Search Results (1,356)

Type I-E and I-F CRISPR-Cas systems were identified in 237 E. coli strains isolated from patients with urinary tract infections (UTIs) between 2004 and 2019. The strains were classified into nine distinct groups (I–IX) based on the presence or absence of cas genes and repeat regions (RRs). Within the type I-E systems, two sequence variants were identified, distinguished by polymorphisms in the casB, cas3, cas7, cas5, and cas6 genes. The direct repeats (DRs) also differed, with I-E-associated RRs ranging from 26 to 32 bp and I-F-associated RRs consistently being 28 bp. We identified 762 unique spacers (29–35 bp in length) across the strain collection, while the number of spacers per strain varied from 1 to 47, and potential DNA targets were determined for 65 spacers, targeting 38 bacteriophage genomes, 19 plasmids, and 8 cas genes of the I-F type CRISPR-Cas system. Multilocus sequence typing (MLST) revealed 68 sequence types and 24 clonal complexes (CCs), with the most prevalent being ST131, CC10, CC69, CC405, CC14, CC38, CC73, and CC648. Significant correlations were observed between specific phylogroups/CCs, the type of CRISPR-Cas system present, and distinct profiles of virulence and antibiotic resistance genes. Full article

Salmonella is a Gram-negative enteric bacterium responsible for the foodborne and waterborne disease salmonellosis, which was the second most reported foodborne gastrointestinal infection in humans in the European Union in 2023. Animals represent the principal reservoir of this pathogen, with animal-derived food products serving as the main route of transmission to humans. In a household context, having numerous animals can be a crucial factor for contracting Salmonella spp. infection. In the present study, we report a case of a familiar outbreak of Salmonella Thompson that occurred in 2024 in central Italy, involving an infant and the companion animals (a dog, a cat and ten birds) of the family’s farm. To support the epidemiological investigations, antimicrobial susceptibility testing and whole-genome sequencing (WGS) were conducted on strains from the human case and from animals. Eleven strains were isolated in total, from fecal samples collected from the child and the animals at different times. WGS confirmed the genetic relatedness between human and animal isolates, supporting the hypothesis of a shared source of infection, but genes or plasmid involved in antibiotic resistance were not found. Moreover, AST revealed that isolates were fully susceptible to major antimicrobial classes tested. Despite being an uncommon serotype, the involved Salmonella Thompson serovar 6,7: k:1,5 O:7 (C1) demonstrated a high pathogenic potential, emphasizing the need for vigilance even toward serotypes not typically associated with major public health concerns. Moreover, these findings underscore the critical need for an integrated One Health approach to effectively monitor, prevent, and control zoonotic infections. Full article

Escherichia coli sequence type 648 (ST648), a lineage within the clinically important phylogroup F, has disseminated worldwide in humans and animals. In this study, we performed whole-genome sequencing and comparative genomic analysis for two New Delhi metallo-beta-lactamase (bla_NDM-5) carrying E. coli strains: ECsOL198, recovered from a wild Eurasian otter in Northern Lebanon, and ECOL247, isolated from a hospitalized leukemia patient. Both isolates belonged to phylogroup F and serotype O9:H4, and exhibited IncFIA, IncFIB, and IncFII plasmids. They shared a similar antimicrobial resistance profile, including a carbapenemase gene (bla_NDM-5), β-lactamase genes (bla_TEM-1, bla_CTX-M-15, and bla_OXA-1), and other genes that confer resistance to aminoglycosides (acc(3)-Ile, aadA2), sulfonamides (sul1), tetracyclines (tet(A)), and fluoroquinolones (mutations in gyrA and parC). Both isolates also carried common virulence-associated genes related to adhesion, iron acquisition, environmental persistence, and immune evasion. Whole-genome multilocus sequence typing (wgMLST) revealed that both isolates formed a distinct subclade closely related to a bloodstream-derived ST648 isolate from India, indicating limited relatedness to global clones. These findings highlight the transmission of nearly clonal multidrug-resistant E. coli ST648 in both clinical and non-clinical settings, raising concerns about the threat to public health. Full article

