Global genomic surveillance has emerged as a foundational pillar of public health in the twenty-first century, enabling real-time tracking of pathogen evolution and informing outbreak response. This chapter examines the strategic architecture of global genomic surveillance, focusing on its application to arboviruses such as chikungunya virus (CHIKV). It explores the integration of genomic data with epidemiological, clinical, and environmental information within a One Health framework, while addressing critical challenges in governance, equity, and interoperability. The discussion covers the entire genomic surveillance workflow, from sample collection and sequencing to bioinformatic analysis and phylogenetic inference, and highlights the transformative role of artificial intelligence (AI) in predictive surveillance. By analyzing global initiatives, operational barriers, and emerging technologies, this chapter underscores the necessity of sustainable, equitable, and interoperable genomic systems to proactively address current and future infectious disease threats.
Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseasesC Z Zhang, S S Lyu, X D Han, H Wang, Y Sun, X D Liu
Objective: To investigate the molecular epidemiological characteristics, antimicrobial resistance mechanisms, and clinical risk factors for infection with carbapenem-resistant Klebsiella pneumoniae (CRKP), and to examine the relationship between antimicrobial resistance and virulence. Methods: A total of 528 Klebsiella pneumoniae (KP) isolates and corresponding clinical data were collected from hospitalized patients at Qingdao Municipal Hospital between November 2016 and October 2023. Based on antimicrobial susceptibility testing results, 80 patients with CRKP infection were assigned to the CRKP group. Patients with carbapenem-susceptible K. pneumoniae (CSKP) isolates recovered within 7 days before or after the CRKP isolation date were selected as matched controls for each patient in the CRKP group. If insufficient eligible controls were available, the matching window was expanded to 30 days before or after the isolation date. Ultimately, 160 matched patients were included in the CSKP group. Whole-genome sequencing was performed on all included isolates to systematically characterize their molecular epidemiological features and resistance and virulence gene profiles. A multivariable logistic regression model was used to identify independent risk factors for CRKP infection. Spearman rank correlation analysis was performed to assess the correlation between resistance and virulence gene scores. Results: Multivariable logistic regression analysis showed that a history of antimicrobial agent use in the 30 days before infection (OR=4.411, 95%CI: 1.749-11.128; Wald χ²=9.882; P<0.01) and invasive abdominal procedures in 30 days before infection (OR=6.846, 95%CI: 3.141-14.922; Wald χ²=23.411; P<0.01) were independent risk factors for CRKP infection. ST11 was the predominant sequence type among CRKP isolates (80.0%), and the blaKPC-2 gene was the predominant resistance determinant (88.8%). The predominant CRKP clone, ST11, underwent a serotype transition from ST11-K25/O5 to ST11-K64/O2a. At the overall population level, the antimicrobial resistance gene score was negatively correlated with the virulence gene score (Spearman ρ=-0.321, P<0.001). However, subgroup analysis showed no significant correlation between the two scores within the same ST11 clone (Spearman ρ=0.020, P=0.872). These findings suggest that the overall negative correlation was a population-level artifact caused by inherent phenotypic differences among distinct clonal groups, rather than an evolutionary trade-off in which the acquisition of antimicrobial resistance within the same clone resulted in reduced virulence. The intensive care unit (ICU) was the central hub for nosocomial clonal transmission of CRKP. The predominant clone may have disseminated from the ICU to general wards through patient transfers, healthcare workers, or medical equipment, thereby forming interdepartmental transmission chains. Conclusions: A history of antimicrobial agent use and invasive abdominal procedures in the 30 days before CRKP infection were independent risk factors for CRKP infection. CRKP isolates frequently carried plasmids coharboring multiple antimicrobial resistance determinants and exhibited extensive antimicrobial resistance.
Bovine Rotavirus (BRV) is the main pathogen responsible for viral diarrhea in calves, which has a serious impact on the cattle industry and leads to economic losses. Therefore, this study aimed to fill the gap in the epidemiological research of yak-sourced rotavirus in Qinghai Province by investigating the infection rate and antibody positive rate of BRVA from yaks in Qinghai Province. We collected a total of 1,195 yak anal swab samples, 95 diarrheal fecal samples, and 834 serum samples from various cities and prefectures in Qinghai Province. The TaqMan probe method and indirect ELISA assay were used to detect and comprehensively analyze the infection rate of BRVA and the positive rate of serum antibodies in different cities and prefectures of Qinghai Province. Additionally, the key factors influencing virus transmission were explored in combination with epidemiological characteristics. The results showed that BRVA infections occurred to varying degrees in Xining City, Haidong City, Haibei Tibetan Autonomous Prefecture, Huangnan Tibetan Autonomous Prefecture, and Haixi Mongolian and Tibetan Autonomous Prefecture. The dominant genotype G6P[5] of the BRVA strains was first identified from yak populations in Qinghai Province. A total of 766 positive sera were detected by indirect ELISA, with an overall antibody positive rate of 91.85%. This study not only provided the latest epidemiological data of bovine rotavirus from yak populations in Qinghai Province, but more importantly, offered crucial data support for formulating targeted prevention and control strategies against BRVA in this region.
The clinical teacherOrlando Carlos Conceição-Neto, Frederico Medeiros Rosas da Silva, Erika Verissimo Villela, Paula Borges de Andrade Lemes, João Pedro Gotti Ferreira, Chiara Gur…
BACKGROUND: Medical biochemistry and molecular genetics stand out as some of the most demanding courses for first-year medical students, who often require repeated exposure to complex pathways and molecular processes. To provide additional support in this early stage of training, we created PodBases, a peer-led educational podcast integrated into an academic mentoring program and made available through a widely accessible global audio-streaming platform. The goal was to offer brief, clinically oriented episodes that reinforced key concepts and complemented traditional teaching. APPROACH: The initiative followed a defined workflow involving close collaboration between student tutors and faculty. Tutors prepared scripts aligned with the weekly course content, which were subsequently reviewed for accuracy. Recordings were made using smartphones and edited with freely accessible audio-editing tools and published on a podcast-hosting service. We documented the entire process to create a practical tutorial that facilitates replication in similar educational settings. EVALUATION: Between May 2023 and January 2026, 30 episodes were published, reaching 13,050 streams across 16 countries. Student feedback highlighted the usefulness of the podcast during commutes and study sessions. Mentors reported skill development in communication, simplification of content and teamwork. IMPLICATIONS: PodBases demonstrates that student-generated podcasts can effectively complement traditional teaching by reinforcing core topics, supporting learner autonomy, enhancing comprehension and developing tutors' pedagogical skills. The experience suggests that peer-led digital resources can enhance comprehension while promoting engagement and professional growth in the foundational years of training. TRIAL REGISTRATION: Not applicable.
MicrobiologyOpenPinar Sagiroglu, Dursun Alp Gundog, Candan Gungor, Kursat Koskeroglu, Mustafa Altay Atalay, Adalet Dishan, Yeliz Ucar, Aytac Akcay, Huseyin Burak Disli, Harun …
This study aimed to assess the genetic diversity and potential epidemiological overlap of Staphylococcus aureus using molecular (spa and SCCmec typing) and phenotypic characterization of 108 isolates obtained along the farm-to-fork continuum (dairy and meat chains) and 50 human clinical isolates. Forty-four spa types, including 17 novel patterns, were identified, with t11284 and t127 predominating among animal-related MRSA and clinical MRSA, respectively. Six SCCmec types (I-VI) were detected in the majority of isolates (85.2%), with SCCmec IVa prevalent in farm-to-fork isolates (67%) and SCCmec III dominant in clinical isolates (28%). Spa repeat-based MST analysis revealed a heterogeneous distribution of isolates across clusters, with identical spa types detected in multiple source categories, indicating genetic relatedness rather than direct transmission events. Overall, 54.6% of isolates exhibited a multidrug-resistant phenotype. Farm-to-fork isolates showed mainly β-lactam resistance (≥ 85%), whereas clinical MRSA exhibited broader resistance profiles, including high fluoroquinolone resistance (≥ 92%). PVL was detected in 41 isolates (38%), predominantly in MRSA, and was associated with SCCmec IV/V and diverse spa types. Toxin genes (tst-1, sea, seb, and sed) were mainly confined to clinical MRSA, suggesting source-associated distribution of virulence determinants. Biofilm formation was observed in 49 isolates (45.3%), more frequently among farm-to-fork isolates. Our study demonstrate marked genetic and phenotypic diversity of S. aureus across farm-to-fork and human clinical sources and suggest the presence of shared genetic lineages among isolates from different sources. The results support the importance of integrated One Health surveillance for monitoring antimicrobial-resistant and virulent S. aureus populations across interconnected ecological compartments.
