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PubMed2024

Contaminant-degrading bacteria are super carriers of antibiotic resistance genes in municipal landfills: A metagenomics-based study.

Municipal landfills are hotspot sources of antimicrobial resistance (AMR) and are also important habitats of contaminant-degrading bacteria. However, high diversity of antibiotic resistance genes (ARGs) in landfills hinders assessing AMR risks in the affected environment. More concerned, whether there is co-selection or enrichment of antibiotic-resistant bacteria and contaminant-degrading bacteria in these extremely polluted environments is far less understood. Here, we collected metagenomic datasets of 32 raw leachate and 45 solid waste samples in 22 municipal landfills of China. The antibiotic resistome, antibiotic-resistant bacteria and contaminant-degrading bacteria were explored, and were then compared with other environmental types. Results showed that the antibiotic resistome in landfills contained 1,403 ARG subtypes, with the total abundance over the levels in natural environments and reaching the levels in human feces and sewage. Therein, 49 subtypes were listed as top priority ARGs for future surveillance based on the criteria of enrichment in landfills, mobilizable and present in pathogens. By comparing to those in less contaminated river environments, we elucidated an enrichment of antibiotic-resistant bacteria with contaminant-degrading potentials in landfills. Bacteria in Pseudomonadaceae, Moraxellaceae, Xanthomonadaceae and Enterobacteriaceae deserved the most concerns since 72.2 % of ARG hosts were classified to them. Klebsiella pneumoniae, Acinetobacter nosocomialis and Escherichia coli were abundant multidrug-resistant pathogenic species in raw leachate (∼10.2 % of total microbiomes), but they rarely carried contaminant-degradation genes. Notably, several bacterial genera belonging to Pseudomonadaceae had the most antibiotic-resistant, pathogenic, and contaminant-degrading potentials than other bacteria. Overall, the findings highlight environmental selection for contaminant-degrading antibiotic-resistant pathogens, and provide significant insights into AMR risks in municipal landfills.

Metagenomics↗

PubMed2025

Multiple clades of regulators contribute to bacterial phosphate homeostasis and pathogenesis.

Phosphate is both essential for life and toxic, necessitating the tight regulation of its acquisition. Based on Escherichia coli, most bacteria are thought to use a single accessory protein that monitors import to regulate phosphate homeostasis. This work reveals that most bacteria possess multiple distinct families of accessory regulators with each family regulating homeostasis in conjunction with a unique importer family. The antibiotic-resistant pathogen Staphylococcus aureus can obtain phosphate from divergent environments and possesses accessory-transporter pairs from all three identified groups. Investigations with S. aureus revealed that all three accessory proteins can regulate phosphate homeostasis, but that there is a hierarchy, which is dictated by the environment. Multiple accessory regulators are independently necessary for S. aureus to cause infection. Thus, microbes possess not one, but multiple distinct groups of accessory regulatory proteins and this diversity enables them to control phosphate homeostasis across environments, including those encountered during infection.

PhoPR↗

PubMed2026

Metal-Organic Framework-Based and Metal-Organic Framework-Derived Nanomaterials for Cancer Theranostics and Antibacterial Applications: Advances, Challenges, and Perspectives.

