A High-Throughput Short Sequence Typing Scheme for Serratia marcescens Pure Culture and Environmental DNA

Bourdin, Thibault; Monnier, Alizee; Benoît, Marie-Eve; Bédard, Émilie; Prévost, Michèle; Quach, Caroline; Déziel, Éric ORCID: https://orcid.org/0000-0002-4609-0115 et Constant, Philippe ORCID: https://orcid.org/0000-0003-2739-2801 (2021). A High-Throughput Short Sequence Typing Scheme for Serratia marcescens Pure Culture and Environmental DNA Applied and Environmental Microbiology , vol. 87 , nº 24:e0139. pp. 1-14. DOI: 10.1128/aem.01399-21.

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Résumé

Molecular typing methods are used to characterize the relatedness between bacterial isolates involved in infections. These approaches rely mostly on discrete loci or whole genome sequences (WGS) analyses of pure cultures. On the other hand, their application to environmental DNA profiling to evaluate epidemiological relatedness amongst patients and environments has received less attention. We developed a specific, high-throughput short sequence typing (HiSST) method for the opportunistic human pathogen Serratia marcescens. Genes displaying the highest polymorphism were retrieved from the core genome of 60 S. marcescens strains. Bioinformatics analyses showed that use of only three loci (within bssA, gabR and dhaM) distinguished strains with a high level of efficiency. This HiSST scheme was applied to an epidemiological survey of S. marcescens in a neonatal intensive care unit (NICU). In a first case study, a strain responsible for an outbreak in the NICU was found in a sink drain of this unit, by using HiSST scheme and confirmed by WGS. The HiSST scheme was also applied to environmental DNA extracted from sink-environment samples. Diversity of S. marcescens was modest, with 11, 6 and 4 different sequence types (ST) of gabR, bssA and dhaM loci amongst 19 sink drains, respectively. Epidemiological relationships amongst sinks were inferred on the basis of pairwise comparisons of ST profiles. Further research aimed at relating ST distribution patterns to environmental features encompassing sink location, utilization and microbial diversity is needed to improve the surveillance and management of opportunistic pathogens. Importance Serratia marcescens is an important opportunistic human pathogen, multidrug resistant and often involved in outbreaks of nosocomial infections in neonatal intensive care unit. Here, we propose a quick and user-friendly method to select the best typing scheme for nosocomial outbreaks in relating environmental and clinical sources. This method, named high-throughput short sequence typing (HiSST), allows to distinguish strains and to explore the diversity profile of non-culturable S. marcescens. The application of HiSST profile analysis for environmental DNA offers new possibilities to track opportunistic pathogens, identify their origin and relate their distribution pattern with environmental features encompassing sink location, utilization and microbial diversity. Adaptation of the method to other opportunistic pathogens is expected to improve knowledge regarding their ecology, which of significant interest for epidemiological risk assessment and elaborate outbreak mitigation strategies.

Type de document:	Article
Mots-clés libres:	HISST; Environmental DNA; Healthcare-Associated Infections (HAI); Molecular Typing; Neonatal Intensive Care Unit (NICU); Opportunistic Pathogens; Sink Environment
Centre:	Centre INRS-Institut Armand Frappier
Date de dépôt:	22 juin 2022 19:21
Dernière modification:	22 juin 2022 19:21
URI:	https://espace.inrs.ca/id/eprint/12306

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