Extended-spectrum β-lactamase- and AmpC β-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study

Toombs-Ruane, Leah; Marshall, Jonathan; Benschop, Jackie; Drinković, Dragana; Midwinter, Anne C.; Biggs, Patrick J.; Grange, Zoë; Baker, Michael G; Douwes, Jeroen; Roberts, M. G.; French, Nigel P.; Burgess, Sara

doi:10.1016/j.ijid.2022.12.013

Cited by 5 publications

(5 citation statements)

References 56 publications

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“…This present study also found that none of the putative AmpC hyperproducing isolates were MDR. This is in line with previous studies that have showed ESBLs and plasmid mediated AmpC, but not overexpressed chromosomal mediated AmpC, being associated with multidrug resistance [41,79].…”

Section: Carriage Of Esbl-/acbl-producing E Coli Within Calves and Da...supporting

confidence: 93%

“…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%

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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: Carriage Of Esbl-/acbl-producing E Coli Within Calves and Da...supporting

confidence: 93%

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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“…In the current study, phylotype B2 was overrepresented in low impact sites (Figure S1 and Table S2 ), which aligns with our previous observations of its increased abundance in pristine bush environments compared to downstream sites impacted by pastoral farming (Cookson et al, 2022 ). Intriguingly, phylotype B2 has also been identified as a human‐associated E. coli phylotype, commonly isolated from urinary tract infections and associated with the extended‐spectrum beta‐lactamase resistant antibiotic resistance phenotype (Toombs‐Ruane et al, 2023 ). Therefore, we hypothesise that there are likely to be multiple pathotypes represented by phylotype B2, including those from forested sites (Petit et al, 2017 ), wildlife (Moinet et al, 2024 ) and humans with contrasting pathotype‐specific genetic characteristics (Johnson et al, 2017 ; Smati et al, 2015 ) which may influence their survival and persistence in the environment.…”

Section: Discussionmentioning

confidence: 99%

Population structure and pathogen interaction of Escherichia coli in freshwater: Implications of land‐use for water quality and public health in Aotearoa New Zealand

Cookson,

Devane,

Marshall

et al. 2024

Environ Microbiol Rep

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Freshwater samples (n = 199) were obtained from 41 sites with contrasting land‐uses (avian, low impact, dairy, urban, sheep and beef, and mixed sheep, beef and dairy) and the E. coli phylotype of 3980 isolates (20 per water sample enrichment) was determined. Eight phylotypes were identified with B1 (48.04%), B2 (14.87%) and A (14.79%) the most abundant. Escherichia marmotae (n = 22), and Escherichia ruysiae (n = 1), were rare (0.68%) suggesting that these environmental strains are unlikely to confound water quality assessments. Phylotypes A and B1 were overrepresented in dairy and urban sites (p < 0.0001), whilst B2 were overrepresented in low impact sites (p < 0.0001). Pathogens ((Salmonella, Campylobacter, Cryptosporidium or Giardia) and the presence of diarrhoeagenic E. coli‐associated genes (stx and eae) were detected in 89.9% (179/199) samples, including 80.5% (33/41) of samples with putative non‐recent faecal inputs. Quantitative PCR to detect microbial source tracking targets from human, ruminant and avian contamination were concordant with land‐use type and E. coli phylotype abundance. This study demonstrated that a potential recreational health risk remains where pathogens occurred in water samples with low E. coli concentration, potential non‐recent faecal sources, low impact sites and where human, ruminant and avian faecal sources were absent.

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“…The ESBL enzymes confer resistance to an extended range of beta-lactam antibiotics, including the first, third and some fourth generation cephalosporins but not the cephamycins or carbapenems [7,8]. CTX-M is the predominant enzyme type associated with human clinical ESBL-producing E. coli [9][10][11]. There are more than 250 bla CTX-M gene variants, with bla CTX-M-15 being the most common amongst human clinical E. coli [12][13][14][15].…”

Section: Introductionmentioning

confidence: 99%

“…There are more than 250 bla CTX-M gene variants, with bla CTX-M-15 being the most common amongst human clinical E. coli [12][13][14][15]. The genes encoding ESBLs are often associated with other antimicrobial resistance genes (ARGs), resulting in a multidrug resistant (MDR) strain [10,11,16]. MDR pathogenic strains of Enterobacteriaceae are of particular concern to the health sector resulting in ESBL-producing Enterobacteriaceae being identified as "critical" on the World Health Organisation's "Priority Pathogens List" [17].…”

Section: Introductionmentioning

confidence: 99%

Genomic epidemiology of ESBL-producingEscherichia colifrom humans and an Aotearoa New Zealand river

Gray,

Biggs,

Midwinter

et al. 2024

Preprint

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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 of 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 outflow point were the main sources of 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%). The most prevalent ESBL genes were both blaCTX-M-27 and blaCTX-M-15 for the clinical isolates (134/307, 43.6%) and blaCTX-M-15 for the environmental isolates (28/45, 62.2%). A core single nucleotide polymorphism 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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Extended-spectrum β-lactamase- and AmpC β-lactamase-producing Enterobacterales associated with urinary tract infections in the New Zealand community: a case-control study

Cited by 5 publications

References 56 publications

The characterisation of antimicrobial resistant Escherichia coli from dairy calves

The characterisation of antimicrobial resistant Escherichia coli from dairy calves

Population structure and pathogen interaction of Escherichia coli in freshwater: Implications of land‐use for water quality and public health in Aotearoa New Zealand

Genomic epidemiology of ESBL-producingEscherichia colifrom humans and an Aotearoa New Zealand river

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