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

Résumé

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.

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