V. furnissii is a marine bacterium capable of infecting both invertebrates and humans. However, the mechanisms underlying its drug resistance and virulence remain largely elusive. In this study, we isolated a multidrug-resistant V. furnissii strain, MT14, from bivalve mollusks. Genomic analysis revealed that MT14 carries a novel pAQU-type plasmid, designated pMT14, which harbors six antibiotic resistance genes: qnrS2, qnrVC6, dfrA31, tetA; sul2, and bla_GMA-1. Notably, bla_GMA-1 and its variants confer resistance to penicillin-class antibiotics, including ampicillin, amoxicillin, and carbenicillin. Comparative genomic analysis further revealed that V. furnissii strains commonly encode T6SS1, T6SS2, and the hemolysin gene vfh, while only five sequenced strains carry zot toxin gene. To our knowledge, this is the first report of zot in V. furnissii. In addition, the absence of drug resistance genes in the majority of genomes (73.3%, 22/30) suggests that such traits are not intrinsic to the species but have been acquired by specific strains, likely through plasmid transfer or other mobile genetic elements. The emergence of bla_GMA-1 and zot in V. furnissii represents a potential public health concern, underscoring the need for enhanced surveillance of antimicrobial resistance in marine pathogens. Full article

Background/Objectives: Providencia stuartii is intrinsically resistant to several antibiotic classes, and acquisition of bla_NDM further restricts treatment options. This study aimed to characterize NDM-producing P. stuartii isolates from a small hospital cluster in Russia and to place them within the global genomic context. Methods: Four isolates recovered between June and July 2023 from a single hospital were analyzed using Illumina and Oxford Nanopore sequencing to assess genetic relatedness and plasmid content. Results: The isolates showed identical extensively drug-resistant profiles and were closely related genomically. All carried nearly identical IncC plasmids harboring multiple antimicrobial resistance genes, including bla_NDM. Comparative analysis indicated that these genomes clustered with recent European isolates but differed in the bla_NDM allele and its genomic location. Highly similar IncC plasmids were also found in our previous Klebsiella pneumoniae dataset, demonstrating that this plasmid backbone occurs in multiple bacterial species in the region. Conclusions: The study highlights the role of IncC plasmids in carbapenemase dissemination and underscores the value of genomic surveillance integrating chromosomal and plasmid analyses to track extensively drug-resistant pathogens. Full article

Background: The efficiency of vermicomposting in reducing antibiotic resistance genes (ARGs) in dairy manure may be compromised by co-pollutants like arsenic (As) and microplastics. Specifically, plasmids serving as carriers and vectors of ARGs were largely distributed in this process. However, the impact of As and microplastics on plasmids carrying ARGs during vermicomposting is largely unknown. Methods: This study utilized a controlled experimental design and applied plasmid metagenomics to investigate the individual and combined effects of As and polyethylene terephthalate (PET) microplastics on plasmid-mediated ARG dynamics during vermicomposting. Results: We found that vermicomposting alone mainly enriched non-mobilizable plasmids, while PET microplastics selectively promoted conjugative and mobilizable plasmids, whereas As significantly increased all plasmid types. Moreover, both PET or As alone and combined exposure (PET and As) increased total ARG abundance, with their combination inducing synergistic ARG enrichment despite unchanged total plasmid abundance. Furthermore, co-occurrence network analysis combined with ARGs/plasmid ratio assessments demonstrated that As influences ARGs through co-selective pressure by enriching ARGs co-localized with As resistance genes (e.g., the ars operon) on plasmids while simultaneously promoting horizontal gene transfer (HGT) via activation of oxidative stress and SOS response pathways. In contrast, PET primarily facilitates ARG dissemination through a “metabolism-resistance” coupling strategy by enriching colonizing bacteria with PET-degrading capacity. Their co-exposure formed As-enrichment hotspots on PET microplastic surfaces, functioning as a “super-mixer” that selectively screened for superbugs carrying potent resistance mechanisms (e.g., bla_OXA-50 and mdtB/mdtE). Conclusions: This study provides the first plasmidome-level evidence of synergistic ARG propagation by As and PET microplastics during vermicomposting, highlighting mobile genetic elements’ critical role in co-pollutant risk assessments. Full article

