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PubMed2026

A standardized, genome-guided MLST scheme for Avibacterium paragallinarum: enhanced epidemiological typing and validation against existing methods.

Avibacterium paragallinarum, the causative agent of infectious coryza (IC), is an important respiratory pathogen of chickens with growing prevalence in commercial and backyard flocks. Current strain-typing methods, including classical serotyping and molecular approaches, such as ERIC-PCR or single-locus HPG2 typing, lack sufficient discriminatory power to investigate the epidemiology or population structure. To address this limitation, we developed a genome-guided multilocus sequence typing (MLST) scheme as a robust and portable tool for A. paragallinarum strain differentiation. Housekeeping genes were identified from 42 whole-genome sequences (WGS); 18 candidates were evaluated; and six were selected for the final MLST scheme. We used the scheme to differentiate 75 A. paragallinarum samples and compared its performance against classical HPG2-based typing, ad hoc core genome MLST (cgMLST), and the MLST scheme published by M. Guo, Y. Jin, H. Wang, X. Zhang, and Y. Wu (Vet Sci 11:208, 2024, https://doi.org/10.3390/vetsci11050208). The new MLST showed higher discriminatory power than HPG2 and outperformed Guo's scheme with higher discriminatory power, particularly for characterizing the samples originating from North and South America. It also showed strong concordance with cgMLST clustering while being more practical for routine use. Overall, the six-locus MLST identified 31 sequence types across 75 samples, revealing epidemiologically meaningful clustering at regional and national scales and capturing temporal persistence of lineages. All allele definitions and sequence types have been deposited in PubMLST, ensuring standardized nomenclature and global accessibility. This scheme represents a reproducible, cost-effective, and globally applicable tool that enhances outbreak investigation, surveillance, and population studies of A. paragallinarum, bridging the gap between low-resolution traditional methods and resource-intensive whole-genome sequencing.IMPORTANCEInfectious coryza (IC) caused by Avibacterium paragallinarum is a major respiratory disease of poultry that causes acute infection, reducing egg production and growth and resulting in significant economic losses in poultry production worldwide. Controlling IC depends on understanding how different strains spread and persist, yet current methods to differentiate strains are either unreliable or too costly for routine use. In this study, we developed a standardized multilocus sequence typing system that provides a simple, accurate, and globally accessible way to identify and compare strains of A. paragallinarum. This scheme identified important links between outbreaks at local and regional levels and showed that certain strains persisted over time. By making the scheme available through PubMLST, laboratories worldwide can use a common tool to track and investigate the pathogen. This accessible tool improves disease surveillance, supports outbreak investigations, and helps poultry producers and veterinarians respond more effectively to IC.

Multilocus Sequence Typing↗

PubMed2026

Core genome and whole genome multi-locus sequence typing of Cronobacter isolates.

UNLABELLED: Cronobacter species, especially C. sakazakii and C. malonaticus, are opportunistic pathogens that are linked to severe infections in infants with high case fatality rates. In this study, we investigated whole genome sequencing (WGS) analysis approaches, specifically 7-gene multi-locus sequence typing (7-gene MLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) to subtype Cronobacter isolates. We analyzed a comprehensive set of 743 Cronobacter isolates derived from clinical, food, and environmental sources. We also evaluated high-quality single nucleotide polymorphism (hqSNP), cgMLST, and wgMLST to cluster epidemiologically related and differentiate sporadic C. sakazakii isolates. Our results indicate that both cgMLST and wgMLST accurately identify closely related isolates and are consistent with epidemiological findings. The allele-based analyses were also comparable with hqSNP analyses, the current gold standard. Our workflow also outputs 7-gene MLST allele calls, Cronobacter sequence types, and clonal complexes, which may be useful for historic comparisons during outbreak investigations. Following the recent classification of Cronobacter infections as nationally notifiable in the United States, our findings demonstrate the efficacy of WGS-based approaches within the PulseNet framework to improve outbreak detection and response strategies for Cronobacter. IMPORTANCE: Cronobacter species, specifically C. sakazakii and C. malonaticus, are opportunistic pathogens linked to severe infections in infants with high case fatality rates. This study highlights the critical importance of advanced molecular techniques in public health surveillance, using whole genome sequencing (WGS) methodologies such as multi-locus sequence typing (7-gene MLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST). The validation of these WGS-based approaches within the PulseNet framework is timely, especially following the recent classification of Cronobacter infections as nationally notifiable in the United States. WGS methods not only enhance outbreak detection but can also inform public health guidance aimed at preventing infections and reducing mortality in vulnerable populations, especially infants. Our research supports implementation of cgMLST as a standardized approach for routine PulseNet surveillance of Cronobacter, with wgMLST and hqSNP analyses providing additional discriminatory power for outbreak investigations and high resolution phylogenetic analysis.

