Journal Articles

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    Genomic epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli from humans and a river in Aotearoa New Zealand.
    (Microbiology Society, 2025-01-10) Gray HA; Biggs PJ; Midwinter AC; Rogers LE; Fayaz A; Akhter RN; Burgess SA
    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.
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    Leech breach: a first record of the invasive freshwater leech Helobdella europaea (Hirudinea: Glossiphoniidae) in Fiji
    (CSIRO Publishing, 2023-07-03) Rashni B; Brown KT; McLenachan PA; Lockhart PJ; Southgate PC; Lal MM; Calver M
    Context: The freshwater flat leech Helobdella europaea Kutschera, 1987 is a small annelid indigenous to South America. This invasive species feeds on the haemolymph of host aquatic invertebrates, with occurrences reported from Europe, USA, Taiwan, North Africa, Hawai'i, Australia and New Zealand. A large number of individuals were discovered in the Ba River catchment, Fiji, during a 2015-2020 freshwater biodiversity survey, raising concerns of potential impacts on endemic Fijian aquatic invertebrate fauna and ecosystem integrity. Aims: To facilitate assessments of its spread and ethology, this study employed morphological and phylogenetic analyses for verification of taxonomic identity. Methods: Phylogenetic trees were constructed using a 658 bp fragment of the mitochondrial DNA cox1 (COI) gene. The first complete mitochondrial genome sequence of H. europaea was also determined using selective multiple displacement amplification and Oxford Nanopore Technology to provide a reference for future comparative analyses and source tracking of spread to other regions. Key results: Morphological and COI analyses identified all Fijian leech specimens collected (n = 16) as H. europaea, reporting the first occurrence of this species on a south-west Pacific Island. The complete mitochondrial genome was sequenced. Conclusions: Confirmation of its presence in Fiji is a national biosecurity concern and will guide the Biosecurity Authority of Fiji and national agencies in further ecosystem assessment and response strategies. Implications: With the complete mitochondrial genome of H. europaea now available, transmission pathway traceability is possible in other regions where this species may be detected.
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    Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites.
    (2022-10) Burgess SA; Moinet M; Brightwell G; Cookson AL
    Extended-spectrum beta lactamase (ESBL)-producing Escherichia coli are often isolated from humans with urinary tract infections and may display a multidrug-resistant phenotype. These pathogens represent a target for a One Health surveillance approach to investigate transmission between humans, animals and the environment. This study examines the multidrug-resistant phenotype and whole genome sequence data of four ESBL-producing E. coli isolated from freshwater in New Zealand. All four isolates were obtained from a catchment with a mixed urban and pastoral farming land-use. Three isolates were sequence type (ST) 131 (CTX-M-27-positive) and the other ST69 (CTX-M-15-positive); a phylogenetic comparison with other locally isolated strains demonstrated a close relationship with New Zealand clinical isolates. Genes associated with resistance to antifolates, tetracyclines, aminoglycosides and macrolides were identified in all four isolates, together with fluoroquinolone resistance in two isolates. The ST69 isolate harboured the bla CTX-M-15 gene on a IncHI2A plasmid, and two of the three ST131 isolates harboured the bla CTX-M-27 genes on IncF plasmids. The last ST131 isolate harboured bla CTX-M-27 on the chromosome in a unique site between gspC and gspD. These data highlight a probable human origin of the isolates with subsequent transmission from urban centres through wastewater to the wider environment.