Prevalence and Abundance of Florfenicol and Linezolid Resistance Genes in Soils Adjacent to Swine Feedlots.

Qin Zhao,Xiang-Dang Du,Zheng Wang,Xi Xia,Jianzhong Shen,Yongning Wu,Haiyang Jiang,Shuangyang Ding,Yang Wang,Bingrui Zhou,Shaolin Wang,Zhangqi Shen,Congming Wu

doi:10.1038/srep32192

Abstract

Florfenicol is extensively used in livestock to prevent or cure bacterial infections. However, it is not known whether the administration of florfenicol has resulted in the emergence and dissemination of florfenicol resistance genes (FRGs, including fexA, fexB, cfr, optrA, floR, and pexA) in microbial populations in surrounding farm environments. Here we collected soil samples for the detection of FRGs and the residue of florfenicol from six swine farms with the record of florfenicol usage. Quantitative polymerase chain reaction and metagenomic sequencing revealed a significantly higher relative abundance of FRGs in the soils adjacent to the three swine farms where florfenicol was heavily used compared with the other sites. Meanwhile, the detectable levels of florfenicol were also identified in soils from two of these three farms using ultra-performance liquid chromatography tandem mass spectrometry. It appears that amount of florfenicol used on swine farms and the spreading of soils with swine waste could promote the prevalence and abundance of FRGs, including the linezolid resistance genes cfr and optrA, in adjacent soils, and agricultural application of swine manure with florfenicol may have caused a residual level of florfenicol in the soils.

Highlights

Soil is the predominant reservoir for bacteria harboring genes associated with the antibiotic resistance, with a number of antibiotic resistance determinants identified from soil bacteria[9] and various resistance bacteria were cultured from soil samples[10]
This conclusion could be supported by the following observations: first, both the metagenomic and quantitative polymerase chain reaction (qPCR) via culture-independent methods revealed that florfenicol resistance genes (FRGs) can be detected in the soils adjacent to the farms with florfenicol usage, but not in the control samples
It has been reported that the variety of ARGs and antibiotic residues in agricultural soils are correlated with soil type, manure application rate and environment conditions[30,31]

Summary

Introduction

Soil is the predominant reservoir for bacteria harboring genes associated with the antibiotic resistance, with a number of antibiotic resistance determinants identified from soil bacteria[9] and various resistance bacteria were cultured from soil samples[10]. In addition to fexA, fexB, cfr, optrA, and floR, phenicol exporter gene pexA was identified in metagenomic libraries of cloned DNA isolated from Alaskan soils[14] All of these genes, apart from pexA14, coexist with bacterial mobile genetic elements such as plasmids, transposons, or integrons[21,25,26,27,28], which aid the horizontal transfer of florfenicol resistance genes (FRGs) to numerous bacterial species and genera. More than one decade ago, the usage of chloramphenicol in the livestock and aquaculture industries has been completely banned and florfenicol became the only available antimicrobial agent from the phenicol class in China It is not clear whether the use of florfenicol in agriculture has contributed to the environmental accumulation of florfenicol and FRGs, especially the cfr and optrA genes conferring resistance to other antimicrobial agents, which are critically important in the human medicine. We quantified six FRGs (fexA, fexB, cfr, optrA, floR and pexA) using quantitative polymerase chain reaction (qPCR) via a culture-independent method and detected the florfenicol residue concentrations using ultra performance liquid chromatography-tandem mass spectrometry (UPLC–MS/MS) in soils from different farms

Methods

Results

Conclusion