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.
American journal of public healthBrian C Castrucci, Madyson Popalis, Lekshmi Rita Venugopal, Jessica Arrazola, Wences Arvelo, Janet Hamilton
Objectives. To assess the competencies of the state and local governmental epidemiology workforce. Methods. We analyzed 2024 Public Health Workforce Interests and Needs Survey data from 4341 epidemiologists (weighted n = 18 177) in the United States. Respondents rated proficiency across 5 domains. Skills were dichotomized and summed to a composite score (0-5; α = 0.81). Frequencies and ordinal logistic regression examined the associations with education, training, and tier. Results. Data modernization (42.3%) and information systems (36.8%) had the lowest proficiency. Mean competency score was 3.28 (SE = 0.04). A master's (adjusted odds ratio [AOR] = 1.80) and doctoral degree (AOR = 2.96) were associated with greater proficiency (both P < .01), as was epidemiology specialization (AOR = 1.63; P < .01). Epidemiology tier showed a positive gradient, with odds increasing (all P < .01). Conclusions. Many epidemiologists reported limited proficiency. Overall proficiency gaps were larger among early-career epidemiologists and those without education or training. Data modernization and informatics showed the largest gaps across all groups. Public Health Implications. Expanding curricula and training to include data modernization and informatics, investing in professional development, and building equitable capacity across jurisdictions are essential to strengthening epidemiological readiness. (Am J Public Health. 2026;116(S5):S436-S445. https://doi.org/10.2105/AJPH.2026.308699).
Pharmacoepidemiology and drug safetyI Truter, J Hugo, H Smith, S Bansal, A Vira
PURPOSE: The primary aim was to conduct a longitudinal pharmacoepidemiological study on the dispensing patterns of the influenza and pneumococcal vaccines in a section of the private healthcare sector in South Africa in the presence of the COVID-19 vaccine to document the dispensing of these two respiratory vaccines alongside COVID-19 vaccines. METHODS: A quantitative cross-sectional pharmacoepidemiological study on health insurance data covering 5 years (2017-2021) was conducted. The study population consisted of approximately 3.8 million individuals. Profile analysis was used to compare annual dispensing patterns of both vaccines. Ethical approval for the study was obtained. RESULTS: The annual dispensing patterns of the pneumococcal and influenza vaccines differed significantly for the period 2017-2021 (p-value < 0.01), with the influenza vaccine dispensed most frequently from March to June. A similar pattern was observed for both the pre-COVID-19 period (2017-2019) (p-value < 0.01) and the post-COVID-19 period (2020-2021) (p-value < 0.01). At the 5% level of significance, there was a slight increase in the dispensing pattern of pneumococcal vaccines post-COVID-19, when compared to the dispensing pattern pre-COVID-19 (p-value < 0.05). For the period March to June, there was, however, a significant increase in the dispensing pattern of influenza vaccines post-COVID-19 (p-value < 0.01). CONCLUSIONS: The presence of the COVID-19 vaccine has collectively not had a significant impact on the dispensing patterns of pneumococcal and influenza vaccines. When considering the vaccines separately, however, for the months between March and June, significantly more influenza vaccines were dispensed post-COVID-19.
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.
Pharmacoepidemiology and drug safetyByeong Yeob Choi
BACKGROUND: In observational pharmacoepidemiology, estimating average treatment effects (ATEs) is often challenging due to a lack of practical positivity. In highly selective clinical settings, certain patients almost always or never receive treatment, causing ATE estimators to rely on unstable extrapolation. Incremental propensity score interventions (IPSIs) offer a stochastic alternative by shifting each patient's probability of treatment, providing a more clinically realistic framework that circumvents positivity violations. METHODS: We illustrate the IPSI approach, including key identification results and inferential procedures. Using observational data from a cohort of 996 patients undergoing percutaneous coronary intervention (PCI), we evaluated the effect of shifting each patient's probability of receiving abciximab by a predetermined amount on six-month mortality. Propensity scores (PSs) and outcome predictions were estimated using a machine learning ensemble (Super Learner) with 10-fold sample splitting. RESULTS: The ATE estimate suggested that abciximab administration reduced the 6-month mortality risk by 5.9 percentage points compared with PCI alone (risk difference = -0.059, 95% CI: -0.104 to -0.015). However, the practical interpretability of the ATE estimate may be limited because it implicitly assumes that patients with a near-certain probability of treatment could realistically be assigned to withhold abciximab. In contrast, shifting each patient's treatment propensity by odds ratios ranging from 0.1 to 10 showed that 6-month mortality would be significantly reduced under a strong treatment policy promoting abciximab administration. CONCLUSIONS: IPSIs provide a robust and practical alternative to conventional causal inference methods in pharmacoepidemiology settings where treatment assignment is highly selective and the strict positivity is violated.