Multilocus Sequence Typing↗

PubMed2026

An analysis of Wolbachia incidence and genetics in non-ant Hymenoptera diversity.

Wolbachia bacteria are widespread maternally inherited symbionts of Nematoda and diverse Arthropoda hosts. Their evolutionary success is determined by the ability to affect the biology of the host in different ways, promoting the relative fitness of females harbouring Wolbachia, as well as sporadic cases of horizontal transmission of Wolbachia between different host species. Here, we revised Wolbachia infection in the Hymenoptera with respect to the symbiont occurrence in host taxa and Wolbachia genetics. The representatives of about half of the extant families and 1000 out of 140,000 non-ant hymenopteran species have been tested for Wolbachia infection. We concluded that Wolbachia are found in all major hymenopteran families. More than 75% of Wolbachia diversity belongs to the A supergroup, whereas other variants belong to the B supergroup and only two isolates belong to the supergroup F. One of the main results of this study is the discovery of a specific Wolbachia genetic pattern (based on multilocus sequence typing [MLST]) in Apoidea hosts. Two haplotypes, ST-479 and ST-wH14, along with their alleles within other sequence types (STs), form the core of symbiont diversity, comprising 81% of unique host-Wolbachia ST associations. These haplotypes have not been reported beyond the Apoidea superfamily or Hymenoptera order. The reasons and mechanisms underlying this pattern in Apoidea remain unknown. Another important result of our study concerns the use of the MLST protocol, which has been previously criticised. We analysed 51 Wolbachia genomes for the average nucleotide identity (ANI) and MLST data, and found that genome and MLST variation are highly correlated. Therefore, the MLST protocol for Wolbachia remains reliable for many research tasks.

Animals↗

PubMed2026

A new highly discriminatory typing scheme for Treponema pallidum reveals similar levels of genetic variability across lineages.

UNLABELLED: The global resurgence of treponematoses, particularly syphilis, poses a growing public health challenge. Despite advances in sequencing technologies, obtaining complete Treponema pallidum genome sequences for epidemiological studies remains challenging due to clinical sampling and methodological constraints. There is, therefore, a need for rapid, cost-effective, and accessible typing methods. Based on the analysis of 121 T. pallidum genomes spanning all three subspecies (TPA, TPE, and TEN) from diverse regions, we selected seven highly variable genes (tp0136, tp0326, tp0548, tp0705, tp0858, tp0865, and tp1031) to form a new typing system, combined with analysis of macrolide resistance mutations in the 23S rRNA gene. The scheme was validated on 542 global T. pallidum samples, using either Sanger reads or whole genome sequence data, obtaining 82 sequence types (STs) among the 415 fully typed samples. Macrolide resistance mutations were frequently detected, highlighting the need for ongoing epidemiological surveillance. Phylogenetic analyses based on concatenated multilocus typing (MLST) loci recovered the expected subspecies and lineage structure. Consistently, almost all sequence types formed monophyletic groups, indicating strong concordance between MLST-based classification and whole-genome phylogenies. In addition, population genetic analyses revealed comparable levels of within-lineage diversity across subspecies and lineages, despite pronounced differences in geographic distribution, and identified distinct regional genetic clusters consistent with localized transmission dynamics. Importantly, the scheme employs a single-step PCR for all seven targets, facilitating implementation in standard laboratories and is publicly accessible through PubMLST. Overall, our novel MLST scheme offers a rapid, cost-effective tool to advance molecular epidemiology of T. pallidum, facilitate transmission and resistance tracking, and support global surveillance to strengthen public health interventions for syphilis and endemic treponematoses control. IMPORTANCE: We have developed a new multilocus typing (MLST) scheme useful for all Treponema pallidum lineages after the analysis of 121 complete genome sequences of this species. The new scheme can be used directly with uncultured clinical samples, thus providing an excellent contribution to the molecular surveillance of syphilis and other treponematoses. The application of this MLST scheme to over 500 samples from all lineages and main geographical regions has revealed similar levels of genetic variation within them. Furthermore, the analyses show a complex pattern of spread, with global and local contributions to the observed distribution of genetic variation in the syphilis-producing sublineages. The new scheme represents a significant improvement over previous proposals and also reveals unsuspected levels of variability in T. pallidum lineages.

