identified as a common source of multidrug resistant (MDR) Escherichia coli .

Gap statement. E. coli strains isolated from dairy calves and the location of their resistance genes (plasmid or chromosomal) have not been well characterised.

Aim. To characterise the phenotypic and genotypic features as well as the population structure of antimicrobial-resistant E. coli isolated from calves located on dairy farms that feed waste-milk to their replacement calves.

Methodology. Recto-anal swab enrichments from 40 dairy calves (≤ 14 days old) located on four dairy farms were examined for tetracycline streptomycin ciprofloxacin and third-generation cephalosporin resistant E. coli . Whole genome sequencing was performed using both short- and long-read technologies on selected antimicrobial resistant E. coli .

Results. Fifty-eight percent (23/40) of calves harboured antimicrobial resistant E. coli : 43 % (17/40) harboured tetracycline resistant and 23 % (9/40) harboured chromosomal mediated AmpC producing E. coli . Whole genome sequencing of 27 isolates revealed five sequence types with ST88 being the dominant ST (17/27 63 % of the sequenced isolates) followed by ST1308 (3/27 11 %) along with the extraintestinal pathogenic E. coli lineages ST69 (3/27 11 %) ST10 (2/27 7 %) and ST58 (2/27 7 %). Additionally 16 isolates were MDR harbouring additional resistance genes that were not tested phenotypically. Oxford Nanopore long-read sequencing technologies enabled the location of multiple resistant gene cassettes in IncF plasmids to be determined.

Conclusion. Our study identified a high incidence of tetracycline and streptomycin-resistant E. coli in dairy calves and highlighted the presence of multidrug-resistant strains emphasising the need for further investigation into potential associations with farm management practices.