Pharmacoepidemiology and drug safetyJames M Gwinnutt, Rodrigo de Oliveira, Miriam J Haviland, Julien H Shippee, Elizabeth Eldridge, Lenon Mendes Pereira, Emily Bratton, Jay Nanavati, Christina De…
Large language models (LLMs) represent a type of generative artificial intelligence (GenAI) that generate and interpret text, with some LLMs able to process multimodal content (e.g., images, audio, video), and can be deployed as part of agents to perform users' tasks. LLMs can perform natural language processing functions such as summarization, translation, and extraction giving them the potential to enhance and scale pharmacoepidemiological and real-world research by performing tasks such as literature review, data extraction, and medical writing. Despite the growing integration of GenAI tools into research workflows, their technical foundations and methodological implications remain unfamiliar to many pharmacoepidemiologists, who are often responsible for the reliability and accuracy of research that relies on these tools. This paper aims to inform pharmacoepidemiologists about the capabilities and limitations of LLMs to support responsible integration into the field of pharmacoepidemiology, providing an intuitive overview of how LLMs work, focusing on training and text generation, and reviews current and emerging applications in drug effectiveness and safety research and epidemiology. The article addresses challenges associated with LLM use in real-world evidence generation, including concerns regarding reproducibility, bias, hallucinations, plagiarism, data privacy, and the need for validation.
Health expectations : an international journal of public participation in health care and health policyJulie Rigoureau, Manon Verroul, Valentine Vieillard, Anne Termoz, Laurie Panse, Anaïs Havet, Marie Viprey, Julie Haesebaert
BACKGROUND: Patient and public involvement in pharmacoepidemiology using healthcare administrative databases remains limited despite its potential to enhance research relevance and societal impact. We evaluated the feasibility and benefits of involving patients as research partners in a Patient Committee for a pharmacoepidemiological study using the French nationwide health insurance database (SNDS). METHODS: A participatory feasibility study was conducted through the establishment of a Patient Committee alongside the study's Scientific Committee. A mixed-methods evaluation assessed feasibility combining quantitative indicators, analysis of group dynamics, and thematic analysis of the transcription of the second meeting. Benefits were evaluated based on changes made in protocol, statistical analysis, and civil society dissemination plans based on patients' proposals. The McMaster tool was used to assess the involvement process. RESULTS: Three patients were recruited out of the minimum expected five. Of the five meetings, three were attended by all participants. Consensus was reached on most points discussed and a good cohesion was observed within the Committee. The questions asked to the moderators focused primarily on the progress of the research and on the availability of data beyond the reimbursement-related data available in the SNDS, as data related to the patient's perspective (quality of life or anxiety). At the second meeting, only 13% of coded exchanges fell within the categories previously predefined according to the meeting's objectives. The remaining themes were unrelated to their illness, drug utilisation or care pathways. Patient involvement led to an effective modification of a primary outcome in the research protocol and an additional statistical analysis. Patient Committee also contributed several points for discussion and produced two visual abstracts. Finally, patients expressed satisfaction with their participation, feeling that their opinions had been listened to and taken into account. Project team members involved in project management appeared satisfied with the process, except in logistical needs (very long research timeline with specific deadlines to be met). CONCLUSION: Although benefits of patient involvement were observed, feasibility was partial due to several obstacles related to participant recruitment and patients' understanding of the SDNS. To improve feasibility, future initiatives should co-construct appropriate methodologies with stakeholders and provide adequate training tailored to the complexity of pharmacoepidemiology research. PATIENT AND PUBLIC CONTRIBUTION: The study was conducted in collaboration with the patient partner from the research laboratory. She was involved in recruiting the Patient Committee and drafting the recruitment materials (flyer and email). The patient partner also proofread the content of the training session.
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.
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.
