Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water
Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water
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DOI：
10.1128/aem.02703-16
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发表时间：
2017-03-01
影响因子：
4.4
通讯作者：
Yoneda, Minoru
中科院分区：
文献类型：
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作者：
Gomi, Ryota;Matsuda, Tomonari;Yoneda, Minoru
地表水被耐药细菌和致病菌污染是一个令人关注的问题。在这项研究中，从日本大和河获得的531株大肠杆菌对25种抗菌素的耐药性进行了表型评估。多药耐药（MDR） 76株（14.3%），1 ~ 2类药物不敏感66株（12.4%），敏感389株（73.3%）。采用Illumina技术对所选菌株进行全基因组测序。共对155株菌株的基因组序列进行了抗生素耐药性决定因素和系统发育特征分析。检测到50多种不同的抗性决定因素，包括获得性抗性基因和染色体抗性突变。在已测序的MDR菌株（n = 66）中，序列型155 （ST155）复合体（n = 9）、ST10复合体（n = 9）和ST69复合体（n = 7）最为常见。在58株肠外致病性大肠杆菌中，普遍存在ST95复合体（n = 18）、ST127复合体（n = 8）、ST12复合体（n = 6）、ST14复合体（n = 6）、ST131复合体（n = 6）等具有临床重要意义的克隆群，显示了环境型大肠杆菌的克隆分布。fimH基因分型显示ST131复合体菌株携带fimH22或fimH41，未检出fimH30亚群菌株。对ST95复合体（引起社区发病感染的主要克隆型大肠杆菌群之一）菌株的精细系统发育分析和毒力基因含量分析显示，环境菌株和临床菌株之间无显著差异。结果表明，地表水污染大肠杆菌属临床重要克隆群。由于地表水被用作饮用水、灌溉和娱乐用途的水源，地表水中抗菌素耐药和致病性大肠杆菌菌株的流行令人担忧。本研究对河流水体中的MDR和exic菌株进行了基因组测序和分析。我们检测到50多个耐药决定因素，并鉴定出MDR和exc菌株特有的克隆群。该研究表明，地表水污染大肠杆菌菌株属于临床重要的克隆群。总的来说，本研究促进了我们对环境MDR和exic菌株的理解。
Contamination of surface waters by antimicrobial-resistant bacteria and pathogenic bacteria is a great concern. In this study, 531 Escherichia coli isolates obtained from the Yamato River in Japan were evaluated phenotypically for resistance to 25 antimicrobials. Seventy-six isolates (14.3%) were multidrug resistant (MDR), 66 (12.4%) were nonsusceptible to one or two classes of agents, and 389 (73.3%) were susceptible. We performed whole-genome sequencing of selected strains by using Illumina technology. In total, the genome sequences of 155 strains were analyzed for antibiotic resistance determinants and phylogenetic characteristics. More than 50 different resistance determinants, including acquired resistance genes and chromosomal resistance mutations, were detected. Among the sequenced MDR strains (n = 66), sequence type 155 (ST155) complex (n = 9), ST10 complex (n = 9), and ST69 complex (n = 7) were prevalent. Among extraintestinal pathogenic E. coli (ExPEC) strains (n = 58), clinically important clonal groups, namely, ST95 complex (n = 18), ST127 complex (n = 8), ST12 complex (n = 6), ST14 complex (n = 6), and ST131 complex (n = 6), were prevalent, demonstrating the clonal distribution of environmental ExPEC strains. Typing of the fimH (type 1 fimbrial adhesin) gene revealed that ST131 complex strains carried fimH22 or fimH41, and no strains belonging to the fimH30 subgroup were detected. Fine-scale phylogenetic analysis and virulence gene content analysis of strains belonging to the ST95 complex (one of the major clonal ExPEC groups causing community-onset infections) revealed no significant differences between environmental and clinical strains. The results indicate contamination of surface waters by E. coli strains belonging to clinically important clonal groups.IMPORTANCE The prevalence of antimicrobial-resistant and pathogenic E. coli strains in surface waters is a concern because surface waters are used as sources for drinking water, irrigation, and recreational purposes. In this study, MDR and ExPEC strains in river water were characterized by genomic sequencing and analysis. We detected more than 50 resistance determinants and identified clonal groups specific to MDR and ExPEC strains. This study showed contamination of surface waters by E. coli strains belonging to clinically important clonal groups. Overall, this study advances our understanding of environmental MDR and ExPEC strains.