In animal husbandry and livestock farming, with the spread of the plasmid-mediated MCR-1 gene, polymyxin E, as the last line of defense against drug-resistant Gram-negative bacteria, is facing severe challenges. This study investigated the in vitro and in vivo synergistic effects and mechanisms of QUE combined with polymyxin E against MCR-1-positive chicken E. coli JD37. In vitro experiments showed that QUE could restore the sensitivity of E. coli JD37 to polymyxin E (FIC = 0.34375) and enhance the bactericidal effect of polymyxin E by increasing cell membrane permeability, fluidity, and membrane potential, downregulating the expression of the AcrAB-TolC efflux pump and LPS-related genes. Molecular docking further identified the key residues for QUE binding to the MCR-1 protein. The in vivo chick infection model confirmed that combination therapy increased survival rates, reduced bacterial load in tissues, alleviated pathological damage, and decreased levels of intestinal inflammatory factors. Our results demonstrate the synergistic bactericidal effect of the QUE-polymyxin E combination against MCR-1-positive E. coli and elucidate its underlying mechanism. Full article

Colistin, a polymyxin antibiotic considered a last-line treatment for multidrug-resistant Gram-negative infections, has been widely used in livestock, promoting resistance in bacterial populations that can disseminate through the environment. Although rarely used in companion animals, dogs and cats can acquire and spread colistin-resistant strains through shared environments, acting as potential reservoirs of resistance. Reliable detection of resistant strains remains challenging due to technical limitations of routine susceptibility tests. Despite these constraints, epidemiological studies demonstrate the global presence of colistin-resistant bacteria in companion animals, with multiple plasmid-mediated colistin-resistant genes (mcr) identified in different bacteria species. Evidence of clonal and plasmid-mediated sharing of resistant strains between companion animals, humans, and, in some cases, food-producing animals highlights the complex and multidirectional nature of transmission. Although the directionality of transmission remains difficult to establish, the detection of colistin-resistant bacteria in companion animals is concerning. Addressing this challenge requires a One Health approach, integrating coordinated surveillance and infection and control measures in veterinary practices to safeguard the effectiveness of this critical last-resort antibiotic. This review summarizes current knowledge on colistin resistance mechanisms, diagnostic challenges, epidemiology, and the potential for interhost transmission, highlighting the role of dogs and cats as potential reservoirs of colistin resistance. Full article

Toxin–antitoxin (TA) modules represent sophisticated regulatory networks that have evolved from simple plasmid maintenance factors into multifunctional genetic modules orchestrating bacterial stress responses, pathogenesis, and ecological adaptation. This review highlights a compelling correlation between the abundance of toxin–antitoxin (TA) modules and bacterial pathogenicity, as exemplified by Mycobacterium tuberculosis (M.tb), which encodes 118 TA loci—significantly more than the fewer than 10 found in closely related saprophytic species. The clinical significance of TA modules extends beyond traditional stress response roles to encompass antimicrobial persistence, where systems like VapBC and MazEF facilitate dormant subpopulations that survive antibiotic therapy while maintaining chronic infections. Recent discoveries have revealed TA modules as sophisticated bacterial defense mechanisms against bacteriophage infection, with DarTG and ToxIN systems representing novel antiviral immunity components that complement CRISPR-Cas and restriction–modification systems. The immunomodulatory capacity of TA modules demonstrates their role in host–pathogen interactions, where systems such as VapC12 in M.tb promote macrophage polarization toward permissive M2 phenotypes while inducing anti-inflammatory cytokine production. Large-scale genomic analyses reveal that TA modules function as drivers of horizontal gene transfer networks, with their signatures enabling accurate prediction of plasmid community membership and serving as determinants of microbial community structure. The biotechnological applications of TA modules have expanded to include genetic circuit stabilization, biocontainment device construction, and multi-species microbial community engineering, while therapeutic strategies focus on developing multi-target inhibitors against conserved TA protein families as promising approaches for combating drug-resistant bacterial infections. The evolutionary conservation of TA modules across diverse bacterial lineages underscores their fundamental importance as central organizing principles in bacterial adaptation strategies, where their multifunctional nature reflects complex selective pressures operating across environmental niches and host-associated ecosystems. This review provides an integrated perspective on TA modules as dynamic regulatory elements that support bacterial persistence, immune evasion, and ecological versatility, establishing them as genetic elements with truly “many faces and functions” in prokaryotic biology. Full article

