Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant Escherichia coli isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans

The aim of the study was to identify the plasmid-encoded factors contributing to the emergence and spread of epidemic IncI1-I␥ plasmids obtained from Escherichia coli and Salmonella enterica isolates from animal and human reservoirs. For this, 251 IncI1-I␥ plasmids carrying various extended-spectrum ␤-lactamase (ESBL) or AmpC ␤-lactamase genes were compared using plasmid multilocus sequence typing (pMLST). Thirty-two of these plasmids belonging to different pMLST types were sequenced using Roche 454 and Illumina platforms. Epidemic IncI1-I␥ plasmids could be assigned to various dominant clades, whereas rarely detected plasmids clustered together as a distinct clade. Similar phylogenetic trees were obtained using only the plasmid backbone sequences, showing that the differences observed between the plasmids belonging to distinct clades resulted mainly from differences between their backbone sequences. Plasmids belonging to the various clades differed particularly in the presence/absence of genes encoding partitioning and addiction systems, which contribute to stable inheritance during cell division and plasmid maintenance. Despite this, plasmids belonging to the various phylogenetic clades also showed marked resistance gene associations, indicating the circulation of successful plasmid-gene combinations. The variation in traY and excA genes found in IncI1-I␥ plasmids is conserved within pMLST sequence types and plays a role in incompatibility, although functional study is needed to elucidate the role of these genes in plasmid epidemiology.

Section: Resultsmentioning

confidence: 96%

Characterization of Epidemic IncI1-Iγ Plasmids Harboring Ambler Class A and C Genes in Escherichia coli and Salmonella enterica from Animals and Humans

Smith

Bossers

Harders

et al. 2015

“…In this context, foodproducing animals have acquired an important role as reservoirs for CTX-M-15-producing bacteria, which can be transmitted to the community (1,2). In this report, we describe for the first time the isolation of CTX-M-15-producing Escherichia coli in commercial swine in Brazil, highlighting a new reservoir of CTX-M-15-producing isolates with zoonotic potential in South America.…”

mentioning

confidence: 89%

First Characterization of CTX-M-15-Producing Escherichia coli Strains Belonging to Sequence Type (ST) 410, ST224, and ST1284 from Commercial Swine in South America

Silva

Moreno

Cabrera

et al. 2016

T he rapid spread of the bla CTX-M-15 gene, which encodes the currently most widely distributed extended-spectrum ␤-lactamase (ESBL) enzyme in Gram-negative bacteria, is a global challenge to human and veterinary medicine. In this context, foodproducing animals have acquired an important role as reservoirs for CTX-M-15-producing bacteria, which can be transmitted to the community (1, 2). In this report, we describe for the first time the isolation of CTX-M-15-producing Escherichia coli in commercial swine in Brazil, highlighting a new reservoir of CTX-M-15-producing isolates with zoonotic potential in South America.In 2012, during a study conducted to assess the occurrence of ESBL-producing bacteria in swine production, eight (3%) ceftiofur-resistant CTX-M-15-producing E. coli isolates were recovered from 267 fecal swabs collected from male and female nursery (40 days) and finishing (90 days) pigs from 28 farms in seven Brazilian states. In this regard, ceftiofur-resistant strains were isolated by using MacConkey agar supplemented with 2 g/ml of ceftiofur. E. coli isolates were identified by the MALDI Biotyper (Bruker Daltonics, Germany), and the antibiotic resistance profiles were determined by the Kirby-Bauer method, with MICs determined by the microdilution technique by using Sensititre ESBL-confirmatory MIC plates (Trek Diagnostic Systems, Thermo Fisher) and/or the agar dilution method (3, 4). ESBL production was screened by the double-disk synergy test, and the presence of bla CTX-M -type genes was examined by PCR amplification and sequencing. E. coli isolates were further characterized by phylogenetic grouping (5) and multilocus sequence typing (MLST) (http: //mlst.warwick.ac.uk/mlst/dbs/Ecoli). Next, plasmids were extracted and used to transform electrocompetent E. coli TOP10 recipient cells (Invitrogen) by electroporation. The transformant E. coli TOP10 strains were selected on Mueller-Hinton agar supplemented with 2 g/ml of cefotaxime and further analyzed by replicon typing (6), plasmid MLST experiments (http://pubmlst .org/plasmid/), and partial plasmid sequencing to elucidate the bla CTX-M-15 genetic environment.The eight ceftiofur-resistant E. coli isolates produced CTX-M-15 and exhibited high MICs of human and veterinary cephalosporins (Table 1). Additionally, E. coli strains were resistant to ciprofloxacin, enrofloxacin, norfloxacin, tetracycline, sulfonamide-trimethoprim, and gentamicin (7). Otherwise, all isolates remained susceptible to amikacin, cephamycins, and carbapenems. The isolates belonged to three clonal lineages of sequence type (ST) 224 (5 strains from farm X in Minas Gerais State, southeastern Brazil), ST410 (CC23; 1 strain from farm Y in Minas Gerais State), and ST1284 (2 strains from farm Z in Paraná State, southern Brazil). While none of the eight isolates belonged to phylogroup B2, phylogroups A and B1 were identified among CTX-M-15-producing E. coli strains. For E. coli ST224 and ST410 strains, the bla CTX-M-15 gene was successfully transferred to TOP10 E. coli isolates by trans...

“…Whole-genome sequencing of the plas-mids of the isolate was performed with a PacBio RS II system. Analysis and annotation of the plasmid sequences were performed as described previously (9).…”

mentioning

confidence: 99%

First Report of Klebsiella oxytoca Strain Simultaneously Producing NDM-1, IMP-4, and KPC-2 Carbapenemases

Wang

Yuan

Chen

et al. 2017

Self Cite

The nucleotide sequences of five plasmids from one Klebsiella oxytoca isolate were determined using the PacBio RS II system. Plasmid analysis revealed that bla NDM-1 was carried on an IncX3 plasmid. The bla IMP-4 and bla KPC-2 genes were located on IncN and IncP-6 plasmids, respectively. Comparative sequence analysis highlighted the successful spread of carbapenemase-harboring plasmids among different enterobacterial species. We report for the first time, to our knowledge, coproducing NDM-1, KPC-2, and IMP-4 carbapenemases on a K. oxytoca isolate.