Treponema pallidum↗

PubMed2026

Potential dissemination and persistence of Clostridium perfringens along the slaughtering process in French cattle, pig or poultry slaughterhouses.

Clostridium perfringens is a major foodborne pathogen associated with meat products, yet its dissemination routes and persistence within slaughterhouses remain poorly understood. In this study, whole-genome sequencing combined with multilocus sequence typing (MLST), core genome MLST (cgMLST), and core single nucleotide polymorphism (SNP) analysis was applied to 286 C. perfringens isolates collected from cattle, pig, and poultry slaughterhouses in France. MLST analysis revealed extensive genetic diversity, with most isolates assigned to novel allelic profiles rather than previously described sequence types. Phylogenetic analyses based on cgMLST and SNP data revealed frequent recovery of closely related isolates from feces, meat, surfaces, and air, highlighting widespread dissemination of strains within slaughterhouses during processing. Notably, close genetic related isolates recovered from air and other sample types are consistent with air-associated dissemination within slaughterhouse environments. In addition, the detection of closely related strains across different sampling campaigns suggests the potential persistence of C. perfringens within slaughterhouse environments over time. Most isolates were classified as toxinotype A (97.9%), with a few belonging to toxinotypes D (1.0%) and G (1.0%), and in silico analyses revealed a broad distribution of virulence-associated genes. Antimicrobial resistance genes (ARGs) were commonly detected, particularly those conferring resistance to tetracyclines, although isolates carrying multiple ARGs remained infrequent. Overall, this study provides new insights into the genomic diversity, dissemination pathways, and persistence of C. perfringens in multi-species slaughterhouses. These findings highlight the potential role of air-associated dissemination in contamination dynamics and underscore the importance of improved hygiene control strategies to mitigate food safety risks along the meat production chain.

Antimicrobial resistance gene (ARG)↗

PubMed2003

How clonal is Staphylococcus aureus?

Staphylococcus aureus is an important human pathogen and represents a growing public health burden owing to the emergence and spread of antibiotic-resistant clones, particularly within the hospital environment. Despite this, basic questions about the evolution and population biology of the species, particularly with regard to the extent and impact of homologous recombination, remain unanswered. We address these issues through an analysis of sequence data obtained from the characterization by multilocus sequence typing (MLST) of 334 isolates of S. aureus, recovered from a well-defined population, over a limited time span. We find no significant differences in the distribution of multilocus genotypes between strains isolated from carriers and those from patients with invasive disease; there is, therefore, no evidence from MLST data, which index variation within the stable "core" genome, for the existence of hypervirulent clones of this pathogen. Examination of the sequence changes at MLST loci during clonal diversification shows that point mutations give rise to new alleles at least 15-fold more frequently than does recombination. This contrasts with the naturally transformable species Neisseria meningitidis and Streptococcus pneumoniae, in which alleles change between 5- and 10-fold more frequently by recombination than by mutation. However, phylogenetic analysis suggests that homologous recombination does contribute toward the evolution of this species over the long term. Finally, we note a striking excess of nonsynonymous substitutions in comparisons between isolates belonging to the same clonal complex compared to isolates belonging to different clonal complexes, suggesting that the removal of deleterious mutations by purifying selection may be relatively slow.

Alleles↗

PubMed2024

Rapid inference of antibiotic susceptibility phenotype of uropathogens using metagenomic sequencing with neighbor typing.

