Decoding antibiotic resistance in tuberculosis: Role of RRDR and non-RRDR mutations in diagnostic perspectives.

The snowy sheathbill (Chionis albus (Gmelin, 1789)) is a coastal Antarctic bird that breeds on Antarctic and sub-Antarctic islands. In this study, we report the first complete mitochondrial genome sequence of C. albus. The mitogenome is circular, 19,116 bp in length, and contains 13 protein-coding genes (PCGs), including an ND3 gene with an extra nucleotide, 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). Notably, a duplicated region of ∼2.3 kb includes ND6 and two tRNAs. The overall nucleotide composition is 30.29% A, 30.37% C, 14.56% G, and 24.78% T, with a GC content of 44.93%. Phylogenetic analysis based on all 13 PCGs placed C. albus firmly within Charadriiformes and clustered with C. minor and, more distantly, with Burhinus bistriatus. This newly characterized mitogenome provides valuable resources for future studies on the phylogeny, molecular evolution, and biogeography of Charadriiformes and the family Chionidae.

Background: Colistin is a last-resort antimicrobial agent for treating multidrugresistant Enterobacterales. However, resistance has emerged globally through plasmid-mediated mcr genes and chromosomal mutations. Reports of wholegenome sequencing of colistin-resistant Escherichia coli from clinical settings in Thailand remain limited. Objectives: To characterize the molecular and phenotypic features of colistinresistant E. coli isolated from a tertiary hospital in Thailand using wholegenome sequencing (WGS). Materials and methods: Fourteen colistin-resistant E. coli isolates were collected from clinical specimens between 2021 and 2022. Antimicrobial susceptibility testing was performed using broth microdilution. WGS was applied to identify resistance determinants, plasmid replicons, virulence genes, phylogroups, and sequence types. Results: The prevalence of colistin-resistant E. coli was 1.2% (14/1203 isolates). Most isolates exhibited an ESBL-like multidrug-resistant profile with preserved carbapenem susceptibility. WGS revealed diverse sequence types (including ST131, ST95, ST58, ST69) and phylogroups, indicating polyclonal dissemination. Two mcr variants (mcr-1.1 and mcr-3.5) were identified on mobile plasmids (IncX4, IncI2, IncFII, IncHI2), with some isolates carrying both variants. Several isolates without mcr carried chromosomal mutations in mgrB, phoPQ, or pmrAB. Virulence genes, particularly adhesins, siderophore systems, and capsule- related determinants, were widely distributed. The detection of mcr-3.5, previously reported in livestock, within clinical isolates highlights potential zoonotic or foodborne transmission. Conclusion: Colistin-resistant E. coli in Thailand shows significant genetic diversity and frequent coexistence of mcr and ESBL genes, often on plasmids with high potential for horizontal transfer. These findings emphasize the importance of antimicrobial stewardship, stricter control of drug use in animals, and integrated genomic surveillance under a One Health framework to mitigate the dissemination of colistin resistance.

Integrated genomic surveillance, combining whole genome sequencing (WGS) of bacterial isolates with patient movement data, promises improved detection and prevention of pathogen transmission. However, evidence on its cost-effectiveness and clinical utility remains limited, not least because the full extent of transmission in hospital settings is difficult to capture. We conducted a 28-month observational study at Rigshospitalet, Copenhagen, collecting patient movement data and sequencing 18 438 bacterial isolates from 7398 patients across diverse species, infection sites, and resistance profiles. We estimated the hypothetical benefits of implementing integrative WGS surveillance, assuming that continued transmission could be prevented when WGS information was acted upon immediately. We found that 1975 of 7398 of culture-positive hospitalized patients (26.7%) harboured a pathogen genetically related to another patient's isolate. Of those, 1359 (68.8%) had an epidemiological link in the hospital, with Enterococcus faecium by far being the most prevalent bacteria involved in transmissions. WGS-informed prevention could hypothetically generate a net savings of €1.35 million annually if transmission was stopped once a clonal isolate was detected in a second patient. Furthermore, this approach could potentially have prevented an estimated 1284 hospital-acquired infections over the 28-month study period, including 94 cases characterized by the recovery of bloodstream isolates. Our integrated genomic surveillance approach reveals previously unexplored transmission landscapes. We discovered that transmission is widespread, varies between species, and is not limited to resistant isolates. Our results emphasize the potential of integrated genomic surveillance, the identification of local transmission hotspots, potential for greater savings by including susceptible isolates, and an incremental cost-effectiveness ratio classification by pathogen species.