Metal-organic frameworks (MOFs), constructed through coordination-driven self-assembly of metal ions/clusters and organic linkers, have emerged as a uniquely versatile class of porous nanomaterials with broad biomedical potential. Despite substantial clinical progress, both oncological treatment and antimicrobial intervention remain constrained by inadequate tumor-targeting selectivity, multidrug resistance, immunosuppressive tumor microenvironments, and the global proliferation of antibiotic-resistant pathogens, limitations that conventional nanocarrier platforms have addressed only in part. MOF-based and MOF-derived nanomaterials, distinguished by tunable pore architecture, structurally and compositionally adaptable metal nodes, high surface areas, and stimulus-responsive degradability, offer a rational framework for overcoming these barriers. This review systematically examines the synthetic strategies underlying MOF-based and MOF-derived nanomaterials, including pyrolysis, chemical etching, composite modification, and functional group introduction, and their structural determinants of performance. In cancer theranostics, we critically evaluate their roles as multimodal imaging contrast agents, stimulus-responsive drug delivery carriers, and platforms for combination therapies encompassing photodynamic, photothermal, chemodynamic, and immunomodulatory modalities. In antibacterial applications, we analyze the mechanistic basis of MOF-based and MOF-derived activity, including physical membrane disruption, reactive oxygen species-mediated oxidative stress, and sustained metal ion release, alongside strategies targeting biofilm formation and antibiotic resistance. Multifunctional platforms that concurrently integrate cancer theranostic and antibacterial capabilities are further discussed. This review also addresses the principal barriers to clinical translation, encompassing large-scale manufacturing, long-term biosafety, and regulatory approval, and proposes future directions incorporating artificial intelligence-assisted design and materials genomics, underscoring the transformative potential of MOF-based and MOF-derived nanomaterials as next-generation precision nanomedicines. This review establishes a unified mechanistic framework grounded in the intrinsic physicochemical properties of MOF-derived nanomaterials, systematically integrating their applications in cancer theranostics and antibacterial therapy. Critically, it bridges fundamental advances with translational reality by incorporating a rigorous assessment of regulatory pathways, scalable manufacturing constraints, and clinical implementation barriers, and offers a comprehensive, practice-oriented reference for the rational design and responsible translation of MOF-based and MOF-derived nanomaterials.

Theranostic Nanomedicine↗

PubMedDate not supplied

Emergence of antibiotic resistance in hospitals, 1935-1975.

A limited review of the changes in susceptibility of common bacterial pathogens to available antibacterial agents is presented. Significant developments in recent years include the following: (1) the emergence of Streptococcus pneumoniae with decreased resistance to penicillin and of some strains resistant to several antibiotics; (2) a decline in prevalence of multi-drug-resistant Staphylococcus aureus after 1960 following their increasing prevalence in the preceding years (these changes were methicillin-resistant (and multi-drug-resistant) S. aureus and the marked differences in their prevalence in different areas (these changes also were related to appearance of new phages in those organisms); (4) an increasing resistance to multiple drugs among enterococci but not among viridans streptococci or among nonenterococcal group D streptococci; (5) the emergence of beta-lactamase-producing Neisseria gonorrhoeae; (6) the emergence and spread of sulfonamide-resistant Neisseria meningitidis; (7) the occurrence of beta-lactamase-producing strains of Haemophilus influenzae and occasional strains resistant to chloramphenicol; (8) the focal occurrence of chloramphenicol-resistant Salmonella typhi in Vietnam and in epidemic form in Mexico; (9) the demonstration of marked differences in prevalence of resistance to multiple drugs in common pathogens to the most widely used antibiotics in different geographic areas. The dominant factor in the emergence and spread of antibiotic-resistant bacterial pathogens, whether in hospital wards or in the community, is clearly the intensive use of the antibiotic agents to which resistance emerges and then spreads.

Bacteria↗

PubMed2026

Mobile genetic elements-driven partitions of mega-plasmids resistome in Salmonella Infantis.