Emerging infectious diseasesLingzi Xiaoli, Taylor Griswold, G Sean Stapleton, Lee S Katz, Zachary Ellison, Kaitlin A Tagg, Hattie E Webb, Katharine Benedict, Jessica C Chen
Nontyphoidal Salmonella enterica serovar Hadar causes poultry-associated salmonellosis outbreaks in the United States. One persisting strain of Salmonella Hadar caused 5 multistate outbreaks resulting in ≈2,000 human cases during 2020-2023. The Centers for Disease Control and Prevention designated the strain as reoccurring, emerging, or persisting (REP), related within 26 core-genome allele differences. That REP strain has caused human illnesses by consumption of commercial poultry food products or contact with backyard poultry. To investigate the REP strain's evolution and identify possible markers for source attribution, we performed phylogenetics and molecular clock analysis on 404 genomes subsampled from routine surveillance and outbreaks. The most recent common ancestor likely emerged in early 2018. We identified 2 clades: clade 1, associated with backyard poultry and other food sources, and clade 2, predominantly linked to commercial poultry products. We found 2 clade-specific single-nucleotide polymorphism markers; in silico screening of additional isolates supported their use for source attribution.
Antimicrobial resistance (AMR) constrains effective treatment and carries implications for infection control, surveillance, and public health. The World Health Organization (WHO) priority bacterial pathogen framework has intensified the need for diagnostic innovation by redefining research priorities around organisms combining high disease burden with complex resistance profiles. Molecular diagnostics have accordingly moved beyond culture-based workflows, integrating rapid pathogen identification, resistance-marker detection, genomic surveillance, and clinical decision support. The present study conducted a bibliometric mapping of the literature on WHO priority pathogens. Rather than addressing resistance at a general level or a single pathogen or technology, it integrates priority pathogens, molecular platforms, and resistance markers within a single framework, tracing their joint thematic and temporal evolution along an explicit pathogen-platform-marker axis. Scopus-indexed articles and reviews (2000-2025) were retrieved, yielding 1746 publications after screening adapted from the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Analyses used Bibliometrix/Biblioshiny, R, and VOSviewer. The literature expanded markedly after 2018, led by China and the United States. Methicillin-resistant Staphylococcus aureus (MRSA), Mycobacterium tuberculosis, Enterococcus faecium, and the Enterobacterales-carbapenemase axis constituted the principal thematic cores, whereas conventional polymerase chain reaction (PCR)/nucleic acid amplification testing (NAAT) and whole-genome sequencing were the dominant platforms. Overall, the field has evolved from pathogen detection into an AMR-centered translational domain encompassing resistance prediction, genomic epidemiology, surveillance, and clinical decision support. Diagnostic development, stewardship, and surveillance depend on hybrid workflows coupling rapid marker-targeted assays with genome-based characterization, delivering actionable resistance within clinically meaningful timeframes, and extending coverage to underrepresented pathogens and platforms.
Emerging infectious diseasesNgoc Anh Bui, Zoe Yi Song, Samuel M S Cheng, Duy Tung Dao, Lydia D J Chang, Gigi Y Z Liu, Quang Huy Nguyen, Thi Hang Dang, Quoc Hung Nguyen, Tom L Y Woo, Coco …
Swine influenza A viruses (IAV-S) caused the 2009 H1N1 pandemic and pose a future zoonotic and pandemic threat. Vietnam represents a critical hotspot for IAV-S emergence within East and Southeast Asia, with dense swine and human populations and intensive livestock trade. We conducted genomic surveillance of IAV-S in Vietnam during 2020-2024, extending previous surveillance from 2013-2019. We identified multiple co-circulating H1 and H3 clades, including pandemic H1N1, Eurasian avian-like, and European lineages, by conducting phylogenetic analysis of 56 IAV-S isolates (21 H1N1, 31 H1N2, and 4 H3N2). Three H1 clades persisted exclusively in Vietnam, circulating up to 12 years. Phylogeographic analysis revealed multiple independent introduction events from North America, Europe, China, Thailand, and Cambodia. We detected extensive reassortment that frequently involved pandemic H1N1 virus internal genes. We identified several lineage-specific mutations associated with mammalian adaptation. Our findings underscore the ongoing IAV-S evolution and need for sustained surveillance in Vietnam.
Trends in biochemical sciencesJosé Sotelo-Silveira, Alexander de Luna Fors, Thomas Kislinger, Bianca Zingales, Alicia González-Manjarrez
The Pan-American Association for Biochemistry and Molecular Biology (PABMB) has promoted scientific exchange, education, and research in the molecular biosciences across the Americas for more than five decades. By linking national societies operating in markedly different scientific environments, PABMB provides a regional framework for meetings, training, researcher mobility, and international collaboration, with particular emphasis on early-career scientists.
MycopathologiaGabriela Ladeira Sanzo, Renata Osório de Faria, Juliana Tasende Ferrando, Marcela Brandão Costa, Isabela de Souza Morales, Giulia Batista Freitas, Lara Costa G…
Sporotrichosis, a subcutaneous mycosis caused by Sporothrix spp., has emerged as a major zoonotic disease in Brazil, primarily driven by Sporothrix brasiliensis. The southern state of Rio Grande do Sul exhibits distinctive ecological and climatic conditions that may shape the persistence and distribution of this pathogen in this region. This study conducted molecular and epidemiological surveillance of feline and canine sporotrichosis in southern Rio Grande do Sul, Brazil. A total of 100 isolates from the culture collection of the Veterinary Mycology Laboratory at the Federal University of Pelotas (UFPel) were analyzed by PCR targeting the calmodulin (CAL) gene for species identification. Fourteen representative isolates were sequenced and subjected to phylogenetic analysis using the Maximum Likelihood method, including reference sequences from Brazil, Paraguay, and Argentina. Epidemiological and clinical variables, including host species, sex, lesion site, and morphology, were evaluated to characterize the epidemiological and clinical profiles of sporotrichosis in the study region. S. brasiliensis and S. schenckii were identified in 97% and 3% of the isolates, respectively. The CAL-based phylogeny confirmed the monophyly of S. brasiliensis and revealed low intraspecific variability with regional clustering among southern Brazilian isolates. When interpreted within the Southern Cone context, the topology indicated a close genetic affinity between isolates from Rio Grande do Sul and reference sequences from Argentina and Paraguay. These findings confirm the territorial expansion of S. brasiliensis across southern Brazil and emphasize the importance of molecular surveillance for detecting and tracking the circulating lineages. Continuous regional monitoring is crucial for strengthening One Health strategies and mitigating the zoonotic spread of sporotrichosis in the Southern Cone.
Genome medicineNicole Ullrich, Roland Diel, Karen Meywald-Walter, Christian Schwarzbach, Matthias I Gröschel, Martin Kuhns, Inna Friesen, Stefan Niemann, Viola Dreyer
BACKGROUND: Tuberculosis (TB) epidemiology in low-incidence settings is increasingly influenced by the importation of Mycobacterium tuberculosis complex (Mtbc) strains from high-incidence regions. Globally, more virulent "generalist" lineages such as Lineage 2 (L2) and Lineage 4 (L4) contrast with geographically restricted "specialist" lineages (L1, L3, L5-L9), reflecting differences in transmissibility and adaptation. The introduction of strains of diverse lineages can alter local transmission dynamics and drug susceptibility patterns, underscoring the need for high-resolution genomic surveillance. METHODS: We performed whole genome sequencing (WGS) on 3,131 Mtbc strains collected from patients with TB in Hamburg, Germany, over 25 years (1997-2021). We analysed population structure and transmission dynamics in relation to patients' self-reported geographical origins. RESULTS: Strains from major Mtbc lineages L1-L6 and M. bovis were detected, with L4 strains being most prevalent (74.6%, n = 2,337). Lineage distribution shifted over time: L4 strains decreased from 83.5% in the first five years to 63.0% in the last five years, while L3 strains increased from 4.8% to 18.1%. These changes correlated with an increasing number of foreign-born patients rather than enhanced transmission of strains of specific lineages. L4 strains accounted for most clusters (81%, 218/269). In-depth analyses revealed heterogeneity in transmission potential among L4 sublineages, underscoring the importance of sublineage-level resolution. Strains of sublineages L4.1.2.1, L4.8, and L4.3 were detected in patients born in over 15 regions each, with >57% of cases from Europe, supporting their representation as globally successful generalist lineages. CONCLUSIONS: Migration substantially increased the genetic diversity of the Mtbc population in Hamburg but did not fundamentally alter local transmission dynamics. Transmission remained lineage-specific and was predominantly driven by established L4 strains, suggesting that successful transmission is mediated by locally adapted sublineages. Predominant L4.1.2.1 and L4.8 sublineages occurred in individuals from a wide range of countries, supporting the generalist-specialist hypothesis at the sublineage level. These findings highlight the interplay between pathogen characteristics and host demographics in shaping transmission and the value of integrating genomic, demographic, and epidemiological data to distinguish imported cases from sustained local transmission in low-incidence settings.
