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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)↗

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

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↗

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↗

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

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

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↗

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

Whole genome analysis of a multidrug-resistant blaNDM-5-carrying Escherichia coli Sequence Type (ST) 167 strain isolated from seafood in Mumbai, India.

BACKGROUND: E. coli ST167 is an emerging extraintestinal pathogenic Escherichia coli (ExPEC) clone. This study reports the whole genome sequence analysis of a multidrug-resistant, blaNDM-5 harboring E. coli ST167 (EC121) isolated from seafood. The antibiotic susceptibility pattern was determined using the standard disc diffusion method. Genomic DNA was extracted, purified, and sequenced using the Illumina platform. The whole genome sequence was analyzed to determine the genome characteristics, including sequence type, serotype, phylogroup, antibiotic resistance genes, virulence attributes, and phylogenetic analysis. RESULTS: Phenotypically, this isolate was resistant to 26 of the 33 antibiotics tested, which correlated well with in-silico prediction. Multilocus sequence typing (MLST) analysis revealed that this strain belonged to sequence type 167, serotype O101:H9, and phylogroup A and harbored different virulence genes, suggesting it was a potential human pathogen. Many acquired antibiotic resistance genes were detected, including blaNDM-5, blaCMY-42, blaOXA-1, blaTEM-116, catA1, sul2, and tet(B). Point mutations in gyrA and parC responsible for quinolone resistance were also detected. CONCLUSION: The combinations of virulence and antibiotic resistance genes in this strain highlight the significant risk associated with emerging E. coli clonal types contaminating the seafood supply chain. Fecal contamination of seafood can contribute to the community dissemination of multidrug-resistant E. coli, necessitating effective monitoring measures.

Seafood↗

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

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

Isolation and Molecular Characterization of Three Staphylococcus pseudintermedius Strains from Dogs and Humans in Egypt.

Staphylococcus pseudintermedius is an opportunistic pathogen that is largely associated with canine hosts but is becoming more widely recognized as a zoonotic pathogen. Understanding its genetic and phenotypic properties, such as virulence factors and antimicrobial resistance (AMR) profiles, is critical for infection control and vaccine development. In this study, we isolated and molecularly characterized three S. pseudintermedius isolates from dogs (hereafter referred to as S. pseudintermedius D8) and humans (hereafter referred to as S. pseudintermedius H10 and S. pseudintermedius H11) in Egypt. All three isolates showed 100% sequence identity with the nuc gene of the S. pseudintermedius SP_11304-3A reference genome. Multilocus sequence typing (MLST) revealed novel sequence types (STs) in the three isolates. The AMR determinants varied substantially among the isolates. While the mecA gene was absent, blaZ was detected in the canine isolate, indicating beta-lactamase-mediated penicillin resistance. Additionally, tetK and tetM genes were found conferring tetracycline resistance in different isolates. Resistance genes for aminoglycosides, chloramphenicol, fusidic acid, macrolides, streptothricin, and trimethoprim were also identified. All isolates were positive for key virulence genes, including immune evasion (AdsA), coagulase (coa), immunoglobulin-binding protein (sbi/spsK), exfoliative toxin (speta), enterotoxins (se-int and siet), fibrinogen binding protein gene (fnbB), and two-component pore-forming leukocidin genes (lukF and lukS). The S. pseudintermedius H11 isolate uniquely harbored the neuraminidase gene (nanB), while none of the isolates contained the gene coding for immunoglobulin G binding protein (spsQ). These findings highlight the differences in virulence and antimicrobial resistance genes among these S. pseudintermedius isolates, underlining the need for global surveillance and molecular characterization of this pathogen.

Dogs↗

PubMed2025

Colorectal cancer-associated Streptococcus gallolyticus: a hidden diversity expose.

