Lactiplantibacillus plantarum is widely used in fermented foods and as a probiotic, yet the genomic basis underlying its γ-aminobutyric acid (GABA) production capacity and strain-level functional diversity remains incompletely resolved. We analyzed 1240 publicly available genomes to map species-wide genome architecture, the distribution of GABA-related genes, and accessory drivers of phenotypes. Pangenome analysis identified 45,201 gene families, including 622 strict core genes (1.38%) and 444 soft-core genes (2.36%). The accessory genome dominated (3138 shell and 40,997 cloud genes; 97.64%), indicating a strongly open pangenome. In contrast, the GABA (gad) operon was universally conserved: gadB (glutamate decarboxylase) and gadC (glutamate/GABA antiporter) were present in all genomes regardless of isolates source. Accessory-genome clustering revealed ecological and geographic structure without loss of the operon, suggesting that phenotypes variability relevant to fermentation and probiotic performance is primarily shaped by accessory modules. Accessory features included carbohydrate uptake and processing islands, bacteriocins and immunity systems, stress- and membrane-associated functions, and plasmid-encoded traits. Analysis of complete genomes confirmed substantial variation in plasmid load (median = 2; range = 0–17), highlighting the role of mobile elements in niche-specific adaptation. Carbohydrate-Active Enzymes database (CAZy) and biosynthetic gene cluster (BGC) profiling revealed a conserved enzymatic and metabolic backbone complemented by rare lineage-specific functions. Collectively, these results position L. plantarum as a genetically stable GABA producer with extensive accessory-encoded flexibility and provide a framework for rational strain selection.

Background/Objectives: Pseudomonas aeruginosa is one of the most significant multidrug-resistant bacteria. It poses considerable challenges in terms of treatment and causes hospital-acquired infections that lead to high morbidity and mortality. Colonization by P. aeruginosa in a patient without clinical signs of infection is a concern in hospital settings, as it is an opportunistic pathogen and can potentially be a multidrug-resistant strain. The objective of this study was to characterize and provide a detailed genomic analysis of this strain of the P. aeruginosa PSU9449 genome, an isolate obtained from a patient at Songklanagarind Hospital, Thailand. Methods: Whole-genome sequencing (WGS) and bioinformatics analysis were employed to examine the genomic features of P. aeruginosa PSU9449. We performed sequence type (ST) determination through multilocus sequence typing (MLST), identified antimicrobial resistance genes (ARGs), virulence factor genes (VFGs), and analyzed the presence of mobile genetic elements (MGEs). Additionally, we compared the PSU9449 genome with strains from neighboring countries to understand its phylogenetic relationship. Results: The P. aeruginosa PSU9449 genome contained five insertion sequences and several ARGs, including fosA, aph (3’)-IIb, bla_OXA-50, and catB7. It also harbored VFGs related to flagella (fli, fle, and flg), the type 6 secretion system (hcpA, tssA, and las), and the type 3 secretion system (exoS, exoU, and exoT). MLST identified PSU9449 as ST3777, which was reported in Thailand for the first time. Phylogenetic analysis based on core gene SNPs revealed that PSU9449 was closely related to P. aeruginosa HW001G from Malaysia and P. aeruginosa MyJU45 from Myanmar, forming a distinct clade. Conclusions: This study presents a comprehensive genomic analysis of P. aeruginosa PSU9449, shedding light on its genetic characteristics, antimicrobial resistance profile, and virulence potential. Interestingly, ST3777, the novel STs from the published genomes of P. aeruginosa in Thailand, were assigned in this study. The findings enhance valuable insights into the expanding knowledge of P. aeruginosa PSU9449 and highlight the importance of ongoing surveillance of its genetic diversity.

Background: Stenotrophomonas maltophilia is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR) and ecological adaptation remain poorly resolved, partly due to inconsistent annotations and fragmented genomic datasets. Methods: Approximately 2400 genome assemblies annotated as Stenotrophomonas maltophilia were available in the NCBI Assembly database at the time of query. After pre-download filtering to exclude metagenome-assembled genomes and atypical lineages, 1750 isolate genomes were retrieved and subjected to stringent quality control (completeness ≥ 90%, contamination ≤ 5%, ≤500 contigs, N50 ≥ 10 kb, and ≤1% ambiguous bases), yielding a final curated dataset of 1518 high-quality genomes used for downstream analyses. Genomes were assessed using CheckM, annotated with Prokka, and compared using average nucleotide identity (ANI), pan-genome analysis, core-genome phylogenomics, and functional annotation. AMR genes, mobile genetic elements (MGEs), and metadata (source, host, and geographic origin) were integrated to assess lineage-specific genomic features and ecological distributions. Results: ANI-based clustering resolved the S. maltophilia complex into multiple distinct genomospecies and revealed extensive misidentification of publicly deposited genomes. The pan-genome was highly open, reflecting strong genomic plasticity driven by accessory gene acquisition. Core-genome phylogeny resolved well-supported clades associated with clinical, environmental, and plant-related niches. Resistome profiling showed widespread intrinsic MDR determinants, with certain lineages enriched for efflux pumps, β-lactamases, and trimethoprim–sulfamethoxazole resistance markers. MGE analysis identified lineage-specific integrative conjugative elements, prophages, and transposases that correlated with source and geographic distribution. Conclusions: This large-scale analysis provides the most comprehensive genomic overview of the S. maltophilia complex to date. Our findings clarify species boundaries, highlight substantial taxonomic misannotation in public databases, and reveal lineage-specific AMR and mobilome patterns linked to ecological and clinical origins. The curated dataset and evolutionary insights generated here establish a foundation for global genomic surveillance, epidemiological tracking, and future studies on the evolution of antimicrobial resistance in S. maltophilia.

