Molecular epidemiology of carbapenem-resistant Serratia marcescens outbreak during the COVID-19 pandemic

Letícia Da Rocha¹Grazielle Motta Rodrigues²Gabriella Simões de Oliveira^3,4Aymê Echevarria⁴Priscila Wink⁵Fabiana Caroline Zempulski Volpato⁵Mayana Hernandez^4,5Larissa Lutz¹Dariane Pereira^1,5Afonso Luís Barth^2,4,5*Andreza Martins^2,3,4,5,6

• ¹Unidade de Microbiologia e Biologia Molecular, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio de Janeiro, Brazil
• ²Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
• ³Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas, Universidade Federal do Rio Grande do Sul, Brazil., Porto Alegre, Brazil
• ⁴Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
• ⁵Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio de Janeiro, Brazil
• ⁶Bioinformatic Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil

Serratia marcescens is a significant causative agent of hospital-acquired infections (HAI), particularly in intensive care units (ICU). Carbapenem resistance represents a major concern in HAI management, as carbapenem-resistant bacteria can trigger outbreaks in hospital settings. While molecular evaluation of outbreaks typically relies on PFGE or cgMLST schemes, alternative rapid, reliable, and costeffective methods for assessing clonal relatedness are needed. This study aimed to characterize a carbapenem-resistant S. marcescens outbreak that occurred during the COVID-19 pandemic in a tertiary care hospital applying the flagellin gene as a Single Locus Sequence Typing (SLST) method. Additionally, we evaluated the genetic context of carbapenemase genes through Whole Genome Sequencing. Among 170 carbapenem-resistant Serratia marcescens isolates recovered, high resistance rates to gentamicin, ciprofloxacin and cefepime were observed. The predominant carbapenemase gene detected by qPCR-HRM was blaKPC (92.2%). Phylogenetic analysis of the flagellin gene grouped the sequences into two distinct clades, with all outbreak-related blaKPC-2 positive S. marcescens isolates clustering within clade B. The blaKPC-2 gene was carried on an IncP6 plasmid. Our findings demonstrate that the flagellin gene serves as an effective marker for characterizing carbapenemresistant S.marcescens carrying blaKPC-2, confirming that the outbreak resulted from clonal expansion of isolates harboring blaKPC-2 on an IncP6 plasmid.