Frontiers in public healthVictor Luckyboy Dzramado, Obed U Lasim, William Wilberforce Amoah, Samuel Antwi, Joana Edem Koto, Doris Hagan
INTRODUCTION: Infectious disease outbreaks continue to threaten global health security, with resource-limited settings facing disproportionate challenges in surveillance, outbreak investigation, and applied biostatistical capacity. The WHO International Health Regulations 2005 framework defines preparedness through measurable core capacities, and seminal multi-country analyses of IHR State Party Self-Assessment Annual Reporting data from 182 and 186 countries consistently show that sub-Saharan African countries report the largest preparedness gaps globally. Ghana, despite hosting the first Field Epidemiology and Laboratory Training Programme in West Africa, has not previously been the subject of a comprehensive synthesis of its preparedness across all relevant IHR domains. This review therefore addresses a single integrated question: to what extent is the Ghana Health Service prepared for field epidemiology and applied biostatistics, as assessed through surveillance system performance, outbreak investigation capacity, workforce development, laboratory infrastructure, and statistical modeling capacities aligned with WHO IHR core capacity benchmarks? METHODS: This systematic review followed PRISMA 2020 guidelines and was prospectively registered on PROSPERO (CRD420261299788). Searches were conducted in PubMed, African Index Medicus, AJOL, and Google Scholar, supplemented by grey literature, covering January 2000 to February 2026. Two reviewers independently screened 328 unique records, assessed 75 full-text articles, and included 38 studies with Ghana-specific disaggregated data. Quality was assessed using design-specific tools with transparent reconciliation into low, moderate, and high risk-of-bias categories. Narrative synthesis was the principal analytic approach. RESULTS: Surveillance completeness ranged from 71% to 94% (median 82%); timeliness ranged from 48% to 91% (median 76%), with regional performance substantially exceeding district performance. The GFELTP produced 420 graduates from 2007 to 2017, representing 45% of WHO-benchmarked workforce requirements. Outbreak response times improved from 14 to 3 days for comparable outbreaks. Laboratory capacity remained concentrated in 2 to 6 sentinel sites. No included study examined biostatistical modeling capacity. The 2017 WHO Joint External Evaluation rated overall IHR capacity at 67%. DISCUSSION: Ghana demonstrates advancing but incomplete preparedness. Priority interventions should address workforce expansion, peripheral surveillance strengthening, laboratory decentralization, and indigenous biostatistical capacity development. SYSTEMATIC REVIEW REGISTRATION: https://www.crd.york.ac.uk/PROSPERO/view/CRD420261299788, identifier: CRD420261299788.
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.
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.
Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhiY J Zheng
There is a persistent inconsistency between the definition of period prevalence (PP) and its practical calculation, which poses a challenge in teaching epidemiology. This paper proposes a visual teaching design for a "three-tiered relationship diagram of disease duration, case numbers and population size within a dynamic population", based on a unified timeline. First, cases are classified into four categories according to the relationship between disease duration and the study period, with a clear distinction between new and pre-existing cases. Second, the person-time (area under the curve) interpretations of the integrals of real-time case counts, cumulative case counts, their maximum value, and population size over time are explained. Third, a theoretical PP formula based on the person-time ratio is established, from which two simplified formulas are derived. The relationships among the three formulas are clarified, and their application is demonstrated using examples of type 2 diabetes and influenza. Centered on the relational graph, this teaching design integrates conceptual analysis, formula derivation, and case validation. A small-scale pilot teaching session has shown preliminary effectiveness, and directions for future application and research are discussed.
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.
History and philosophy of the life sciencesDavide Coraci
The trade-off hypothesis plays a foundational role in the theoretical framework of modern evolutionary epidemiology, proposing that pathogen fitness is maximized at intermediate levels of virulence. Despite its influence on the study of host-pathogen interactions, the hypothesis has been criticized for its limited empirical support and the conceptual ambiguities surrounding the definition of virulence. This paper reassesses the scientific status of the trade-off hypothesis by interpreting the dependencies among epidemiological parameters as constitutive principles. Therefore, the results of the seminal 1982 work of Anderson and May are reinterpreted as a shift in the constitutive principles underpinning the paradigm of evolutionary epidemiology. This perspective provides a novel basis for evaluating the empirical support for the trade-off hypothesis and reassessing the debate regarding its validity.
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.
