Aug 2026· Computational biology and chemistry· Vol 125, pp.
109359
· 0 citations· 37 references
Medicine
TL;DR
Accessory genome expansion was associated with higher AMR burden in several species, whereas other species showed no significant association between accessory genome size and AMR burden and no significant enrichment of AMR genes in either genome compartment, highlighting the species-specific nature of AMR evolution.
Abstract
Background
ESKAPE pathogens are major causes of hospital-acquired infections and are characterized by extensive antimicrobial resistance (AMR) and diverse virulence mechanisms. Although species-specific pan-genome studies have revealed substantial genomic diversity, the relationships among genome plasticity, resistance burden, and virulence remain incompletely understood across the ESKAPE complex.
Methods
We analyzed 120 high-quality genomes representing six single-species ESKAPE groups (20 genomes per species). Genome quality was assessed using CheckM2. Species-specific pan-genomes were constructed with Roary, AMR genes were identified using AMRFinderPlus, and virulence factors were detected against the VFDB database using DIAMOND. AMR genes were mapped to core and accessory genome compartments through integration of Prokka annotations and Roary outputs. Statistical associations were evaluated using Fisher's exact tests and correlation analyses, with false discovery rate correction applied within each test family. Core-genome maximum-likelihood phylogenies were reconstructed to provide an evolutionary framework.
Results
Pan-genome sizes ranged from 4720 to 17,272 genes, with Enterobacter and Pseudomonas possessing the largest accessory genomes. Multidrug resistance (MDR; resistance to ≥3 antimicrobial classes) was detected in 93.3% of strains. After false discovery rate correction, AMR genes remained significantly enriched in the accessory genomes of Enterobacter, Enterococcus, Klebsiella, and Staphylococcus, whereas Acinetobacter and Pseudomonas did not show significant enrichment in either genome compartment. Within-species analyses identified significant positive associations between accessory genome size and AMR class burden in Staphylococcus, Enterococcus, and Enterobacter, whereas the moderate Pearson correlation observed in Pseudomonas was not significant after FDR correction. Virulence factor repertoires varied markedly among species, with Pseudomonas exhibiting the highest burden and Enterococcus the lowest.
Conclusions
ESKAPE pathogens display distinct patterns of resistance and virulence. Accessory genome expansion was associated with higher AMR burden in several species, whereas other species showed no significant association between accessory genome size and AMR burden and no significant enrichment of AMR genes in either genome compartment, highlighting the species-specific nature of AMR evolution.
Stenotrophomonas maltophilia
is an emerging opportunistic pathogen characterized by intrinsic multidrug resistance and broad ecological distribution. However, its genomic characteristics across publicly available clinical, environmental, and animal isolates remain incompletely defined.
This study aimed to characterize the taxonomic distribution, antimicrobial resistance genes (ARGs), virulence-associated genes (VAGs), sequence types (STs), predicted mobile genetic elements (MGEs), orthogroup-occupancy patterns, and core-genome sequence variation of publicly available
S. maltophilia
isolates.
A total of 3,343 high-quality
Stenotrophomonas
candidate genomes obtained from NCBI were subjected to average nucleotide identity (ANI)-based taxonomic verification using the NCBI Prokaryotic Genome Annotation Pipeline. Of these, 1,584 genomes unambiguously assigned to
S. maltophilia
were retained for genomic analyses. ARGs were identified using a custom BLASTN-based nucleotide screen validated against AMRFinderPlus, and VAGs, multi-locus sequence types (MLST), and predicted MGEs were characterized using complementary bioinformatic approaches. Source-stratified analyses used the 1,054 genomes with resolved isolation-source metadata. Pangenome composition and lineage-specific core-genome phylogenetic relationships were evaluated separately for 95 ST4 and 113 ST5 genomes.
S. maltophilia
represented 1,584 of the 3,343 candidate genomes (47.4%). Country-level metadata were resolved for 1,044 genomes, representing 35 countries, whereas 540 had missing or unresolved geographic information. Among the 1,054 source-resolved genomes, 856 (81.2%) were human-derived, 154 (14.6%) were environmental, and 44 (4.2%) were animal-derived. The custom ARG screen identified 12,215 loci representing 67 ARG designations, while 38 non-redundant VAGs were detected. The efflux-associated genes
emrA
,
emrB
,
emrC
, and
smeF
, together with the intrinsic β-lactamase gene
blaL1
, were widely distributed, whereas acquired carbapenemase genes were uncommon. Source-associated differences were limited to selected ARGs and VAGs rather than broad changes in ARG or VAG burden. Among 1,388 typeable genomes, 234 STs were identified, with ST5, ST4, ST31, ST162, and ST115 being the most frequently represented. A total of 1,140 predicted ARG–MGE co-localization events were identified; predicted plasmid-associated contigs represented the largest category of ARG–MGE co-localization events, accounting for 898 events (78.8%), although these computational assignments did not establish confirmed plasmid carriage or transferability. In the pangenome comparison, ST4 showed a larger rare-gene and strain-specific orthogroup component, whereas ST5 showed greater core-genome sequence separation according to retained variable-site counts and pairwise SNP-distance metrics. ST4 had higher proportions of strain-specific orthogroups (3.4% versus 1.3%) and unassigned genes (2.7% versus 0.8%), whereas the shell-plus-cloud proportions were similar between ST4 and ST5 (46.7% versus 46.2%). ST5 had a higher orthogroup-assignment rate (99.2% versus 97.3%) and a higher proportion of orthogroups meeting the ≥ 99% core threshold (52.4% versus 49.8%). Core-genome analyses showed a higher pre-recombination variable-site density in ST5 than in ST4 (4.54 versus 3.50 sites/kb), more retained variable sites after recombination filtering (3,269 versus 2,295), and a higher median pairwise SNP distance (127 versus 108 SNPs).