Salmonella enterica serovar Infantis (S. Infantis) becomes the primary pathogen among the top Salmonella serotypes, contributing to numerous cases of foodborne illness annually in the United States. S. Infantis infection has spread rapidly worldwide, especially the clones with pESI-like plasmids. However, the underlying mechanisms regarding the transmission of S. Infantis, particularly mobile genetic elements (MGEs), mediated horizontal gene transfer, are limited. The objective of this study was to evaluate the relationship, if any, among MGEs, antibiotic-resistant genes (ARGs), and virulence factors (VFs) within S. Infantis via genomic analysis. A total of 91 S. Infantis complete genomes with high sequencing quality were selected for downstream bioinformatic analysis. The results showed that the majority of VFs were located in the bacterial chromosomes, while most ARGs were carried by S. Infantis mega-plasmids in an MGE-favored manner. Integrons and transposons were closely associated with certain ARGs, but prophages within mega-plasmids displayed a diverse ARG profile. Collectively, MGE-mediated horizontal gene transfer might lead to ARG acquisition by mega-plasmids, subsequently contributing to the resistome of S. Infantis. Our findings provide insights into the development of MGE-associated resistome in S. Infantis that could inform more effective prevention and intervention strategies to control this pathogen, further ensuring public health and safety.IMPORTANCEThe rapid emergence and transmission of antibiotic-resistant foodborne pathogens pose a significant risk to public health, necessitating the discovery of underlying mechanisms to control multidrug-resistant pathogens. Salmonella enterica serovar Infantis (S. Infantis) has become a pathogen of clinical and epidemiological relevance in recent years, ranking as the top prevalent serovar associated with foodborne illnesses and exhibiting resistance to several antibiotics. The current investigation of multidrug resistance (MDR) S. Infantis strains primarily emphasized the presence of mega-plasmids. However, the question of how mega-plasmids contribute to the transmission of antibiotic-resistant genes (ARG) is unaddressed. Utilizing the genomic characterization of S. Infantis complete genomes with high quality, our study revealed that the resistome of S. Infantis mega-plasmids-the primary ARG reservoirs of S. Infantis-followed a specific pattern of mobile genetic elements (MGEs). Monitoring the spread of MGE-carried ARGs within mega-plasmids should be considered in future surveillance.

Interspersed Repetitive Sequences↗

PubMed2026

Complete genome sequences of Staphylococcus epidermidis phages Cicami, Sazerac, Southeast, Slasher, Spartan, and Undine.

Staphylococci are opportunistic pathogens that cause a variety of antibiotic-resistant infections, and staphylococcal viruses (phages) can be harnessed as alternative therapeutics. Here, we report genome sequences of six Staphylococcus epidermidis phages with siphovirus morphology that lack proteins associated with virulence and lysogeny. Our observations suggest potential uses in therapeutic applications.

bacteriophage therapy↗

PubMed2026

The spatial and temporal distribution of Staphylococcus aureus along a tropical Hawaiian watershed.

Staphylococcus aureus is a leading cause of community-acquired skin and soft-tissue infections worldwide. One major route of exposure is recreating in marine waters, but knowledge is limited regarding the drivers of S. aureus in surface waters that discharge into marine environments. This study explores spatial and temporal distributions of S. aureus, including antimicrobial-resistant and virulence genes, using both culture-dependent and molecular techniques across a tropical Hawaiian watershed with a gradient of human influence. Negative binomial generalized linear mixed models revealed that the interaction between spatial and temporal factors was the strongest predictor of S. aureus and associated genes. Cultured S. aureus was highest at mid-watershed sites in summer, which included a popular swimming hole, suggesting human shedding as a significant source. Molecular detection of S. aureus (femA gene) yielded concentrations two orders of magnitude higher than cultured concentrations and peaked at estuarine sites with the greatest nutrients and water residence times. In the winter at upstream sites with no public access, staphylococci antibiotic-resistant (mecA) and S. aureus virulence gene (etb) were elevated, indicating highly pathogenic S. aureus strains in surface waters may originate from zoonotic sources. Our findings indicate that human and zoonotic sources contribute antibiotic-resistant and virulent S. aureus to watersheds, with streams facilitating environmental transmission to marine waters. This watershed-scale assessment enables the prediction of spatial and temporal conditions associated with elevated S. aureus concentrations, thereby reducing exposure and infections.

Staphylococcus aureus↗

PubMed2026

Chloramphenicol and tetracycline synergize with bacteriophage SeKF_13 to inactivate antimicrobial-resistant Salmonella Typhimurium.