Archives of microbiologyMaged El-Ashker, Shahinda Rezk, Stefan Monecke, Mayada Gwida, Sherine Shawky, Elke Müller, Lisa Schönau, Lukas Rüttiger, Ralf Ehricht
Data regarding the molecular epidemiology, clonal diversity, and resistance mechanisms of methicillin-resistant Staphylococcus aureus (MRSA) causing skin and soft tissue infections (SSTIs) in Egypt remain limited. This study aimed to characterize the clonal structure, resistance determinants, and virulence profiles of MRSA isolates from SSTIs in Alexandria, Egypt. We analyzed 38 non-duplicate MRSA isolates recovered between July and December 2024 from SSTI specimens submitted to a central microbiology laboratory serving hospitals and outpatient clinics in Alexandria, Egypt. Molecular characterization of antimicrobial resistance, virulence, and biofilm-associated genes were performed using DNA microarray analysis, assigning isolates to clonal complexes (CCs). The diagnostic performance of lateral flow assays (LFAs) for penicillin-binding protein 2a (PBP2a) and Panton-Valentine leukocidin (PVL) detection was evaluated against microarray results. Ten distinct CCs were identified, predominantly CC152 (28.9%) and CC1153 (23.7%). A high prevalence of PVL genes (lukS-PV/lukF-PV) was detected (78.9%), demonstrating significant lineage specificity (p < 0.001) among CC152, and CC1153. Analysis of the antimicrobial resistance gene profiles revealed a broad genotypic resistance repertoire across the collection. Notably, 78.9% carried the fusidic acid resistance gene fusC and 71.1% carried the aminoglycoside resistance gene aacA-aphD, both significantly associated with CC152 and CC1153 (p < 0.001). One isolate (2.6%; lineage CC1-MRSA-[V/VT + fus+ccrAB1]) was confirmed as vancomycin-resistant (VRSA). LFAs demonstrated 100% concordance with microarray results for both PBP2a and PVL detection. This study demonstrates a high prevalence of PVL-positive, multidrug-resistant MRSA lineages among SSTI isolates in Alexandria. The frequent detection of CC152 and CC1153 lineages co-carrying mobile genetic element (MGE)-borne resistance genes (fusC and aacA-aphD) highlights the expansion of multidrug resistance profiles among community-associated genetic backgrounds. Furthermore, the detection of a sporadic VRSA strain emphasizes the necessity of routine phenotypic susceptibility testing alongside molecular screening. The 100% concordance of LFAs supports their implementation as rapid, culture-based screening tools in laboratory diagnostic workflows to guide empirical antibiotic therapy and infection control.
BACKGROUND: Leptospirosis is a significant zoonotic disease in Thailand and globally. The causative agents are the spirochete bacteria in the genus Leptospira. An updated assessment of molecular epidemiology in Thailand is needed. METHODOLOGY/PRINCIPAL FINDINGS: Remnant EDTA blood specimens from suspected leptospirosis cases collected between June 2024 and July 2025 from the Central, Northern, Northeastern, and Southern regions of Thailand, were referred to the National Institute of Health. Demographic data were collected. Confirmed cases were diagnosed using TaqMan real-time PCR targeting LipL32 with a positively threshold of Ct < 37. Partial 16S rDNA (approximately 500 bp) was sequenced using Oxford Nanopore (Oxford, UK) and analyze by BLASTn. Among 1,063 suspected cases, 34 (3.2%) were real-time PCR confirmed. The majority of the cases were male (58.8%), primarily residing in Nan province (55.9%), and most positives were from specimens collected during the rainy season (76.5%). Twenty-six of 34 sequences (76.5%) clustered with L. interrogans, and 8 of 34 (23.5%) clustered with L. weilii within the primary pathogenic (P1) clade. Re-examination with published Thai and regional datasets showed broad circulation of L. interrogans and a Northern Thailand-Lao People Democratic Republic (PDR) focus for L. weilii To our knowledge, this is the first evidence of L. weilii detected in human clinical specimens in Thailand. CONCLUSION/SIGNIFICANCE: Pathogenic L. interrogans and L. weilii caused human Leptospirosis in Thailand during 2024-2025. These findings update the epidemiological status of Leptospira spp. in Thailand and can guide surveillance and control.
Journal of clinical virology : the official publication of the Pan American Society for Clinical VirologyLilian Bosibori Obaga, Tharathip Boondouylan, Warinya Nuwong, Navin Horthongkham, Kamol Suwannakarn, Pravech Ajawatanawong, Pravarit Athiprayoon, Atsadang Boon…
INTRODUCTION: Dengue virus serotype 4 (DENV4) co-circulates with other serotypes in Thailand, a hyperendemic setting characterized by cyclical shifts in serotype predominance. During the COVID-19 pandemic, related public health interventions may have influenced dengue detection, transmission and epidemiological dynamics. MATERIALS AND METHODS: A total of 413 dengue NS1/PCR-positive samples collected from 2018 to 2024 at a tertiary hospital in Bangkok were serotyped using a real-time PCR DENV1-4 subtyping assay. Forty-seven DENV4-positive samples (Ct < 32) underwent whole-genome sequencing using the ATOPlex DENV1-4 panel on the DNBSEQ-G99RS platform. Sequencing reads were processed using CLC Genomics Workbench, followed by phylogenetic, mutation, codon-based selection-pressure, and epitope-mapping analyses. RESULTS: DENV4 was identified in 18.2% (75/413) of samples, with 48% of cases requiring hospitalization. Detection increased markedly from 11.8% (22/186) during 2018-2021-23.3% (53/227) during 2022-2024 (proportion ratio, 1.97; p = 0.0025). Among the 47 whole-genome-sequenced samples, most strains clustered within genotype I lineage 4I_A.3 and showed lineage-associated non-synonymous substitutions. NS1-A90T, NS2A-L113F, and NS3-F523Y appeared exclusively during 2022-2024 (p < 0.001), whereas NS2A-L113F, NS5-G223S, and NS5-Q631R showed concordant positive-selection signals by FEL and MEME. CONCLUSIONS: This hospital-based study highlights an increase in DENV4 detection in Bangkok during 2022-2024 compared with 2018-2021, accompanied by predominance of lineage 4I_A.3 distinct from Malaysian and Indonesian strains reported during a similar period. These findings support integrated clinical and genomic surveillance to monitor DENV serotype and genotype dynamics and inform public health and vaccine strategies.
MedicineYoushu Wang, Bo Zhang, Songye Gu, Qizhen Yu, Junwei Chen
This study examined the molecular transmission characteristics of human immunodeficiency virus type 1 (HIV-1) among newly diagnosed HIV/acquired immunodeficiency syndrome cases in Dinghai District, Zhoushan City, Zhejiang Province, with the aim of informing targeted prevention and control strategies. Newly reported HIV/acquired immunodeficiency syndrome cases from 2022 to 2024 were enrolled, and demographic as well as epidemiological information was collected. Plasma samples obtained prior to antiretroviral therapy were subjected to reverse transcription and nested polymerase chain reaction to amplify the polymerase gene. HIV-1 subtypes were determined using Neighbor-Joining phylogenetic analysis, and molecular transmission networks were constructed with Cytoscape 3.6.1 based on Tamura-Nei 1993 (model) genetic-distance thresholds. A total of 147 cases were identified during the study period, among which 121 blood samples were collected and 117 high-quality polymerase gene sequences were successfully obtained. Of these cases, 87.18% were male, 46.15% were aged ≥50 years, and 71.79% had a junior high school education or below. Commercial heterosexual contact was the most frequently reported route of transmission (38.46%). Thirteen HIV-1 subtypes were identified with CRF07_BC (37.61%) and CRF01_AE (23.93%), being the predominant strains. Using a genetic-distance threshold of 1%, 14 molecular clusters comprising 36 sequences were identified, corresponding to an overall clustering rate of 30.77%. The largest cluster included 10 individuals. Notably, 9 high-risk individuals with 4 or more network links were all infected with CRF07_BC and were predominantly older males with lower educational levels who reported commercial heterosexual exposure. In conclusion, CRF07_BC and CRF01_AE were the dominant HIV-1 subtypes circulating in Dinghai District. Middle-aged and older individuals involved in commercial heterosexual activities constituted the core of the local transmission network. Strengthening targeted interventions and expanding HIV testing coverage in this population are essential to prevent further transmission. These findings indicate that molecular transmission-network analysis can provide useful district-level evidence for identifying potential priority populations and optimizing targeted HIV prevention strategies in Dinghai District. The group with higher clustering signals may play an important role in local transmission, but molecular links should not be interpreted as proof of direct transmission.
International journal of molecular sciencesMaría Orosia Lucha-López
Musculoskeletal disorders are among the leading causes of disability worldwide and represent a major driver of physical therapy needs across the life course [...].
Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhiC X Li, Y Yi, W Zhang, H R Zeng, B Q Liu, X L Zheng, B S Li
Objective: To analyze the incidence and genetic characteristics of Sapovirus infection in pediatric diarrhea cases aged ≤5 years in Guangdong Province. Methods: Epidemiological data and stool samples were collected from hospitalized children aged ≤5 years with diarrhea in Guangdong between January 2022 and December 2024. Sapovirus RNA detection from stool samples was conducted by using real-time RT-PCR, and partial VP1 region was amplified and sequenced. Phylogenetic tree analysis was conducted to characterize the genotype of each sequence. Whole-genome sequencing of samples with predominant GⅠ.1 genotype were conducted to analyze its mutation features. Results: In 2 080 pediatric diarrhea cases aged ≤5 years, the positive rate of Sapovirus was 2.45% (51/2 080). The positive rate in boys and girls were 2.20% (28/1 271) and 2.84% (23/809) respectively. The positive rate was highest in age group 13-24 months (4.40%, 22/500), and the detection peak occurred during October-December. Partial VP1 gene sequences were obtained from 31 out of 51 cases, with the GⅠ.1 genotype being predominant (80.65%, 25/31). Phylogenetic analysis indicated close evolutionary relationships among GⅠ.1 strains. Whole-genome sequencing found some amino acid substitutions at multiple conserved sites in GⅠ.1 genotype, and its mutation characteristics were highly consistent with those of the strains circulating in recent years. Conclusions: From 2022 to 2024, Sapovirus infection caused diarrhea occasionally in children aged ≤5 years in Guangdong. Sapovirus GⅠ.1 was the predominant pathogen, and the strains had close evolutionary relationship. It is necessary to further strengthen local surveillance and molecular epidemiological characterization of Sapovirus to provide evidence for epidemic trend analysis and early warning of potential outbreaks.
Pathogens (Basel, Switzerland)Saime Sundus Uygun, Hatice Turk Dagi, Gulsum Alkan, Onur Ural, Baris Otlu, Evrim Kilicli, Osman Selcuk Duysak, Hanifi Soylu, Murat Konak
Ralstonia pickettii is an opportunistic Gram-negative bacterium associated with healthcare-associated infections, particularly in premature infants and other immunocompromised or critically ill patients. This study aimed to investigate a neonatal intensive care unit outbreak of Ralstonia pickettii bacteremia by describing the clinical characteristics of affected infants, identifying the environmental source, and evaluating the genetic relatedness between clinical and environmental isolates. Hospital records from January 2023 through November 2025 were reviewed; the nine included cases occurred between February 2024 and October 2025. Demographic, clinical, and laboratory data were reviewed. Environmental sampling was performed to identify the source of contamination. Genetic relatedness between clinical and environmental isolates was evaluated using arbitrarily primed polymerase chain reaction (AP-PCR), and the molecular findings were interpreted together with microbiological and epidemiological data. This study was initially designed as a retrospective clinical review and was subsequently expanded to include an outbreak investigation after three temporally clustered cases were identified in October 2025. The outbreak involved nine neonates with Ralstonia pickettii bacteremia. Environmental investigation identified Ralstonia pickettii in both opened and unopened sterile distilled water samples. Clinical and environmental isolates demonstrated highly similar AP-PCR banding patterns, supporting genetic relatedness when interpreted together with microbiological and epidemiological findings. Following removal of the contaminated source and implementation of infection control measures, no additional R. pickettii bacteremia cases were identified. Overall mortality was 44.4%, whereas only one death (11.1%) was considered attributable to Ralstonia pickettii bacteremia. Ralstonia pickettii can cause healthcare-associated outbreaks in neonatal intensive care units. Integration of microbiological, environmental, epidemiological, and molecular findings may facilitate timely outbreak source identification and implementation of effective infection control measures.
Signal transduction and targeted therapyDing-Kun Ji, Haozhi Lei, Jia Liu, Fangfang Xia, Xiaobo Gao, Yi-Qing Zhou, Ruiying Li, Yongqi Han, Ruowen Wang, Weihong Tan
Nucleic acid aptamers, often referred to as "chemical antibodies," are versatile, specific, and easily modifiable functional nucleic acids. There is a growing focus on new methods for the selection and target validation of aptamers, with the aim of expanding their biomedical applications in molecular diagnostics and therapeutics, which is currently a research hotspot. This review is composed of eight sections. In the first section, we briefly introduce aptamers and review their development in molecular diagnostics and therapeutics. The "Advantages of aptamers in molecular diagnosis and therapeutics" section summarizes and discusses the advantages of aptamers in these fields. The "New methods for screening aptamers" section presents and discusses nucleic acid aptamer screening methods, including both classical and novel approaches. In the "New methods for target validation" section, we explore new methods for target validation, covering aptamer structure validation, target recognition validation, and aptamer-target interaction validation. The "New methods for molecular diagnostics" section summarizes and discusses recent applications of aptamers in molecular diagnostics, particularly focusing on new mechanisms and detection strategies as well as their applications in various diseases. The "New methods for molecular therapeutics" section summarizes and discusses recent applications of aptamers in molecular therapeutics, emphasizing new mechanisms and aptamer-based therapy strategies, along with their therapeutic applications in different diseases. The "Challenges and future perspectives of nucleic acid aptamers" section addresses the challenges and future perspectives of aptamers in disease diagnosis and treatment. Finally, the "Conclusion" section shares our views on the future directions of aptamers in clinical disease molecular diagnostics and therapeutics.
Pathogens (Basel, Switzerland)Sara Gomes-Gonçalves, Ricardo J Figueiredo, Beatriz Oliveira Alcobia, Luís Cardoso, Ana Cláudia Coelho, João R Mesquita
A total of 100 fecal samples collected from cattle in the district of Viana do Castelo, northern Portugal, were molecularly screened for Cryptosporidium spp., Giardia duodenalis, and Blastocystis sp. This study represents the first molecular survey of enteric protozoa in cattle from the district of Viana do Castelo, northern Portugal. Blastocystis sp. was the most frequently detected protozoan and exhibited considerable subtype diversity, including the zoonotic subtype ST3 and the potentially zoonotic subtypes ST10a and ST14, a circumstance highlighting the occurrence in cattle of Blastocystis subtypes with potential public health relevance and the need to further investigate their cross-host transmission dynamics. Giardia duodenalis was detected at a relatively low occurrence, although unsuccessful multilocus sequence typing (MLST) amplification prevented assessment of its assemblages and zoonotic potential. Cryptosporidium spp. were not detected, likely reflecting the predominance of adult cattle in the sampled population. Overall, these findings contribute to the understanding of the molecular epidemiology of enteric protozoa in Portuguese cattle and provide updated baseline geographical data for northern Portugal. Continued molecular surveillance using optimized genotyping approaches and larger, more representative sample sets will be essential to better characterize the diversity, epidemiology, and zoonotic importance of these parasites within a One Health framework.
BACKGROUND: Streptococcus pneumoniae remains a major cause of pneumococcal disease globally despite widespread use of pneumococcal conjugate vaccines (PCVs). Genomic data from the Arabian Gulf remain limited, and ongoing changes in pneumococcal population structure may complicate serotype-based surveillance and vaccine impact assessment. METHODS: Whole-genome sequencing was performed on 250 S. pneumoniae isolates collected in the United Arab Emirates and Kuwait. Population structure was analysed using Global Pneumococcal Sequence Clusters (GPSCs). Serotypes and sequence types were determined, and capsule switching was assessed by discordance between lineage assignment and capsular type, supported by recombination analysis. RESULTS: Extensive serotype diversity was observed, comprising 51 capsular serotypes with predominance of Serotype 3 (n=33), followed by serotypes 11A (n=15), 8 (n=12), 23B (n=12), 35B (n=11), and 9N (n=11). The isolates were assigned to 61 Global Pneumococcal Sequence Clusters (GPSCs), with four dominant lineages (GPSC10, GPSC12, GPSC6, and GPSC3) accounting for 28.8% of isolates. GPSC10 (n=27) was the predominant lineage and was mainly associated with serogroup 15 (15B/15C), with all isolates exhibiting multidrug resistance. PCV13 serotypes accounted for 29.2% of isolates, increasing to 50.0% and 65.2% for PCV20 and PCV21, respectively. Five sequence types were associated with two distinct serotypes, consistent with putative capsule-switching events and recombination evidence was identified in one lineage. CONCLUSION: Pneumococcal populations in the Arabian Gulf are dominated by globally distributed lineages with substantial serotype diversity. Evidence of capsular switching underscores the limitations of serotype-based surveillance, supporting integration of lineage-resolved genomic surveillance to inform PCV strategies in highly connected regions.
