Rapid Increase in the IS26-Mediated cfr Gene in E. coli Isolates with IncP and IncX4 Plasmids and Co-Existing cfr and mcr-1 Genes in a Swine Farm.

Zhenbao Ma,Jiao Liu,Zhenling Zeng,Xiaoqin Liu,Wenguang Xiong,Jian-Hua Liu,Lin Chen

doi:10.3390/pathogens10010033

Abstract

This paper aimed to investigate the molecular epidemiological features of the cfr gene in E. coli isolates in a typical swine farm during 2014–2017. A total of 617 E. coli isolates were screened for the cfr gene using PCR amplification. A susceptibility test, pulsed-field gel electrophoresis (PFGE), S1-PFGE, southern blotting hybridization, and the genetic context of the cfr gene were all used for analyzing all cfr-positive E. coli isolates. A conjugation experiment was conducted with the broth mating method using E. coli C600 as the recipient strain and 45 mcr-1-cfr-bearing E. coli isolates as the donor strain. Plasmids pHNEP124 and pHNEP129 were revealed by Illumina Miseq 2500. Eighty-five (13.7%) E. coli isolates were positive for the cfr gene and the prevalence of the cfr gene had significantly increased from 1.6% in 2014 to 29.1% in 2017. The Pulsed-Field Gel Electrophoresis (PFGE) analysis indicated that the spread of the cfr gene among E. coli isolates was mainly due to horizontal transfer. In addition, the cfr gene was primarily located on the plasmids between 28.8-kb to 60-kb in size, and the cfr gene was flanked by two copies of IS26 with the same orientation. Sequence analysis suggested that the plasmids pHNEP124 and pHNEP129 co-harboring the cfr and mcr-1 genes belonged to the plasmids IncP plasmid and IncX4 plasmid, respectively. In conclusion, this is the first study to report the high prevalence of the cfr gene among E. coli isolates and the first report of the complete genome sequence of IncP and IncX4 plasmids carrying the mcr-1 and cfr genes. The occurrence and dissemination of the cfr/mcr-1-carrying plasmids among E. coli isolates need further surveillance.

Highlights

The multi-resistant cfr gene, encoded rRNA methyltransferase, confers cross-resistance to five chemically unrelated classes of antimicrobial agents, including phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A [1]
Multidrug-resistant (MDR) Escherichia coli has become a worrisome issue that poses a threat to public health and it is considered to be a major reservoir of antibiotic resistance genes that may be responsible for the treatment failure events in human clinical and veterinary medicine [7]
It is worth noting that 45 (52.9%) cfr-positive E. coli isolates were positive for the mcr-1 gene (Figure 2)

Summary

Introduction

The multi-resistant cfr gene, encoded rRNA methyltransferase, confers cross-resistance to five chemically unrelated classes of antimicrobial agents, including phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A (called PhLOPSA phenotype) [1]. Since the first identified cfr gene in plasmid pSCFS1 from a Staphylococcus sciuri isolate, the transferable cfr gene has been detected in both Grampositive and Gram-negative bacteria such as Staphylococcus, Enterococcus, Bacillus, Macrococcus, Jeotgalicoccus, Streptococcus, Proteus, Escherichia coli, and Morganella morganii [3,4,5]. Mobile gene elements such as insertion sequences (ISs) and plasmids can acquire antimicro- 4.0/). A total of 24 cfr-positive E. coli isolates have been reported in food-producing animals from various sources in seven provinces of China and it is mainly located on various plasmid replicon types such as IncX4, IncF43:A-:B-, and

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