UNLABELLED: Timely diagnostic tools are needed to improve antibiotic treatment. Pairing metagenomic sequencing with genomic neighbor typing algorithms may support rapid clinically actionable results. We created resistance-associated sequence elements (RASE) databases for Escherichia coli and Klebsiella spp. and used them to predict antibiotic susceptibility in directly sequenced (Oxford Nanopore) urine specimens from critically ill patients. RASE analysis was performed on pathogen-specific reads from metagenomic sequencing. We evaluated the ability to predict (i) multi-locus sequence type (MLST) and (ii) susceptibility profiles. We used neighbor typing to predict MLST and susceptibility phenotype of E. coli (64/80) and Klebsiella spp. (16/80) from urine samples. When optimized by lineage score, MLST predictions were concordant for 73% of samples. Similarly, a RASE-susceptible prediction for a given isolate was associated with a specificity and a positive likelihood ratio (LR+) for susceptibility of 0.65 (95% CI, 0.54-0.76) and 2.26 (95% CI, 1.75-2.92), respectively, with an increase in the probability of susceptibility of 10%. A RASE-non-susceptible prediction was associated with a sensitivity and a negative likelihood ratio (LR-) for susceptibility of 0.79 (95% CI, 0.74-0.84) and 0.32 (95% CI, 0.24-0.43) respectively, with a decrease in the probability of susceptibility of 20%. Numerous antibiotic classes could reasonably be reconsidered empiric therapy by shifting empiric probabilities of susceptibility across relevant treatment thresholds. Moreover, these predictions can be available within 6 h. Metagenomic sequencing of urine specimens with neighbor typing provides rapid and informative predictions of lineage and antibiotic susceptibility with the potential to impact clinical decision-making. IMPORTANCE: Urinary tract infections (UTIs) are a common diagnosis in hospitals and are often treated empirically with broad-spectrum antibiotics. These broad-spectrum agents can select for resistance in these bacteria and co-colonizing organisms. The use of narrow-spectrum agents is desirable as an antibiotic stewardship measure; however, it is counterbalanced by the need for adequate therapy. Identification of causative organisms and their antibiotic susceptibility can help direct treatment; however, conventional testing requires days to produce actionable results. Methods to quickly and accurately predict susceptibility phenotypes for pathogens causing UTI could thus improve both patient outcomes and antibiotic stewardship. Here, expanding on previous work showing accurate prediction for certain Gram-positive pathogens, we demonstrate how the use of RASE from metagenomic sequencing can provide informative and rapid phenotype prediction results for common Gram-negative pathogens in UTI, highlighting the future potential of this method to be used in clinical settings to guide empiric antibiotic selection.

Humans↗

PubMed2026

Whole-Genome Analysis Reveals Antimicrobial Resistance and Population Structure of Environmental and Veterinary Acinetobacter baumannii.

Acinetobacter (A.) baumannii is an important multidrug-resistant pathogen increasingly recognized across animal and environmental settings, and carbapenem-resistant A. baumannii (CRAB) is classified as a critical-priority pathogen by the World Health Organization. This study investigated the antimicrobial resistance (AMR) and genomic characteristics of 122 A. baumannii isolates comprising 72 veterinary and 50 environmental isolates collected in Andhra Pradesh, India. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), resistance and virulence gene profiling, multilocus sequence typing (MLST), core-genome analysis, single nucleotide polymorphism (SNP) phylogeny, and pan-genome analysis were performed. Overall, 58.2% of isolates were multidrug-resistant (MDR), and 41.8% were extensively drug-resistant (XDR). Sequence type (ST) 52 predominated among veterinary isolates, whereas ST2 was more frequent among environmental isolates. The presence of carbapenem-resistant isolates along with the ST2 lineage enhances the similarity to clinical A. baumannii. Several intrinsic resistance genes, including blaOXA-23, armA, aph(3″)-Ib, aph(6)-Id, tet(B), mph(E), and msr(E), were more prevalent in the ST2-associated population. Virulence-associated determinants were widely conserved. Core-genome MLST (cgMLST) and core-genome SNP (cgSNP) analyses identified highly related isolates within both lineages, while pairwise SNP differences were 0-7. Pan-genome analysis identified 4204 gene clusters and distinct accessory gene patterns between ST2 and ST52. These findings indicate that resistance gene distribution was closely associated with lineage structure and support integrated genomic surveillance of A. baumannii across animal and environmental reservoirs.

Acinetobacter baumannii↗

PubMed2026

Mycoplasma and Bartonella in cats from the tropical tourist Gili Islands, Indonesia.

Bartonella spp. and haemotropic Mycoplasma spp. are important vector-borne bacteria of veterinary and zoonotic relevance, yet information on their circulation in Indonesian island ecosystems remains limited. We investigated their occurrence and molecular diversity in 117 domestic and free-roaming cats from the Gili Islands, Indonesia, using full-length 16S rRNA nanopore metagenomics followed by targeted PCR, sequencing, phylogenetic analysis and multilocus sequence typing (MLST). Bartonella DNA was detected in 18/117 (15.4%) cats and haemotropic Mycoplasma DNA in 40/117 (34.2%). Sequence analysis identified Bartonella henselae as the predominant species together with Bartonella clarridgeiae. MLST of B. henselae revealed three sequence types (ST1, ST16 and ST42), with ST1, a lineage reported in both feline and human isolates, predominating. Comparison with the PubMLST database showed significant geographical differences in the distribution of ST1 and ST42, supporting regional variation in the circulation of B. henselae lineages. Haemoplasma characterization identified Candidatus Mycoplasma haemominutum, Mycoplasma haemofelis, Candidatus Mycoplasma turicensis and a Mycoplasma feliminutum-like organism, comprising ten distinct sequence variants. Haemoplasma positivity was significantly associated with age, with adults showing higher positivity than younger animals (P < 0.001), whereas Bartonella infection was not associated with age, sex or island of origin. The detection of zoonotically relevant B. henselae lineages and the genetic diversity of feline haemoplasmas provide evidence of the circulation of vector-borne bacteria among cats in this tropical island ecosystem. These findings provide the first molecular epidemiological baseline for this region and contribute to understanding the circulation and genetic diversity of feline vector-borne pathogens in Southeast Asia.

