IncI1 ST3 and IncI1 ST7 plasmids from CTX-M-1-producing Escherichia coli obtained from patients with bloodstream infections are closely related to plasmids from E. coli of animal origin

Abstract

Objectives Fully sequenced IncI1 plasmids obtained from CTX-M-1-producing Escherichia coli of human and animal origin were compared. Methods Twelve E. coli isolates sharing identical ESBL genes and plasmid multilocus STs sequenced on Illumina and MinION platforms were obtained from the Danish antimicrobial resistance surveillance programme, DANMAP. After de novo assembly, the sequences of plasmids harbouring blaCTX-M-1 were manually curated and ORFs annotated. Within-group comparisons were performed separately for the IncI1 ST3 plasmid type and the IncI1 ST7 plasmid type. The IncI1 ST3 plasmid group was obtained from 10 E. coli isolates (2 from patients with bloodstream infections, 6 from food and 2 from animals). The IncI1 ST7 plasmids originated from E. coli isolates obtained from a patient with bloodstream infection and from a pig. Sequences of IncI1 ST3 and IncI1 ST7 plasmids harbouring blaCTX-M-1 with determined origin were retrieved from GenBank and used for comparison within the respective group. Results The 10 IncI1 ST3 blaCTX-M-1 plasmids were highly similar in structure and organization with only minor plasmid rearrangements and differences in the variable region. The IncI1 ST7 blaCTX-M-1 plasmids also showed high similarity in structure and organization. The high level of similarity was also observed when including plasmids from E. coli of animal origin from Australia, Switzerland, the Netherlands and France. Conclusions This study shows broad spread of a very successful CTX-M-1-producing IncI1 type plasmid among E. coli of both human and animal origin.

High-resolution characterisation of ESBL/pAmpC-producing Escherichia coli isolated from the broiler production pyramid

“…Furthermore, the rifampicin resistance gene arr-3, and the aac(6′)Ib-cr gene, which confers resistance to both fluoroquinolones and aminoglycosides, were found in all four ST2179 isolates of this study (Table 1). Although we did not confirm resistance phenotypes by susceptibility testing, previous studies showed high accordance between resistance phenotype and genotype 20,21 . Multi-drug resistance, which is frequently observed in ESBL/pAmpC-EC 22,23 , is crucial for their selection and dissemination by the use of non-β-lactam antimicrobial agents and thus may help to explain the high prevalence of ESBL/pAmpC-EC in broilers even in the absence of cephalosporin use 24 .…”

“…The insertion of the module ISEcp1-bla CTX-M-1 into the shufflon region seems to be common for IncI1 plasmids belonging to pST3, as shown in previous studies identifying this plasmid type from various sources 46,[49][50][51] . A recent study reported identical bla CTX-M-1 -carrying IncI1 pST3 plasmids from chicken, chicken meat, and bloodstream infections in humans 21 . Furthermore, additional resistance genes, mainly tet(A) and sul2 (Table 1), were found on the IncI1bla CTX-M-1 plasmids and their co-localisation with bla CTX-M-1 has been described before 21,45 .…”

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

“…A recent study by Valcek et al on IncI1-pST3 and -pST7 plasmids showed that using combined long-read and short-read sequencing data improves the accuracy of a full plasmid analysis, e.g. of rearrangements [15]. All of studies used either gene presence/absence based or SNP based analysis, but not both, possibly missing subtle differences between various plasmids.…”

“…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].…”

“…This limits the interpretation of plasmid transmission by not providing accurate prediction of the total plasmid sequence. Recently, a combination of short-and long-read sequence data has provided the possibility for more accurate analysis, such as shown in a recent study on IncI1 plasmids of pST 3 and pST7 [15].…”