Presence and Characterization of a Novel cfr-Carrying Tn558 Transposon Derivative in Staphylococcus delphini Isolated From Retail Food

Feng Zhang,Juan Wang,Shi Wu,Qingping Wu,Liang Xue,Jingsha Dai,Runshi Yang,Tao Lei,Jumei Zhang,Jiahui Huang,Yu Ding,Moutong Chen

doi:10.3389/fmicb.2020.598990

Abstract

Antimicrobial resistance has become a major public health threat. Food-related Staphylococcus species have received much attention due to their multidrug resistance. The cfr gene associated with multidrug resistance has been consistently detected in food-derived Staphylococcus species. In this retrospective study, we examined the prevalence of cfr-positive Staphylococcus strains isolated from poultry meat in different geographical areas of China from 2011 to 2016. Two cfr-positive Staphylococcus delphini strains were identified from poultry meat in China. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in the two S. delphini isolates 245-1 and 2794-1. Whole-genome sequencing showed that they both harbored a novel 20,258-bp cfr-carrying Tn558 transposon derivative on their chromosomes. The Tn558 derivative harbors multiple antimicrobial resistance genes, including the transferable multiresistance gene cfr, chloramphenicol resistance gene fexA, aminoglycoside resistance genes aacA-aphD and aadD, and bleomycin resistance gene ble. Surprisingly, within the Tn558 derivative, an active unconventional circularizable structure containing various resistance genes and a copy of a direct repeat sequence was identified by two-step PCR. Furthermore, core genome phylogenetic analysis revealed that the cfr-positive S. delphini strains were most closely related to S. delphini 14S03313-1 isolated from Japan in 2017 and 14S03319-1 isolated from Switzerland in 2017. This study is the first report of S. delphini harboring a novel cfr-carrying Tn558 derivative isolated from retail food. This finding raises further concerns regarding the potential threat to food safety and public health safety. The occurrence and dissemination of similar cfr-carrying transposons from diverse Staphylococcus species need further surveillance.

Highlights

In recent years, resistance in bacteria has spread worldwide and presents a serious threat to human health
We examined the prevalence of cfr-positive Staphylococcus isolates in poultry meat from 2011 to 2016
Antimicrobial susceptibility testing showed that these strains were resistant to chloramphenicol, florfenicol, tiamulin, clindamycin, and linezolid, exhibiting a high level of resistance to florfenicol (MIC = 256 μg/ml), chloramphenicol (MIC > 128 μg/ml), and tiamulin (MIC > 128 μg/ml)

Summary

Introduction

Resistance in bacteria has spread worldwide and presents a serious threat to human health. The cfr gene could mediate resistance to linezolid (Long et al, 2006). This gene encodes a methyltransferase that catalyzes the posttranscriptional methylation of adenosine at nucleotide position 2503 (Escherichia coli numbering) in 23S rRNA, which replaced the target of binding for linezolid (Corinna et al, 2005; Giessing et al, 2009; Anna et al, 2016). Due to overlapping binding sites, cfr methylation confers resistance to four other classes of antimicrobial agents and results in the PhLOPSA multiresistance phenotype, including resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds (Long et al, 2006; Anna et al, 2016). Cfr is often associated with erm, fexA, lsa(B), and tet(L), which can assist in co-selecting the cfr gene and in its spread (Shen et al, 2013; Mendes et al, 2014)

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