Department of Food Engineering, Middle East Technical University, Ankara 06810, Turkey.
Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
Int J Food Microbiol. 2019 Oct 16;307:108275. doi: 10.1016/j.ijfoodmicro.2019.108275. Epub 2019 Jul 27.
Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) isolates were found to have a multi-drug resistance profile (kanamycin, streptomycin, nalidixic acid, tetracycline, sulfonamide, and sometimes to ampicillin) and high prevalence (91%) in Turkish poultry in our previous studies. To investigate the mechanism behind multi-drug antimicrobial resistance (AMR) and high prevalence in Turkish poultry, 23 of the isolates were sequenced for comparative genomic analyses including: SNP-based comparison to S. Infantis from other countries, comparison of antimicrobial resistance genes (AMGs) with AMR phenotypes, and plasmid identification and annotation. Whole-genome SNP-based phylogenetic analysis found that all 23 Turkish S. Infantis isolates formed a distinct, well-supported clade, separate from 243 comparison S. Infantis genomes in GenomeTrakr identified as from the US and EU; the isolates most closely related to the cluster of these Turkish isolates were from Israel and Egypt. AMGs identified by bioinformatic analysis, without differentiating chromosomal or plasmid located genes, implied AMR phenotypes with 94% similarity overall to wet lab data, which was performed by phenotypic and conventional PCR methods. Most of the S. Infantis (21/23) isolates had identifiable plasmids, with 76% (16/21) larger than 100 kb and 48% (10/21) larger than 200 kb. A plasmid larger than 200 kb, with the incompatibility type of IncX1, similar to United States S. Infantis plasmid N55391 (99% query coverage and 99% identity overall), which itself is similar to Italian and Hungarian S. Infantis plasmids. Turkish S. Infantis plasmids had different beta-lactam resistance genes (bla, bla and bla-) than the gene bla found in S. Infantis plasmids from other countries. This is the first observation of these three genes in S. Infantis isolates. The plasmids larger than 200 kb had two distinct regions of interest: Site 1 and Site 2. Site 1 (around 130 kb) had virulence- and bacteriocin- associated genes such as bacteriocin secretion system and type II toxin-antitoxin system genes (vagC, ccdA, ccdB, mchE, cvaB) and an aminoglycoside resistance gene (str). Site 2 (around 75-110 kb) had the antimicrobial resistance genes (aadA, sulI, tetA, tetR) and mercury (mer) resistance gene on tranposons Tn552 and Tn501. Presence of these AMR and virulence genes suggests they may have a role in the emergence of S. Infantis in poultry and support treating this serotype as a an important human health hazard.
先前的研究表明,沙门氏菌肠炎亚种肠炎血清型(S. Infantis)分离株具有多药耐药谱(卡那霉素、链霉素、萘啶酸、四环素、磺胺类药物,有时还有氨苄青霉素)和高流行率(91%),在土耳其家禽中。为了研究土耳其家禽中多药抗微生物耐药(AMR)和高流行率的机制,对 23 株分离株进行了比较基因组分析,包括:基于 SNP 的与来自其他国家的 S. Infantis 比较、与 AMR 表型比较的抗生素耐药基因(AMGs)、以及质粒鉴定和注释。全基因组 SNP 基于系统发育分析发现,所有 23 株土耳其 S. Infantis 分离株形成了一个独特的、得到很好支持的分支,与在 GenomeTrakr 中确定为来自美国和欧盟的 243 株 S. Infantis 基因组分开;与这些土耳其分离株聚类最密切相关的分离株来自以色列和埃及。生物信息学分析鉴定的 AMGs,不区分染色体或质粒定位基因,暗示 AMR 表型与湿实验室数据总体上具有 94%的相似性,这些数据是通过表型和常规 PCR 方法获得的。大多数 S. Infantis(21/23)分离株可识别出质粒,其中 76%(16/21)大于 100kb,48%(10/21)大于 200kb。一个大于 200kb 的质粒,具有 IncX1 的不相容性类型,类似于美国 S. Infantis 质粒 N55391(99%的查询覆盖率和总体 99%的同一性),它本身类似于意大利和匈牙利的 S. Infantis 质粒。土耳其 S. Infantis 质粒具有不同于其他国家 S. Infantis 质粒中发现的 bla 基因的β-内酰胺耐药基因(bla、bla 和 bla-)。这是首次在 S. Infantis 分离株中观察到这三个基因。大于 200kb 的质粒有两个不同的感兴趣区域:Site 1 和 Site 2。Site 1(约 130kb)具有与毒力和细菌素相关的基因,如细菌素分泌系统和 II 型毒素-抗毒素系统基因(vagC、ccdA、ccdB、mchE、cvaB)和氨基糖苷类耐药基因(str)。Site 2(约 75-110kb)在转座子 Tn552 和 Tn501 上具有抗菌药物耐药基因(aadA、sulI、tetA、tetR)和汞(mer)耐药基因。这些 AMR 和毒力基因的存在表明它们可能在沙门氏菌肠炎血清型在禽类中的出现中发挥作用,并支持将该血清型视为人类健康的重要危害。