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Genomic analysis identifies candidate SOS-associated and EPS/envelope-remodeling islands in a drinking-water Stenotrophomonas maltophilia complex isolate.

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Τίτλος: Genomic analysis identifies candidate SOS-associated and EPS/envelope-remodeling islands in a drinking-water Stenotrophomonas maltophilia complex isolate.
Συγγραφείς: Hassan F; Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information, Cairo, Egypt., Türkyılmaz S; Department of Microbiology, Faculty of Veterinary Medicine, Aydın Adnan Menderes University, Aydın, Türkiye., El-Mahdy TS; Department of Microbiology and Immunology, Faculty of Pharmacy, Capital (formerly Helwan) University, Cairo, Egypt. taghrid-elmahdy@pharm.capu.edu.eg.
Πηγή: Scientific reports [Sci Rep] 2026 Jun 28; Vol. 16 (1). Date of Electronic Publication: 2026 Jun 28.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE
Imprint Name(s): Original Publication: London : Nature Publishing Group, copyright 2011-
Ιατρικοί όροι (MeSH): Stenotrophomonas maltophilia*/genetics , Stenotrophomonas maltophilia*/isolation & purification , Stenotrophomonas maltophilia*/drug effects , Stenotrophomonas maltophilia*/classification , Drinking Water*/microbiology , SOS Response, Genetics*/genetics , Extracellular Polymeric Substance Matrix*/genetics , Extracellular Polymeric Substance Matrix*/metabolism , Genomic Islands*, Biofilms/growth & development ; Biofilms/drug effects ; Genomics/methods ; Genome, Bacterial ; Phylogeny
Περίληψη: Drinking-water distribution systems (DWDS) impose ecological pressures shaped by oligotrophy, surface attachment, hydraulic fluctuation, and residual disinfectants. These conditions may favor stress-tolerant and biofilm-capable microorganisms, including members of the Stenotrophomonas maltophilia complex. Although this complex is clinically relevant because of intrinsic multidrug resistance and opportunistic pathogenic potential, the strain-level genomic features that may support persistence in disinfectant-managed water systems remain incompletely characterized. We applied an integrated genome-resolved framework to Stenotrophomonas sp. NG-SM01, a drinking-water isolate assigned to the S. maltophilia complex genomospecies Sgn4. Hybrid sequencing was used to generate a closed genome assembly, followed by phylogenomics and MLST for taxonomic placement, pangenome analysis for gene-content context, and genomic-island mapping to identify candidate accessory regions. Functional profiling included BacMet screening for metal/biocide tolerance-associated loci and genome-scale metabolic reconstruction using gapseq. Phenotypic assays assessed crystal-violet biofilm biomass and acute hydrogen peroxide (H₂O₂) survival as a general oxidative-stress proxy. NG-SM01 clustered within the Sgn4 genomospecies of the S. maltophilia complex and formed a strongly supported sister lineage to its closest available reference genome, GCF_025642255.1 (UFboot = 100). MLST confirmed a newly curated guaA allele (guaA-909), and the allelic profile was assigned ST1409. Disk diffusion showed limited inhibition by several antimicrobial agents; however, categorical interpretation using S. maltophilia-specific CLSI criteria was applied only to levofloxacin and trimethoprim-sulfamethoxazole, both of which were susceptible. Genomic-island analysis highlighted two candidate loci potentially relevant to stress adaptation: GI_6, carrying an EPS/envelope-remodeling cassette including algL and a GT26-family glycosyltransferase within a panel-restricted architecture, and GI_4, an IME-associated region located near SOS-response genes including recA, recX, and lexA. NG-SM01 formed reproducible moderate biofilm biomass under static microtiter conditions and showed plateau-like survival dynamics during acute H₂O₂ exposure. BacMet screening prioritized Tier-1 metal/biocide tolerance-associated signals, including CzcR-like and AdeL-like regulators and a YfeB-like transport component, while gapseq reconstruction predicted broad transport capacity, including 1,920 transporter entries, of which 23% were metal-related. This single-isolate study identifies genomic and phenotypic features potentially relevant to persistence in a drinking-water S. maltophilia complex Sgn4 isolate. The combined evidence supports a hypothesis-generating "Switch-Shield" framework, in which stress-response regulation and mobilome-associated plasticity may represent a candidate "switch," while EPS/envelope remodeling may represent a candidate protective "shield." However, direct causality between GI_4/GI_6 and the observed phenotypes was not demonstrated. Future validation using transcriptomics, mutant-based assays, and DWDS-mimetic free-chlorine or chloramine exposure models, including flow/pipe reactors with detachment and shedding measurements, will be required to test this model.
(© 2026. The Author(s).)
Competing Interests: Declarations. Competing interests: The authors declare no competing interests.
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Contributed Indexing: Keywords: Stenotrophomonas maltophilia complex; Biofilm adaptation; Drinking-water distribution system (DWDS); Environmental surveillance; Genomic islands; Persistence
Substance Nomenclature: 0 (Drinking Water)
Entry Date(s): Date Created: 20260628 Date Completed: 20260628 Latest Revision: 20260726
Update Code: 20260726
PubMed Central ID: PMC13310844
DOI: 10.1038/s41598-026-58581-0
PMID: 42366209
Βάση Δεδομένων: MEDLINE
Περιγραφή
ISSN:2045-2322
DOI:10.1038/s41598-026-58581-0