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High-throughput short sequence typing schemes for pseudomonas aeruginosa and stenotrophomonas maltophilia pure culture and environmental DNA

Thibault Bourdin, Marie-Ève Benoit, Émilie Bédard, Michèle Prévost, Caroline Quach, Éric Déziel and Philippe Constant

Article (2024)

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Abstract

Molecular typing techniques are utilized to determine genetic similarities between bacterial isolates. However, the use of environmental DNA profiling to assess epidemiologic links between patients and their environment has not been fully explored. This work reports the development and validation of two high-throughput short sequence typing (HiSST) schemes targeting the opportunistic pathogens Pseudomonas aeruginosa and Stenotrophomonas maltophilia, along with a modified SM2I selective medium for the specific isolation of S. maltophilia. These HiSST schemes are based on four discriminative loci for each species and demonstrate high discriminating power, comparable to pairwise whole-genome comparisons. Each scheme includes species-specific PCR primers for precise differentiation from closely related taxa, without the need for upstream culture-dependent methods. For example, the primers targeting the bvgS locus make it possible to distinguish P. aeruginosa from the very closely related Pseudomonas paraeruginosa sp. nov. The selected loci included in the schemes are adapted to massive parallel amplicon sequencing technology. An R-based script implemented in the DADA2 pipeline was assembled to facilitate HiSST analyses for efficient and accurate genotyping of P. aeruginosa and S. maltophilia. We demonstrate the performance of both schemes through in silico validations, assessments against reference culture collections, and a case study involving environmental samples.

Uncontrolled Keywords

molecular typing; opportunistic pathogens; neonatal intensive care units (NICUs); healthcare-associated infections (HAIs); selective medium; Pseudomonas paraeruginosa; eDNA; genotyping; opportunistic premise plumbing pathogens (OPPP)

Subjects: 1000 Civil engineering > 1000 Civil engineering
1500 Environmental engineering > 1500 Environmental engineering
1900 Biomedical engineering > 1900 Biomedical engineering
Department: Department of Civil, Geological and Mining Engineering
Funders: NSERC / CRSNG, Canadian Institute of Health Research / Instituts de recherche en santé du Canada, Fonds de Recherche du Québec–Santé (Junior 1), Tier-1 Canada Research Chair in Infection Prevention
Grant number: CHRP 523790-18, CRC-2019-00055
PolyPublie URL: https://publications.polymtl.ca/57386/
Journal Title: Microorganisms (vol. 12, no. 1)
Publisher: MDPI
DOI: 10.3390/microorganisms12010048
Official URL: https://doi.org/10.3390/microorganisms12010048
Date Deposited: 28 Feb 2024 14:05
Last Modified: 29 Apr 2024 19:03
Cite in APA 7: Bourdin, T., Benoit, M.-È., Bédard, É., Prévost, M., Quach, C., Déziel, É., & Constant, P. (2024). High-throughput short sequence typing schemes for pseudomonas aeruginosa and stenotrophomonas maltophilia pure culture and environmental DNA. Microorganisms, 12(1), 48 (15 pages). https://doi.org/10.3390/microorganisms12010048

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