Animals↗

PubMed2025

New Delhi metallo-β-lactamase-producing Acinetobacter baumannii in the USA from October, 2013, to March, 2022: a retrospective molecular epidemiological analysis.

BACKGROUND: Most US carbapenem-resistant Acinetobacter baumannii (CRAB) isolates harbour carbapenem-hydrolysing class D β-lactamases. Other carbapenemases, such as New Delhi metallo-β-lactamase (NDM), are uncommon but emerging. We describe the epidemiology of NDM-producing CRAB reported to the US Centers for Disease Control and Prevention (CDC). METHODS: We defined cases as A baumannii with blaNDM confirmed by molecular testing and isolated from any specimen source from a patient in the USA between Oct 1, 2013, and March 31, 2022, and passively reported to the CDC from regional, state, local public health, and CDC laboratories. Epidemiologically linked cases had epidemiological linkage (eg, overlapping health-care facility stay) with one or more other cases. We assessed case relatedness through analysis of whole-genome sequence data using traditional multilocus sequence typing (MLST; Oxford scheme [sequence typeOX]) and core genome MLST. To understand the potential origins of NDM-CRAB in the USA, we compared sequences of cases to US CRAB without NDM and to NDM-CRAB from non-US locations. FINDINGS: We identified 327 NDM-CRAB cases from 264 patients in 21 US states. Among patients with available epidemiological information, 192 (90%) of 214 had epidemiological linkage to at least one additional case and 13 (7%) of 193 were hospitalised outside the USA 12 months or less before index specimen collection. Five regionally distinct sequence type clusters were identified among the 264 case patients; three (sequence type OX218, sequence type OX281, and sequence type OX1697) were closely related to international NDM-CRAB isolates. INTERPRETATION: We identified regionally distinct NDM-CRAB strains, suggesting localised transmission in the USA. Some NDM-CRAB strains in the USA are closely related to strains identified outside the USA, suggesting that spread followed importation. FUNDING: None.

Acinetobacter baumannii↗

PubMed2026

Screening Equine Skin and Mucous Membranes for Carriage of Coagulase-Positive Staphylococci.

BACKGROUND: Commensal populations of coagulase-positive Staphylococcus spp. (CoPS) in healthy horses are not well-defined. OBJECTIVE: To determine the point prevalence, anatomical distribution, antimicrobial susceptibility and genomic characteristics of CoPS in healthy horses. ANIMALS: One-hundred and fifty privately owned, systemically healthy horses from seven facilities were enrolled in this study. MATERIALS AND METHODS: Horses were sampled from the nares, buccal mucosa and three skin sites. Isolates were identified using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry, and antimicrobial susceptibility testing was performed by gradient diffusion. Whole-genome sequencing with multilocus sequence typing (MLST) characterised Staphylococcus aureus lineages. In silico PCR differentiated Group A and Group B Staphylococcus delphini. Sampling site sensitivity was calculated using a multisite composite reference. Mixed-effects logistic regression evaluated associations between demographic factors and carriage. RESULTS: Carriage of any staphylococcal species occurred in 111 of 150 (74%) horses: S. aureus 28 of 150 horses (18.7%) and S. delphini 23 of 150 horses (15.3%). Increasing age was associated with decreased odds of CoPS isolation (odds ratio 0.92/year; 95% confidence interval 0.86-0.98). The nares were the most sensitive single sampling site, whereas multisite sampling improved detection. Meticillin-resistance was absent in all CoPS isolates, and S. delphini isolates were fully susceptible to all antimicrobials tested. MLST revealed multiple S. aureus sequence types, some of which were shared across multiple horses at some boarding facilities. Both groups of S. delphini lineage were identified, although many isolates were nontypable. CONCLUSIONS AND CLINICAL RELEVANCE: Healthy horses harbour S. aureus and S. delphini, with minimal antimicrobial resistance. Shared S. aureus sequence types within facilities suggest possible lateral transmission.