Male mammals are of particular interest for molecular systematics as their cells contain two non-recombinant markers, the mitochondrial genome and the male-specific Y chromosome (MSY), which provide information on maternal and paternal evolutionary histories, respectively. Here, we assembled four single-copy MSY genes (AMELY, DDX3Y, SRY and ZFY), three homologs on theXchromosome, the mitogenome, and 21 autosomal introns from whole genome sequencing (WGS) data available for 123 male giraffes. We detected several instances of introgression between giraffe subspecies involving the mitogenome, MSY, and X-linked genes. The analysis of MSY haplotypes supports a deep separation in Africa between northern giraffes (subspecies antiquorum, peralta, rothschildi, and reticulata) and southern giraffes, with a large gap between intragroup and intergroup DNA distances (referred to as the 'MSY barcoding gap'). At a finer scale, southern giraffes can be divided into two geographic MSY groups that are distributed in East Africa (comprising the subspecies tippelskirchi and thornicrofti) and southern Africa (comprising the subspecies giraffa and wardi). These relationships are all supported by several exclusive synapomorphies in most DNA datasets. Our results provide strong support for two species of Giraffa, i.e., G. camelopardalis (northern giraffes) and G. giraffa (southern giraffes), but with ZFX alleles showing evidence of ancient introgression between the two taxa. The delimitation of Giraffa in two species is consistent with skull morphology and the evolution of highly distinctive phenotypes (reticulated versus Masai) in the hybrid zone between northern and southern species in southern Kenya which may have promoted the reinforcement of prezygotic isolation, thus limiting gene flow between them.

Functional DNA methylation abnormalities are a hallmark of human cancers and may be a promising biomarker for their early diagnosis. Moreover, the largest methylation differences can improve the sensitivity of noninvasive diagnoses of solid tumors. We combined whole-genome bisulfite sequencing (WGBS) and mRNA-seq data from 33 paired hepatocellular carcinoma (HCC) and adjacent tissues to identify methylation markers that could be used for noninvasive diagnosis in blood samples. Methylation markers were selected according to the following criteria: differentially methylated regions (DMR) located in the promoter region with large differences in methylation (Δβ > 0.3) and inverse correlation with matched gene expression (cor < -0.3). Cell-free DNA (cfDNA) from 48 patients with HCC and 24 normal participants was used to verify the performance of meTSPYL5 using qMSP. Integrated WGBS and transcriptomic data analysis identified eight target promoter hyper-DMRs. After confirming the WGBS profiles of genes in peripheral blood mononuclear cells, meTSPYL5 was selected to further verify the plasma cfDNA samples by qMSP. The results of plasma validation showed that the methylation detection of meTSPYL5 was sensitive for identifying HCC, with a sensitivity and specificity of 85.4% and 100%, respectively. Pan-cancer analysis found that the methylation level of TSPYL5 was elevated in multiple cancer types, indicating that it lacks cancer-type specificity; however, this result does not affect its application value in monitoring high-risk populations of HCC. By analyzing and integrating all available high-throughput epigenomic and transcriptomic data from human HCC tissues, we identified eight regions as potential diagnostic biomarkers for HCC. Integrative analyses of epigenomic and transcriptomic data provide an efficient method to identify diagnostic biomarkers for human cancers. Methylated TSPYL5 in plasma is a promising biomarker for the detection and screening of HCC.

Phenotypic and genotypic characterization of antimicrobial-resistant uropathogens in community settings of India: A multicentric cross-sectional study.

A novel chimpanzee-derived adenovirus, a recombinant of Mastadenovirus exoticum and Mastadenovirus blackbeardi members, reveals lineage-specific recombination hotspots in simian adenoviruses.