Hemorrhagic septicemia (HS) is a fulminant bovine disease across Asia and Africa, yet Pasteurella multocida (P. multocida) isolated from yak is poorly reported. We isolated strain NQ01 from a fatal HS case in Xizang, China and identified it as P. multocida B:2 by morphology, Gram stain, and PCR (kmt1⁺, bcbD⁺, LPS L2). NQO1 formed smooth, non-hemolytic colonies. After Gram staining, the cells appeared as red rods with bipolar staining. Antimicrobial testing showed broad susceptibility to β-lactams, aminoglycosides, tetracyclines, fluoroquinolones, midecamycin, florfenicol, polymyxin, and vancomycin, with resistance to metronidazole, trimethoprim sulfamethoxazole, and clindamycin. Streptomycin and ofloxacin had intermediate activity. In mice, the intraperitoneal and intranasal LD₅₀ values were 40.64 CFU/mL and 9.53 × 10⁶ CFU/mL, respectively. The intranasal fatal cases were characterized by bacteremia with multifocal disseminated intravascular coagulation involving lung, liver, and spleen. The complete genome comprises a single 2.33 Mb chromosome (40.47% GC, 2115 CDS, no plasmids) with only one resistance gene (Eco_EFTu_PLV) and 28 virulence genes spanning adhesion (tadA, rcpA, ppdD, pilB, tuf/tufA, htpB, PM_RS00430, PM_RS00425, PM_RS08640), immune modulation (lpxB/C/D, msbB, manB, rfaE/F, gmhA/lpcA, kdsA, pgi, wecA, galE, bexD’, ABZJ_RS06285, ABD1_RS00310), and nutritional/metabolic factor (hgbA, hemR, hemN), plus a YadA-like factor. Phylogenetically, NQ01 clusters with regional B:2 bovine/yak isolates. Collectively, these data define NQ01 as a highly virulent, low-resistance yak isolate and a practical model for natural-route HS pathogenesis and targeted control in high-altitude pastoral settings yaks. Full article

Cronobacter sakazakii is a foodborne pathogen of major concern due to its link with severe neonatal infections through powdered infant formula (PIF). However, its genomic epidemiology in Bangladesh remains uncharacterized. We report the first whole-genome analysis of three isolates from PIF. Two isolates (S41_PIFM and S44_RUTF) belonged to ST83, a lineage repeatedly associated with neonatal meningitis, septicemia, and persistence in PIF production environments, while the third (S43_TF) represented ST789, a recently described and rare lineage of unknown pathogenic potential. Pan-genome and comparative analyses identified 39 virulence determinants, 19 antimicrobial-resistance genes, and diverse mobile genetic elements. ST83 isolates harbored plasmid replicons IncFII(pCTU2) and pESA2, while the ST789 isolate carried insertion sequence ISKpn34, indicating horizontal gene transfer potential. All strains encoded I-E CRISPR-Cas systems. The detection of globally recognized high-risk ST83 clones alongside the novel ST789 lineage highlights emerging public health risks. This study provides the first genomic insights into C. sakazakii in Bangladesh and underscores the urgent need for genomic surveillance and strengthened food safety monitoring to protect infant health in low- and middle-income countries. Full article

