Coexistence of seven different carbapenemase producers in a single hospital admission screening confirmed by whole-genome sequencing

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance Pub Date : 2024-10-16 DOI:10.1016/j.jgar.2024.09.005

Frieder Fuchs , Kyriaki Xanthopoulou , Tessa Burgwinkel , Rocío Arazo del Pino , Esther Wohlfarth , Florian Pavlu , Ralf M. Hagen , Paul G. Higgins

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引用次数: 0

Abstract

Objective

To molecularly characterize several extensively drug-resistant isolates from a single hospital admission screening of a war-injured patient from Ukraine.

Methods

Admission screening included swabs from skin, wounds, catheters, nasopharyngeum and rectum. Bacterial identification, antimicrobial susceptibility testing and rapid multiplex PCR assays targeting resistance genes were performed during routine diagnostics. Isolates positive by PCR had their genomes sequenced using short- and long read-platforms (MiSeq and MinION) to confirm species, identify resistance genes and plasmids and investigate clonality with core-genome MLST.

Results

Seven Gram-negative pathogens (Acinetobacter baumannii (n = 2; ST78, ST2), Klebsiella pneumoniae (n = 2; ST395), Pseudomonas aeruginosa (n = 1; ST1047), Escherichia coli (n = 1; ST46), Enterobacter cloacae complex (n = 1; ST231)) were molecularly confirmed non-identical. Antimicrobial susceptibility testing showed resistance to carbapenems (7/7 isolates) and last-resort treatment options such as ceftazidime-avibactam (6/7 isolates) and cefiderocol (4/7 isolates). All isolates were colistin susceptible. Sequencing identified the E. cloacae complex as Enterobacter hormaechei subsp. xiangfangensis. Six acquired carbapenemase genes (bla_IMP-1, bla_NDM-1, bla_OXA-48, bla_NDM-5, bla_OXA-23 and bla_OXA-72) were detected. Both A. baumannii isolates differed in sequence type, carbapenemases and cefiderocol susceptibility. Both K. pneumoniae isolates shared sequence type and some resistance genes on an IncR plasmid but were different in core-genome MLST and carbapenemases (OXA-48 or NDM-1). One vancomycin-resistant Enterococcus faecium was also detected (VanA).

Conclusions

War-injured patients from Ukraine may carry different clones of multidrug-resistant pathogens with limited treatment options and diverse resistance genes at risk for dissemination. Infection control measures should include early molecular characterization of isolates for detection of routes of transmission.

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通过全基因组测序，证实在一次入院筛查中同时存在七种不同的碳青霉烯酶生产者。

目的对来自乌克兰的一名战争伤员的一次入院筛查中分离出的几种广泛耐药菌株进行分子鉴定：入院筛查包括从皮肤、伤口、导管、鼻咽和直肠采集拭子。在常规诊断过程中进行了细菌鉴定、抗菌药物药敏试验（AST）和针对耐药基因的快速多重 PCR 检测。利用长短读取平台（MiSeq 和 MinION）对 PCR 检测结果呈阳性的分离菌进行基因组测序，以确认菌种、鉴定耐药基因和质粒，并利用核心基因组 MLST（cgMLST）研究克隆性：结果：7 种革兰氏阴性病原体（鲍曼不动杆菌（n=2；ST78、ST2）、肺炎克雷伯氏菌（n=2；ST395）、铜绿假单胞菌（n=1；ST1047）、大肠埃希菌（n=1；ST46）、复合泄殖腔肠杆菌（n=1；ST231））经分子鉴定为非同种。AST 显示出对碳青霉烯类（7/7 个分离株）和头孢唑肟-阿维巴坦（6/7 个分离株）和头孢克洛（4/7 个分离株）等最后治疗方案的耐药性。所有分离物均对秋水仙碱敏感。通过测序，确定泄殖腔大肠杆菌复合体为 E. hormaechei 亚种 xiangfangensis。检测到六个获得性碳青霉烯酶基因（blaIMP-1、blaNDM-1、blaOXA-48、blaNDM-5、blaOXA-23 和 blaOXA-72）。这两种鲍曼尼氏菌分离物在序列类型、碳青霉烯酶和头孢羟氨苄敏感性方面存在差异。两个肺炎克氏菌分离株共享序列类型和 IncR 质粒上的一些耐药基因，但在 cgMLST 和碳青霉烯酶（OXA-48 或 NDM-1）方面存在差异。此外，还检测到一种耐万古霉素的粪肠球菌（VanA）：结论：乌克兰的战争伤员可能携带不同克隆的耐多药病原体，治疗方案有限，耐药基因多样，存在传播风险。感染控制措施应包括及早对分离物进行分子鉴定，以检测传播途径。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of global antimicrobial resistance INFECTIOUS DISEASES-PHARMACOLOGY & PHARMACY

CiteScore

8.70

自引率

2.20%

发文量

285

审稿时长

34 weeks

期刊介绍： The Journal of Global Antimicrobial Resistance (JGAR) is a quarterly online journal run by an international Editorial Board that focuses on the global spread of antibiotic-resistant microbes. JGAR is a dedicated journal for all professionals working in research, health care, the environment and animal infection control, aiming to track the resistance threat worldwide and provides a single voice devoted to antimicrobial resistance (AMR). Featuring peer-reviewed and up to date research articles, reviews, short notes and hot topics JGAR covers the key topics related to antibacterial, antiviral, antifungal and antiparasitic resistance.