Whole genome sequencing as a reliable alternative for Salmonella serotyping: a comparative study with the gold-standard method

Irene Mileto¹Greta Romano^1*Stefano Gaiarsa¹Giulia Grassia¹Jessica Bagnarino¹Antonio Piralla¹Vincenzina Monzillo¹PATRIZIA CAMBIERI¹Fausto Baldanti^1,2Marta Corbella¹

• ¹San Matteo Hospital Foundation (IRCCS), Pavia, Italy
• ²Universita degli Studi di Pavia Dipartimento di Scienze Clinico Chirurgiche Diagnostiche e Pediatriche, Pavia, Italy

Introduction:Salmonella is a major foodborne pathogen of significant global health concern, leading to conditions like gastroenteritis, with symptoms such as diarrhea, abdominal cramps, and fever. Although most cases are self-limiting, S. enterica can cause bacteremia or typhoid fever in some cases. There are over 2,600 known serotypes of S. enterica. Each serotype differs in its surface antigens (somatic O and flagellar H), which is how they are classified. Considering that traditional phenotypic typing is laborious and time-consuming, the goal of this study is to evaluate whole genome sequencing (WGS) application in this field. Methods: From January 2021 to December 2024, 282 isolates of S. enterica were collected at the Microbiology and Virology department of Fondazione IRCCS Policlinico San Matteo (Italy). The isolates were serotyped for O and H antigens with a serum agglutination method (gold-standard). WGS was performed using Illumina MiSeq and quality-filtered reads were used to perform serotype prediction using SeqSero2 and SISTR tools. Results: the genomic typing of both tools shows an optimal concordance level with the gold-standard method, accurately predicting the serotype (both O and H antigens) for 236 out of 282 (95%) of analyzed isolates. In addition, 34 isolates were correctly typed by the genomic methods, whereas typing with the gold-standard was not possible due to the lack of specific antisera. The genomic typing was able to classify all isolates while staying as close as possible to the present classification of Salmonella into subspecies and serovars. Discussions: WGS has proven to be a robust and reliable method for Salmonella typing. It allows for the simultaneous analysis of multiple samples, shortens processing times, and reduces hands-on time. Moreover, WGS enabled the recovery of identifications that could not be obtained using the gold-standard method.