UNLABELLED: Non-typhoidal Salmonella is estimated to cause up to 1 billion cases of global foodborne illness per year. Salmonella Typhimurium is a serovar of gravest worldwide concern as it is capable of infecting animal and human hosts and can also acquire antimicrobial resistance (AMR) determinants at a rapid rate. Recent advances in phage research have positioned them as especially useful for inactivation of Salmonella where antibiotics have proven no longer effective. Even more recently, phage-antibiotic synergy (PAS) has been proposed as a solution for AMR Salmonella, where synergistic combinations of phages and antibiotics are more effective than application of phage or antibiotic alone. Utilizing an in-house phage isolate, SeKF_13, we sought to determine the existence of PAS against a strain of Salmonella enterica serovar Typhimurium 14028 2a that is clinically resistant to bacteriostatic antibiotics chloramphenicol and tetracycline. Checkerboard assays revealed the presence of synergy when sub-lethal (sub-MIC) levels of either tetracycline or chloramphenicol were combined with phage SeKF_13 (P < 0.05; two-way ANOVA). Compared to tetracycline or chloramphenicol alone, the addition of phage also decreased the MICs of both antibiotics twofold. We also monitored the development of resistance and found that PAS significantly suppressed emergence of resistance compared to the antibacterial agents alone (P < 0.05; Tukey's HSD). Whole-genome sequencing revealed that SeKF_13 is devoid of genes encoding integrase, antimicrobial resistance, and virulence, ensuring safety in future applications. Together, our results suggest that combined treatment of phage and antibiotic can improve antimicrobial efficacy against antibiotic-resistant Salmonella enterica. IMPORTANCE: Salmonella enterica is a foodborne pathogen that causes one of the highest rates of foodborne illness worldwide. They are also capable of becoming resistant to antimicrobials very rapidly (i.e., antimicrobial resistance; AMR) due to their ability to acquire AMR determinants, undermining the effectiveness of current treatments. Bacteriophages (phages), viral predators of bacteria, have been proven to be effective in some cases, but recently, phage-antibiotic synergy has been proposed as a more effective solution than phages or antibiotics alone. We found this was, indeed, the case; using phage SeKF_13 and tetracycline or chloramphenicol (to which the Salmonella strain was resistant), we found that combination treatment was significantly more effective than either treatment alone. These results demonstrate that combined treatment of phage and antibiotic can bolster treatment efficacy against AMR Salmonella.

Salmonella typhimurium↗

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

Complete genome sequence of an antibiotic-resistant and virulent Escherichia marmotae isolate recovered from a urinary tract infection.

OBJECTIVES: We aimed at analyzing the whole genome of the antibiotic-resistant Escherichia marmotae isolate 23-MO01035-0, which was obtained from a urinary tract infection of a male patient in Germany. The study focused on the characterization of mobile genetic elements and genetic factors that contribute to antibiotic resistance and pathogenicity. METHODS: Phenotypic antimicrobial susceptibility testing was performed and genomic DNA was sequenced using Illumina NextSeq (2 × 151 bp) and a MinION Mk1C device followed by de novo hybrid assembly using Unicycler v0.4.8. Resistance genes, virulence factors, plasmids, and mobile elements were identified with the bakcharak pipeline and PathogenFinder. RESULTS: The isolate belonged to sequence type ST133 and the 5,041,084 bp whole genome, consisting of one chromosome and five plasmids with an average GC content of 50.4%, revealed resistance genes for various antibiotic classes on an IncFII plasmid that had not yet been described. The isolate was predicted to be a potential human pathogen due to the presence of multiple virulence genes. CONCLUSION: Here, we report one of the first detailed genomic characterization of an antibiotic-resistant and virulent E. marmotae isolate from Germany. Considering that this bacterium was isolated from the urinary tract and possibly belonged to the faecal microbiota of the patient at that time, E. marmotae might contribute to the spread of antibiotic resistance in humans. This underscores the importance of genomic surveillance of E. marmotae, which causes human infections, but may be misidentified as E. coli.

Escherichia marmotae↗

PubMed2026

Emergence and persistence of ESBL- and carbapenemase-producing Klebsiella pneumoniae-related species in Barcelona wastewater treatment plants.

