Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom.
Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom.
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对粪肠球菌的基因组监测显示，英国牲畜和人类之间的菌株和抗性基因的共享有限。
DOI：
10.1128/mbio.01780-18
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发表时间：
2018-11-06
期刊：
影响因子：
6.4
通讯作者：
Peacock SJ
中科院分区：
文献类型：
--
作者：
Gouliouris T;Raven KE;Ludden C;Blane B;Corander J;Horner CS;Hernandez-Garcia J;Wood P;Hadjirin NF;Radakovic M;Holmes MA;de Goffau M;Brown NM;Parkhill J;Peacock SJ
1988 年至 2000 年代欧洲耐万古霉素屎肠球菌 (VREfm) 菌株引起的人类感染率上升，有人认为与从牲畜中获得该菌株有关。因此，欧盟禁止在牲畜饲料中使用糖肽药物阿伏霉素作为生长促进剂。虽然一些研究报告牲畜的 VREfm 有所减少，但其他研究报告没有减少。在此，我们报告了自 2003 年以来英国首次进行的牲畜 VREfm 患病率调查，以及首次使用全基因组测序来调查牲畜和人类中屎肠球菌菌株之间关系的大规模研究。我们发现零售肉类中 VREfm 的流行率较低，并且最近牲畜和人类之间存在血流感染菌株共享的证据有限。有证据表明，这些宿主之间编码抗生素耐药性的基因共享有限，这一发现需要进一步研究。耐万古霉素屎肠球菌 (VREfm) 是医院感染的主要原因，被世界卫生组织全球抗生素耐药细菌优先清单列为高度优先考虑的细菌。过去，牲畜被认为是感染人类的耐药屎肠球菌菌株的假定宿主，并且在两个宿主中都发现了相同谱系的分离株。我们进行了横断面调查，从英国的畜牧场、零售肉类和废水处理厂中分离出屎肠球菌（包括 VREfm）。对来自这些来源的 600 多个分离株进行了测序，并将它们的相关性和抗生素抗性基因与来自英国和爱尔兰血流感染患者的近 800 个粪肠球菌分离株的基因组进行了比较。从 28/29 农场分离出屎肠球菌；这些分离株均不是 VREfm，这表明自 2003 年英国上次牲畜调查以来，VREfm 患病率有所下降。然而，VREfm 从 1% 至 2% 的零售肉类产品中分离出来，并且在废水处理厂中普遍存在。系统发育比较表明，大多数人类和牲畜相关分离株在遗传上是不同的，尽管 2001 年至 2004 年期间，来自三个农场的猪分离株与人类分离株在遗传上更为相关（至少 50 个单核苷酸多态性 [SNP]）。辅助（可变）基因的分析为独特的生态位适应提供了进一步的证据。对获得性抗生素抗性基因及其变体的分析表明，人类和牲畜之间的共享有限。我们的研究结果表明，感染患者的大多数屎肠球菌菌株与该环境下家畜的菌株有很大不同，菌株和抗性基因的共享有限。
The rise in rates of human infection caused by vancomycin-resistant Enterococcus faecium (VREfm) strains between 1988 to the 2000s in Europe was suggested to be associated with acquisition from livestock. As a result, the European Union banned the use of the glycopeptide drug avoparcin as a growth promoter in livestock feed. While some studies reported a decrease in VREfm in livestock, others reported no reduction. Here, we report the first livestock VREfm prevalence survey in the UK since 2003 and the first large-scale study using whole-genome sequencing to investigate the relationship between E. faecium strains in livestock and humans. We found a low prevalence of VREfm in retail meat and limited evidence for recent sharing of strains between livestock and humans with bloodstream infection. There was evidence for limited sharing of genes encoding antibiotic resistance between these reservoirs, a finding which requires further research. Vancomycin-resistant Enterococcus faecium (VREfm) is a major cause of nosocomial infection and is categorized as high priority by the World Health Organization global priority list of antibiotic-resistant bacteria. In the past, livestock have been proposed as a putative reservoir for drug-resistant E. faecium strains that infect humans, and isolates of the same lineage have been found in both reservoirs. We undertook cross-sectional surveys to isolate E. faecium (including VREfm) from livestock farms, retail meat, and wastewater treatment plants in the United Kingdom. More than 600 isolates from these sources were sequenced, and their relatedness and antibiotic resistance genes were compared with genomes of almost 800 E. faecium isolates from patients with bloodstream infection in the United Kingdom and Ireland. E. faecium was isolated from 28/29 farms; none of these isolates were VREfm, suggesting a decrease in VREfm prevalence since the last UK livestock survey in 2003. However, VREfm was isolated from 1% to 2% of retail meat products and was ubiquitous in wastewater treatment plants. Phylogenetic comparison demonstrated that the majority of human and livestock-related isolates were genetically distinct, although pig isolates from three farms were more genetically related to human isolates from 2001 to 2004 (minimum of 50 single-nucleotide polymorphisms [SNPs]). Analysis of accessory (variable) genes added further evidence for distinct niche adaptation. An analysis of acquired antibiotic resistance genes and their variants revealed limited sharing between humans and livestock. Our findings indicate that the majority of E. faecium strains infecting patients are largely distinct from those from livestock in this setting, with limited sharing of strains and resistance genes.