scholarly journals The epidemiology of AmpC-producing Escherichia coli isolated from dairy cattle faeces on pasture-fed farms

2021 ◽  
Vol 70 (10) ◽  
Author(s):  
Sara A. Burgess ◽  
Adrian L. Cookson ◽  
Lisa Brousse ◽  
Enrico Ortolani ◽  
Jackie Benschop ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sequence Analysis ◽  
Type Species ◽  
Dairy Farms ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Analysis ◽  
Content Type ◽  
E Coli ◽  
Link Type

Introduction. Antibiotic use, particularly amoxicillin-clavulanic acid in dairy farming, has been associated with an increased incidence of AmpC-hyperproducing Escherichia coli . Gap statement. There is limited information on the incidence of AmpC-hyperproducing E. coli from seasonal pasture-fed dairy farms. Aim. We undertook a New Zealand wide cross-sectional study to determine the prevalence of AmpC-producing E. coli carried by dairy cattle. Methodology. Paddock faeces were sampled from twenty-six dairy farms and were processed for the selective growth of both extended-spectrum beta-lactamase (ESBL)- and AmpC-producing E. coli . Whole genome sequence analysis was carried out on 35 AmpC-producing E. coli . Results. No ESBL- or plasmid mediated AmpC-producing E. coli were detected, but seven farms were positive for chromosomal mediated AmpC-hyperproducing E. coli . These seven farms were associated with a higher usage of injectable amoxicillin antibiotics. Whole genome sequence analysis of the AmpC-producing E. coli demonstrated that the same strain (<3 SNPs difference) of E. coli ST5729 was shared between cows on a single farm. Similarly, the same strain (≤15 SNPs difference) of E. coli ST8977 was shared across two farms (separated by approximately 425 km). Conclusion. These results infer that both cow-to-cow and farm-to-farm transmission of AmpC-producing E. coli has occurred.

scholarly journals Whole genome sequence analysis of Shigella from Malawi identifies fluoroquinolone resistance

2021 ◽  
Vol 7 (5) ◽  
Author(s):  
George E. Stenhouse ◽  
Khuzwayo C. Jere ◽  
Chikondi Peno ◽  
Rebecca J. Bengtsson ◽  
End Chinyama ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Antimicrobial Resistance ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Fluoroquinolone Resistance ◽  
Whole Genome ◽  
Genome Sequence Analysis ◽  
Content Type ◽  
Link Type ◽  
Global Priority

Increasing antimicrobial resistance and limited alternative treatments have led to fluoroquinolone-resistant Shigella strain inclusion on the WHO global priority pathogens list. In this study we characterized multiple Shigella isolates from Malawi with whole genome sequence analysis, identifying the acquirable fluoroquinolone resistance determinant qnrS1.

scholarly journals Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

2020 ◽  
Vol 6 (7) ◽  
Author(s):  
Bede Constantinides ◽  
Kevin K. Chau ◽  
T. Phuong Quan ◽  
Gillian Rodger ◽  
Monique I. Andersson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Type Species ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Antimicrobial Resistance Genes

Escherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonized with diverse populations of E. coli , Klebsiella pneumoniae and Klebsiella oxytoca , including both antimicrobial-resistant and susceptible strains. Using whole-genome sequencing of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies, which may vary as a result of different inputs and selection pressures. Whole-genome sequencing of 46 contemporaneous patient isolates identified one (2 %; 95 % CI 0.05–11 %) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10 % of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including bla CTX-M, bla SHV and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention. This article contains data hosted by Microreact.

scholarly journals Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population

2021 ◽  
Vol 7 (5) ◽  
Author(s):  
Frédéric Auvray ◽  
Alexandre Perrat ◽  
Yoko Arimizu ◽  
Camille V. Chagneau ◽  
Nadège Bossuet-Greif ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Type Species ◽  
Whole Genome Sequence ◽  
Active Metabolites ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Sequence Types ◽  
Trna Locus ◽  
Integrative And Conjugative Element