Microbial genomicsGrace Thandekire Sibande, Charlotte E Chong, Anmol Kiran, Belson Kutambe, Mary Charles, Victor Maiden, Kate S Baker, Jennifer Cornick
Antimicrobial resistance (AMR) in Shigella is rising globally, complicating shigellosis management. Whole-genome sequence analysis (WGSA) has advanced our understanding of AMR and transmission dynamics, yet contemporary whole-genome sequencing data from Shigella in sub-Saharan Africa remain scarce. In this study, we applied WGSA to 27 Shigella isolates collected from children presenting with diarrhoea at Ndirande Health Centre in Malawi (2022-2023), as part of the Enterics for Global Health Shigella surveillance study. Serotyping, AMR profiling and phylogenetic analysis revealed Shigella sonnei as the dominant serogroup, with distinct genetic clustering relative to global reference strains among S. sonnei, Shigella flexneri and Shigella boydii. We identified 16 AMR genes linked to ten antimicrobial classes with qnrS1 and qnrB19 genes conferring resistance to fluoroquinolone, alongside IncFIB(K) and IncFII plasmid replicon markers. Importantly, no azithromycin resistance determinants were detected both genotypically and phenotypically, providing baseline evidence that warrants continued surveillance of current first-line treatment. However, the detection of fluoroquinolone resistance genes with plasmid replicon markers in the absence of phenotypic resistance might indicate a silent reservoir with epidemic potential. This is the first contemporary Shigella data from a large-scale diarrhoea disease surveillance study in Malawi, providing essential baseline information for guiding antibiotic treatment and future vaccine development efforts, contributing to the efforts to combat shigellosis in Malawi and other similar regions.
Journal of medical virologyKamol Suwannakarn, Chutikarn Chaimayo, Atsadang Boonmee, Charussri Leeyaphan, Pattriya Jirawattanadon, Pravarit Athiprayoon, Natsada Saengdao, Piyarat Taiphakp…
Since 2022, human monkeypox virus (hMPXV) has emerged in non-endemic regions, including Thailand. However, the genomic dynamics and clinical correlates of local transmission remain incompletely defined. Whole-genome sequencing was performed on hMPXV from 16 patients in Thailand (2023-2024) using targeted amplicon NGS. Phylogenetic analyses integrated global reference sequences. Mutational profiles, specifically non-synonymous substitutions and APOBEC3-associated signatures, were analyzed in relation to clinical data. Phylogenetic reconstruction identified three temporal phases. Early 2022 cases (clade IIb lineages A and B) were interspersed with global sequences, consistent with multiple introductions. In contrast, 2023-2024 cases were dominated by lineage C.1. All 16 genomes belonged to C.1 (one C.1.1), and formed a distinct mid-2023 cluster, designated C.1/Thai/Cluster, supporting sustained local transmission. APOBEC3-associated mutations were pervasive across the C.1 lineage overall, including within C.1/Thai/Cluster, without evidence of significant enrichment specific to this cluster. The cohort comprised exclusively male patients (81% HIV-positive, MSM), with predominantly genital painful lesions and a median recovery time of 23 days. No significant associations were detected between viral genetic variation and clinical outcomes. Mpox transmission in Thailand evolved from multiple introductions to sustained C.1-dominated local spread, underscoring the importance of continued genomic surveillance.
Journal of medical virologySahel Abyar, Seyed Reza Mohebbi, Seyed Masoud Hosseini, Shabnam Kazemian, Amir Sadeghi, Mohammad Reza Zali
Human T-lymphotropic virus 1 (HTLV-1) and Human Immunodeficiency Virus 1 (HIV-1) can be transmitted through similar routes, so co-infection may occur, especially in endemic regions. Since there is limited data on this co-infection, its genotypes, and genetic variations in Iran, we aimed to investigate HTLV-1/HIV-1 co-infection to gain a better understanding of its epidemiology. Whole blood and plasma of 282 HIV-1-infected patients were sampled in Tehran, Iran. Briefly, plasma samples were used to investigate HTLV I/II antibody seroprevalence by ELISA, and PBMCs were used for molecular analysis of Tax, LTR, and ENV regions. Then, amplified LTR and ENV were subjected to sequencing, phylogenetic analysis, and variation determination. Out of 282 HIV-1-infected individuals (31.9% female and 68.1% male, with a mean age of 43.80 ± 11.25), 6 samples (2.1%) were seropositive, and provirus was detected in 2 samples (0.7%). Both samples belonged to HTLV-1aTC, and after genetic variation analysis for both LTR and ENV regions, the ENV region displayed 6 and 7 point mutations in each isolate, respectively, relative to the ATK HTLV-1 prototype, with 5 and 4 of these mutations being nonsynonymous. Analysis of the LTR region identified 8 mutations in each isolate, comprising 7 point mutations and one deletion. This survey confirms the prevalence of HTLV-1 among people living with HIV-1, highlighting the need for ongoing monitoring of this population. Additionally, the findings in this study indicate that HTLV-1aTC is predominant among the studied population, consistent with previous reports worldwide, and nucleotide variations are present in both investigated HTLV-1 regions.
Veterinary medicine and scienceMd Arif Khan, Pronesh Dutta, Md Kaisar Rahman, Abdullah-Al Mamun, Jade K Forwood, Shariful Islam, Ariful Islam
BACKGROUND: Peste des petits ruminants (PPR) is a highly contagious viral disease of sheep and goats that causes substantial economic losses through high morbidity, mortality and rapid transmission among small ruminants. Molecular epidemiological data on circulating PPR virus (PPRV) strains in Bangladesh remain limited. OBJECTIVES: To investigate the molecular epidemiology and phylogenetic characteristics of PPRV among fat-tailed sheep and goats traded in livestock markets in Bangladesh. METHODS: A cross-sectional survey was conducted in livestock markets in Dhaka city, Bangladesh, during the Eid-ul-Adha festival between August and October from 2015 to 2018. Oral, nasal and rectal swabs were collected from 161 animals comprising 141 sheep (including 111 fat-tailed sheep) and 20 goats. Samples were screened for PPRV using conventional hemi-nested polymerase chain reaction (PCR) targeting the nucleocapsid gene. Positive amplicons were sequenced, analysed phylogenetically and subjected to three-dimensional (3D) structural prediction of the RNA-dependent RNA polymerase protein. RESULTS: The overall prevalence of PPRV in small ruminants was 2.5% (95% confidence interval [CI]: 0.7-6.2). In fat-tailed sheep, the prevalence was 3.6% (95% CI: 1.0-8.9), whereas no positive cases were detected among goats. A significantly higher (p < 0.05) prevalence was observed in animals sampled from the Gabtoli livestock market. Phylogenetic analysis revealed that two of the four positive samples clustered closely with PPRV strains from India and the United Arab Emirates, whereas the other two clustered with strains from China and Tibet. CONCLUSIONS: These findings demonstrate the transboundary circulation of genetically diverse PPRV strains among small ruminants traded in livestock markets in Bangladesh. Strengthened molecular surveillance in livestock markets and coordinated regional control strategies are needed to support PPR prevention and eradication.
The Journal of general virologyJianguo Shen, Yujie Jin, Shayidan Wufuer, Zhenguo Du, Fangluan Gao
Maize chlorotic mottle virus (MCMV) represents a major quarantine pathogen that poses a serious threat to global maize production, yet its spatiotemporal evolutionary dynamics remain incompletely characterized. In this study, we reconstructed the global molecular epidemiology of MCMV by analysing 117 complete genome and 214 coat protein (CP) gene sequences. We employed whole-genome data for Bayesian phylodynamic inference while utilizing CP sequences for phylogenetic reconstruction and population genetic analyses. Our phylodynamic analyses estimated a mean evolutionary rate of 2.07×10-4 substitutions per site per year, with the global most recent common ancestor traced to the Americas around 1938. Following its emergence, the MCMV population diversified into two major clades: a basal American lineage (Clade I) and a recently emerged, rapidly diversifying lineage (Clade II, originating ~1952). Within Clade II, we identified a monophyletic East African cluster - representing the most extensively sampled geographic population - that is phylogenetically nested within a broader assemblage of Asian isolates. This East African population, dating to the mid-1980s, exhibits signatures of a recent founder effect, characterized by minimal intra-regional genetic differentiation and lower nucleotide diversity (π=0.003) relative to Asian (0.008) and American (0.026) populations. Phylodynamic demographic reconstructions reveal that regional establishment in East Africa coincided with a pronounced global expansion in effective population size (N e) from the mid-1990s through the mid-2000s, subsequently followed by demographic stabilization. These findings provide structural and temporal insights into the global population structure and spatiotemporal dynamics of MCMV, establishing a foundation for international surveillance strategies and phytosanitary control measures.
