Chromosomal integration of blaCTX-M genes in diverse Escherichia coli isolates recovered from river water in Japan

Gomi, Ryota; Yamamoto, Masaki; Tanaka, Michio; Matsumura, Yasufumi

doi:10.1016/j.crmicr.2022.100144

Cited by 8 publications

(4 citation statements)

References 35 publications

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“…High rates of bla CTX-M chromosomal integration are being increasingly reported, reaching, for example, 64% in a Japanese study. 19 Moreover, we detected multiple chromosomal insertion sites over a large part of the genome suggesting frequent and repeated events. Of note, most of the insertions were localized in regions outside the oriC macrodomain and encompassing the terminus of replication, a region known for hyper-recombination.…”

Section: Discussionmentioning

confidence: 87%

Tricycle surveillance in Antananarivo, Madagascar: circulation of both extended-spectrum beta-lactamase producingEscherichia colistrains and plasmids among humans, chickens and the environment

Milenkov

Proux

Rasolofoarison

et al. 2023

Preprint

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Background: Antimicrobial resistance is a major public health threat, affecting not only humans but also animals and the environment. Although the "One Health" dimension of resistance is well recognized, data are lacking on the circulation of resistance, particularly in low-income countries. The World Health Organization has proposed a protocol called Tricycle, focusing on extended-spectrum beta-lactamase (ESBL)-Escherichia coli surveillance in the three sectors. We implemented Tricycle in Madagascar to assess ESBL-E. coli prevalence and describe intra- and inter-sector circulation of ESBL-E. coli and plasmids. Methods: 289 pregnant women, 246 farm chickens and 28 surface waters were sampled in Antananarivo (the capital city) area and tested for ESBL-E. coli. Isolates were sequenced by short- (Illumina) and long- (Nanopore) read methods. Findings: ESBL-E. coli prevalence was 29.8%, 56.9% and 100% in pregnant women, chickens, and the environment, respectively. The wet season was associated with higher rates of carriage in humans (OR=3.1, 95%CI 1.8-5.3) and animals (OR=2.8 95%CI 1.7-4.8). Sequencing of 277 non-duplicated isolates (82, 118 and 77 from each sector, respectively) showed high genetic diversity (90 STs identified) with differences between sectors. Single nucleotide polymorphism (SNP) analysis revealed 169/277 (61%) isolates grouped into 44 clusters (≥2 isolates) of closely related isolates (<40 SNPs), of which 24 contained isolates from two sectors and five contained isolates from all three sectors. ESBL genes were all blaCTX-M (77.6% blaCTX-M-15), chromosomally integrated in 57.4% (159/277) of isolates, and plasmidic in 40.8% (113/277). The 114 ESBL-carrying plasmids were mainly IncF (55.2%, n=63) and IncY (36.8%, n=42). The F31/36:A4:B1 (n=13) and F-:A-:B53 (n=8) subtypes, and all IncY plasmids, highly conserved, were observed in isolates of differing genetic backgrounds from all sectors. Interpretation: Despite varying strain population structures in the three sectors, both ESBL-E. coli strains and plasmids are circulating among humans, chickens and the environment in the capital of Madagascar. Funding: Fondation Merieux, INSERM, Universite Paris Cite. Keywords: Extended spectrum beta-lactamase (ESBL), Escherichia coli, Tricycle, One Health, circulation

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Section: Discussionmentioning

confidence: 87%

Tricycle surveillance in Antananarivo, Madagascar: circulation of both extended-spectrum beta-lactamase producingEscherichia colistrains and plasmids among humans, chickens and the environment

Milenkov

Proux

Rasolofoarison

et al. 2023

Preprint

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“…Some other ARGs, bla CTX-M alleles being a key example, had a distribution disconnected from that of the class 1 integron, indicating that they were mobilized separately in ST1193. It is notable that chromosomal integration of bla CTX-M genes is on the rise in E. coli ( 49 ), including clinically relevant E. coli lineages that carry pUTI89, such as ST963 ( 50 ) and ST131 ( 32 ).…”

Section: Discussionmentioning

confidence: 99%

Global Phylogeny and F Virulence Plasmid Carriage in Pandemic Escherichia coli ST1193

et al. 2022

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We have generated an updated ST1193 phylogeny using publicly available sequences, reinforcing previous assertions that Escherichia coli ST1193 is a human-associated lineage, with many examples sourced from human extraintestinal infections. ST1193 from urban-adapted birds, wastewater, and companion animals are frequent, but isolates from animal agriculture are notably absent.

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“…Detailed analyses of genetic contexts of chromosomal bla CTX-M genes and adjacent AMR genes are provided in Figure S3. We note that recent studies have also shown the frequent occurrence (more than 50%) of chromosomal bla CTX-M integration among E. coli isolates using both short-and long-read sequencing (Gomi et al, 2022;Milenkov et al, 2023). Chromosomal integration of AMR genes might have been previously underestimated due to the inability of PCR or short-read sequencing to determine the location of AMR genes.…”

Section: Locations and Genetic Contexts Of Amr Genes In Isolates From...mentioning

confidence: 73%

Genomic surveillance of antimicrobial-resistantEscherichia coliin fecal sludge and sewage in Uganda

Gomi

Matsumura

Yamamoto

et al. 2023

Preprint

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The global increase of antimicrobial resistance (AMR) is a major public health concern. An effective AMR surveillance tool is needed to track the emergence and spread of AMR. Wastewater surveillance has been proposed as a resource-efficient tool for monitoring AMR carriage in the community. Here, we performed genomic surveillance of antimicrobial-resistantEscherichia coliobtained from fecal sludge and sewage in Uganda to gain insights intoE. coliepidemiology and AMR burden in the underlying population. Selective media containing different antibiotic combinations (cefotaxime, ciprofloxacin, cefotaxime + ciprofloxacin + gentamicin) were used to obtain antimicrobial-resistantE. colifrom fecal sludge and sewage. Short-read sequencing was performed for the obtained isolates, and a subset of isolates (selected from predominant sequence types (STs)) was also subjected to long-read sequencing. Genomic analysis of the obtainedE. coliisolates (n = 181) revealed the prevalence of ST10 complex, including ST167 (n = 43), ST10 (n = 28), ST1284 (n = 17), and ST617 (n = 4), in both fecal sludge and sewage, irrespective of antibiotics used for selection. We also detected global high-risk clones ST1193 (n = 10) and ST131 (n = 2 clade A, n = 3 subclade C1-M27, and n = 1 subclade C2). Diverse AMR determinants, including extended-spectrum β-lactamase genes (mostlyblaCTX-M-15) and mutations ingyrAandparC, were identified. Analysis of the completed genomes revealed that diverse IncF plasmids and chromosomal integration were the major contributors to the spread of AMR genes in the predominant STs. This study showed that a combination of sewage surveillance (or fecal sludge surveillance) and whole-genome sequencing can be a powerful tool for monitoring AMR carriage in the underlying population.

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Chromosomal integration of blaCTX-M genes in diverse Escherichia coli isolates recovered from river water in Japan

Cited by 8 publications

References 35 publications

Tricycle surveillance in Antananarivo, Madagascar: circulation of both extended-spectrum beta-lactamase producingEscherichia colistrains and plasmids among humans, chickens and the environment

Tricycle surveillance in Antananarivo, Madagascar: circulation of both extended-spectrum beta-lactamase producingEscherichia colistrains and plasmids among humans, chickens and the environment

Global Phylogeny and F Virulence Plasmid Carriage in Pandemic Escherichia coli ST1193

Genomic surveillance of antimicrobial-resistantEscherichia coliin fecal sludge and sewage in Uganda

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