Henares Desiree, Cubero Meritxell, Martinez-de-Albeniz Irene, Arranz Alba, Rocafort Muntsa, Brotons Pedro, Perez-Argüello Amaresh, Troyano Maria Jose, Gene Amadeu, Lluansi Aleix, Iriondo-Sanz Marti, Jordan Iolanda, Fortuny Claudia, Urrea Mireia, Muñoz-Almagro C
Department of RDI Microbiology, Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain.
Infectious Diseases and Microbiome Research Group, Institut de Recerca Sant Joan de Déu (IRSJD), Santa Rosa 39-57, 08950 Esplugues de Llobregat, Spain.
Antimicrob Resist Infect Control. 2025 Jun 4;14(1):63. doi: 10.1186/s13756-025-01582-x.
Serratia marcescens is a frequent cause of outbreaks in high-risk hospital settings such as neonatal intensive care units (NICU). This study investigated a potential S. marcescens outbreak in the NICU of a reference children's hospital using Whole Genome Sequencing (WGS). Additionally, it assessed the performance of third-generation sequencing for the rapid and accurate identification and characterization of the outbreak's clonal strain.
A prospective study was conducted from September 8th to November 12th 2021, following a sharp increase in invasive S. marcescens infections in the NICU of University Children's Hospital Sant Joan de Déu (Barcelona, Spain). This study included all patients admitted to NICU and other hospital wards from whom S. marcescens was isolated in any sample type. Nanopore sequencing was performed on S. marcescens isolates. Genomic characterization included phylogenetic analyses and detection of antimicrobial resistance genes.
Twenty-nine patients (16 NICU and 13 non-NICU patients) infected/colonized by S. marcescens were detected during the study period, accounting for a total of 61 isolates. The genomic characterization was performed on 24 isolates from 14 NICU-patients and 10 isolates from eight non-NICU patients. Phylogenetic analyses evidenced three clusters of closely related strains; cluster I (n = 22), II (n = 2) and III (n = 5). The remaining isolates (n = 5) did not cluster. Cluster I contained most isolates from NICU patients (20/24), and most isolates from NICU-patients with confirmed invasive disease (7/8). Cluster II contained two isolates from two NICU-patients, one presenting with invasive disease. The resistance gene blaSRT was found in 97% of S. marcescens isolates (33/34). All isolates exhibited the amikacin-tobramycin aac(6') resistance gene and three multi-drug efflux pumps genes; sdeY, sdeB and smfY. The tetracycline tet(41) resistance gene was found in non-clustered isolates (4/34). The first results were available less than one month after the outbreak's alarm, and complete genomic study after two months.
Two clonal strains were co-circulating in the NICU setting, with one being the major strain responsible for the outbreak. Rapid molecular characterization with nanopore sequencing confirmed the outbreak. It revealed the phylogenetic relationships among isolates and their antimicrobial potential. This approach enabled effective contextualization of the outbreak and allowed for monitoring its progression.
粘质沙雷氏菌是新生儿重症监护病房（NICU）等高风险医院环境中暴发感染的常见原因。本研究使用全基因组测序（WGS）调查了一家参考儿童医院NICU中潜在的粘质沙雷氏菌暴发情况。此外，还评估了第三代测序在快速、准确鉴定和表征暴发的克隆菌株方面的性能。
在西班牙巴塞罗那圣琼德迪乌大学儿童医院NICU中侵袭性粘质沙雷氏菌感染急剧增加之后，于2021年9月8日至11月12日进行了一项前瞻性研究。该研究纳入了所有入住NICU及其他医院病房且任何样本类型中分离出粘质沙雷氏菌的患者。对粘质沙雷氏菌分离株进行了纳米孔测序。基因组特征分析包括系统发育分析和抗菌药物耐药基因检测。
在研究期间检测到29例感染/定植粘质沙雷氏菌的患者（16例NICU患者和13例非NICU患者），共分离出61株菌株。对来自14例NICU患者的24株分离株和来自8例非NICU患者的10株分离株进行了基因组特征分析。系统发育分析证明存在三个密切相关菌株簇；簇I（n = 22）、簇II（n = 2）和簇III（n = 5）。其余分离株（n = 5）未聚类。簇I包含大多数来自NICU患者的分离株（20/24），以及大多数确诊侵袭性疾病的NICU患者分离株（7/8）。簇II包含来自两名NICU患者的两株分离株，其中一名患有侵袭性疾病。在97%的粘质沙雷氏菌分离株（33/34）中发现了耐药基因blaSRT。所有分离株均表现出对阿米卡星-妥布霉素的aac(6')耐药基因以及三个多药外排泵基因；sdeY、sdeB和smfY。在未聚类的分离株中发现了四环素tet(41)耐药基因（4/34）。在暴发警报发出后不到一个月获得了初步结果，两个月后完成了完整的基因组研究。
两种克隆菌株在NICU环境中共同传播，其中一种是导致暴发的主要菌株。通过纳米孔测序进行的快速分子特征分析证实了暴发情况。它揭示了分离株之间的系统发育关系及其抗菌潜力。这种方法能够有效地将暴发情况置于背景中，并允许监测其进展。
