European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK; Department of Medicine, University of Cambridge, Cambridge, UK.
National Hospital for Tropical Diseases, Hanoi, Viet Nam; Hanoi Medical University, Hanoi, Viet Nam.
Lancet Microbe. 2022 Nov;3(11):e857-e866. doi: 10.1016/S2666-5247(22)00181-1. Epub 2022 Oct 4.
Viet Nam has high rates of antimicrobial resistance (AMR) but little capacity for genomic surveillance. This study used whole genome sequencing to examine the prevalence and transmission of three key AMR pathogens in two intensive care units (ICUs) in Hanoi, Viet Nam.
A prospective surveillance study of all adults admitted to ICUs at the National Hospital for Tropical Diseases and Bach Mai Hospital was done between June 19, 2017, and Jan 16, 2018. Clinical and environmental samples were cultured on selective media, characterised with MALDI TOF mass spectrometry, and sequenced with Illumina. Phylogenies based on the de-novo assemblies (SPAdes) were constructed with MAFFT (PARsnp), Gubbins, and RAxML. Resistance genes were detected with Abricate against the US National Center for Biotechnology Information database.
3153 Escherichia coli, Klebsiella pneumoniae, and Acinetobacter baumannii isolates from 369 patients were analysed. Phylogenetic analysis revealed predominant lineages within A baumannii (global clone 2, sequence types ST2 and ST571) and K pneumoniae (ST15, ST16, ST656, ST11, and ST147) isolates. Isolation from stool was most common with E coli (87·0%) followed by K pneumoniae (62·5%). Of the E coli, 85·0% carried a bla variant, while 81·8% of K pneumoniae isolates carried bla (54·4%), or bla (45·1%), or both. Transmission analysis with single nucleotide polymorphisms identified 167 clusters involving 251 (68%) of 369 patients, in some cases involving patients from both ICUs. There were no clear differences between the lineages or AMR genes recovered between the two ICUs.
This study represents the largest prospective surveillance study of key AMR pathogens in Vietnamese ICUs. Clusters of closely related isolates in patients across both ICUs suggests recent transmission before ICU admission in other health-care settings or in the community.
UK Medical Research Council Newton Fund, Viet Nam Ministry of Science and Technology, Wellcome Trust, Academy of Medical Sciences, Health Foundation, and UK National Institute for Health and Care Research Cambridge Biomedical Research Centre.
越南的抗生素耐药率（AMR）很高，但进行基因组监测的能力有限。本研究使用全基因组测序，检测了越南河内两家重症监护病房（ICUs）中三种关键 AMR 病原体的流行情况和传播情况。
2017 年 6 月 19 日至 2018 年 1 月 16 日，对国家热带病医院和巴查马伊医院 ICU 收治的所有成年患者进行了前瞻性监测研究。对选择性培养基上培养的临床和环境样本进行了 MALDI-TOF 质谱鉴定，并进行了 Illumina 测序。基于从头组装（SPAdes）的系统发育树，使用 MAFFT（PARsnp）、Gubbins 和 RAxML 进行了构建。使用 Abricate 针对美国国家生物技术信息中心数据库检测了耐药基因。
对 369 名患者的 3153 株大肠埃希菌、肺炎克雷伯菌和鲍曼不动杆菌进行了分析。系统发育分析显示，鲍曼不动杆菌（全球克隆 2、ST2 和 ST571）和肺炎克雷伯菌（ST15、ST16、ST656、ST11 和 ST147）分离株中存在主要谱系。粪便中分离到的大肠埃希菌最为常见（87.0%），其次是肺炎克雷伯菌（62.5%）。85.0%的大肠埃希菌携带 bla 变体，而 81.8%的肺炎克雷伯菌携带 bla（54.4%）或 bla（45.1%）或两者。通过单核苷酸多态性进行的传播分析确定了 167 个包含 369 名患者中的 251 名（68%）的簇，在某些情况下，这些患者来自两个 ICU。两个 ICU 之间分离株的谱系或 AMR 基因没有明显差异。
本研究代表了越南 ICU 中关键 AMR 病原体最大的前瞻性监测研究。两个 ICU 中密切相关的患者分离株的聚集表明，在 ICU 入院前，在其他医疗机构或社区中发生了近期传播。
英国医学研究理事会牛顿基金、越南科技部、惠康信托基金会、英国医学科学院、英国健康基金会和英国国家卫生与保健研究院剑桥生物医学研究中心。
