ST131 fimH22 Escherichia coli isolate with a blaCMY-2/IncI1/ST12 plasmid obtained from a patient with bloodstream infection: highly similar to E. coli isolates of broiler origin

Roer, Louise; Overballe‐Petersen, Søren; Hansen, Frank; Johannesen, Thor Bech; Stegger, Marc; Bortolaia, Valeria; Leekitcharoenphon, Pimlapas; Korsgaard, Helle; Seyfarth, Anne Mette; Mossong, Joël; Wattiau, Pierre; Boland, Cécile; Hansen, Dennis Schrøder; Hasman, Henrik; Hammerum, Anette M.; Hendriksen, René S.

doi:10.1093/jac/dky484

Cited by 40 publications

(44 citation statements)

References 15 publications

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“…1A). These findings underscore the potential of IncI1-I␥ plasmids to be transferred in strains from Salmonella and E. coli outside the poultry environment (13,(35)(36)(37)(38). The genetic environment of bla CMY-2 in most IncI1-I␥/ST12 plasmids and ST12 SLVs was similar and characterized upstream by insertion sequence ISEcp1 and downstream by blc and sugE (Fig.…”

mentioning

confidence: 56%

Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring bla _CMY-2 and bla _SHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries

Castellanos

Bloois

Donado-Godoy

et al. 2019

Antimicrob Agents Chemother

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The objective of this study was to elucidate the genetic and evolutionary relatedness of blaCMY-2- and blaSHV-12-carrying IncI1-Iγ plasmids. Phylogenomic analysis based on core genome alignments and gene presence/absence was performed for different IncI1-Iγ sequence types (STs). Most IncI1-Iγ/ST12 and IncI1-Iγ/ST231 plasmids had near-identical core genomes. The data suggest that widely occurring blaCMY-2-carrying IncI1-Iγ/ST12 plasmids originate from a common ancestor. In contrast, blaSHV-12 was inserted independently into different IncI1-Iγ/ST231-related plasmids.

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mentioning

confidence: 56%

Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring bla _CMY-2 and bla _SHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries

Castellanos

Bloois

Donado-Godoy

et al. 2019

Antimicrob Agents Chemother

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“…A high degree of similarity between IncI1-pST12 plasmids was previously reported [12][13][14]. However, these studies either contained only plasmids extracted from one E. coli sequence type (ST131) [12], or included plasmids were primarily of poultry origin [14]. Moreover, these studies predominately used in silico reference-based plasmid reconstructions of short-read sequence data rather than performing a hybrid assembly of both short-and long-read sequence data.…”

Section: Discussionmentioning

confidence: 99%

“…(https://github.com/tseemann/snippy) the number of single nucleotide polymorphisms (SNP) was determined between the extracted plasmid components using a blaCMY-2 gene containing IncI1-pST12 plasmid extracted from the GenBank (accession number: MH472638.1) as reference [12]. A pan-genome was constructed, and a gene-presence or absence was determined for all extracted plasmid components using roary v3.12 [31].…”

Section: Plasmid Analysismentioning

confidence: 99%

“…Incompatibility group I1 (IncI1) plasmids of the plasmid sequence type (pST) 12 have been associated with the spread of blaCMY-2, the most common AmpC beta-lactamase gene [9][10][11]. Recent studies show that the sequence of IncI1 plasmids is highly conserved [12][13][14][15]. Most studies to date are based on short-read sequence data [13,14].…”

Section: Introductionmentioning

confidence: 99%

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Limited genetic diversity ofbla_CMY-2-containing IncI1-pST12 plasmids from Enterobacteriaceae of human and broiler chicken origin in the Netherlands

Drijver

Stohr

Verweij

et al. 2020

Preprint

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AbstractDistinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1-pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1-pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNP) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1-pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1-pST12 plasmids revealed a low number of SNP differences (range of 0-9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. NGS-analysis of blaCMY--2-containing IncI1-pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.

