Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use

Biggs, Patrick J.; Wilkinson, David A.

doi:10.1128/aem.00277-22

Cited by 10 publications

(21 citation statements)

References 74 publications

(106 reference statements)

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“…The genome sequences of the ESBL-producing E. coli isolated from the freshwater sites were compared with the genome sequences of 271 other New Zealand sequence type (ST)131 and ST69 strains previously sequenced by other institutes (Table S1) [3, 19, 27, 28]. The sequence reads were downloaded from the NCBI Sequence Read Archive database and processed using the Nullarbor pipeline (v.2.0.20191013).…”

Section: Methodsmentioning

confidence: 99%

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Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites

2022

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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.

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Section: Methodsmentioning

confidence: 99%

“…In New Zealand, E. coli levels in waterways are measured and faecal source tracking has identified the main sources of faecal pollution in these waterways [19, 20]. However, little is known about the source of antimicrobially resistant E.…”

Section: Introductionmentioning

confidence: 99%

Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites

2022

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“…Strains were obtained as part of a study examining the impact of contrasting land uses on Escherichia spp. and were cultured as described previously ( 8 ). Genomic data from E. coli and the new Escherichia spp.…”

Section: Announcementmentioning

confidence: 99%

Draft genome sequences of Escherichia spp. isolates from New Zealand environmental sources

Biggs,

Moinet,

Rogers

et al. 2024

Microbiol Resour Announc

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Escherichia coli is often used as a fecal indicator bacterium for water quality monitoring. We report the draft genome sequences of 500 Escherichia isolates including newly described Escherichia species, namely Escherichia marmotae , Escherichia ruysiae, and Escherichia whittamii , obtained from diverse environmental sources to assist with improved public health risk assessments.

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“…The sequence reads of other New Zealand ST10, ST69 strains as well as ST88 cattle and calf isolates previously sequenced by other institutes (Table S3) [39][40][41][42][43][44][45][46], were downloaded from the NCBI Sequence Read Archive database and processed using the Nullarbor pipeline (v. 2.0.20191013). Whole genome multi-locus sequence typing (wgMLST) was undertaken using Fast-GeP (v. 1.0) [47] and Single Nucleotide Polymorphism (SNP) analyses using Snippy (v. 4.3.6, https://github.com/tseemann/snippy).…”

Section: Genome Sequences and Bioinformaticsmentioning

confidence: 99%

The characterisation of antimicrobial resistant Escherichia coli from dairy calves

Mwenifumbo

Zhao

Ahmed

et al. 2023

Journal of Medical Microbiology

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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.

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Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use

Cited by 10 publications

References 74 publications

Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites

Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites

Draft genome sequences of Escherichia spp. isolates from New Zealand environmental sources

The characterisation of antimicrobial resistant Escherichia coli from dairy calves

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