The World Health Organization classifies extended-spectrum beta-lactamase (ESBL) and carbapenemase-producing Klebsiella pneumoniae as critical-priority pathogens due to their high incidence, mortality, transmissibility, rapid resistance acquisition, and limited treatment options. Beyond clinical settings, their detection in wastewater treatment plants (WWTPs) provides an opportunity to assess their prevalence, persistence, and circulation within wastewater systems. This study characterized 37 antibiotic-resistant K. pneumoniae-related species strains isolated from two WWTPs in the metropolitan area of Barcelona, analyzing their antimicrobial resistance (AMR) profiles, antimicrobial resistance genes (ARGs), biocide and heavy metal tolerance genes (HMTGs), virulence factor genes (VFGs), biofilm-forming capacity, and conjugation ability. Among them, 70.3% were multidrug-resistant (MDR), and 16.2% were extensively drug-resistant. Whole-genome sequencing revealed diverse ARGs; all strains carried β-lactam resistance genes (14 ESBL and 12 carbapenemase producers), nearly all (96.9%) carried biocide or HMTGs, 64.9% harbored integrases, and all carried VFGs. Core-genome SNP analysis identified closely related strains across sampling periods and treatment stages, suggesting long-term persistence within the wastewater treatment system, despite biological and chemical processes in secondary treatment. Most strains (67.6%) displayed biofilm-forming capacity, and conjugation assays confirmed horizontal gene transfer in five of the seven ESBL-producing strains tested. High-risk clones were predominantly detected in the IFAS secondary treatment stage of the Gavà-Viladecans WWTP. The three strains recovered from the reclaimed water of the Baix Llobregat WWTP were ESBL or carbapenemase producers. Altogether, these results provide genomic and phenotypic evidence of the persistence and circulation of antibiotic-resistant K. pneumoniae-related species within wastewater treatment systems.IMPORTANCEWWTPs are essential for urban sanitation and environmental protection. Understanding how clinically relevant pathogens, such as ESBL and carbapenemase-producing K. pneumoniae-related species strains, behave in these settings may inform public health considerations. Investigating the presence and persistence of high-risk MDR pathogens in WWTPs helps identify circulation of AMR, assess the risk of gene transfer, and evaluate the potential for co-selection with other contaminants. This knowledge supports efforts to improve wastewater treatments, strengthen environmental surveillance, and develop integrated One Health strategies to limit the spread of AMR across human, animal, and environmental sectors.

Wastewater↗

PubMed2024

Shedding light on Klebsiella pneumoniae virulence: Engineering of broad host range bioluminescence reporter vectors for transcriptional analysis in drug resistant pathogens.

In this work, we report the construction of four bacterial luciferase-based promoter probe vectors with an expanded set of selectable markers, designed to facilitate their use in antibiotic-resistant bacteria. These vectors contain the low-copy-number, broad-host-range pBBR origin of replication and an origin of transfer, allowing efficient conjugative transformation into various bacterial genera. The broad host range origin also enables their use in bacterial strains that harbor other plasmids, as the pBBR origin is compatible with a wide variety of other plasmid replication systems. The utility of these vectors was demonstrated by quantifying capsule gene expression in both classical and hypervirulent Klebsiella pneumoniae strains lacking tolC, which encodes the outer membrane pore protein for tripartite transport systems. Our results revealed that the tolC mutation reduced capsule gene expression, highlighting a critical role for tolC in K. pneumoniae pathobiology and the utility of bioluminescence for studying gene expression in real time. These new vectors provide a flexible platform for circumventing antibiotic resistance phenotypes and studying gene expression across diverse bacterial species, including strains containing additional plasmids.

Klebsiella pneumoniae↗

PubMed2026

Multi-omics evidence reveals robust airborne-human resistome connectivity driven by high-risk ARGs and mediated by Staphylococcus.