Background: Acinetobacter baumannii is a major nosocomial pathogen with extensive antimicrobial resistance, yet the extent to which resistome burden covaries with mobilome architecture across clonal backgrounds remains unclear at the global scale. Using a curated dataset of 10,500 high-quality genomes, this study examined lineage-resolved relationships among AMRFinder-detected resistance determinants, insertion sequence (IS) burden, plasmid diversity, predicted plasmid mobility, and virulence-associated gene presence. Results: The population structure was highly uneven and dominated by a small number of lineages. Using total AMRFinder burden, genome-level associations with IS burden and plasmid replicon diversity were modest (Spearman rho = 0.259 and 0.246, respectively). In a sensitivity analysis using an acquired-like burden metric that excluded OXA-51 family hits, bla_ADC family hits, predefined intrinsic or conserved chromosomal background loci, and non-antibiotic resistance classes, the median burden decreased from 17 to 9 hits per genome. Under this filter, acquired-like burden remained associated with IS/mobile genetic element burden (rho = 0.237) and showed a slightly stronger association with plasmid replicon diversity (rho = 0.285), with both relationships persisting after excluding genomes from China and the United States. Mobilome features remained markedly heterogeneous across lineages, whereas virulence-associated gene presence profiles were comparatively conserved. Conclusions: These findings support a lineage-structured view of resistance-associated genomic variation in A. baumannii. However, the observed genome-wide associations were small in magnitude and should be interpreted as patterns of co-occurrence rather than direct evidence of mechanism or causality. Sensitivity analyses suggest that plasmid-related features show a more robust relationship with acquired-like resistance burden than IS counts alone. This distinction is relevant for genomic surveillance, but it should be interpreted together with lineage imbalance, sampling bias, and the limitations of gene-presence-based inference.

Acinetobacter baumannii sequence type 2 (ST2), corresponding to international clone II (IC2), is the most globally disseminated high-risk lineage associated with healthcare settings. Yet, despite its epidemiological prominence, the extent to which global ST2 diversification reflects deep phylogenetic subdivision versus repeated clonal expansion with accessory-gene turnover remains unresolved.,Here, we analyzed 5,612 high-quality ST2 genomes from public databases using lineage-focused population genomics, pairwise core-accessory distance profiling, class-level resistome summaries, predicted plasmid mobility, temporal summaries of resistance and plasmid-mobility signatures, and SNP-based phylogeny. PopPUNK assigned 5,604 of 5,612 genomes (99.86%) to one dominant cluster, supporting a globally cohesive ST2 background for downstream genome-level analyses.,The SNP-based analysis contained those 5,604 genomes plus one retained reference sequence (5,605 sequences total) and resolved an internally structured but connected lineage. Pairwise SNP distances among the 5,604 genomes spanned 0-4911 SNP (median, 314; IQR, 40-1029), with dense enrichment of short-distance links consistent with recurrent clonal expansion rather than a few deeply separated global clades. At the class-level antimicrobial resistance gene (ARG) resolution used here, a stable high-prevalence resistome co-occurred with geographic and phylogenetic variation in accessory resistance content.,Predicted plasmid mobility varied across phylogenetic and geographic backgrounds: 52.6% of genomes were classified as conjugative because at least one predicted conjugative plasmid was detected, 42.7% were classified as mobilizable because at least one predicted mobilizable plasmid but no predicted conjugative plasmid was detected, and 4.7% were classified as non-mobilizable. Host-range assignments were usually confined to class or genus rank. The association between detected mobile genetic element (MGE) burden and ARG burden was statistically significant but weak (Spearman ρ = 0.191), indicating only limited genome-wide coupling that did not persist after de-duplication to independent lineages. Together, these findings support a cautious model in which global ST2 is a cohesive but internally structured lineage with accessory resistance and predicted plasmid mobility varying among phylogenetic and geographic backgrounds, while genome-wide mobilome-resistome association remains weak.

Background/Objectives: Bacteroides species are key members of the human gut microbiota but can act as opportunistic pathogens. This study investigated the genomic features of clinical Bacteroides isolates from southern Thailand. Methods: Sixteen isolates were collected from body fluids, tissues, and pus at Songklanagarind Hospital (2022–2024). Whole-genome sequencing was performed on the BGI platform, followed by genome assembly, annotation, average nucleotide identity (ANI), pairwise single-nucleotide polymorphism (SNP) analysis, antimicrobial resistance (AMR) gene profiling, plasmid prediction, virulence screening, and phylogenetic analysis. Results: ANI and SNP analysis revealed two clusters: one comprising B. ovatus, B. intestinigallinarum, and B. thetaiotaomicron, and another mainly B. fragilis with one B. hominis isolate. All isolates were resistant to ampicillin, cephalothin, and penicillin; six B. fragilis strains were resistant to all tested antibiotics. The β-lactamase gene cepA was detected in all B. fragilis isolates, and plasmids were predicted in two genomes. Three virulence types (capsule formation, lipopolysaccharide modification, and stress response) were identified. Phylogenomic analysis confirmed species-level assignments and revealed underrecognized lineages, emphasizing the value of genome-based approaches for accurate classification. Conclusions: Clinical Bacteroides isolates display diverse resistance and virulence profiles, highlighting the importance of strain-level genomic surveillance.