Hawai'i journal of health & social welfareHelene Le Mouellic, Gillian Dunn
The Pacific Island Health Officers Association supports health workforce capacity building in the United States-Affiliated Pacific Islands by implementing a Field Epidemiology Training Program (FETP) called Strengthening Health Interventions in the Pacific (SHIP). This study presents a secondary analysis of survey and interview data from a 2023 mixed-methods external evaluation to identify and examine stakeholder perspectives on the program. Quantitative survey data from 83 respondents were analyzed using descriptive statistics, with Wilcoxon signed-rank tests used to compare retrospective self-assessed proficiency ratings. Qualitative data from 52 key informant interviews and open-ended survey responses were analyzed using thematic coding. Analysis identified 6 themes grouped within 2 domains: the SHIP learning model and participant skills development and application. Stakeholders identified workplace-based learning, academic accreditation, inclusion of non-communicable disease epidemiology, and support from supervisors and instructors as important features of the learning model. Survey respondents reported high satisfaction with the program, frequent application of SHIP-acquired skills in routine public health practice and outbreak response, and significant improvements in retrospective self-assessed proficiency across all competencies (P<.001). Because competency ratings were retrospective self-assessments, the findings reflect perceived rather than objectively measured improvements in proficiency. Nevertheless, the consistency of the quantitative and qualitative findings suggests that FETPs may benefit from aligning training with workplace responsibilities, incorporating local disease priorities into the curriculum, providing recognized academic accreditation, and investing in strong instructional and supervisory support. The model may offer lessons for strengthening epidemiology capacity in small island jurisdictions and other resource-constrained public health settings.
Pharmacoepidemiology and drug safetyMette Reilev, Lotte Rasmussen, Jonas Kanstrup Olsen, Martin Thomsen Ernst, Saad Hanif Abbasi, Rikke Wesselhoeft, Mette Bliddal, Jesper Hallas, Henrik Støvring
BACKGROUND: In pharmacoepidemiologic research, correct assignment of the length of single dispensation is critical to build treatment episodes. The parametric reverse waiting time distribution (rWTD) is a particularly attractive data-driven method to estimate dispensation lengths. AIM: To provide an easily accessible resource of estimated dispensation lengths covering all commonly used drugs for use in treatment episode building in applied pharmacoepidemiologic research. METHODS: We used a random 20% sample of the Danish population alive after 1st January 2000 and identified all their prescriptions filled between 2010 and 2022. We applied the rWTD with five random index dates for each individual to estimate parameters that allow calculation of dispensation length estimates. Parameters were estimated with and without age, sex, and dispensed amount as covariates. RESULTS: We present estimated dispensation lengths for the 20 most prescribed drugs and drug classes in Denmark. Estimated dispensation lengths for all drugs are provided online, and in a spreadsheet. The most prescribed drug was paracetamol with an estimated dispensation length of 194 days, while atorvastatin was the most commonly used drug indicated for long-term use with an estimated dispensation length of 165 days. The dispensation lengths for drugs varied according to age, dispensed volume, sex, and over time. CONCLUSIONS: This is a comprehensive overview of dispensation lengths for all commonly prescribed drugs registered in the Danish National Prescription Registry. Data presented in an online resource can be utilized and modified by other researchers providing optimal conditions for high quality pharmacoepidemiologic research.
Journal of managed care & specialty pharmacyChijioke M Okeke, Regina Nechi, Javeria Khalid, Ibraheem M Karaye, J Douglas Thornton, Ismaeel Yunusa
BACKGROUND: Real-world evidence (RWE) is increasingly used to inform regulatory and payer policy decisions and health technology assessment, yet appraising the methodological credibility of RWE studies remains time-intensive and requires specialized expertise. The appraisal task could involve using an appraisal tool that provides a structured approach for evaluating bias in observational studies of comparative effectiveness and safety. Large language models (LLMs) may offer a scalable means to support this appraisal process, but their performance on structured bias assessment tasks has not been fully characterized. OBJECTIVE: To compare the performance of LLMs from 6 major artificial intelligence (AI) technology providers against human expert assessments in appraising bias in published RWE studies using the Appraisal of Potential Bias in Real-World Evidence Studies framework. METHODS: We conducted a comparative diagnostic accuracy study evaluating 40 LLMs from OpenAI, Anthropic, Google, xAI, Meta, and DeepSeek. Ten published RWE studies representing diverse pharmacoepidemiological designs and data sources were appraised by each LLM using a structured chain-of-thought prompt with conditional rubric injection based on the Appraisal of Potential Bias in Real-World Evidence Studies framework. Two independent human reviewers with pharmacoepidemiology training evaluated each study, with a third adjudicator resolving disagreements to establish the reference standard. LLM performance was assessed using overall accuracy and macro-averaged precision, recall, and F1 scores. Assessment time was compared between models and benchmarked against human reviewers. Bootstrap method was used to construct 95% CI for performance measures. RESULTS: Across 280 item-level assessments per model (10 studies × 28 items), overall accuracy ranged from 12.9% to 66.1%. The highest-performing model was Claude-Sonnet-4.6 (66.1%), followed by o3 (65.4%) and Gemini-3.1-pro-preview (65.0%). Macro-averaged F1 scores ranged from 30.9% to 66.9%; o3 achieved the highest F1 score (66.9%), followed by GROK-4 (65.5%) and Gemini-3.1-pro-preview (65.4%). Human reviewers required an average of 61.05 minutes per study; all LLMs completed assessments substantially faster, with average time per study ranging from 0.80 to 17.22 minutes relative to humans. CONCLUSIONS: LLMs hold considerable promise for automating methodological appraisal of RWE studies; however, their performance is variable and model dependent. Their greatest value may lie in enhancing efficiency and supporting human-led appraisal as decision-support tools rather than replacing expert review. Future research should assess performance across larger, more diverse RWE study collections and evaluate output reproducibility across repeated runs.