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“…The long read genome assemblies illuminated significant variation in plasmids, MGEs and bla CTX-M gene composition that was not captured by short reads. ST131 is a globally pandemic E. coli clonal group [15] with diverse sources of transmission [25]. Phylogenetic comparison with published genomes [8,42] showed that five out of six isolates were from subclade C2 with one from C1.…”

Section: Discussionmentioning

confidence: 99%

Complete assembly ofEscherichia coliST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

Decano

Ludden

Feltwell

et al. 2019

Preprint

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22The incidence of infections caused by extraintestinal Escherichia coli (ExPEC) is rising globally, 23 which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been 24 associated with excess mortality, prolonged hospital stays and higher healthcare costs. E. coli ST131 is 25 a major ExPEC clonal group worldwide with variable plasmid composition, and has an array of genes 26 enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genes blaCTX-M-27 14/15/27, which are often rearranged, amplified and translocated by mobile genetic elements (MGEs).28 Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow 29 MGE structures encoding blaCTX-M genes to be fully determined. Here, we performed long read 30 sequencing to decipher the genome structures of six E. coli ST131 isolated from six patients. Most 31 long read assemblies generated entire chromosomes and plasmids as single contigs, contrasting with 32 more fragmented assemblies created with short reads alone. The long read assemblies highlighted 33 diverse accessory genomes with blaCTX-M-15, blaCTX-M-14 and blaCTX-M-27 genes identified in three, one 34 and one isolates, respectively. One sample had no blaCTX-M gene. Two samples had chromosomal 35 blaCTX-M-14 and blaCTX-M-15 genes, and the latter was at three distinct locations, likely transposed by the 36 adjacent MGEs: ISEcp1, IS903B and Tn2. This study showed that AMR genes exist in multiple 37 different chromosomal and plasmid contexts even between closely-related isolates within a clonal 38 group such as E. coli ST131. 39 40 Importance 41 Drug-resistant bacteria are a major cause of illness worldwide and a specific subtype called 42 Escherichia coli ST131 cause a significant amount of these infections. ST131 become resistant to 43 treatment by modifying their DNA and by transferring genes among one another via large packages of 44 genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a 45 better understanding of what plasmids are being exchanged and their exact contents. To achieve this, 46we applied new high-resolution DNA sequencing technology to six ST131 samples from infected 47 patients and compared the output to an existing approach. A combination of methods shows that drug-48 resistance genes on plasmids are highly mobile because they can jump into ST131's chromosomes. We 49 found that the plasmids are very elastic and undergo extensive rearrangements even in closely related 50 samples. This application of DNA sequencing technologies illustrates at a new level the highly 51 dynamic nature of ST131 genomes. 52 53 54 55 56 57 Reported cases of bloodstream and urinary tract infections caused by extraintestinal pathogenic 58 Escherichia coli (ExPEC) are increasing globally at an alarming rate [1]. As a key source of ExPEC 59 isolates worldwide, E. coli sequence type 131 (ST131) is regarded as a serious threat to public health, 60 given its high level of a...

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ST131 fimH22 Escherichia coli isolate with a blaCMY-2/IncI1/ST12 plasmid obtained from a patient with bloodstream infection: highly similar to E. coli isolates of broiler origin

Cited by 40 publications

References 15 publications

Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring bla _CMY-2 and bla _SHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries

Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring bla _CMY-2 and bla _SHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries

Limited genetic diversity ofbla_CMY-2-containing IncI1-pST12 plasmids from Enterobacteriaceae of human and broiler chicken origin in the Netherlands

Complete assembly ofEscherichia coliST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

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ST131 fimH22 Escherichia coli isolate with a blaCMY-2/IncI1/ST12 plasmid obtained from a patient with bloodstream infection: highly similar to E. coli isolates of broiler origin

Cited by 40 publications

References 15 publications

Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring bla CMY-2 and bla SHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries

Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring bla CMY-2 and bla SHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries

Limited genetic diversity ofblaCMY-2-containing IncI1-pST12 plasmids from Enterobacteriaceae of human and broiler chicken origin in the Netherlands

Complete assembly ofEscherichia coliST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

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Product

Resources

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Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring bla _CMY-2 and bla _SHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries

Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring bla _CMY-2 and bla _SHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries

Limited genetic diversity ofbla_CMY-2-containing IncI1-pST12 plasmids from Enterobacteriaceae of human and broiler chicken origin in the Netherlands