The Journal of antimicrobial chemotherapyQin Fan, Jiafeng Zhang, Jun Jiang, Xiaohong Pan, Yaping Yao, Hui Xing, Yi Feng, Hehe Zhao, Xiaobei Ding, Yan Xia, Yun Xu, Xin Zhou, Chengliang Chai
OBJECTIVE: To characterize the epidemiology, subtype distribution and transmission dynamics of pre-treatment drug resistance (PDR) among newly diagnosed antiretroviral therapy (ART)-naive individuals with human immunodeficiency virus type 1 (HIV-1) in Zhejiang Province, Eastern China, in 2023. METHODS: In this province-wide cross-sectional molecular epidemiological study, the HIV-1 pol gene was amplified and Sanger-sequenced. Genotypic resistance was interpreted using the Stanford HIV Drug Resistance Database, subtypes were assigned by phylogenetic analysis, and transmission networks were inferred at a pairwise genetic distance threshold of 0.01 substitutions/site, with sensitivity analysis across 0.001-0.015 substitutions/site thresholds. RESULTS: Among 3466 valid pol sequences, 241 PDR cases were identified, yielding an overall PDR prevalence of 6.95% [95% confidence interval (CI): 6.11%-7.80%], with the highest prevalence observed in Jinhua (10.02%; 95% CI: 7.39%-12.65%). Of the 241 PDR cases, 10 distinct HIV-1 subtypes were detected, among which CRF07_BC (43.57%, 105/241) and CRF01_AE (38.17%, 92/241) predominated. Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance was most frequent (67.66%, 159/235), driven by the resistance-associated mutation (RAM) K103N/S (46.47%, 112/241); high-level resistance was highest for nevirapine (63.07%, 152/241) and efavirenz (54.77%, 132/241). Overall, 42.32% of PDR cases clustered into 51 resistance-associated transmission clusters (RTCs); 18 medium/large RTCs (≥4 individuals) carried high-level NNRTI resistance, 8 with mean pairwise distances ≤0.005 substitutions/site, suggesting high sequence homology and suggestive of close epidemiological linkage among clustered strains. CONCLUSIONS: In this study, PDR cases in Zhejiang were dominated by NNRTI resistance with substantial regional clustering, indicating putative transmission networks. Scaled-up standardized PDR surveillance, optimized first-line ART regimens and cluster-targeted interventions are urgently needed to curb resistant HIV-1 transmission and inform national HIV drug resistance policy.
Journal of infection in developing countriesMajda El-Hassouni, Asmae Hazzaz, Reda A Souhli, El Mehdi El Ghorba, Hanaa El Mamouny, Kawtar El Harrak, Nouhaila Chahid, Youssra Amekran, Karima Rissoul
INTRODUCTION: Carbapenemase-producing Enterobacterales (CPE) have widely emerged as a global health threat due to the spread of resistance genes such as New Delhi metallo-β-lactamase (blaNDM) and oxacillinase-48-like β-lactamases (blaOXA-48-like). Data on the molecular epidemiology of CPE in northern Morocco remain limited. Hence, this study aimed to report the epidemiological profile of carbapenem-resistant Enterobacterales and their molecular analysis. METHODOLOGY: A prospective study was conducted from July 2024 to July 2025 at Mohammed VI University Hospital, Tangier. Ninety-two non-duplicate Enterobacterales isolates were collected across different departments. Species were identified via the matrix-assisted laser desorption/ionization - time-of-flight (MALDI-TOF MS) technique and antimicrobial susceptibility testing was performed according to the guidelines of the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Carbapenemase production was screened using GeneXpert® Carba-R (Cepheid, Sunnyvale, USA). Associations between clinical, microbiological, and molecular data were assessed using Chi square or Fisher's exact tests. RESULTS: Klebsiella pneumoniae dominated across all isolates (75/92; 81.5%), followed by Escherichia. coli (8/92; 8.7%). BlaNDM was found in 65/92 (70.6%), blaOXA-48-like in 17/92 (18.5%), and both in 10/92 (10.9%). Most cases occurred in neonatal (38%) and intensive care units (31.5%). Resistance exceeded 70% for several major antibiotics; 29.3% were colistin-resistant. Mortality was 46.7%. Diabetes (p < 0.01) and severe burns (p < 0.01) were significantly associated with carbapenemase carriage. CONCLUSIONS: CPE, especially NDM-producing Klebsiella pneumoniae, represent a major threat in northern Morocco, notably in neonatal and critical care units. Their high resistance and mortality highlight the urgent need for reinforced infection control, molecular surveillance, and rapid diagnostics.
Since NADC30-like PRRSV-2 was first detected in Henan Province in 2012, it has continued to spread and has become one of the predominant PRRSV-2 groups in mainland China. However, the long-term spatiotemporal dynamics, interprovincial transmission patterns, transmission drivers and recombination associated evolutionary features of sublineage L1C (L1C; NADC30-like) remain incompletely resolved. Here, we analysed 9541 quality-controlled lineage 1 ORF5 sequences from 12 countries, including ORF5 sequences from 62 laboratory-derived complete genomes assigned to L1C. Globally, 3787 sequences were classified as L1C. Among the 1648 lineage 1 sequences from China, 1362 were assigned to L1C, accounting for 82.65% of Chinese lineage 1 sequences. Phylodynamic analysis dated the global common ancestor of L1C to around 2002 and suggested that strains circulating in mainland China were likely introduced from US-related strains around 2008. Before the African swine fever (ASF) outbreak, inferred interprovincial transmission links were concentrated in a limited number of key provinces. During the early ASF period, observable links decreased, but they subsequently recovered and expanded across more provinces. Transmission-driver analysis suggested that pig inventory and pig output were associated with stronger inferred interprovincial L1C transmission links, whereas geographic distance was associated with a spatial-decay effect. Whole-genome recombination analysis revealed extensive recombination signals in L1C genomes involving other PRRSV-2 lineages. Among inter-lineage associations, L8E (HP-PRRSV/JXA1-like) was the most frequently implicated background, followed by L5 and L3. These findings provide systematic evidence for the persistent prevalence, regional transmission and recombination-driven evolution of L1C in mainland China, and support molecular surveillance, regional risk warning and optimization of PRRSV-2 control strategies.
Frontiers in public healthXueli Yi, Bin Luo, Yuanyuan Dai, Ying Wei, Shimao Zhong, Ying Deng, Chunfang Wang, Yuanji Teng
BACKGROUND: Streptococcus suis (S. suis) is an important zoonotic pathogen and a common colonizer of the upper respiratory tract of pigs. Human infections have been reported in several regions of China, including Guangxi, but genomic and antimicrobial resistance data from this region remain limited. This study investigated the molecular epidemiology, antimicrobial susceptibility, and genomic characteristics of human S. suis isolates collected in Baise City, Guangxi, from 2015 to 2021. METHODS: This retrospective study included 39 non-duplicate clinical isolates confirmed as S. suis by whole-genome analysis. Antimicrobial susceptibility testing was performed using a broth microdilution-based system and interpreted according to the Clinical and Laboratory Standards Institute guidelines. Serotypes were determined by agglutination using type-specific antisera. Whole-genome sequencing was used for species confirmation, multilocus sequence typing, detection of antimicrobial resistance and virulence-associated genes, and core-protein phylogenetic analysis. RESULTS: The median patient age was 55 years, and 36/39 (92.3%) patients were male. Meningitis was documented in 34/39 (87.2%) patients, and hearing impairment occurred in 21/39 (53.8%). Pig- or pork-related exposure was recorded in 15/39 (38.5%) patients. Resistance was highest to tetracycline (38/39, 97.4%), followed by erythromycin and clindamycin (26/39, 66.7% each). Four isolates (10.3%) showed intermediate susceptibility to penicillin, but none were resistant. All isolates remained susceptible to ampicillin, ceftriaxone, levofloxacin, linezolid, vancomycin, and meropenem. Serotype 2 predominated (32/39, 82.1%), followed by serotype 14 (7/39, 17.9%), while ST1 (29/39, 74.4%) and ST7 (7/39, 17.9%) were the two major sequence types. Resistance genes were mainly associated with tetracyclines, macrolides, lincosamides, and aminoglycosides. All ST1 isolates carried mrp and lacked tet(40), while all ST7 isolates showed the reverse pattern. CONCLUSION: Serotype 2 and ST1 predominated among the human S. suis isolates collected at this center. Resistance to tetracycline, erythromycin, and clindamycin was common, while susceptibility to the β-lactams tested was largely preserved. Differences in virulence- and resistance-associated gene profiles were also observed between the major lineages, indicating distinct genetic characteristics among the locally circulating isolates.