Animals↗

PubMed2005

Population structure and properties of Candida albicans, as determined by multilocus sequence typing.

We submitted a panel of 416 isolates of Candida albicans from separate sources to multilocus sequence typing (MLST). The data generated determined a population structure in which four major clades of closely related isolates were delineated, together with eight minor clades comprising five or more isolates. By Fisher's exact test, a statistically significant association was found between particular clades and the anatomical source, geographical source, ABC genotype, decade of isolation, and homozygosity versus heterozygosity at the mating type-like locus (MTL) of the isolates in the clade. However, these associations may have been influenced by confounding variables, since in a univariate analysis of variance, only the clade associations with ABC type and anatomical source emerged as statistically significant, providing the first indication of possible differences between C. albicans strain type clades and their propensity to infect or colonize different anatomical locations. There were no significant differences between clades with respect to distributions of isolates resistant to fluconazole, itraconazole, or flucytosine. However, the majority of flucytosine-resistant isolates belonged to clade 1, and these isolates, but not flucytosine-resistant isolates in other clades, bore a unique mutation in the FUR1 gene that probably accounts for their resistance. A significantly higher proportion of isolates resistant to fluconazole, itraconazole, and flucytosine were homozygous at the MTL, suggesting that antifungal pressure may trigger a common mechanism that leads both to resistance and to MTL homozygosity. The utility of MLST for determining clade assignments of clinical isolates will form the basis for strain selection for future research into C. albicans virulence.

Analysis of Variance↗

PubMed2025

Comparative genomics of carbapenem-resistant Acinetobacter baumannii isolated from pediatric patients in a tertiary care hospital.

Acinetobacter baumannii is a short gram-negative bacillus, notable for its intrinsic multidrug resistance and genomic plasticity, which facilitates the acquisition of additional resistance genes via mobile genetic elements. Due to its increasing carbapenem resistance, the World Health Organization has classified it as a critical priority pathogen. This study performed a comparative genomic analysis of 20 carbapenem-resistant A. baumannii clinical strains isolated from the Hospital Infantil de México Federico Gómez (CRAB-HIMFG), alongside 11 genomes from other Mexican strains. The pangenome was determined to be open, and core genome single-nucleotide polymorphism-based analysis grouped the CRAB-HIMFG strains within CC758/IC5 and CC92/IC2. A novel sequence type (ST) in the MLST-Pasteur scheme was identified, related to STPas156, and in the MLST-Oxford scheme, associated with STOxf758 and STOxf1054. Virulence and resistance genes comprised 0.61% to 2.23% of the pangenome. Oxacillinase genes and efflux pumps primarily mediated carbapenem resistance, while virulence genes included those encoding biofilm and type IV pili. Capsule typing revealed a correlation with established international clones, IC2 and IC5. Plasmids exhibited high diversity, harboring maintenance modules and toxin-antitoxin systems, with the dissemination of resistance genes linked to insertion sequences. Biofilm formation and twitching motility were not always expressed, as they depend on additional environmental factors. Our study shows that comparative genomics is an essential tool to analyze clinically and epidemiologically significant genomes, providing critical insights into gene distribution, genomic architecture, and horizontal gene transfer mechanisms in microbial populations.IMPORTANCEIn recent years, a reported increase in the mortality rate associated with infections caused by A. baumannii, along with a rise in carbapenem resistance, poses a serious clinical challenge. The WHO considered this microorganism critical for research into alternative therapies and epidemiological surveillance. Despite advances in bioinformatics, genomic studies have yet to fully elucidate the structural rearrangements and secretion systems of A. baumannii. This knowledge gap hinders our understanding of its remarkable genomic plasticity and its ability to acquire and spread resistance and virulence genes through horizontal gene transfer.

Acinetobacter baumannii↗

PubMed2026

Genomic and virulence characteristics of Staphylococcus aureus isolates from foodborne outbreak cases.