The pks island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of Escherichia coli strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine E. coli isolates, we identified 109 strains carrying a highly conserved pks island, mostly from phylogroup B2, but also from phylogroups A, B1 and D. Different scenarios of pks acquisition were deduced from whole genome sequence and phylogenetic analysis. In the main scenario, pks was introduced and stabilized into certain sequence types (STs) of the B2 phylogroup, such as ST73 and ST95, at the asnW tRNA locus located in the vicinity of the yersiniabactin-encoding High Pathogenicity Island (HPI). In a few B2 strains, pks inserted at the asnU or asnV tRNA loci close to the HPI and occasionally was located next to the remnant of an integrative and conjugative element. In a last scenario specific to B1/A strains, pks was acquired, independently of the HPI, at a non-tRNA locus. All the pks-positive strains except 18 produced colibactin. Sixteen strains contained mutations in clbB or clbD, or a fusion of clbJ and clbK and were no longer genotoxic but most of them still produced low amounts of potentially active metabolites associated with the pks island. One strain was fully metabolically inactive without pks alteration, but colibactin production was restored by overexpressing the ClbR regulator. In conclusion, the pks island is not restricted to human pathogenic B2 strains and is more widely distributed in the E. coli population, while preserving its functionality.

scholarly journals Enterohaemorrhagic Escherichia coli O121:H19 acquired an extended-spectrum β-lactamase gene during the development of an outbreak in two nurseries

2019 ◽  
Vol 5 (7) ◽  
Author(s):  
Koji Kikuchi ◽  
Kenichi Lee ◽  
Hiroyuki Ueno ◽  
Kentaro Tomari ◽  
Sumie Kobori ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Type Species ◽  
Secondary Infection ◽  
Elderly Care ◽  
Whole Genome Sequence ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Enterohaemorrhagic Escherichia Coli ◽  
Extended Spectrum

Enterohaemorrhagic Escherichia coli (EHEC) is an important human pathogen worldwide. Although serotype O157 is currently the most dominant and important EHEC strain, serotypes O26, O111, O91, O103 and O121 are also recognized as serious pathogens that affect public health. EHEC outbreaks often occur in nurseries and elderly care facilities. In 2012, a nursery outbreak of EHEC O121 occurred during which the bacterium acquired a plasmid-borne extended-spectrum β-lactamase (ESBL) gene. ESBL-producing E. coli O86 was concurrently isolated from one of the EHEC patients. Therefore, we investigated the isolates by whole-genome sequence (WGS) analysis to elucidate the transmission dynamics of the EHEC strains and the ESBL plasmid. According to WGS-based phylogeny, all 17 EHEC O121 isolates were clonal, while E. coli O86 was genetically distant from the EHEC O121 isolates. The complete sequence of an ESBL plasmid encoding the CTX-M-55 β-lactamase was determined using S1-PFGE bands, and subsequent mapping of the WGS reads confirmed that the plasmid sequences from EHEC O121 and E. coli O86 were identical. Furthermore, conjugation experiments showed that the plasmid was capable of conjugative transfer. These results support the hypothesis that EHEC O121 acquired an ESBL-producing plasmid from E. coli O86 during the outbreak. This report demonstrates the importance of implementing preventive measures during EHEC outbreaks to control both secondary infection and the spread of antimicrobial resistance factors.

scholarly journals Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands

2020 ◽  
Vol 6 (6) ◽  
Author(s):  
Ethan R. Wyrsch ◽  
Piklu Roy Chowdhury ◽  
Louise Wallis ◽  
Max L. Cummins ◽  
Tiziana Zingali ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Type Species ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Inland Wetlands ◽  
Novel Variants ◽  
Sequence Types

Wildlife, and birds in particular, play an increasingly recognized role in the evolution and transmission of Escherichia coli that pose a threat to humans. To characterize these lineages and their potential threat from an evolutionary perspective, we isolated and performed whole-genome sequencing on 11 sequence types (STs) of E. coli recovered from the desiccated faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands located in geographically different regions of New South Wales, Australia. Carriage of virulence-associated genes was limited, and no antimicrobial resistance genes were detected, but novel variants of an insertion element that plays an important role in capturing and mobilizing antibiotic resistance genes, IS26, were identified and characterized. The isolates belonged to phylogroups B1 and D, including types known to cause disease in humans and animals. Specifically, we found E. coli ST58, ST69, ST162, ST212, ST446, ST906, ST2520, ST6096 and ST6241, and a novel phylogroup D strain, ST10208. Notably, the ST58 strain hosted significant virulence gene carriage. The sequences of two plasmids hosting putative virulence-associated factors with incompatibility groups I1 and Y, an extrachromosomal integrative/conjugative element, and a variant of a large Escherichia phage of the family Myoviridae, were additionally characterized. We identified multiple epidemiologically relevant gene signatures that link the ibis isolates to sequences from international sources, plus novel variants of IS26 across different sequence types and in different contexts.