Frontiers in cellular and infection microbiologyTao Hu, Feiyang Zheng, Weizhe Zhang, Yulu Sun, Hanyun Qin, Liang Zhao, Huazhang Lai, Jingwen Chen, He Li, Bo Yang, Xiaoli Zhang, Fengkun Yang
INTRODUCTION: Enterocytozoon bieneusi is a zoonotic parasite causing diarrheal disease in rural settings with frequent human-animal contact. METHODS: We conducted a cross-sectional study in Heilongjiang, China, enrolling 69 households across 10 villages. Humans and domestic animals were sampled. Nested PCR targeting the ITS region was performed. Genotypes were determined by sequencing, and genetic diversity was assessed using DnaSP. RESULTS: Human prevalence was 11.0% (13/118), while overall animal prevalence was 23.4% (162/693), with sheep being the highest (66.7%), followed by pigs (46.1%) and geese (20.5%). Prevalence was significantly higher in mammals than poultry (32.9% vs. 13.9%; p < 0.001). Sequence analysis yielded 29 distinct genotypes (10 known, 19 novel), with EbpC (36.0%), BEB6 (13.7%), EbpA (13.7%), and D (11.4%) being the most prevalent, most clustering within zoonotic Group 1. DISCUSSION: Notably, zoonotic genotypes EbpC and EbpA were identified in chickens and geese, extending the known host range of these genotypes. Human-animal genotype sharing was observed in only one household (genotype EbpC between humans, pigs, chickens, and geese), while intraspecies circulation and occasional animal-animal genotype sharing were more common. Phylogenetic and network analyses suggested localized diversification, though single-locus ITS limits definitive evolutionary inference. E. bieneusi is highly prevalent in rural domestic animals in Heilongjiang, with genetically diverse and potentially zoonotic genotypes circulating in livestock and poultry. Although household-level human-animal transmission appears limited in this dataset, the presence of shared zoonotic genotypes highlights the need for expanded surveillance incorporating environmental sampling and multi-locus typing to clarify transmission pathways and inform One Health strategies.
Irish medical journalJ B Sarma, V Murray, C McFadden
AIM: To characterise the genomic epidemiology of Clostridioides difficile infection (CDI) at Letterkenny University Hospital (LUH) using core-genome Multi Locus Sequence Typing (cgMLST), quantify true nosocomial transmission, distinguish relapse from reinfection, and examine the relationship between CDI patterns and institutional antimicrobial consumption. METHODS: In 2023 and 2024, 1,510 and 1,754 stool samples were screened, respectively for suspected CDI. GDH screening was positive in 153 (10.1%) and 226 (12.9%) with toxin EIA detecting active toxin in 86 (56.2%) and 106 (46.9%), respectively. PCR identified toxin genes in a further 44 (65%) and 72 (60%) of toxin-negative GDH-positive samples. Of these, 117, toxin-positive isolates from 94 patients underwent whole-genome sequencing and cgMLST. Molecular clusters were defined as ≤2 allelic differences, and epidemiological linkage required shared ward location and overlapping admission periods. National antimicrobial-use deciles were reviewed for CDI-associated agents. RESULTS: cgMLST identified 28 sequence types, with ST11 predominating (19, 16.2%). Of 48 clusters, only one represented confirmed nosocomial transmission. Recurrent CDI occurred in 10 out of 94 (11%), with 90% representing molecular relapse. LUH ranked among the highest national consumers of CDI-associated antimicrobials. DISCUSSION: CDI at LUH is driven primarily by endogenous activation of community-acquired strains rather than hospital transmission. High-risk antimicrobial use is the key modifiable driver, highlighting the need for strengthened antimicrobial stewardship supported by ongoing WGS surveillance.
Bovine coronavirus (BCoV) is a key pathogen causing calf diarrhea and bovine respiratory diseases, bringing sustained economic losses to the cattle industry. As an RNA virus, BCoV possesses high mutation and recombination capacities, leading to prominent genomic genetic diversity. The genome contains hypervariable and conserved regions, with the S (especially S1), HE and Open Reading Frame (ORF4) genes serving as major variation hotspots linked to viral antigenicity, tissue tropism shift and immune evasion. Host immune pressure drives strong positive selection on S protein antigenic variation. This review discusses existing research limitations and proposes future directions including genomic surveillance, reverse genetics verification and broad-spectrum vaccine development to support BCoV prevention and control.
Scientific reportsMaysa Ragab, Yassir A Almofti, Yazeed A Rauouf, Nick J Knowles, Donald P King, Jemma Wadsworth, Hayley M Hicks, Haitham Saeed, Omima Abd Algalil, Ibrahim Albok…
Foot-and-mouth disease (FMD) is a highly contagious transboundary viral disease causing significant economic losses in livestock. This study investigated the serotype distribution and molecular epidemiology of FMD viruses (FMDV) circulating in Sudan between 2019 and 2022. A total of 51 epithelial tissue samples were collected from outbreaks in Khartoum, Blue Nile and Northern States. Samples were analyzed via virus isolation in bovine thyroid cell culture (BTY), antigen detection ELISA, and real-time reverse transcription PCR (rRT-PCR). Antigen detection ELISA successfully typed 13 of 51 (25.5%) epithelial tissue samples, of which 10 were identified as serotype A and 3 as serotype O. In contrast, rRT-PCR detected FMDV RNA in 33 of the 35 samples (94.3%) that were suitable for molecular analysis, showing the superior diagnostic sensitivity of this molecular method. FMDV positive samples were further characterized by sequencing the VP1-coding region. These data demonstrated the presence of two serotypes (A and O), while SAT serotypes were not detected during the study period. Serotype A was detected in outbreaks during 2019, 2021 and 2022, while serotype O predominated in 2020. Phylogenetic analysis of VP1-coding sequences showed that serotype A sequences clustered within the A/AFRICA topotype, lineage G-IV and were closely related to strains from Egypt and Ethiopia. Serotype O sequences were clustered within the EAST AFRICA-3 (EA-3) topotype and showed ≥ 96% identity with the Egyptian isolates. VP1 analysis revealed conserved functional motifs alongside variability within the immunodominant antigenic region, suggestive of ongoing viral evolution with potential implications for vaccine effectiveness. These results suggested the persistent circulation of FMDV serotypes A and O in Sudan with close genetic relationships to viruses recovered from neighboring countries. These findings suggested the transboundary transmission of FMDVs and a role for cross-border livestock movements in virus dissemination. Continuous molecular surveillance and regional cooperation are essential to improve vaccine matching and strengthen FMD control strategies in endemic regions.
Journal of visualized experiments : JoVEEitan Halper-Stromberg, Suguna Narayan, Vincent Laufer, Melvin Limson, Tracy Busse, Jeremy P Segal, Dara L Aisner, Jennifer J D Morrissette, Helga Thorvaldsdot…
The integrative genomics viewer (IGV) is a pivotal tool in clinical genomics, enabling the visualization and interpretation of complex sequencing data. Bringing clinical knowledge to bear with visual evaluation of sequencing results is the primary means by which molecular pathologists and other professionals assess and finalize cases. A variety of software tools can assist, but their relationship to the underlying data must be understood and applied systematically. This study includes essential background on next-generation sequencing (NGS) data file types (e.g., FASTQ, BAM, VCF) with a discussion of their format and purpose. We then describe features of IGV that derive nuances from these files. We utilize a series of curated practical cases based on clinical vignettes through which the reader will interact with clinical NGS sequencing data using the IGV software to review various types of clinically relevant variants relative to the human reference genome. These clinical vignettes have been curated to describe examples of some of the complexities of interpretation of genomic data, and how utilizing IGV as part of a routine workflow can provide additional interpretive information for variants beyond routine bioinformatic software algorithm variant calls. The visual inspection of genomic variants utilizing the tools within IGV can unmask subtle contextual cues (i.e., variant allele frequency, strand bias, tissue-specific context) that can influence the interpretation of genomic variants. Although this study focuses on using IGV for the detection and interpretation of somatic variants, the provided applications can be extrapolated for use in the germline setting, including analysis of complex variants and detection of mosaicism.
Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated diarrhoea and a marker of antimicrobial exposure and healthcare quality, yet Central Asia is almost absent from the indexed literature. We reviewed available evidence on CDI epidemiology, antimicrobial use and molecular typing across Kazakhstan, Uzbekistan, Kyrgyzstan, Tajikistan and Turkmenistan, searching PubMed/MEDLINE, Google Scholar and accessible regional sources, and identified priorities for surveillance development. The retrievable evidence is sparse and fragmented. The strongest direct data came from Uzbekistan, where paediatric cohorts documented toxigenic C. difficile in up to 47% of the aetiological structure of antibiotic-associated diarrhoea in early-aged children. Nationwide surveys in Kazakhstan showed substantial antimicrobial use (38.2-40.2% of inpatients) and measurable healthcare-associated infection burdens (2.4-3.8%), indicating environments in which CDI may go unrecognised. No national CDI surveillance, ribotyping or resistance-gene data were identified for any of the five countries, whereas evidence from China, Thailand and other Asian settings indicates that ribotype 017 (sequence type 37) predominates in those countries. This absence appears more consistent with underdiagnosis, fragmented reporting and limited laboratory capacity than with true absence of disease. Sentinel surveillance, standardised diagnostic algorithms, integration with antimicrobial stewardship and infection prevention programmes, and regional typing collaborations are the practical priorities.