This analysis of publicly available
S. maltophilia
genomes identified widely distributed intrinsic resistance determinants, uncommon acquired carbapenemases, selected source-associated gene differences, and frequent computational co-localization of ARGs with sequences predicted to be plasmid-associated. ST4 contained a larger strain-specific and unassigned-gene component, whereas ST5 showed greater core-genome sequence separation according to variable-site density and pairwise SNP-distance metrics. These findings support continued genomic surveillance across clinical, environmental, and animal sources while emphasizing the need for epidemiologically representative sampling, complete genome assemblies, and experimental validation of predicted ARG mobility.
Rong-Zheng Sun, Yan-Dan Liu, Xiaoli Cao et al.· Frontiers in Microbiology· 0 citations
ABSTRACT Brucella melitensis has a highly conserved genome, but the distribution of core-genome, gene-content, virulence-associated, mobile-element-associated, and antimicrobial-resistance-relevant variation among available sub-Saharan African genomes has not been examined in an integrated regional analysis. We analyzed 51 curated B. melitensis genomes from human and animal hosts using core-genome phylogenomics, pangenome reconstruction, virulence profiling, mobile genetic element (MGE) analysis, and mutation-based screening of antimicrobial resistance (AMR)-associated loci. A phylogeny reconstructed from 6,060 shared SNP sites resolved a dominant ST12-associated lineage, together with ST7, ST8, ST42, and novel sequence type branches. Individual genomes differed from the reference by 1,677–2,579 SNPs. The pangenome comprised 3,457 gene families, including 3,049 persistent families, indicating strong genome conservation, and limited accessory expansion. Virulence profiling identified 66 VFDB-associated genes; 48 genomes carried all 66, and the remaining three retained more than 98% of the virulence repertoire. Conserved determinants included the VirB type IV secretion system, lipopolysaccharide biosynthesis, intracellular survival pathways, and stress-response functions. MGE-associated variation was restricted to a small number of regions dominated by transposases and insertion-sequence-associated proteins. A GspF-domain-containing secretion-associated locus was detected only in BM2, although no complete type II secretion system gene cluster was identified. Recurrent substitutions occurred in AMR-relevant chromosomal loci, including rpoB, gyrA, gyrB, parC, parE, folA, folP, bepCDEFG, and mprF, but none corresponded to validated resistance-conferring alleles. The available regional genomes therefore comprise multiple phylogenetic lineages within a strongly conserved gene and intracellular virulence framework, with diversity concentrated in core-genome SNPs and localized genomic regions. IMPORTANCE Brucella melitensis is a major zoonotic pathogen at the livestock-human interface, but genome-resolved evidence from sub-Saharan Africa remains limited. This study curates available regional genomes and shows that the population is dominated by a conserved intracellular virulence backbone, strong core-genome conservation, and focal genomic diversification rather than by extensive accessory-genome expansion. By integrating phylogenomics, pangenome analysis, virulence profiling, mobile-element characterization, and mutation screening of antimicrobial-resistance-associated loci, the work provides a regional framework for One Health genomic surveillance and identifies candidate loci requiring phenotype-linked validation. Brucella melitensis is a major zoonotic pathogen at the livestock-human interface, but genome-resolved evidence from sub-Saharan Africa remains limited. This study curates available regional genomes and shows that the population is dominated by a conserved intracellular virulence backbone, strong core-genome conservation, and focal genomic diversification rather than by extensive accessory-genome expansion. By integrating phylogenomics, pangenome analysis, virulence profiling, mobile-element characterization, and mutation screening of antimicrobial-resistance-associated loci, the work provides a regional framework for One Health genomic surveillance and identifies candidate loci requiring phenotype-linked validation.