This study investigated the molecular epidemiology, virulence, antimicrobial resistance, and mobile genetic elements (MGEs) of Salmonella enterica serovar I 4,[5],12:i:- isolates collected in Jeollanam-do, South Korea, between 2021 and 2023. A total of 135 isolates were tested for antimicrobial susceptibility and 14 virulence-associated genes were screened by PCR. Pulsed-field gel electrophoresis (PFGE) assessed clonal relatedness, and whole-genome sequencing (WGS) enabled multilocus sequence typing (MLST), core genome MLST (cgMLST), SNP phylogeny, resistance gene detection, and MGE analysis. Nine virulence profiles (VP1–VP9) were identified. VP1 (74.1%) was strongly associated with multidrug resistance (MDR), while VP2 (14.8%), which carried plasmid-encoded spv genes, remained largely susceptible. Overall, 83.7% of isolates were resistant to at least one antimicrobial, and 65.2% were MDR, with ampicillin and tetracycline consistently forming the backbone of MDR phenotypes. PFGE revealed high genetic diversity, with 72 pulsotypes, yet certain clones (e.g., SMOX01.006, SMOX01.012) were widely distributed and corresponded to VP2 isolates. WGS confirmed two dominant sequence types, ST34 (n = 24) and ST19 (n = 20), with SNP phylogeny showing VP1 isolates mainly clustered with ST34 and VP2 with ST19. Genotype–phenotype concordance showed strong agreement for most antimicrobials, except cefoxitin, ciprofloxacin, amikacin, and trimethoprim/sulfamethoxazole. MGE analysis revealed that tet(B) was consistently associated with ISVsa5, while ISEc59 was linked to multiple resistance genes, though only aac(3)-IV was phenotypically expressed. These findings demonstrate that MDR and virulence gene composition were closely associated with clonal clustering and that MGEs may contribute to resistance gene expression. This study provides a basis for understanding the dissemination of resistant and virulent Salmonella in the region and underscores the need for continuous genomic surveillance. Full article

Background: Escherichia coli strains associated with poultry are increasingly recognized as reservoirs of both virulence and resistance genes, posing significant zoonotic risks throughout the food production chain. However, the genotypic architecture and pathogenic potential of isolates from large-scale turkey farms remain under characterized, particularly in the context of extended-spectrum β-lactamase (ESBL) production. Methods: A total of 160 ESBL-producing E. coli isolates were collected from healthy turkeys on intensive Hungarian farms. Whole genome sequencing (WGS) was performed to characterize virulence factors. Functional annotation included screening for fimbrial adhesins, iron acquisition systems, secretion pathways, and autotransporter toxins, using VirulenceFinder and Prodigal-based genome annotations. Data analysis included assembly quality control with QUAST and BUSCO, and comprehensive virulome profiling. Results: The isolates exhibited a functionally diverse virulence profile encompassing classical ExPEC-associated colonization factors (type I, P, S fimbriae; curli; ECP), multiple iron acquisition systems (enterobactin, salmochelin, aerobactin, yersiniabactin, and heme uptake), and key secretion systems (LEE-associated T3SS and T2SS). Genetic hallmarks of avian pathogenic E. coli (APEC), uropathogenic pathogenic E. coli (UPEC), and enteropathogenic E. coli (EPEC) pathotypes co-occurred in 44% of the isolates, indicating a mosaic virulence landscape. Notably, serine protease autotransporters of Enterobacteriaceae (SPATE) toxins (Vat, Pic) and ColV-type plasmid-associated modules were frequently detected. All isolates were confirmed by ESBL producers, highlighting their antimicrobial resistance potential. Conclusions: This study reveals that E. coli strains isolated from turkeys possess a complex, host-adapted virulence repertoire capable of supporting both enteric and extraintestinal infections. The co-occurence of APEC-, UPEC-, and EPEC-like traits—combined with ESBL production—underscores their One Health relevance. These findings support the need for host-specific surveillance, functional validation, and integrative control strategies in poultry systems. Full article

Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a critical global health threat, with ST101 identified as a major circulating clone in Saudi Arabia. We used whole genome sequencing and plasmid reconstruction to investigate the molecular characteristics of CRKP ST101 isolates from Saudi Arabia (2018–2021), analyzing antimicrobial resistance genes (ARGs), virulence factors, and plasmid structure and replicon types. Clinical isolates were obtained from the Ministry of National Guard Health Affairs (MNGHA) hospitals in Saudi Arabia between 2018 and 2021. Whole-genome sequencing was performed using the Illumina MiSeq^® platform, followed by comprehensive bioinformatic analysis of ARGs, virulence factors, and plasmid content. All ten isolates belonged to ST101 and harbored extensive antimicrobial resistance (AMR) and virulence determinants. Nine isolates (90%) carried bla_OXA-48, with three co-harboring bla_NDM-1, representing dual-carbapenemase producers. These carbapenemase genes were located on plasmids with distinct replicon types, including IncL/M, IncHI1B/IncFIB, and IncFIA/IncR. All isolates were multidrug-resistant (MDR), with half classified as extensively drug-resistant (XDR). Four isolates exhibited hypervirulent profiles, harboring aerobactin and yersiniabactin siderophores. This study provides comprehensive genomic characterization of CRKP ST101 in Saudi Arabia, revealing complex resistance mechanisms mediated by diverse plasmid types. The findings highlight the importance of genomic surveillance to track the evolution and dissemination of high-risk MDR and XDR lineages and inform targeted infection control strategies. Full article

Background/Objectives: This study assessed the risk associated with third-generation cephalosporin- and fluoroquinolone-resistant Salmonella from pork consumption by integrating phenotypic resistance profiles with genetic data to characterize the risks and transmission pathways. Methods: Salmonella were isolated from raw pork meat samples (n = 793) collected from fresh markets and hypermarkets across Bangkok during 2021–2022, of which 150 were extended-spectrum β-lactamase (ESBL)-producing and 31 were fluoroquinolone-resistant isolates. Phenotypic and genotypic resistance profiles were characterized. Quantitative antimicrobial resistance risk assessment (AMR RA) was conducted using a dose–response model. Results: Salmonella spp. was detected in 42.75% of pork samples, with a higher prevalence in fresh markets (75.5%) than in hypermarket samples and with concentrations ranging from 1.3 to 180 MPN/g. Twenty-eight percent of isolates were ESBL producers, with ciprofloxacin and levofloxacin resistance observed in 5.3% and 3.0%, respectively. The bla_CTX-M55 genes were located on conjugative plasmids. Whole genome sequencing revealed both vertical and horizontal gene transfer. IncHI2/N and IncC plasmids shared conserved backbones and resistance gene architectures, indicating horizontal dissemination of resistance genes. Phylogenomics suggested possible clonal transmission among pigs, pork, and humans. AMR RA estimated 88,194 annual illness cases per 100,000 people from ESBL-producing Salmonella and 61,877 from ciprofloxacin-resistant strain, compared with 95,328 cases predicted by QMRA from Salmonella contamination. Cooking pork at ≥64 °C for 3 min eliminated the risk in all scenarios. Sensitivity analysis identified initial contamination level and cooking temperature as key determinants. Conclusions: Raw pork meat consumption represents the highest risk, which can be mitigated by thorough cooking (>64 °C, ≥3 min), while integrating genomic data enhances AMR hazard identification, source attribution, and exposure assessment. Therefore, promoting well-cooked meat consumption and safe cooking practices, alongside the use of AMR genetic data to inform targeted interventions, is recommended. Full article