PBP4 and PBP5 are involved in regulating exopolysaccharide synthesis during Escherichia coli biofilm formation

Microbiology ◽  
2021 ◽  
Vol 167 (3) ◽  
Author(s):  
Sathi Mallick ◽  
Shanti Kiran ◽  
Tapas Kumar Maiti ◽  
Anindya S. Ghosh
Keyword(s):  
Escherichia Coli ◽  
Biofilm Formation ◽  
Type Species ◽  
Pentose Phosphate ◽  
Bacterial Cells ◽  
Surface Adhesion ◽  
Content Type ◽  
Penicillin Binding Proteins ◽  
E Coli ◽  
Link Type

Escherichia coli low-molecular-mass (LMM) Penicillin-binding proteins (PBPs) help in hydrolysing the peptidoglycan fragments from their cell wall and recycling them back into the growing peptidoglycan matrix, in addition to their reported involvement in biofilm formation. Biofilms are external slime layers of extra-polymeric substances that sessile bacterial cells secrete to form a habitable niche for themselves. Here, we hypothesize the involvement of Escherichia coli LMM PBPs in regulating the nature of exopolysaccharides (EPS) prevailing in its extra-polymeric substances during biofilm formation. Therefore, this study includes the assessment of physiological characteristics of E. coli CS109 LMM PBP deletion mutants to address biofilm formation abilities, viability and surface adhesion. Finally, EPS from parent CS109 and its ΔPBP4 and ΔPBP5 mutants were purified and analysed for sugars present. Deletions of LMM PBP reduced biofilm formation, bacterial adhesion and their viability in biofilms. Deletions also diminished EPS production by ΔPBP4 and ΔPBP5 mutants, purification of which suggested an increased overall negative charge compared with their parent. Also, EPS analyses from both mutants revealed the appearance of an unusual sugar, xylose, that was absent in CS109. Accordingly, the reason for reduced biofilm formation in LMM PBP mutants may be speculated as the subsequent production of xylitol and a hindrance in the standard flow of the pentose phosphate pathway.

scholarly journals d-Serine induces distinct transcriptomes in diverse Escherichia coli pathotypes

Microbiology ◽  
2021 ◽  
Vol 167 (10) ◽  
Author(s):  
James P. R. Connolly ◽  
Natasha C. A. Turner ◽  
Jennifer C. Hallam ◽  
Patricia T. Rimbi ◽  
Tom Flett ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Type Species ◽  
Pathogenic Bacteria ◽  
Neonatal Meningitis ◽  
Published Data ◽  
Toxic Metabolite ◽  
Transcriptional Responses ◽  
Content Type ◽  
E Coli ◽  
Link Type

Appropriate interpretation of environmental signals facilitates niche specificity in pathogenic bacteria. However, the responses of niche-specific pathogens to common host signals are poorly understood. d-Serine (d-ser) is a toxic metabolite present in highly variable concentrations at different colonization sites within the human host that we previously found is capable of inducing changes in gene expression. In this study, we made the striking observation that the global transcriptional response of three Escherichia coli pathotypes – enterohaemorrhagic E. coli (EHEC), uropathogenic E. coli (UPEC) and neonatal meningitis-associated E. coli (NMEC) – to d-ser was highly distinct. In fact, we identified no single differentially expressed gene common to all three strains. We observed the induction of ribosome-associated genes in extraintestinal pathogens UPEC and NMEC only, and the induction of purine metabolism genes in gut-restricted EHEC, and UPEC indicating distinct transcriptional responses to a common signal. UPEC and NMEC encode dsdCXA – a genetic locus required for detoxification and hence normal growth in the presence of d-ser. Specific transcriptional responses were induced in strains accumulating d-ser (WT EHEC and UPEC/NMEC mutants lacking the d-ser-responsive transcriptional activator DsdC), corroborating the notion that d-ser is an unfavourable metabolite if not metabolized. Importantly, many of the UPEC-associated transcriptome alterations correlate with published data on the urinary transcriptome, supporting the hypothesis that d-ser sensing forms a key part of urinary niche adaptation in this pathotype. Collectively, our results demonstrate distinct pleiotropic responses to a common metabolite in diverse E. coli pathotypes, with important implications for niche selectivity.

