Characterization of the genetic environment of blaESBL genes, integrons and toxin-antitoxin systems identified on large transferrable plasmids in multi-drug resistant Escherichia coli

Abstract

Objectives: Previously 14 conjugative plasmids from multi-drug resistant (MDR) Escherichia coli from healthy humans and food-producing animals in Switzerland were sequenced. The aim of this study was to extend the genetic characterization of these plasmids with a focus on blaESBL genes including blaCTX-M-1 and blaTEM, class 1 integrons and toxin-antitoxin (TA) systems contained therein.Methods: The nucleotide sequences and subsequent annotation therein of 14 conjugative plasmids were previously determined from their corresponding transconjugants. The TA loci were confirmed by RASTA-Bacteria.Results: Eight of the conjugative plasmids identified were found to encode genes expressing ESBLs. Structural heterogeneity was noted in the regions flanking both the blaCTX-M-1 and blaTEM genes. The blaCTX-M-1 genes were associated with the common insertion sequences ISEcp1 and IS26, and uniquely with an IS5 element in one case; while blaTEM genes were found to be associated with IS26 and Tn2. A new blaTEM-210 gene was identified. Seven class 1 integrons were also identified and assigned into 3 groups, denoted as In54, In369 and In501. Sixteen TA loci belonging to 4 of the TA gene families (relBE, vapBC, ccd and mazEF) were identified on 11 of these plasmids.Conclusions: Comparative sequence analysis of these plasmids provided data on the structures likely to contribute to sequence diversity associated with these accessory genes, including IS26, ISEcp1 and Tn2. All of them contribute to the dissemination of the corresponding resistance genes located on the different plasmids. There appears to be no association between β-lactam encoding genes and TA systems.

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks

“…In similarity to the bla CTX−M−1 located next to a mobile element (ISECp1), we found another class C beta-lactamase gene in S. enterica CVM 22462, again found next to a mobile transposase locus. We speculate that colocalization to mobile elements might affect locus stability and explains the scattered prevalence of these resistances in the plasmid homologs (Wang et al, 2014b ) (Figure 7 ).…”

Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae

“…Only one amino acid, K104E, distinguishes TEM-52 from TEM-20 (Arlet et al, 1999). Tn2 and Tn3 transposons have been associated with both bla TEM-20 and bla TEM-52 variants (Wang et al, 2015) (Cloeckaert et al, 2007). The pMLST database contains 2 bla TEM-20 and 39 bla TEM-52 -IncI1 records.…”

IncHI2 Plasmids Are Predominant in Antibiotic-Resistant Salmonella Isolates

“…The dissemination of undesirable antibiotic resistance in Gram-negative bacteria has been largely attributed to the acquisition of multiple plasmid-located antibiotic resistance genes by horizontal gene transfer (HGT; Carattoli, 2013 ; Wang et al, 2015 ). The emergence of plasmid-mediated quinolone resistance (PMQR) predominantly encoded by qnr variants, aac(6′)-Ib-cr , qepA , and oqxAB genes in Salmonella , has further facilitated selection of high-level chromosomal quinolone resistance via mutations in topoisomerase genes, as well as the wide spread of quinolone resistance via HGT ( Jiang et al, 2014 ; Skov et al, 2015 ).…”

“…Transmissible plasmids contain a full set of conjugation-encoding genes facilitating their spread over large taxonomic distances, and they harbor drug-resistance determinants, virulence factors and addiction systems promoting their stability and maintenance in bacterial hosts under different environmental conditions. It is essential to clarify the roles of these genetic elements and the corresponding surrounding genetic structures by plasmid sequencing in order to trace the transmission and persistence of antibiotic resistance ( Carattoli, 2013 ; Wang et al, 2015 ).…”