This study aimed to investigate the genomic characteristics, enterotoxin production, and antimicrobial resistance profiles of Staphylococcus aureus isolates associated with foodborne outbreaks. A total of 19 bacterial isolates were collected from foodborne outbreaks in Guizhou Province, China between 2014 and 2023. Following biochemical identification, all isolates were confirmed as S. aureus. Phylogenetic analysis divided the 19 strains into seven branches. Enterotoxin production was detected using standard microbiological techniques and immunoassays. Antimicrobial susceptibility was evaluated using the broth microdilution method. Whole-genome sequencing and subsequent bioinformatic analyses were conducted to characterize virulence genes, antimicrobial resistance genes, multilocus sequence typing (MLST) genotypes, and phylogenetic relationships among the isolates. This study found that all strains produced classical staphylococcal enterotoxins, with staphylococcal enterotoxin (SEA) showing the highest detection rate (63.16%). Virulence gene profiling revealed widespread presence of hlb, hlgA, nuc, clfB, spa, and set genes. All strains were resistant to penicillin, with high resistance rates for erythromycin and cefoxitin. Multidrug resistance occurred in 11 of the 19 strains, and 22 resistance genes were identified. MLST analysis showed that ST6 and ST59 were the dominant types, with ST59 methicillin-resistant S. aureus (MRSA) strains displaying stronger resistance and more virulence determinants. These findings provide insights into the virulence, resistance, and molecular epidemiology of S. aureus strains involved in foodborne outbreaks, and may provide useful information for future surveillance and risk assessment.

Staphylococcus aureus↗

PubMed2026

Correlation assessment of SARS-CoV-2 variants and their subvariants present in clinical and wastewater samples in Oregon, USA (February 7, 2021 - February 26, 2022) using the Freyja bioinformatics approach.

BACKGROUND: Wastewater surveillance is a valuable tool for monitoring SARS-CoV-2 at the community level. As the virus diversified into many variants and subvariants that share overlapping mutations, resolving them accurately from wastewater becomes a key bioinformatic challenge. OBJECTIVES AND AIMS: This study evaluated two distinct bioinformatic approaches, multilocus sequence typing (MLST) and Freyja, for identifying SARS-CoV-2 variants and subvariants in Oregon wastewater samples collected from February 2021 to February 2022. METHODS: The MLST approach identified SARS-CoV-2 variants using unique mutations curated from clinical samples. In contrast, the Freyja approach resolved variant and subvariant abundances using genome wide mutation profiles weighted by sequencing depth. In this study, the variant and subvariants relative abundances produced by both approaches were compared against those observed in clinical surveillance data. RESULTS: Both approaches identified SARS-CoV-2 variants at relative abundances that agreed closely with those observed in clinical surveillance data. However, only the Freyja approach identified over 200 Delta subvariants, divided into three clades (21A, 21I and 21J) and two levels (Level 1 and 2) based on Pango subvariants. Delta subvariants showed strong agreement at Level 1 subvariants (rs = 0.892-0.944), while agreement at Level 2 subvariants was inconsistent (rs = 0.324-0.903). CONCLUSIONS: The Freyja approach provided enhanced resolution of SARS-CoV-2 variants and subvariants in wastewater, at abundances that agreed with clinical surveillance. This added resolution is a critical advantage for public health surveillance as SARS-CoV-2 continues to evolve and share mutations across variants and subvariants.

Oregon↗

PubMed2026

Genomic insights into Aeromonas infections in diarrheal patients: high diversity, emerging resistance, and potential outbreak in Beijing.