Birth defects researchGabra Nohmie, Marc Lanovaz, Odile Sheehy, Cristina Longo, Robert Platt, Audrey Durand, Christine Damase-Michel, Anick Bérard
BACKGROUND: With approximately 50% of pregnancies being unplanned, there is an unintended exposure to potential feto-toxic drugs that may cause major congenital malformations (MCM). This study aims to compare the predictive performance between traditional pharmacoepidemiologic (PE) and machine learning (ML) models. METHODS: We conducted a cohort study within the Quebec Pregnancy Cohort, including all pregnancies covered by Quebec's prescription drug insurance program and their children from 01/1998 to 12/2015. Medication exposures, comorbidities, and women's characteristics 12 months before pregnancy and during the first trimester were considered. Robust Poisson models were used to obtain adjusted risk ratios (aRR) and 95% confidence intervals (CI) of predictors. Logistic regression, robust Poisson, K-Nearest Neighbors, Random Forest, XGBoost, Naïve bayes, Multilayer Perceptron, and Support Vector Machine were developed to predict pregnancies at risk of MCM. Sensitivity, specificity, PPV, NPV, accuracy, ROC-AUCs, PR-AUCs, and F1-score were used to evaluate the performance of predictive models. RESULTS: We analyzed 213,744 pregnancies, finding a 9.7% prevalence of MCM. Logistic regression had the highest discriminative power across models at predicting MCM, with a ROC-AUC of 53.3% and the highest sensitivity (41.5%) and F1-score (46.6%). KNN had the highest specificity (97.9%) but the lowest sensitivity (2.3%). Robust Poisson performed similarly to logistic regression, with the highest accuracy (52.3%). Robust Poisson performed slightly better than logistic regression at classifying organ-specific malformations. All models showed poor overall predictive performance. Results were robust across sensitivity analyses. CONCLUSION: There is insufficient evidence for the superiority of ML over traditional pharmacoepidemiologic modeling in predicting MCM.
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.
Pharmacoepidemiology and drug safetyChristopher T Rentsch, Vincent Lo Re, Melissa Skanderson, Kathleen A McGinnis, Farah Kidwai-Khan, Charles Alcorn, Anne C Black, Kristina Crothers, Vincent C Ma…
The Veterans Aging Cohort Study (VACS)-National is a large, longitudinal real-world data resource derived from electronic health records within the Department of Veterans Affairs (VA), the largest integrated healthcare system in the United States. As of December 2025, VACS-National includes > 14.9 million Veterans who have received care in the VA since 2000. It captures information on VA-related outpatient and inpatient care and includes structured (e.g., diagnostic codes, laboratory results, vital signs, dispensed medical products), semi-structured (e.g., radiology and pathology reports) and unstructured (e.g., progress notes) fields, collected from over 1300 points of care nationwide. Its longitudinal structure supports extended follow-up across demographically and clinically diverse populations within an integrated healthcare system. Key features for pharmacoepidemiological research include near real-time availability of data on dispensed medications, including biologics, vaccines, and devices; routinely-collected laboratory measurements; and computable phenotypes, including validated natural language phenotypes. The resource includes linkages to Centers for Medicare and Medicaid Services (CMS) data, VA Community Care data, National Death Index, and deeply phenotyped VACS sub-cohorts with an extensive library of biomarkers and survey data. VACS-National has supported a wide range of research, including drug utilization, drug safety, comparative effectiveness, and epidemiologic and health outcomes research. Strengths include its national scale, longitudinal follow-up, and rich clinical record; limitations include a small proportion of women and potential incomplete capture of care outside the system or not recoverable through linked datasets. VACS-National provides a comprehensive platform for generating real-world evidence to inform clinical, regulatory, and public health decision-making.
Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletinSimon Brinkwirth, Lena Ella Schneider, Ida Sperle, Petra von Berenberg-Gossler, Katharina Alpers, Sofie Gillesberg Lassen
INTRODUCTIONField epidemiology training programmes (FETPs) strengthen public health workforce capacity for infectious disease surveillance and outbreak response. The Postgraduate Training for Applied Epidemiology (PAE) is a 2-year FETP aligned with European and global training standards.AIMWe evaluated the contribution of PAE to a strengthened public health workforce for infection protection in Germany.METHODSOur evaluation consisted of three components: a semi-structured desk review of programme outputs (1996-2025), an online graduate survey (cohorts 1996-2023), and an online workshop with experts from local, federal state and national health authorities. We analysed quantitative data descriptively, and qualitative data through a simplified content analysis.RESULTSBy December 2025, PAE had 126 graduates with the following outputs: 197 peer-reviewed publications, 193 accepted conference abstracts, and 205 conducted outbreak investigations. In total, 72% (91/126) graduates responded to the survey. Most respondents remained in the German public health workforce (70%; 64/91), reported high satisfaction (90%; 82/91), and would recommend the programme (96%; 87/91). Graduates reported roles in crisis and outbreak management (70%; 64/91), holding leadership roles (59%; 54/91), and engaging in knowledge dissemination (86%; 78/91). Qualitative findings highlighted shared methodological approaches and technical language, and strong networks as key facilitators of collaboration across all levels of the German public health service.CONCLUSIONWe found that PAE contributes to strengthening and sustaining an infection protection workforce in Germany that regularly applies and disseminates learnt skills. Most graduates have held or currently hold leadership roles and frequently contribute to outbreak and public health crisis management.
Journal of evaluation in clinical practiceMahyar Etminan, Ramin Rezaeianzadeh, Antonios Douros
RATIONALE: The rapid expansion of medical literature has led to variability and contradictions in study findings, making it increasingly difficult to distinguish meaningful signals from noise. Much of this variability arises from methodological limitations, including confounding, selection bias, and reverse causation. Although artificial intelligence (AI)-assisted tools exist for risk-of-bias assessment, most are designed for systematic reviews and are not tailored to identifying epidemiologic biases in observational studies. Structured, scalable approaches are needed to evaluate validity in real-world evidence research. AIMS AND OBJECTIVES: To develop and validate EpiVise, an AI-assisted, expert-informed, rule-based framework for identifying major sources of bias in pharmacoepidemiologic studies and to assess its agreement with expert epidemiologist evaluations. METHODS: Recently published pharmacoepidemiologic studies from high-impact journals (post- July 2025) were independently evaluated by EpiVise and two expert epidemiologists across predefined bias domains, including measured confounding, confounding by indication, selection bias, immortal time bias, and disease latency bias. Agreement was assessed using weighted kappa statistics. In addition, synthetic study scenarios with predefined embedded biases were constructed to evaluate framework performance under controlled conditions. RESULTS: Among published studies (10 studies; 60 ratings), agreement between EpiVise and expert assessments was substantial (weighted κ = 0.75; 95% confidence interval [CI], 0.63-0.87). Twelve ratings (20.0%) were discordant, all limited to adjacent categories. In synthetic scenarios (10 studies; 50 ratings), agreement was also substantial, with 40 of 50 ratings concordant (80.0%) and a weighted κ of 0.72 (95% CI, 0.61-0.83). CONCLUSION: EpiVise demonstrated substantial agreement with expert epidemiologist assessments in both published and synthetic study evaluations. As a scalable and reproducible framework for identifying common epidemiologic biases, EpiVise may enhance evidence appraisal, peer review, and clinical or regulatory decision-making. Further validation across broader study designs and therapeutic areas is warranted.
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.