scholarly journals Whole-Genome Sequence of Phage-Resistant Strain Escherichia coli DH5α

2018 ◽  
Vol 6 (10) ◽  
Author(s):  
Jingchao Chen ◽  
Yi Li ◽  
Kun Zhang ◽  
Hailei Wang
Keyword(s):  
Escherichia Coli ◽  
Comparative Analysis ◽  
Genome Sequence ◽  
Resistant Strain ◽  
Resistance Mechanism ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
T4 Bacteriophage

ABSTRACT The genomes of many strains of Escherichia coli have been sequenced, as this organism is a classic model bacterium. Here, we report the genome sequence of Escherichia coli DH5α, which is resistant to a T4 bacteriophage (CCTCC AB 2015375), while its other homologous E. coli strains, such as E. coli BL21, DH10B, and MG1655, are not resistant to phage invasions. Thus, understanding of the genome of the DH5α strain, along with comparative analysis of its genome sequence along with other sequences of E. coli strains, may help to reveal the bacteriophage resistance mechanism of E. coli .

scholarly journals Proposal to rename Carnobacterium inhibens as Carnobacterium inhibens subsp. inhibens subsp. nov. and description of Carnobacterium inhibens subsp. gilichinskyi subsp. nov., a psychrotolerant bacterium isolated from Siberian permafrost

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 556-561 ◽  
Author(s):  
Wayne L. Nicholson ◽  
Kateryna Zhalnina ◽  
Rafael R. de Oliveira ◽  
Eric W. Triplett
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Fatty Acid Content ◽  
Optimal Growth ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Positive Staining ◽  
The Novel ◽  
Content Type ◽  
Link Type

A novel, psychrotolerant facultative anaerobe, strain WN1359T, was isolated from a permafrost borehole sample collected at the right bank of the Kolyma River in Siberia, Russia. Gram-positive-staining, non-motile, rod-shaped cells were observed with sizes of 1–2 µm long and 0.4–0.5 µm wide. Growth occurred in the range of pH 5.8–9.0 with optimal growth at pH 7.8–8.6 (pH optimum 8.2). The novel isolate grew at temperatures from 0–37 °C and optimal growth occurred at 25 °C. The novel isolate does not require NaCl; growth was observed between 0 and 8.8 % (1.5 M) NaCl with optimal growth at 0.5 % (w/v) NaCl. The isolate was a catalase-negative, facultatively anaerobic chemo-organoheterotroph that used sugars but not several single amino acids or dipeptides as substrates. The major metabolic end-product was lactic acid in the ratio of 86 % l-lactate : 14 % d-lactate. Strain WN1359T was sensitive to ampicillin, chloramphenicol, fusidic acid, lincomycin, monocycline, rifampicin, rifamycin SV, spectinomycin, streptomycin, troleandomycin and vancomycin, and resistant to nalidixic acid and aztreonam. The fatty acid content was predominantly unsaturated (70.2 %), branched-chain unsaturated (11.7 %) and saturated (12.5 %). The DNA G+C content was 35.3 mol% by whole genome sequence analysis. 16S rRNA gene sequence analysis showed 98.7 % sequence identity between strain WN1359T and Carnobacterium inhibens . Genome relatedness was computed using both Genome-to-Genome Distance Analysis (GGDA) and Average Nucleotide Identity (ANI), which both strongly supported strain WN1359T belonging to the species C. inhibens . On the basis of these results, the permafrost isolate WN1359T represents a novel subspecies of C. inhibens , for which the name Carnobacterium inhibens subsp. gilichinskyi subsp. nov. is proposed. The type strain is WN1359T ( = ATCC BAA-2557T = DSM 27470T). The subspecies Carnobacterium inhibens subsp. inhibens subsp. nov. is created automatically. An emended description of C. inhibens is also provided.

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