BACKGROUND: Aeromonas species are ubiquitous aquatic bacteria that have emerged as significant foodborne enteric pathogens worldwide, yet their genomic landscape in clinical settings remains poorly delineated, particularly in Beijing. METHODS: To address this gap, we performed active surveillance for Aeromonas among 691 consecutive diarrheal outpatients in a Beijing district from January to December 2024. Isolates were recovered using enrichment culture coupled with PCR screening and identified by MALDI-TOF MS. Antimicrobial susceptibility was tested against 17 agents. Whole-genome sequencing was conducted on all isolates, enabling average nucleotide identity (ANI) analysis, comprehensive annotation of antimicrobial resistance and virulence genes, multilocus sequence typing (MLST), and core-genome SNP (cgSNP)-based phylogenetics. RESULTS: Aeromonas was detected in 3.3% (23/691) of patients, with Aeromonas veronii (56.52%, 13/23) and Aeromonas caviae (26.09%, 6/23) predominating. Co-infections with other enteric pathogens occurred in 65.2% of positive cases. Resistance rates were notably high for ampicillin/ampicillin-sulbactam (78.26%), nalidixic acid (56.52%), and ertapenem (21.73%), and 65.21% of isolates were multidrug-resistant. Genotypic-phenotypic concordance was robust, with β-lactamase genes ampS (60.87%) and blaCEPH-A3 (47.83%) being most prevalent. Strikingly, mcr-3.25 and mcr-3.3, which belong to the mcr family (originally described as mobile colistin resistance genes), were identified in 8.70% of isolates, exhibiting perfect correlation with phenotypic resistance. Plasmer analysis suggested both mcr genes to be chromosomally encoded. Comparative genomic analysis of virulence-associated genes revealed striking species-specific specialization: A. veronii predominantly carried complete T3SS clusters (61.5%), A. caviae and Aeromonas enteropelogenes were enriched in T6SS genes, and a single A. dhakensis isolate possessed an extensive arsenal including T3SS, T6SS, and a full RTX toxin cluster. MLST resolved the 23 isolates into 22 sequence types, 18 of which were novel. Phylogenetic reconstruction identified a tight monophyletic cluster of three A. veronii isolates (9-27 SNP differences) recovered within a 96-h window, suggestive of a potential cluster that warrants further epidemiological investigation. Comparative genomic analysis of the rare species Aeromonas allosaccharophila demonstrated that the Beijing clinical isolate S14 differs from the U.S. clinical strain ATCC 35942 by 42,099 SNPs, confirming its distinct genetic lineage. CONCLUSION: Collectively, this study delineates high genetic diversity, emerging chromosomal colistin resistance, and species-specific virulence specialization among Aeromonas isolates from diarrheal patients in Beijing. The detection of a potential outbreak cluster and a rare clinical isolate underscores the power of genomics-based surveillance for detecting and mitigating foodborne pathogen threats.

Aeromonas↗

PubMed2026

Genomic Characterization of Aeromonas dhakensis Isolated From a Fatal Dolphin Case.

Aeromonas dhakensis has emerged as a significant pathogen affecting both aquatic animals and humans; however, genomic data for isolates from marine mammals remain scarce. In this study, we characterised the genome of A. dhakensis strain KDL-001, isolated from a fatal dolphin case, using whole-genome sequencing and comparative genomics. Taxonomic analyses, including MLST and average nucleotide identity (ANI), confirmed the isolate as A. dhakensis. Core-genome phylogeny further revealed that KDL-001 is closely related to strains derived from fish and aquatic environments. Notably, in silico screening of virulence-associated genes showed that the virulence-associated gene profile of the dolphin isolate was broadly comparable to those of other A. dhakensis strains, with no isolate-specific virulence-associated genes being identified within the limits of this analysis. These findings demonstrate that the dolphin-derived isolate is genomically comparable to previously described A. dhakensis strains and possesses conserved virulence-associated genes commonly found within the species.

Animals↗

PubMed2026

Comparative Genomic Analysis of Multidrug-Resistant Escherichia coli Across Poultry-Human-Environmental Interfaces.

The emergence of multidrug-resistant (MDR) Escherichia coli in poultry represents a critical One Health concern, particularly in developing countries. This study employed a comparative genomic approach to investigate the genomic characteristics, antimicrobial resistance (AMR) profiles, virulence determinants, of poultry-derived MDR E. coli isolates from Bangladesh. Whole-genome sequencing of three representative MDR isolates, identified with 83 globally diverse poultry, human, and environmental E. coli genomes. Pangenome analysis identified the characteristic open pangenome of E. coli, with core genes comprising only 4.6% of the combined dataset. Resistome analysis shown diverse AMR determinants, including blaCTX-M, blaTEM, sul, tet, and qnrS1, associated with antibiotic inactivation and efflux mechanisms. Virulence profiling revealed diverse genes involved in adhesion (fim, csg), iron acquisition (ent, fep, chu), motility, and secretion systems, with core virulence genes exhibiting > 90% sequence identity, whereas accessory virulence genes were more variable. Plasmid analysis demonstrated heterogeneous replicon types, predominantly IncF and Col plasmids, indicating their role in horizontal gene transfer. Jaccard similarity indices revealed moderate to high genetic overlap with global strains (~0.63 for virulence genes and ~0.55 for AMR profiles), suggesting shared evolutionary backgrounds. Phylogenomic and MLST identified all Bangladeshi isolates as ST457, clustering within a globally distributed clonal complex linked to ST10 and ST131 lineages. These findings suggest that the three Bangladeshi poultry-derived E. coli isolates are genetically related to globally circulating strains while harboring extensive resistance and virulence determinants, emphasizing poultry as an important reservoir of MDR pathogens and reinforcing the need for strengthened antimicrobial stewardship and genomic surveillance.

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