Airborne microbiomes are considered an important source of human antimicrobial resistance (AMR) exposure, yet multi-omics evidence linking airborne and human nasal resistomes remains limited. Here, we integrated metagenomic sequencing and whole-genome sequencing of antibiotic-resistant Staphylococcus isolates to investigate the connectivity between air and human nasal resistomes in dairy farm environments. Metagenomic taxonomic profiling showed that Staphylococcus was prominent in total suspended particles (TSP) and consistently detected across all samples. Among environmental reservoirs, TSP resistomes exhibited the strongest similarity to human nasal resistomes. This connectivity was supported by multiple lines of evidence, including highly similar resistome profiles, extensive homologous antibiotic resistance gene (ARG) pairs, strain-level similarity of resistant Staphylococcus isolates, and conserved mobile ARG genetic contexts. Notably, this connectivity was primarily driven by high-risk ARGs, while Staphylococcus was frequently associated with mobile ARGs and represented the only shared pathogenic genomes carrying both ARGs and virulence factor genes between airborne and nasal samples. Although lower ARG diversity, nasal resistomes exhibited higher ARG burden, risk scores, antibiotic-resistant bacterial genome abundance, and prevalence of resistant Staphylococcus. Occupational exposure further increased total and high-risk ARG burdens among farm workers. Together, these findings indicate that TSP can serve as an important route of occupational AMR exposure, with high-risk ARGs and Staphylococcus contributing to connectivity between airborne and nasal resistomes. Incorporating the host microbiome may therefore provide a more complete assessment of human-associated AMR exposure within a One Health framework.

Airborneresistome↗

PubMed2025

Uncovering encrypted antimicrobial peptides in health-associated Lactobacillaceae by large-scale genomics and machine learning.

BACKGROUND: Antimicrobial peptides (AMPs) are well known for their broad-spectrum activity and have shown great promise in addressing the antibiotic-resistant crisis. The Lactobacillaceae family, recognized for its health-promoting effects in humans, represents a valuable source of novel AMPs. However, the global prevalence and distribution of AMPs within Lactobacillaceae remains largely unknown, which limits the efficient discovery and development of novel AMPs. RESULTS: We analyzed all available genomes (10,327 genomes), encompassing 38 genera and 515 species, to investigate the biosynthetic potential (indicated by the number of AMP sequences in the genome) of AMP in the Lactobacillaceae family. We demonstrated Lactobacillaceae species had ubiquitous (69.90%) biosynthetic potential of AMPs. Overall, 9601 AMPs were identified, clustering into 2092 gene cluster families (GCFs), which showed strong interspecies specificity (95.27%), intraspecies heterogeneity (93.31%), and habitat uniqueness (95.83%), that greatly expanded on the AMP sequence landscape. Novelty assessment indicated that 1516 GCFs (72.47%) had no similarity to any known AMPs in existing databases. Machine learning predictions suggested that novel AMPs from Lactobacillaceae possessed strong antimicrobial potential, with 664 GCFs having an additive minimum inhibitory concentration (MIC) below 100 μM. We randomly synthesized 16 AMPs (with predicted MIC < 100 μM) and identified 10 AMPs exhibiting varied-spectrum activity against 11 common pathogens. Finally, we identified one Lactobacillus delbrueckii-originated AMP (delbruin_1) having broad-spectrum (all 11 pathogens) and high antimicrobial activity (average MIC = 38.56 µM), which proved its potential as a clinically viable antimicrobial agent. CONCLUSIONS: We uncovered the global prevalence of AMPs in Lactobacillaceae and proved that Lactobacillaceae is an untapped and invaluable source of novel AMPs to combat the antibiotic-resistance crisis. Meanwhile, we provided a machine learning-guided framework for AMP discovery, offering a scalable roadmap for identifying novel AMPs not only in Lactobacillaceae but also in other organisms. Video Abstract.

Machine Learning↗

PubMed2025

Municipal sewage as a pathway for multidrug-resistant KPC-producing Klebsiella pneumoniae from hospital effluent to urban stream: challenges for wastewater management.

