Empowering active surveillance of Carbapenem-resistant Enterobacterales: Insights from one year of genomic surveillance

IF 4.8 3区医学 Q1 INFECTIOUS DISEASES

Journal of Infection and Public Health Pub Date : 2026-04-01 Epub Date: 2026-02-26 DOI:10.1016/j.jiph.2026.103187

Greta Petazzoni , Stefano Gaiarsa , Irene Mileto , Angela Kuka , Marta Corbella , Cristina Merla , Antonio Piralla , Marina Ramus , Aurora Piazza , Vittoria Mattioni Marchetti , Roberta Migliavacca , Alba Muzzi , Patrizia Cambieri , Fausto Baldanti

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引用次数: 0

Abstract

Background

Healthcare-associated infections (HAIs) in Europe affect millions of patients annually, driving antimicrobial resistance and imposing significant economic burdens. Carbapenem-resistant Enterobacterales (CRE) are particularly concerning due to their ability to spread, making genomic surveillance essential for tracking their transmission.

Methods

From October 2022 to September 2023, we sequenced and analysed the genome of 340 CRE obtained from patients admitted to Fondazione IRCCS Policlinico San Matteo ( Italy). Sequencing was performed using a short-read approach and genomes were in-silico characterized to identify Sequence Types (STs), antimicrobial resistance and virulence determinants, and plasmid content. Moreover, a core SNP-based phylogeny was performed to identify potential epidemic clusters within the same clone.

Results

Among the 340 CRE isolated from surveillance (N = 234) and other clinical specimens (N = 106), 87.7% belonged to the Klebsiella genus, primarily K. pneumoniae (CR-Kp, N = 284). Escherichia coli (CR-Ec) accounted for 8.5% (N = 29); while the remaining species were Enterobacter spp. (N = 13) and Citrobacter spp. (N = 9). bla_KPC and bla_NDM gene variants were detected in 55.9% and 25.6% of CRE, respectively. The most prevalent CR-Kp clones were ST307, ST6668, ST258, and ST512, whereas ST131 was dominant among CR-Ec. Large epidemic clusters (ECs; ≥ 5 strains in each clade) were mainly found in CR-Kp associated with ST307 and ST6668, with 80.63% of CR-Kp grouped into nine ECs. Conversely, other species were observed as sporadic cases or within transmission clusters with limited spread.

Conclusion

Our comprehensive analysis of CRE circulation at HSM revealed that their dissemination was largely driven by highly successful clones, shedding light on several of them.

查看原文本刊更多论文

授权碳青霉烯抗性肠杆菌的主动监测：从一年的基因组监测的见解。

背景：欧洲医疗保健相关感染（HAIs）每年影响数百万患者，推动抗菌素耐药性并造成重大经济负担。碳青霉烯耐药肠杆菌（CRE）由于其传播能力特别令人担忧，因此基因组监测对于跟踪其传播至关重要。方法：从2022年10月至2023年9月，我们对来自意大利圣马泰奥基金会（Fondazione IRCCS Policlinico San Matteo）收治的340例CRE患者的基因组进行了测序和分析。测序采用短读法，并对基因组进行了计算机表征，以确定序列类型（STs）、抗菌素耐药性和毒力决定因素以及质粒含量。此外，还进行了基于核心snp的系统发育，以确定同一克隆中潜在的流行病聚集性。结果：监测分离到的340株CRE （N = 234）和其他临床标本（N = 106）中，克雷伯氏菌属占87.7%，以肺炎克雷伯氏菌（CR-Kp, N = 284）为主。大肠杆菌（CR-Ec）占8.5% (N = 29)；其余菌种为肠杆菌（N = 13）和柠檬酸杆菌（N = 9）。在CRE中分别检测到55.9%和25.6%的blaKPC和blaNDM基因变异。CR-Kp无性系以ST307、ST6668、ST258和ST512最为普遍，而CR-Ec无性系以ST131为主。与ST307和ST6668相关的CR-Kp主要存在大流行聚集性（ECs，每个进化支≥5株），其中80.63%的CR-Kp归为9个ECs。相反，其他物种为散发病例或传播聚集性病例，传播有限。结论：我们对HSM的CRE循环进行了综合分析，发现它们的传播主要是由非常成功的克隆驱动的，从而揭示了其中一些克隆。

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 Infection and Public Health PUBLIC, ENVIRONMENTAL & OCCUPATIONAL HEALTH -INFECTIOUS DISEASES

CiteScore

13.10

自引率

1.50%

发文量

203

审稿时长

96 days

期刊介绍： The Journal of Infection and Public Health, first official journal of the Saudi Arabian Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences and the Saudi Association for Public Health, aims to be the foremost scientific, peer-reviewed journal encompassing infection prevention and control, microbiology, infectious diseases, public health and the application of healthcare epidemiology to the evaluation of health outcomes. The point of view of the journal is that infection and public health are closely intertwined and that advances in one area will have positive consequences on the other. The journal will be useful to all health professionals who are partners in the management of patients with communicable diseases, keeping them up to date. The journal is proud to have an international and diverse editorial board that will assist and facilitate the publication of articles that reflect a global view on infection control and public health, as well as emphasizing our focus on supporting the needs of public health practitioners. It is our aim to improve healthcare by reducing risk of infection and related adverse outcomes by critical review, selection, and dissemination of new and relevant information in the field of infection control, public health and infectious diseases in all healthcare settings and the community.