Streptococcus gallolyticus subsp. gallolyticus (SGG) is a bacterial pathogen implicated in bacteremia and endocarditis and is often associated with colon tumors in elderly individuals. The development of colorectal cancer (CRC) has been linked to intestinal dysbiosis, characterized by increased proportions of SGG and other intestinal microbes. In this study, we present the complete nucleotide sequence of five novel clinical isolates of SGG associated with colorectal cancer, revealing unexpected genetic diversity. Sequencing an additional 30 SGG clinical isolates provided a more comprehensive description of this genetic diversity. We did not identify a pathogenicity island specific to CRC-associated SGG isolates. Most of these human-derived SGG isolates exhibit resistance to multiple antibiotics. Our findings also offer additional insights into multilocus sequence typing (MLST), capsular loci, and pilus organization. Analysis of the repertoire of surface proteins reveals high potential for binding and foraging complex polysaccharides. Finally, comparative genomics with the phylogenetically closest non-pathogenic subspecies S. gallolyticus subsp. macedonicus confirmed that SGG pathogenicity-associated factors mostly rely on a large repertoire of surface proteins involved in host colonization, presence of C5a peptidase to avoid innate immunity, bile salt hydrolase to persist in the gut, and of specific bacteriocin and type VII-dependent effectors to colonize the host colon. Additionally, the presence of extracellular polysaccharides in SGG probably helps the bacterium survive in harsher conditions.IMPORTANCEStreptococcus gallolyticus subsp. gallolyticus (SGG) was the first intestinal bacterium associated with colorectal cancer. It is now widely accepted that colonic microbiota dysbiosis contributes to oncogenesis, with a higher relative abundance of several potentially pro-carcinogenic bacteria. For example, the oncogenic role of Escherichia coli pks+ and enterotoxinogenic Bacteroides fragilis in colorectal cancer has been well established, identifying the role of genetic loci encoding toxins. Through the sequencing and analysis of 11 clinical SGG isolates from CRC patients and comparisons with non-CRC isolates, we uncovered a significant diversity among CRC-associated strains. Our findings suggest that SGG association with CRC is complex and is not linked to a specific strain or pathogenicity island, thus highlighting the opportunistic and versatile nature of SGG.

Humans↗

PubMed2026

Multidrug resistance and genomic characteristics of nontypeable Haemophilus influenzae isolates from the respiratory tract of pediatric patients.

UNLABELLED: Nontypeable Haemophilus influenzae (NTHi) is a common colonizer of the human upper respiratory tract and one of the major pathogens responsible for pediatric respiratory tract infections. Given the increasing severity of its multidrug resistance (MDR), this study comprehensively investigated the genomic characteristics of circulating NTHi isolated from sputum and bronchoalveolar lavage fluid (BALF). A total of 104 H. influenzae isolates (69 from sputum; 35 from BALF) were collected from pediatric patients between January 2024 and January 2025. All isolates underwent whole-genome sequencing and antimicrobial susceptibility testing, followed by core/pan-genome phylogenetic analysis, multilocus sequence typing (MLST), and resistome profiling. Among them, 103 were identified as NTHi. We identified 29 known sequence types (STs) and 10 novel STs, with ST-107 (14.4%), ST-57 (10.6%), and ST-11 (8.7%) being the major circulating lineages. However, core-genome phylogenetic analysis provided a more granular view of the genetic variation within these identical STs. All the isolates showed high resistance to ampicillin (98.1%) and cefuroxime (84.6%). Genomically, the multidrug efflux pump gene hmrM was ubiquitous (100%). Ampicillin resistance was predominantly driven by blaTEM-1 carriage (77.9%), with minor contributions from chromosomal ftsI mutations. Fifteen plasmid replicons were predicted from 25 isolates, which highly coincided with the carriage of blaTEM-1 and other acquired resistance genes. This study demonstrates that MDR in pediatric NTHi is primarily driven by acquired resistance genes and chromosomal mutations, with specific resistant clones persisting and enriching under clinical antibiotic pressures. These findings underscore the importance of continuous high-resolution genomic surveillance in guiding rational antibiotic stewardship. IMPORTANCE: This study highlights the critical importance of high-resolution genomic surveillance in managing pediatric nontypeable Haemophilus influenzae (NTHi) infections. By utilizing whole-genome sequencing, we uncovered the pathogen's highly dynamic population structure and complex multidrug resistance (MDR) mechanisms. Crucially, our findings reveal a strong, non-random coupling between core genomic architectures, virulence factors, and MDR elements, driven by dual environmental and pharmacological pressures. This "virulence-MDR" co-evolutionary trend underscores the persistent clinical threat of locally adapted high-risk clones. These findings provide important insights for guiding rational clinical antibiotic stewardship, optimizing treatment strategies, and improving regional infection control.