Carbapenemase-producing Klebsiella pneumoniae is among the mainly reasons for death from bacterial infection associated with antibiotic resistance. Its widespread dissemination, especially due to KPC enzyme, is one of the main challenges in One Health perspective. Here, we studied 42 KPC-producing K. pneumoniae isolates from hospital wastewater, municipal wastewater from wastewater treatment plant (WWTP), and urban stream which receives treated municipal effluent. The isolates presented broad resistance to β-lactams antibiotics, as well as to fluoroquinolones, and show antibiotic resistance profile very similar, even those from out-of-hospital settings. Along to blaKPC gene, blaCTX-M-1 (33,3 %, n = 14), blaCTX-M-8 (19 %, n = 8), qnrB (52,3 %, n = 22), qnrS (2,38 %, n = 1), and rmtB (19 %, n = 8) were detected. There was a predominance of gene that confers tolerance to silver and copper metals, as well as to virulence factor related to enterobactin and colibactin production. Macrorestriction genomic analysis by XbaI enzyme demonstrated several pulsotype, but some ones are related. Isolates from hospital wastewater were detected after 4 months at the same sampling point, as well as similar to those detected in WWTP and urban stream demonstrating the effluents role as spreaders of antibiotic resistance. This study provides data on the characterization of KPC-producing K. pneumoniae, which contributes to the epidemiological characterization of human pathogens transmitted by aquatic matrices. In view of the universal sanitation and control of antimicrobial resistance in the One Health perspective, greater investment in effluent treatment is necessary to avoid contamination and environmental dissemination of antibiotic-resistant bacteria.

Klebsiella pneumoniae↗

PubMed2025

Global diversity and evolution of Salmonella enterica serovar Panama: a genomic epidemiology study.

BACKGROUND: Non-typhoidal Salmonella is a globally important bacterial pathogen, typically associated with foodborne gastrointestinal infection. Some non-typhoidal Salmonella serovars can also colonise typically sterile sites in people to cause invasive non-typhoidal Salmonella disease. Salmonella enterica serovar Panama is responsible for a substantial number of cases of human bloodstream infection, but despite its global dissemination, numerous outbreaks, and a reported association with invasive non-typhoidal Salmonella disease, S enterica serovar Panama (S Panama) is understudied. We aimed to describe the genomic epidemiology and evolutionary history of S Panama to provide a vital baseline of understanding for this globally important serovar. METHODS: In this genomic epidemiology study, we analysed S Panama genomes derived from historical collections, national surveillance datasets, and publicly available epidemiological and whole-genome sequencing data which span the years 1931-2019. Maximum likelihood and Bayesian phylodynamic approaches were used to investigate population structure and evolutionary history and to infer geotemporal dissemination. A combination of different bioinformatic approaches with short-read and long-read data were used to characterise geographical and clade-specific trends in antimicrobial resistance (AMR) and genetic markers for invasiveness. FINDINGS: We analysed 836 S Panama genomes, of which 559 (67%) were sequenced as part of this study. The collection represents all inhabited continents and includes isolates collected between 1931 and 2019. We identified the presence of four geographically linked S Panama clades (C1 [ie, the Latin America and the Caribbean clade; n=338], C2 [ie, the European clade; n=124], C3 [ie, the Martinique clade; n=131], and C4 [ie, the Asia and Oceania clade; n=104]) and regional trends in AMR profiles. Most isolates (715 [86%] of 836) were pan-susceptible to antibiotics and belonged to clades circulating in Latin America and the Caribbean (64%, n=458). Most antibiotic-resistant isolates in our collection (113 [93%] of 121) fell within clades C4 (ie, the Asia and Oceania clade) and C2 (ie, the European clade), the latter of which had the highest invasiveness index values based on the conservation of 196 extraintestinal predictor genes. INTERPRETATION: This first large-scale phylogenetic analysis of S Panama has revealed important information about the population structure, AMR, global ecology, and genetic markers of invasiveness of the identified genomic subtypes. Our findings provide an important baseline for understanding S Panama infection. The presence of multidrug-resistant clades with elevated invasiveness index values should be monitored through ongoing surveillance, as such clades could pose an increased public health risk. FUNDING: UK Research and Innovation Global Challenges Research Fund and Biotechnology and Biological Sciences Research Council, UK Medical Research Council, Wellcome Trust, John Lennon Memorial Scholarship, Institut Pasteur, Santé publique France, Fondation Le Roch-Les Mousquetaires, Investissement d'Avenir Programme, and Australian National Health and Medical Research Council.