Urban broiler production is rapidly expanding in East Africa, raising public health concerns about zoonotic pathogens such as Campylobacter and the spread of antibiotic resistance. This study investigated the occurrence and phenotypic and genotypic antibiotic resistance of Campylobacter from broilers in urban and peri‑urban Uganda. A total of 194 samples, including cloacal swabs (n = 157) and boot socks (n = 37), were collected from 28 randomly selected farms in three districts. Campylobacter was isolated according to ISO 10272-1 and tested for susceptibility to nalidixic acid, ciprofloxacin, tetracycline, streptomycin, and erythromycin by disk diffusion following European Committee on Antimicrobial Susceptibility Testing guidelines. Species identification and resistance genotypes were determined by whole-genome sequencing. Isolates that could not be re-cultivated were excluded from further analyses. Campylobacter was isolated from all 194 samples (100%). Of the 157 sequenced isolates, 54% (n = 84) were Campylobacter coli and 46% (n = 73) were Campylobacter jejuni. Of the 170 isolates tested for antibiotic susceptibility, 16% (n = 28) were resistant to all five antibiotics. No isolate was susceptible to ciprofloxacin. Multidrug resistance occurred in 61% (51/84) of C. coli and in 6% (4/72) of C. jejuni isolates. Strong concordance was observed between quinolone resistance and gyrA T86I mutation, tetracycline resistance and tet(O/32/O) or tet(O) genes, and in C. coli, streptomycin resistance and ant(6)-Ia gene. Broilers in urban and peri‑urban Uganda are frequently colonized with antibiotic-resistant Campylobacter, highlighting the need for strengthened biosecurity and antibiotic stewardship to mitigate public health risks.

Rapid identification of non-tuberculosis mycobacteria in simulated positive blood cultures with MALDI-TOF MS and Mycobacterium multiplex PCR detection panel.

Panton-Valentine leukocidin-positive sequence type 88 methicillin-resistant Staphylococcus aureus emerging as nosocomial pathogen in Brazil.

Epidemiological characteristics and viral molecular evolution analysis of severe fever with thrombocytopenia syndrome in Shandong Province, China.

Human adenoviruses (HAdVs) are important respiratory pathogens that circulate globally and frequently cause outbreaks, particularly among pediatric populations. Despite their clinical relevance, recent data on genome-wide evolution and recombination of circulating HAdVs in Korea remain limited. In this study, we characterized the epidemiological dynamics and genomic evolution of HAdVs detected in Gwangju, South Korea, between 2023 and 2025. Molecular epidemiological surveillance of respiratory samples was conducted, followed by phylogenetic and whole-genome sequencing analyses. Adenovirus positivity increased sharply during an outbreak from August to October 2023, with pediatric cases predominating. Phylogenetic analysis identified eight genotypes from species B and C, with genotype B114 as the principal outbreak strain. Whole-genome sequencing revealed recombination events in both species, involving antigenic, replication, and packaging regions. These findings indicate that circulating HAdVs undergo continuous genome-wide recombination, resulting in genotype-specific outbreaks that are not fully captured by capsid-based classification alone. Our study highlights the importance of whole-genome approaches for understanding adenovirus evolution and provides insights into the genomic diversity underlying recent outbreaks.

Multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium (S. Typhimurium) poses a growing threat to food safety and animal health, particularly in the swine industry. In this study, we characterized a highly resistant ST strain isolated from a Quebec swine farm using whole-genome sequencing and phenotypic assays. The isolate harbored two plasmids, one of which encoded resistance to seven major antibiotic classes, including β-lactams, aminoglycosides, and sulfonamides, along with multiple virulence factors. To counteract these resistance mechanisms, we developed a nano-enabled antibacterial combination therapy (NeACT) by co-encapsulating amoxicillin (AMOX) and the β-lactamase inhibitor tazobactam into cyclodextrin encapsulated in liposomes (LP-CAT). Physicochemical analysis confirmed optimal particle size, charge, and stability, while checkerboard assays demonstrated strong drug synergism. The LP-CAT formulation drastically restored antimicrobial efficacy, reducing the AMOX minimum inhibitory concentration (MIC) from >2000 µg/mL to ~60 µg/mL. Using porcine intestinal epithelial (IPEC-J2) cells as an intracellular infection model, our study showed the potential of LP-CAT to remove >94% of intracellular bacteria with no cytotoxic effect. The ability of LP-CAT to resolve intestinal infection was further verified in Caenorhabditis elegans (C. elegans) intestinal infection model. These findings establish LP-CAT as a safe and effective strategy to revive antibiotic potency against intracellular MDR pathogens, offering a novel tool for combating antimicrobial resistance in livestock and safeguarding public health.

