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

Burgess, Sara; Moinet, Marie; Brightwell, Gale

doi:10.1099/mgen.0.000893

Cited by 5 publications

(11 citation statements)

References 78 publications

(113 reference statements)

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“…To give insights into the transmission of these resistant E. coli from a One Health perspective a core SNP analysis was undertaken on the ST10 and ST69 isolates ( and S1) [39]. The New Zealand dairy calf isolates from this study were distinct from the other New Zealand derived isolates but were closely related to each other, with the ST10 isolates from farms VCF77 and VCF80 differing by six SNPs suggesting they were derived from a shared source or that there was farm to farm transmission (Table S4).…”

Section: Resultsmentioning

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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Section: Resultsmentioning

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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“…The use of the CHROMagar ESBL media for ESBL-E. coli enumeration and isolation were in line with previous studies [34,35]. Samples were processed by homogenizing 25 g of soil or vegetable samples or mixing 25 ml of irrigation water with 225 ml of buffered peptone water, diluted serially, followed by incubation for 24 h at 37˚C.…”

Section: Esbl Enumeration Isolation and Identificationmentioning

confidence: 96%

Multidrug-resistant extended spectrum β-lactamase (ESBL)-producing Escherichia coli from farm produce and agricultural environments in Edo State, Nigeria

et al. 2023

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Antimicrobial resistance (AMR) is a major public health concern, especially the extended-spectrum β-lactamase-producing (ESBL) Escherichia coli bacteria are emerging as a global human health hazard. This study characterized extended-spectrum β-lactamase Escherichia coli (ESBL-E. coli) isolates from farm sources and open markets in Edo State, Nigeria. A total of 254 samples were obtained in Edo State and included representatives from agricultural farms (soil, manure, irrigation water) and vegetables from open markets, which included ready-to-eat (RTE) salads and vegetables which could potentially be consumed uncooked. Samples were culturally tested for the ESBL phenotype using ESBL selective media, and isolates were further identified and characterized via polymerase chain reaction (PCR) for β-lactamase and other antibiotic resistance determinants. ESBL E. coli strains isolated from agricultural farms included 68% (17/25) from the soil, 84% (21/25) from manure and 28% (7/25) from irrigation water and 24.4% (19/78) from vegetables. ESBL E. coli were also isolated from RTE salads at 20% (12/60) and vegetables obtained from vendors and open markets at 36.6% (15/41). A total of 64 E. coli isolates were identified using PCR. Upon further characterization, 85.9% (55/64) of the isolates were resistant to ≥ 3 and ≤ 7 antimicrobial classes, which allows for characterizing these as being multidrug-resistant. The MDR isolates from this study harboured ≥1 and ≤5 AMR determinants. The MDR isolates also harboured ≥1 and ≤3 beta-lactamase genes. Findings from this study showed that fresh vegetables and salads could be contaminated with ESBL-E. coli, particularly fresh produce from farms that use untreated water for irrigation. Appropriate measures, including improving irrigation water quality and agricultural practices, need to be implemented, and global regulatory guiding principles are crucial to ensure public health and consumer safety.

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“…To give insights into the transmission of these resistant E. coli from a One Health perspective a core SNP analysis was undertaken on the ST10 and ST69 isolates (Figure 4, Supplementary Figure1, and Table S3) (Burgess et al, 2022). The New Zealand dairy calf isolates from this .…”

Section: Population Structure Of Ampc-producing Tetracycline Resistan...mentioning

confidence: 99%

“…Bioinformatics, 3025-3027. (Burgess et al, 2022) generated using 17218 core SNPs. AGR6137 was used as the reference.…”

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confidence: 99%

“…The symbols represent the source (dog, natural environment, human, or cattle/calf) of the isolate, the coloured strip represents the year of isolation, the circles represent the presence of the bla CTX-M gene, the stars the presence of the bla CMY or bla DHA-1 gene and the squares the presence of other antimicrobial resistance genes. Burgess, S.A., Moinet, M., Brightwell, G., Cookson, A.L., 2022. Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites. Microbial Genomics 8.…”

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confidence: 99%

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The characterisation of antimicrobial resistantEscherichia colifrom dairy calves

Mwenifumbo¹,

Zhao²,

Ahmed³

et al. 2023

Preprint

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Dairy calves, particularly pre-weaned calves have been identified as a common source of multidrug (MDR) resistant E. coli. However, the strains and whether their resistance genes are plasmid or chromosomally located have not been well characterised. Our study examined the phenotype and genotype of antimicrobial resistant E. coli isolated from young calves (≤ 14 days old). Recto-anal swab enrichments from 40 dairy calves located on four dairy farms were examined for tetracycline, streptomycin, ciprofloxacin, and third-generation cephalosporin resistant E. coli. Fifty-eight percent (23/40) of calves harboured antimicrobial resistant E. coli: 18/40 (45%) harboured tetracycline resistant and 25% (10/40) 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), ST10 (2/27, 7%), and ST58 (1/27, 4%). 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. A phylogenetic comparison of the ST10 and ST69 isolates demonstrated that the calf derived isolates were distinct from other New Zealand animal, human, and environmental isolates. and highlights the importance of understanding the sources of antimicrobial resistance.

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

Cited by 5 publications

References 78 publications

The characterisation of antimicrobial resistant Escherichia coli from dairy calves

The characterisation of antimicrobial resistant Escherichia coli from dairy calves

Multidrug-resistant extended spectrum β-lactamase (ESBL)-producing Escherichia coli from farm produce and agricultural environments in Edo State, Nigeria

The characterisation of antimicrobial resistantEscherichia colifrom dairy calves

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