Samweli Y. Bahati, E. Mwakalapa, H. Mung’ong’o et al.· Microbiology spectrum· 0 citations
Background Acinetobacter baumannii is a critical multidrug-resistant pathogen whose genomic landscape in Mexico has been reshaped by the COVID-19 pandemic. While global studies have highlighted distinctive sequence type distributions, systematic analyses in Mexico remain limited. Methods We analyzed 194 genomes, including 47 newly sequenced post-COVID isolates (MIQ), alongside 147 publicly available genomes (HPG). Whole-genome sequencing was combined with phylogenetic reconstruction, resistome and virulome profiling based on gene presence and absence, mobilome analysis, and biosynthetic gene cluster (BGC) characterization. Results Two major clades dominated by Oxford STs 758, 208, 417, and 369 were identified. Resistome profiling uncovered 128 distinct resistome profiles (combinations of genes) and 44 emerging antimicrobial resistance genes (ARGs), with an increased number of resistance genes in the strains obtained during the pandemic. Virulome analysis revealed enrichment of metabolic adaptation genes (argG, carA, ilvC) in MIQ strains. Mobilome profiling demonstrated enrichment of ISAbA1 and ISAbA3 elements, known to mobilize carbapenemase genes. Mobilome profiling demonstrated enrichment of ISAba1 and ISAba3 elements, including novel associations such as blaOXA-72 with ISAba27 and blaOXA-66 with ISAba1. BGC analysis showed conserved siderophores involved in virulence, alongside diversification of the secondary metabolite repertoires in MIQ genomes. Additional observations included geographic mixing of clades across Jalisco, Aguascalientes, and Mexico City and referral bias toward carbapenemase-positive isolates. Because post-COVID isolates were enriched for referred high-risk cases, resistance estimates likely reflect a worst-case hospital scenario rather than community prevalence. Conclusion The genomic landscape of A. baumannii in Mexico has diversified post-COVID, with evidence of inter-regional transmission, virulome expansion, mobilome-driven ARG dissemination, and metabolic adaptation. These findings underscore the urgent need for coordinated genomic surveillance, functional and clinical validation of adaptation signals, and regionally integrated infection control strategies to mitigate resistance trajectories.
Moisés A. Alejo, Miriam Sarahi Lozano Gamboa, Brian Muñoz Gomez et al.· Frontiers in Public Health· 0 citations
This study provides new insights into the pangenome of Magnaporthe oryzae and introduces a method for the identification of functionally important genes in fungal species.
Yi Wang, Qi Wu, Jin-bin Li et al.· Journal of Advanced Research· 0 citations
BACKGROUND
Antimicrobial resistance (AMR) in Helicobacter pylori is increasingly compromising eradication therapies worldwide. Despite growing concern, comprehensive global genomic analyses integrating resistance determinants, geographic distribution, and evolutionary patterns remain limited.
METHODS
A total of 6876 high-quality H. pylori genomes collected from 85 countries between 1900 and 2024 were analyzed. Resistance determinants were identified using AMRFinderPlus, followed by lineage profiling, geographic mapping, temporal trend analysis, and resistome characterization. The distribution of virulence-associated genes and resistance gene presence patterns was also evaluated.
RESULTS
Twenty-two AMR determinants were identified, predominantly chromosomal mutations. The most prevalent mutation was pbp1a S543R, associated with amoxicillin resistance, detected in 24.03% (1652/6876) of genomes across 63 countries since 1983. Fluoroquinolone resistance-associated gyrA N87K demonstrated a marked temporal increase, reaching approximately 50% prevalence by 2023. Additional gyrA and pbp1a variants were widely distributed globally. Acquired resistance genes, including blaTEM,aph(3')-IIIa, and catA1, were rare and primarily confined to sequence type 181. Among 2877 resistant isolates, 103 distinct resistance profiles were observed, with single-mutation patterns predominating. Geographic analysis revealed pbp1a S543R prevalence exceeding 40% in multiple Asian and African countries, while gyrA N87K exceeded 30% in parts of Asia and South America. The resistome exhibited an open structure, whereas 134 virulence-associated genes remained highly conserved.
CONCLUSIONS
This large-scale global genomic study demonstrates the extensive dissemination and ongoing evolution of AMR in H. pylori, particularly against amoxicillin and fluoroquinolones. The findings indicate that empirical treatment strategies based on these agents are becoming increasingly unsustainable worldwide. Implementation of susceptibility-guided therapy, rapid molecular diagnostics, and international genomic surveillance programs is urgently required to preserve eradication efficacy and limit further resistance expansion.
L. B. Alhusseini, Ali R. Laftah, F. N. Jaafar et al.· Infection, Genetics and Evol...· 0 citations
It is demonstrated that homologous recombination, genome plasticity, and lineage-specific diversification are major drivers of adaptation, ecological fitness, and pathogenic evolution in this emerging phytopathogen P. jejuense across diverse hosts and geographic regions.
Dario Arizala, S. Dobhal, Gamze Boluk et al.· bioRxiv· 0 citations
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