Di Pilato Vincenzo, Henrici De Angelis Lucia, Aiezza Noemi, Baccani Ilaria, Niccolai Claudia, Parisio Eva Maria, Giordano Cesira, Camarlinghi Giulio, Barnini Simona, Forni Silvia, Righi Lorenzo, Mechi Maria Teresa, Giani Tommaso, Antonelli Alberto, Rossolini Gian Maria
Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy; Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.
Department of Medical Biotechnologies, University of Siena, Siena, Italy.
Lancet Microbe. 2022 Mar;3(3):e224-e234. doi: 10.1016/S2666-5247(21)00268-8. Epub 2022 Feb 4.
Carbapenemase-producing Enterobacterales (CPE), particularly those producing metallo-β-lactamases, are among the most challenging antibiotic-resistant pathogens, causing outbreaks of difficult-to-treat nosocomial infections worldwide. Since November 2018, an outbreak of New Delhi metallo-β-lactamases-positive CPE (NDM-CPE) has emerged in Tuscany, Italy. In this study, we aimed to investigate the NDM-CPE associated with the outbreak and characterise the responsible Klebsiella pneumoniae clone.
We used whole-genome sequencing and bioinformatic analysis to characterise NDM-CPE isolates that caused bloodstream infections in 53 patients at 11 hospitals in Tuscany and that were collected between Jan 1, 2018, and July 5, 2019 (ie, the early phase of the outbreak and preceding months). The CPE isolates characterised in this study were isolated and identified at the species level and as NDM producers by six diagnostic microbiology laboratories that serve the 11 hospitals. We used comparative genomic analysis, antimicrobial susceptibility testing, plasmid conjugal transfer assays, evaluation of virulence potential in the Galleria mellonella infection model, and serum bactericidal assays to further characterise the clone causing the outbreak.
The outbreak was sustained by an ST147 K pneumoniae producing NDM-1, which had a complex resistome that mediated resistance to most antimicrobials (except cefiderocol, the aztreonam-avibactam combination, colistin, and fosfomycin). The clone belonged to a sublineage of probably recent evolution, occurred by the sequential acquisition of an integrative and conjugative element encoding the yersiniabactin siderophore, an FIB(pQil)-type multiresistance plasmid carrying bla, and a transferable chimeric plasmid, derived from virulence elements of hypervirulent K pneumoniae, carrying several resistance and virulence determinants. Infection of G mellonella larvae revealed a variable virulence potential. The behaviour in serum bactericidal assays was different from typical hypervirulent K pneumoniae strains, with variable grades of serum resistance apparently associated with mutations in specific chromosomal loci (csrD, pal, and ramR).
This description of a sublineage of ST147 K pneumoniae with a complex resistome and virulome that is capable of sustaining a large regional outbreak adds to existing research on the evolutionary trajectories within high-risk clones of K pneumoniae. Global surveillance programmes are warranted to track the dissemination of these lineages, and to prevent and control their spread.
Italian Ministry of Health and Department of Experimental and Clinical Medicine, University of Florence.
产碳青霉烯酶肠杆菌目细菌（CPE），尤其是那些产金属β-内酰胺酶的细菌，是最具挑战性的耐药病原体之一，在全球范围内引发了难以治疗的医院感染暴发。自2018年11月以来，意大利托斯卡纳出现了新德里金属β-内酰胺酶阳性CPE（NDM-CPE）的暴发。在本研究中，我们旨在调查与此次暴发相关的NDM-CPE，并鉴定出相关的肺炎克雷伯菌克隆。
我们使用全基因组测序和生物信息学分析来鉴定2018年1月1日至2019年7月5日期间（即暴发早期及之前几个月）在托斯卡纳11家医院导致53例患者血流感染的NDM-CPE分离株。本研究中鉴定的CPE分离株由为这11家医院服务的6个诊断微生物实验室进行分离、菌种鉴定及NDM产生菌鉴定。我们使用比较基因组分析、抗菌药物敏感性测试、质粒接合转移试验、在大蜡螟感染模型中评估毒力潜能以及血清杀菌试验来进一步鉴定导致此次暴发的克隆。
此次暴发由一株产NDM-1的ST147肺炎克雷伯菌持续传播引起，该菌株具有复杂的耐药基因组，介导对大多数抗菌药物（除头孢地尔、氨曲南-阿维巴坦合剂、黏菌素和磷霉素外）的耐药性。该克隆属于一个可能近期进化而来的亚谱系，通过依次获得一个编码耶尔森菌素铁载体的整合和接合元件、一个携带bla的FIB(pQil)型多耐药质粒以及一个源自高毒力肺炎克雷伯菌毒力元件的可转移嵌合质粒而产生，该嵌合质粒携带多个耐药和毒力决定簇。大蜡螟幼虫感染显示出不同的毒力潜能。血清杀菌试验中的表现与典型的高毒力肺炎克雷伯菌菌株不同，不同程度的血清耐药性显然与特定染色体位点（csrD、pal和ramR）的突变有关。
对具有复杂耐药基因组和毒力基因组且能够维持大规模区域暴发的ST147肺炎克雷伯菌亚谱系的这一描述，丰富了关于肺炎克雷伯菌高风险克隆进化轨迹的现有研究。有必要开展全球监测计划来追踪这些谱系的传播，并预防和控制其扩散。
意大利卫生部以及佛罗伦萨大学实验与临床医学系。