Humans↗

PubMed2026

Salmonella Pullorum strain SPullorum-YN-07 from dead embryos of Yanjin black-bone chickens: Complete genome with IncFII(S) and Col(pVC) plasmids and pathogenicity.

Salmonella Pullorum is a host-adapted pathogen that causes Pullorum disease in chickens and can be vertically transmitted via eggs, leading to embryonic mortality. The susceptibility and vertical transmission of S. Pullorum may vary among chicken breeds, yet genomic characterization of strains from dead embryos of indigenous breeds remains limited. This study isolated and characterized a Gram-negative short rod, designated Salmonella Pullorum strain SPullorum-YN-07, from dead embryos of Yanjin black-bone chickens, a native breed in Yunnan, China. The strain formed colorless colonies on MacConkey agar and red, non-H2S colonies on XLD agar, with biochemical reactions consistent with the genus Salmonella. Whole-genome sequencing using Illumina and PacBio platforms generated a complete genome consisting of one circular chromosome and four circular plasmids; plasmid replicon types IncFII(S) and Col(pVC) were identified in two of the plasmids. On the chromosome, a total of 340 virulence-associated genes were detected, including those involved in secretion systems, adhesion, motility, and immune modulation. Resistance gene analysis identified the acquired aminoglycoside resistance gene aac(6')-Iaa, alongside multiple intrinsic resistance determinants related to efflux pumps and target alteration. Multilocus sequence typing (MLST) assigned the strain to sequence type ST92, and core-genome phylogenetic analysis confirmed its clustering within the Salmonella Pullorum lineage. In a chick infection model, the strain induced depression, white diarrhea, and growth retardation, with clinical scores peaking at 10 days post-infection and a mortality rate of 10%. Bacterial colonization was highest in the cecum, and histopathological lesions were observed in the liver, spleen, and cecum. This study provides the first complete genomic characterization and pathogenicity assessment of an S. Pullorum strain isolated from dead embryos of Yanjin black-bone chickens, offering a foundation for understanding host-pathogen interactions in indigenous breeds and assessing cross-transmission risks to commercial poultry populations.

Complete genome↗

PubMed2026

Global Diffusion of IncC Plasmid Harboring blaNDM-1in the High-Risk Escherichia coli ST131 Clone.

AIMS: The global expansion of quinolone-resistant Escherichia coli (QR-EC) is increasingly associated with β-lactam resistance and mobile genetic elements that facilitate resistance dissemination. This study investigated the molecular mechanisms underlying fluoroquinolone and β-lactam resistance in clinical QR-EC isolates and explored the plasmid type associated. METHODS AND RESULTS: A total of 123 non-duplicate QR-EC clinical isolates responsible mainly for gastrointestinal colonization were collected between 2019 and 2021. Plasmid-mediated quinolone resistance (PMQR), extended-spectrum β-lactamase (ESBL), and carbapenemase genes were screened by PCR. Mutations in the quinolone resistance-determining regions (QRDR) of gyrA and parC were analyzed using sequencing and mismatch amplification mutation assay PCR (MAMA-PCR). Selected isolates underwent multilocus sequence typing (MLST). Whole-genome sequencing (WGS) of a representative extensively drug-resistant strain carrying multiple quinolone resistance determinants, ESBL genes, and carbapenemase genes, was performed. PMQR genes were prevalent among QR-EC, dominated by aac(6')-Ib-cr (60.9% of isolates). ESBL genes were identified in 93.5% of isolates, predominantly blaCTX-M (95.7%). Among ertapenem-resistant isolates (QCR-EC) (n=18), blaNDM-1 and blaOXA-48 were detected in 13 and 11 isolates, respectively. QRDR mutations were highly frequent, particularly gyrA83 (98.4%) and parC80 (30.9%). Major QCR-EC genotypes belonged to sequence types ST167 (n=2), ST1196, ST469, and ST410. High-risk E. coli ST131 clone harboring IncC plasmid encoding blaNDM-1 was described for the first time in Africa, following its emergence, in two continents, Asia and America. Despite the very rare description of these strains worldwide, their description in three continents sign their global diffusion. CONCLUSIONS: This finding highlights the ongoing spread of carbapenem resistance and underscores the urgent need for strengthened genomic surveillance.

