Draft Genome Sequences of Seven Extended-Spectrum β-Lactamase-Producing Escherichia coli Strains Isolated from New Zealand Waterways

Indigenous food sources as vectors of Escherichia coli and antibiotic resistance

The contamination of surface waters by fecal bacteria, measured by the number of Escherichia coli, is a significant public health issue. When these bacteria are also resistant to antimicrobials, infections are more complicated to treat. While water is regularly tested at recreational sites, wild-harvested foods, known as mahinga kai by the indigenous Māori people of Aotearoa New Zealand, are commonly overlooked as a source of exposure to potential pathogens and antimicrobial resistance (AMR). We investigate two likely sources of risk from harvesting aquatic wild foods. The first is water contact, and the second is contact with/ingestion of the harvest. We used E. coli as a proxy for microbial water quality at harvesting sites. Two popular mahinga kai species were also harvested and assessed. We found antibiotic-resistant bacteria on watercress (Nasturtium officinale) and cockles (Austrovenus stutchburyi). One-third of E. coli isolates were conjugative donors of at least one resistance phenotype. Tank experiments were used to track the internalization of E. coli by Greenshell/lip mussels (Perna canaliculus). Greenshell mussels kept at environmentally relevant concentrations of E. coli were colonized to levels considered unsafe for human consumption in 24 h. Finally, we measured horizontal gene transfer between bacteria within the shellfish, what we termed 'intra-shellular' conjugation. The transmission frequency of plasmid RP4 was significantly higher in mussels than in water alone. Our results indicate that shellfish could promote the dissemination of antibiotic resistance. They highlight the need to limit or reduce human pathogenic bacteria where food is gathered.

Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments

Antimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, the role antimicrobial usage on pasture-based dairy farms, such as those in NZ, plays in driving the spread of AMR within the dairy farm environment remains equivocal. Culture-based methods were used to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli from farm environmental samples collected over a 15-month period from two NZ dairy farms with contrasting management practices. Whole genome sequencing was utilised to understand the genomic epidemiology and antimicrobial resistance gene repertoire of a subset of third-generation cephalosporin resistant E. coli isolated in this study. There was a low sample level prevalence of ESBL-producing E. coli (faeces 1.7%; farm dairy effluent, 6.7% from Dairy 4 and none from Dairy 1) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3% and 8.3%; farm dairy effluent 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). ESBL- and AmpC-producing E. coli were isolated from faeces and farm dairy effluent in spring and summer, during months with varying levels of antimicrobial use, but no ESBL- or AmpC-producing E. coli were isolated from bulk tank milk or soil from recently grazed paddocks. Hybrid assemblies using short- and long-read sequence data from a subset of ESBL- and AmpC-producing E. coli enabled the assembly and annotation of nine plasmids from six E. coli, including one plasmid co-harbouring 12 antimicrobial resistance genes. ESBL-producing E. coli were infrequently identified from faeces and farm dairy effluent on the two NZ dairy farms, suggesting they are present at a low prevalence on these farms. Plasmids harbouring several antimicrobial resistance genes were identified, and bacteria carrying such plasmids are a concern for both animal and public health. AMR is a burden for human, animal and environmental health and requires a holistic “One Health” approach to address.

Antimicrobial Resistance in New Zealand-A One Health Perspective

Antimicrobial resistance (AMR) is an increasing global threat that affects human, animal and, often less acknowledged, environmental health. This complex issue requires a multisectoral One Health approach to address the interconnectedness of humans, animals and the natural environment. The prevalence of AMR in these reservoirs varies widely among countries and thus often requires a country-specific approach. In New Zealand (NZ), AMR and antimicrobial usage in humans are relatively well-monitored and -understood, with high human use of antimicrobials and the frequency of resistant pathogens increasing in hospitals and the community. In contrast, on average, NZ is a low user of antimicrobials in animal husbandry systems with low rates of AMR in food-producing animals. AMR in New Zealand’s environment is little understood, and the role of the natural environment in AMR transmission is unclear. Here, we aimed to provide a summary of the current knowledge on AMR in NZ, addressing all three components of the One Health triad with a particular focus on environmental AMR. We aimed to identify knowledge gaps to help develop research strategies, especially towards mitigating AMR in the environment, the often-neglected part of the One Health triad.