Humans↗

PubMed2026

Therapeutic potential of a novel virulent bacteriophage XQ-1 against avian pathogenic Escherichia coli infection in broiler chickens.

Avian Pathogenic Escherichia coli (APEC) represents a significant subgroup within extraintestinal pathogenic Escherichia coli strains and constitutes a substantial threat to the global poultry industry. Although the negative impacts of APEC have been mitigated considerably through antibiotic use, this practice has concurrently facilitated the widespread emergence and dissemination of antibiotic-resistant APEC strains worldwide. Consequently, bacteriophage has emerged as a promising alternative to antibiotics. In the current study, a novel virulent bacteriophage, designated XQ-1, was isolated from a sewage sample collected at a broiler chickens farm in Hubei Province, China. Notably, this bacteriophage exhibited the capability to lyse multiple APEC strains, including O1, O2, and O78 serotypes. The optimal multiplicity of infection (MOI) for bacteriophage XQ-1 was determined to be 0.001, yielding a maximum viral titer of 4.73 ± 0.31 × 1011 plaque-forming units (PFU) per milliliter. This bacteriophage displayed a latent period of 30 min, and a burst period of 80 minutes, corresponding to a burst size of 348 PFU per infected cell. Additionally, bacteriophage XQ-1 retained high lytic activity across a temperature range of 4-50 °C and maintained tolerance with a pH range of 3-11. Further in vitro studies demonstrated that bacteriophage XQ-1 holds potential as an effective disinfectant capable of directly lysing APEC strain JZ-1. In chick models subjected to intraperitoneal injection, exposure to APEC resulted in 100% mortality in chicks. However, treatment with bacteriophage XQ-1 significantly improved the survival rates of infected broiler chickens, reduced organ indexes, decreased bacterial loads in the liver and heart organs, and mitigated intestinal damage caused by APEC infection. Collectively, these findings suggest that bacteriophage XQ-1 represents a promising candidate for the prevention and treatment of APEC infections in poultry.

APEC↗

PubMed2025

Comprehensive genomic analysis of antibiotic resistance plasmids in animal-associated Staphylococcus aureus in France.

UNLABELLED: In Staphylococcus aureus, an animal pathogen and zoonotic agent, plasmids play a pivotal role in the acquisition and spread of antibiotic resistance genes (ARGs). This study investigated the plasmid content of 329 S. aureus isolates from livestock and companion animals collected in France between 2010 and 2021. Plasmids (n = 211) were identified from 139 isolates. The major families identified-rep7a, rep20, and rep10-were associated with specific resistance genes (str, cat, blaZ, erm(C)) and exhibited widespread horizontal transfer across different S. aureus sequence types (STs) and animal hosts. In temporal analysis, the rep7a/str and rep7a/cat plasmids circulating in horses were progressively replaced by a rep7a plasmid carrying both str and cat genes. The study also highlighted the presence of mosaic plasmids, which combined elements from different bacterial species/genera, confirming the broad host range of S. aureus plasmids and their ability to acquire ARGs from diverse sources. Moreover, the occurrence of hybrid plasmids (carrying multiple rep genes) underscores the plasticity of these vectors of ARGs. This study emphasizes the need to investigate the mechanisms driving the spread and persistence of antibiotic-resistant plasmids in S. aureus, with a view to developing strategies aimed at combating antibiotic resistance. IMPORTANCE: The spread of antibiotic resistance in Staphylococcus aureus is a growing concern, particularly in animals that can serve as reservoirs for resistant strains. This study highlights the crucial role of plasmids in transmitting resistance genes among different animal hosts and S. aureus lineages. The characterization of 329 isolates collected over 10 years revealed how certain plasmid families are associated with specific resistance genes and how they evolve over time. The occurrence of mosaic and hybrid plasmids further underscores the ability of S. aureus to acquire resistance from diverse bacterial sources. These findings provide key insights into the mechanisms shaping antibiotic resistance in this pathogen and emphasize the fact that understanding plasmid-driven resistance is essential for developing effective interventions to limit the spread of multidrug-resistant S. aureus in both veterinary and human medicine.

Animals↗