Escherichia coli↗

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↗

PubMed2026

Genomic determinants of fluoroquinolone resistance in Escherichia coli in Nigeria: dominance of QRDR mutations and limited contribution of PMQR in a cross-sectional study.

BACKGROUND: Fluoroquinolone-resistant Escherichia coli is a major global clinical threat, particularly in low- and middle-income countries like Nigeria. However, the full genomic landscape, including the relative contributions of chromosomal mutations, plasmid-mediated resistance, and the role of high-risk clones, remains poorly characterized in this setting. This study aimed to define the genomic mechanisms, clonal distribution, and genotype-phenotype relationships of fluoroquinolone resistance in clinical E. coli isolates from Nigeria. METHODS: A cross-sectional study of 107 clinical E. coli isolates was conducted. Phenotypic susceptibility to ciprofloxacin and nalidixic acid was determined using VITEK 2 and broth microdilution. Whole-genome sequencing was performed, and analysis included detection of quinolone resistance determining region (QRDR) mutations (gyrA, parC, parE) and plasmid-mediated quinolone resistance (PMQR) genes, multilocus sequence typing (MLST), and phylogenetic analysis. Statistical associations were evaluated using chi-squared tests or Fisher's exact tests. RESULTS: Ciprofloxacin non-susceptibility was high at 86.0%. Resistance was primarily driven by a conserved chromosomal mutation profile; the combination of gyrA S83L, gyrA D87N, and parC S80I was present in 85 isolates and was associated with ciprofloxacin non-susceptibility in all affected isolates in this cohort. Isolates with only gyrA mutations were resistant to nalidixic acid but susceptible to ciprofloxacin, consistent with a stepwise resistance pathway. In this cohort, the triple QRDR signature (gyrA S83L + gyrA D87N/Y + parC S80I) was a perfect positive predictor of ciprofloxacin non-susceptibility (85/85; 100%). The ST131 lineage dominated, accounting for 21.5% of isolates and universally carrying the complete triple QRDR profile; notably, no ST131 isolate carried a PMQR determinant. Plasmid-mediated quinolone resistance (PMQR) genes were detected in 15.0% of isolates but were not independently associated with ciprofloxacin non-susceptibility in this cohort in the absence of concomitant QRDR mutations. Efflux pump genes were ubiquitous and non-predictive. Notably, six isolates, all from urine, were non-susceptible (R/I) despite lacking all known QRDR and PMQR determinants, pointing to uncharacterized mechanisms. In a multivariable logistic regression model that included ST131 status, PMQR carriage, and parE mutation status, ST131 was associated with ciprofloxacin non-susceptibility (adjusted OR 5.96, 95% CI 1.21-29.4, p = 0.028), whereas PMQR carriage was not (adjusted OR 0.94, 95% CI 0.18-4.85, p = 0.94). The triple QRDR signature was not included in this model because it perfectly predicted ciprofloxacin non-susceptibility in this cohort. Resistance patterns varied by clinical source, with the highest burden in bloodstream and wound infections. This stepwise hierarchy from first-step gyrA mutations to the classic triple QRDR profile is summarised in the graphical abstract, Fig. 1. CONCLUSIONS: Fluoroquinolone resistance in Nigerian clinical E. coli is predominantly driven by chromosomal QRDR mutations within successful clones like ST131. PMQR genes and efflux pumps appeared to play a supplementary role rather than being independent drivers of ciprofloxacin resistance in this cohort. These data support prioritising key QRDR mutations in genomic reporting and local stewardship decisions, while the QRDR-negative resistant urine isolates require further investigation.

Escherichia coli↗