Institute of Hygiene, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang 310013, China.
Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, China.
J Glob Antimicrob Resist. 2019 Jun;17:198-200. doi: 10.1016/j.jgar.2019.04.007. Epub 2019 Apr 18.
Escherichia coli and Enterobacter cloacae are two major pathogens causing urinary tract infection (UTI). Here we characterised the genome of an NDM-1-producing E. cloacae strain and an extended-spectrum β-lactamase (ESBL)-producing E. coli strain that were co-isolated from a UTI.
The genomes of E. cloacae strain EC32 and E. coli strain EC33 were sequenced using an Illumina HiSeq platform. The whole genome sequences were assembled using CLC Genomics Workbench and were annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) server. Genomic analysis was further performed.
The draft genome sequences of E. cloacae EC32 (ST66) and E. coli EC33 (ST1139) consisted of 89 contigs comprising 5 178 393 bp and 62 contigs comprising 5 057 666 bp, respectively. Including the bla gene, in total 13 resistance genes were identified in E. cloacae EC32 conferring resistance to β-lactams, rifampicin, phenicols, fosfomycin, macrolides, quinolones, sulfonamides and tetracycline. Nine resistance genes were identified in E. coli EC33 including the ESBL-encoding gene bla.
To our knowledge, this is the first report of genomic characterisation of NDM-1-producing E. cloacae and ESBL-producing E. coli co-isolated from a UTI in China. The two strains inhabiting in the same environment may allow the possibility of horizontal transfer of bla and bla, making clinical treatment even difficult. This report also sheds light on geographically distinct Enterobacteriaceae strains from China enabling a comparative analysis of NDM-1- or ESBL-producing strains.
大肠埃希菌和阴沟肠杆菌是引起尿路感染（UTI）的两种主要病原体。在这里，我们对从 UTI 中分离出的一株产 NDM-1 的阴沟肠杆菌和一株产超广谱β-内酰胺酶（ESBL）的大肠埃希菌进行了基因组特征分析。
采用 Illumina HiSeq 平台对阴沟肠杆菌 EC32 株和大肠埃希菌 EC33 株的基因组进行测序。使用 CLC Genomics Workbench 对全基因组序列进行组装，并使用 NCBI Prokaryotic Genome Annotation Pipeline（PGAP）服务器进行注释。进一步进行基因组分析。
阴沟肠杆菌 EC32（ST66）和大肠埃希菌 EC33（ST1139）的草图基因组序列分别由 89 个和 62 个组成，分别包含 5178393bp 和 5057666bp。包括 bla 基因在内，阴沟肠杆菌 EC32 共鉴定出 13 个耐药基因，可赋予其对β-内酰胺类、利福平、酚类、磷霉素、大环内酯类、喹诺酮类、磺胺类和四环素类的耐药性。大肠埃希菌 EC33 中鉴定出 9 个耐药基因，包括 ESBL 编码基因 bla。
据我们所知，这是首次报道中国从 UTI 中分离出的产 NDM-1 的阴沟肠杆菌和产 ESBL 的大肠埃希菌的基因组特征。这两株在同一环境中定植的菌株可能允许 bla 和 bla 的水平转移，使临床治疗更加困难。本报告还为中国不同地理位置的肠杆菌科菌株提供了参考，为比较分析产 NDM-1 或 ESBL 的菌株提供了依据。
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