VirusesEsraa Al-Fraihat, Amal Irshaid, Mohammed Sallam, Johan Snygg, Rasha Awawdeh, Hasanain Al-Shakerchi, Sama Al-Baidhani, Malik Sallam
The molecular epidemiology and antiretroviral (ARV) drug resistance of human immunodeficiency virus type 1 (HIV-1) remain incompletely outlined in the Middle East and North Africa (MENA). The aim of this retrospective molecular epidemiology study was to analyze MENA HIV-1 sequences for phylogenetic clustering and to delineate surveillance drug-resistance mutations (SDRMs) for nucleoside reverse-transcriptase inhibitors (NRTIs), non-nucleoside reverse-transcriptase inhibitors (NNRTIs), and protease inhibitors (PIs) across various periods, locations, and subtypes/circulating recombinant forms (CRFs). Viral sequences were retrieved from the Los Alamos HIV Sequence Database as of 15 April 2026. Analyses were done using multiple sub-gene regions (two env regions (n = 224 and n = 60) and PR (n = 2413) and RT (n = 2103) of the pol gene). Phylogeny construction was conducted using maximum-likelihood estimation, while ARV drug resistance analysis was conducted using the Stanford HIVdb algorithm. The HIV-1 MENA sequences showed a remarkable genetic diversity, with co-circulation of multiple subtypes/CRFs, including subtype B in the Maghreb, Levant, and Egypt sub-regions, subtypes A1, G, CRF01_AE, and CRF02_AG in the Gulf Cooperation Council (GCC) and Yemen sub-region, and subtypes C and D in the Horn of Africa and Sudan sub-region. The percentage of MENA HIV-1 sequences in clusters was 10.3% for env1, 8.3% for env2, 22.0% for PR and 37.2% for RT. Phylogenetic reconstruction hinted at a structured epidemic dominated by small transmission units, with most clusters comprising dyads (n = 260) or networks (n = 142) and a limited number of large clusters (n = 8) that were largely confined within national boundaries, with only occasional cross-border linkages (n = 8). Overall SDRM prevalence was 3.2% in the PR region and 14.9% in the RT region, with a higher percentage of NNRTI-associated mutations (10.0%) than NRTI-associated mutations (9.1%) and dual-class resistance observed in 4.1% of sequences. Phylogenetic clustering was not associated with the probability of harboring SDRMs; however, negative binomial models showed that non-clustered sequences had a greater burden of NRTI-associated mutations, whereas no such association was observed for NNRTI- or PI-associated mutations. The findings showed predominantly localized and fragmented MENA HIV-1 transmission dynamics. Heterogeneous ARV drug resistance dynamics indicated that resistance emergence might be shaped by broader epidemiologic and treatment-related factors rather than ongoing clustered transmission. There is a need for coordinated molecular surveillance and optimized ART strategies across the MENA countries.
Frontiers in public healthShiteng Huang, Bingdong Zhan, Min Wang, Lei Lyu, Jialing You, Ruijun Yang, Hui Yang
OBJECTIVE: To elucidate the epidemiological distribution patterns of avian influenza virus (AIV) in the external environment of western Zhejiang from 2014 to 2025, analyze the molecular epidemiological characteristics of the H9N2 subtype, and assess its public health risks. METHODS: According to the Zhejiang Provincial Surveillance Program for Avian Influenza in Occupationally Exposed Populations and External Environments, real-time RT-PCR was used to detect AIV subtypes in environmental specimens. H9N2-positive samples with cycle threshold values <30 were inoculated into specific pathogen-free (SPF) embryonated chicken eggs for virus isolation, followed by whole-genome sequencing and bioinformatics analysis for phylogenetic and molecular characterization. RESULTS: A total of 7,762 specimens were tested from 2014 to 2025, with an overall positivity rate of 34.64% (2,689/7,762) for AIV. Significant differences in positivity rates were observed in seasons, regions, sampling sites, and specimen types (all p < 0.001). AIV activity peaked in winter and spring, with the highest rates detected in live poultry markets and chopping board swabs. The H9 was the predominant subtype, with co-circulation of multiple subtypes. All 48 H9N2 subtype isolates belonged to the G57 genotype, with the hemagglutinin (HA) and neuraminidase (NA) genes falling into the Y280-like branch, while the internal genes exhibited a mosaic pattern combining G1-like and F/98-like lineages. Molecular characterization analysis revealed multiple mammalian adaptive mutations, involving alterations in receptor-binding sites (T163N, H191N, T197D, T198V, Q234L, Q235M), antigenic epitopes (D280G, N285S), and glycosylation sites (218NRTF, 313NCSK). NA stalk deletion (62-64 aa), along with multiple mutations in the hemadsorption site (E/K368N, D369S/G, D401G/V, N402D, W403L/R, Q432H). Additionally, multiple key amino acid substitutions were also identified in the internal proteins. CONCLUSION: The external environment in western Zhejiang exhibits a high prevalence of AIVs with pronounced spatiotemporal clustering. H9 was the dominant subtype and co-circulated with multiple subtypes, with live poultry markets and slaughterhouses identified as high-risk settings. The H9N2 subtype AIV has accumulated multiple mammalian adaptive mutations, and exhibits genetic linkages across eastern Chinese provinces. These findings collectively underscore the need for an integrated One Health surveillance and early-warning system to reduce the risk of human infections with avian influenza.
Frontiers in cellular and infection microbiologyArockiasamy Arun Prince Milton, Kandhan Srinivas, Sabia Khan, Archana Thakur, Zakir Hussain, M Saminathan, Sandeep Ghatak, G Bhuvana Priya, Hosterson Kylla, La…
BACKGROUND: African swine fever (ASF), caused by Asfivirus haemorrhagiae, entered India through its northeastern frontiers in 2020. Following the initial outbreaks in Arunachal Pradesh and Assam, the next state to report ASF was Meghalaya, a tribal dwelling, pork-deficit state landlocked between Assam and the neighboring country of Bangladesh. MATERIALS: In this study, we undertook an exploratory spatio-temporal analysis and economic cost analysis based on a total of 115 outbreak events involving 1603 animals were recorded involving 7 of the erstwhile 11 districts between July 2020 and April 2025. Additionally, we also regularly screened field samples from various districts of Meghalaya and tried to understand the molecular epidemiology based on p72 and p54 based phylogenetic analysis. RESULTS AND DISCUSSION: Phylogenetic analysis of representative strains from the outbreaks based on p72 and p54 regions assigned the strains to Genotype II, and more specifically sub-genotype IIa, respectively. Economic losses directly arising from assumed pork sales of affected animals yielded a conservative estimate of INR 2,74,45,883 (USD 305,225). Further, exploratory spatial autocorrelation analysis indicated clustering of outbreaks in 2020 and 2021. Moreover, exploratory temporal autocorrelation analysis hinted at weak but insignificant seasonal (p > 0.05) and annual trends at lag 12 frequency, which was also the feature observed in temporal decomposition of ASF outbreaks. Conclusions: The current study offers baseline data on which forecasting models can be developed and effectively prevent and contain future outbreaks by collaborative efforts of the stakeholders.
Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhiT Li, Y N Huang, D M He, J J Liu, F Z Ouyang, B X Ke, Y H Shi, B S Li
Objective: To investigate the drug resistance profiles and molecular epidemiological characteristics of Aeromonas species isolated from human clinical samples. Methods: A total of 72 Aeromonas isolates were collected and identified to the species level using biochemical tests, mass spectrometry, and average nucleotide identity based on whole-genome sequencing. Antimicrobial susceptibility testing was performed by the broth microdilution method. The phylogenetic relationships among isolates were reconstructed based on core single-nucleotide polymorphisms. Whole-genome sequencing data were used to determine multilocus sequence types and identify the virulence genes. The correlation between identified resistance genes and the corresponding resistant phenotypes was assessed. Results: Conventional biochemical and mass spectrometry methods yielded inconsistent species identification results for some Aeromonas strains compared with whole-genome sequencing. The predominant strains of human Aeromonas infections were Aeromonas veronii (48/72, 66.66%). The prevalent sequence types were ST425 (5/72, 6.94%). Antibiotic susceptibility testing revealed that human-derived Aeromonas species were sensitive to most antimicrobial agents, with slightly higher resistance rates to tetracycline (18.06%) and compound sulfamethoxazole (13.89%). A high concordance rate was observed between the antimicrobial resistance genotypes and phenotypes of Aeromonas. The number of toxin gene-positive strains is large, and the number of toxin gene-positive strains of different species of Aeromonas is different. Conclusions: Aeromonas veronii was the predominant species among human-derived Aeromonas isolates, and the sequence types showed high diversity. The overall antimicrobial resistance rate was low, with most resistance phenotypes mediated by resistance genes, and the number of positive strains of Aeromonas toxin genes is different among different species.