Optimizing genomic mating in sturgeon by incorporating dominance effects from whole-genome sequencing

Genome analysis of blaNDM-5 and blaKPC-2 co-occurrence in ST45-K62 carbapenem-resistant Klebsiella pneumoniae isolate from China.

Beijing, a large urban center with complex food supply chains, faces increasing challenges from foodborne Campylobacter infections. However, local data on antimicrobial resistance, source attribution, and pathogenic characteristics remain limited. This study aimed to clarify long-term trends, resistance patterns, and likely infection sources of Campylobacter in Beijing to inform prevention and treatment strategies. From 2016 to 2023, 27,691 stool samples were collected from patients with foodborne diseases in 45 hospitals across Beijing. Campylobacter isolates were recovered and identified, followed by antimicrobial susceptibility testing, and whole-genome sequencing. A core-genome MLST-based extreme gradient boosting (XGBoost) model was applied for machine-learning source attribution. A total of 1204 Campylobacter isolates were identified, including 1005 C. jejuni, 198 C. coli and one C. fetus. The proportion of C. coli increased compared with the early surveillance years and reached its highest level in 2023. Both C. jejuni and C. coli showed >90% resistance to fluoroquinolones and tetracyclines, and C. coli has a much higher resistance rate to macrolide. Machine-learning analysis identified chicken as the major source for C. coli infections, accounting for 75.76% cases. This 8-year genomic surveillance highlights the sustained and increasing contribution of C. coli and extensive resistance in Beijing, supporting targeted control measures and antibiotic stewardship in foodborne disease management.

An emerging tick-borne spotted fever group Rickettsia in China: Isolation, genomics, and human infection of Rickettsia koreansis.

This study assessed longitudinal trends in antimicrobial resistance (AMR) among Enterobacterales causing companion animal infections in Portugal between 2020 and 2023 and characterized carbapenemase-producing Enterobacterales (CPE). A collection of 4155 non-duplicate clinical Enterobacterales isolates underwent antimicrobial susceptibility testing mainly through disk diffusion, targeting β-lactams, fluoroquinolones, aminoglycosides and folate pathway inhibitors. Possible bacteria-AMR associations and temporal trends were statistically assessed. Potential CPE were selected on Brilliance™ CRE Agar, confirmed by multiplex PCR and characterized by whole-genome sequencing (Illumina NovaSeq). In silico MLST was performed and the clonality of the strains was evaluated through maximum likelihood phylogenetic trees and pairwise SNP matrixes. Klebsiella spp. and Enterobacter spp. exhibited a higher likelihood of AMR than Escherichia coli (P < 0.001, ORs between 2.56 and 14.32). Most AMR phenotypes remained stable or declined over time, although fluoroquinolone resistance increased toward the end of the study period. Eighteen CPE mostly associated with high-risk global STs (E. coli ST410 and ST457, Klebsiella pneumoniae ST11, ST147 and ST307, respectively) were detected, carrying blaKPC-3, blaNDM-5, blaOXA-181 or blaOXA-244. Genomic analysis showed four CPE strain pairs from epidemiologically unrelated sources had < 10 SNPs differences, indicating possible recent clonal transmission of E. coli ST4981 and K. pneumoniae ST147 and ST273 strains. Overall, this study presents longitudinal AMR surveillance data from companion animal Enterobacterales infections and characterizes the genetic diversity of CPE, having detected international high-risk clones and possible transmission events. These findings reinforce the importance of integrating companion animals into One Health surveillance systems and antimicrobial stewardship strategies.

A national study confirms a low occurrence of antimicrobial resistance amongst Escherichia coli isolates from the caecae of Australian meat chickens.