Genomic insights into the spread of vancomycin- and tigecycline-resistant Enterococcus faecium ST117.

IF 4.6 2区医学 Q1 MICROBIOLOGY

Annals of Clinical Microbiology and Antimicrobials Pub Date : 2025-06-11 DOI:10.1186/s12941-025-00806-7

Marie Brajerova, Otakar Nyc, Pavel Drevinek, Marcela Krutova

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引用次数: 0

Abstract

Background: Since the incidence of vancomycin-resistant enterococci (VRE) is increasing and treatment options remain limited, we aimed to investigate the epidemiology of vancomycin- and tigecycline-resistant enterococci in a university hospital using whole genome sequencing (WGS).

Methods: Between April and December 2021, 102 VRE isolates were collected from a single tertiary care hospital in the Czech Republic. Forty selected isolates underwent antimicrobial susceptibility testing and WGS (Illumina short reads and long reads with MinION in selected isolates).

Results: All Enterococcus faecium isolates were resistant to ampicillin, carrying the PBP5_Met485Ala, PBP5_Glu629Val, and fluoroquinolones carrying the GyrA_Ser83Ile and ParC_Ser80Ile substitutions. The vanA operon was found on pELF2-like plasmids and plasmids carrying rep17 and/or rep18b genes. The novel Tn1546 structural variants were identified in vanA-carrying isolates. The vanB operon was located on the chromosome within a Tn1549 structural variant. Linezolid resistance was detected in one isolate carrying the 23S rDNA_G2576T substitution. Twenty-two isolates were resistant to tigecycline (tet(L), tet(M) and rpsJ_del 155-166 or RpsJ_Lys57Arg). Discrepancies between phenotypic and genotypic resistance profiles were observed for daptomycin (RpoB_Ser491Phe), trimethoprim/sulfamethoxazole (dfrG gene), nitrofurantoin (NmrA_Gln48Lys substitution without the EF0404 and EF0648 genes) and tetracycline (truncated TetM). The two multilocus sequence typing (MLST) schemes identified different numbers of STs: 5 STs, with ST117 as the predominant one (n = 32, 80%), versus 10 STs, with ST138 (27.5%), ST136 (25%), and ST1067 (20%) being the most frequent, respectively. The whole genome MLST revealed clonal clustering (0-7 allele differences) among isolates of the same ST. When comparing ST117 isolates from our study with 2,204 ST117 isolates from 15 countries, only one Czech isolate clustered closely with strains from Germany and the Netherlands, differing by just 16 alleles.

Conclusions: The spread of E. faecium isolates ST117 resistant to vancomycin and tigecycline was identified. The discrepancies between resistance genotypes and phenotypes highlight the importance of combining molecular and phenotypic surveillance in antimicrobial resistance monitoring.

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对万古霉素和替加环素耐药屎肠球菌ST117传播的基因组分析。

背景：由于万古霉素耐药肠球菌（VRE）的发病率正在增加，治疗方案仍然有限，我们旨在利用全基因组测序（WGS）研究某大学医院万古霉素和地加环素耐药肠球菌的流行病学。方法：2021年4月至12月，从捷克共和国一家三级医院收集了102株VRE分离株。选取40株菌株进行了抗菌药敏试验和WGS（选定菌株的Illumina短读段和长读段带有MinION）。结果：所有粪肠球菌分离株均对氨苄西林耐药，携带PBP5_Met485Ala、PBP5_Glu629Val，氟喹诺酮类携带GyrA_Ser83Ile和ParC_Ser80Ile取代基。在pelf2样质粒和携带rep17和/或rep18b基因的质粒上发现了vanA操纵子。在携带钒的分离株中发现了新的Tn1546结构变异。vanB操纵子位于Tn1549结构变异的染色体上。一株携带23S rDNA_G2576T取代的分离株检测到利奈唑胺耐药。22株对替加环素耐药(tet（L)、tet(M)和rpsJ_del 155-166或RpsJ_Lys57Arg）。结果表明，达托霉素（RpoB_Ser491Phe）、甲氧苄啶/磺胺甲新唑（dfrG基因）、呋喃妥英（NmrA_Gln48Lys替代，不含EF0404和EF0648基因）和四环素（截断的TetM）的表型和基因型耐药谱存在差异。两种多位点序列分型（MLST）方案鉴定出不同数量的STs: 5个STs，以ST117为主（n = 32,80%）， 10个STs，分别以ST138（27.5%）、ST136（25%）和ST1067（20%）最常见。在与来自15个国家的2204株ST117分离株进行比较时，只有1株捷克分离株与来自德国和荷兰的ST117分离株紧密聚集，仅相差16个等位基因。结论：发现了对万古霉素和替加环素耐药的粪肠杆菌ST117的传播。耐药基因型和表型之间的差异突出了分子监测和表型监测相结合在抗菌素耐药性监测中的重要性。

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

Annals of Clinical Microbiology and Antimicrobials MICROBIOLOGY-

CiteScore

8.60

自引率

0.00%

发文量

审稿时长

>12 weeks

期刊介绍： Annals of Clinical Microbiology and Antimicrobials considers good quality, novel and international research of more than regional relevance. Research must include epidemiological and/or clinical information about isolates, and the journal covers the clinical microbiology of bacteria, viruses and fungi, as well as antimicrobial treatment of infectious diseases. Annals of Clinical Microbiology and Antimicrobials is an open access, peer-reviewed journal focusing on information concerning clinical microbiology, infectious diseases and antimicrobials. The management of infectious disease is dependent on correct diagnosis and appropriate antimicrobial treatment, and with this in mind, the journal aims to improve the communication between laboratory and clinical science in the field of clinical microbiology and antimicrobial treatment. Furthermore, the journal has no restrictions on space or access; this ensures that the journal can reach the widest possible audience.