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PubMed2026

Portable metagenomics for preventive surveillance and outbreak control in livestock and poultry: Pathogen detection, resistome profiling, and antimicrobial stewardship.

Conventional diagnostics for livestock and poultry outbreaks commonly rely on culture or targeted PCR panels, which may be too slow or too narrow to guide early control decisions. Portable metagenomics, particularly real-time nanopore sequencing, offers a route to broad pathogen detection, antimicrobial-resistance gene profiling, and outbreak investigation within an integrated workflow. This implementation-focused review evaluates how near-point-of-care metagenomics may support preventive veterinary medicine through earlier detection, surveillance, cohorting, biosecurity decisions, and antimicrobial stewardship. We synthesize sample-to-answer workflows for enteric and respiratory disease in food-producing animals, including sampling, nucleic-acid extraction, host depletion or target enrichment, library preparation, sequencing, bioinformatics, quality control, and interpretation. Applications in calf diarrhea, bovine respiratory disease, poultry outbreaks, mastitis, and resistome monitoring are considered alongside the central limitation that detection alone does not establish causation. Pathogen and resistance-gene signals must therefore be interpreted with clinical signs, lesions, epidemiology, controls, and confirmatory testing. We also propose a minimum reporting checklist, intended as a practical framework rather than a validated consensus standard. Portable metagenomics is not a replacement for conventional diagnostics, but appropriately validated workflows can reduce uncertainty during time-sensitive outbreaks and support more judicious antimicrobial use.

Animals↗
PubMed2026

Nosocomial Outbreak of Lassa Fever in Conakry, Guinea, 2022.

BACKGROUND: Lassa fever is endemic in Guinea, with high seroprevalence in the forest region. However, clinical cases have been only anecdotally reported. In August 2022, a nosocomial outbreak occurred at a private clinic in the capital, Conakry, an area previously considered low risk. METHODS: Suspected cases were confirmed by real-time reverse-transcription polymerase chain reaction within 24 hours. Viremia was monitored during hospitalization, and whole-genome sequencing was performed in-country within 13 days of outbreak detection. Outbreak investigation involved rodent testing in the home village of the suspected primary case. RESULTS: Six cases were laboratory-confirmed, 5 of which were healthcare workers of the clinic. The case fatality rate was 16.7%. Viral RNA remained detectable in blood of survivors for a median of 26 days (interquartile range, 24-41 days) post-disease onset. Epidemiological investigations identified a suspected primary case, who had died of a febrile disease compatible with Lassa fever, had contact with all secondary cases, and had a travel history from Kissidougou area. Three near-complete and 1 partial Lassa virus genomes were recovered from the secondary cases, which phylogenetically clustered with genomes from central Guinea. Consistent with a common transmission source, the 4 genomes were almost identical. Rodent testing revealed a new reservoir area in eastern-central Guinea. CONCLUSIONS: This outbreak highlights the vulnerability of healthcare settings in low-prevalence areas of West Africa to nosocomial Lassa virus transmission due to human mobility. Facilitated by capacity-building programs for viral hemorrhagic fevers, rapid diagnosis, genomic analysis, and ecological assessment enabled an efficient outbreak response and control.

Lassa Fever↗
PubMed2026

Agricultural sprinkler irrigation systems as environmental reservoirs and airborne dissemination sources of Legionella pneumophila.

Sprinkler irrigation systems are critical for modern agriculture but represent largely unrecognized aquatic environments capable of sustaining opportunistic human pathogens. Among them, Legionella pneumophila is of particular concern due to its ability to colonize engineered water systems, persist under fluctuating environmental conditions, and be transmitted through aerosols. In this study, we conducted a comprehensive microbiological and genomic investigation of irrigation ponds and ditches in a rural area of north-east Spain where two zones were sampled. Metagenomic profiling revealed highly diverse microbial communities encompassing more than 20,000 species, including 21 airborne-transmissible bacterial pathogens of clinical relevance. Notably, L. pneumophila was detected in both zones, with a relative abundance of up to 4.6 %. Culture-based isolation confirmed the presence of L. pneumophila serogroup 1, Pontiac group, Benidorm subgroup, sequence type 15. Phylogenetic analysis demonstrated a close relationship between this environmental strain and clinical isolates obtained during a Legionnaires' disease outbreak occurred in 2015, which had remained without a confirmed environmental source. Meteorological data from the exposure period revealed wind conditions favouring long-distance aerosol dispersion from irrigated fields toward residential areas. Our findings provide evidence that irrigation infrastructures can act as environmental reservoirs and dissemination routes of L. pneumophila among other airborne pathogens. These results underscore the need to incorporate agricultural irrigation systems into routine environmental surveillance, outbreak investigations, and public health risk assessments.

Legionella pneumophila↗
PubMed2026

Clustering and Source Association of Clinical and Nonclinical Listeria monocytogenes Isolates, New York, USA, 2000-20211.

We analyzed whole-genome sequencing data for 1,046 human clinical and 1,332 nonclinical Listeria monocytogenes isolates collected across New York, USA, during 2000-2021. Several hypervirulent clonal complexes (CCs) were significantly associated with clinical isolates, and several hypovirulent CCs were associated with nonclinical isolates. Specific CCs also showed association with specific food categories (e.g., processed meat); specific genetic markers (e.g., inlA premature stop codons) were also significantly associated with processed meat isolates. Analysis of clusters that contained food isolates, as well as subsequently identified clinical isolates, showed that time of isolation between food isolates and clinical isolates was significantly shorter for produce isolates than for isolates from meat, dairy, or fish. This finding suggests unique transmission pathways for produce, which might reflect short shelf life or limited L. monocytogenes persistence (e.g., in agricultural environments). This study highlights new opportunities for use of whole-genome sequencing to improve outbreak investigations and source attribution.

Listeria monocytogenes↗
PubMed2025

Crimean-Congo Hemorrhagic Fever Outbreak in Podor, Northern Senegal in 2022: Two Independent Emergences and Unprecedented Mortality.

Crimean-Congo hemorrhagic fever (CCHF) is a lethal zoonotic disease transmitted through tick bites and contact with infected animals or humans. As CCHF continues to expand worldwide, we report on the first severe outbreak in Senegal (Podor, Saint-Louis region) in 2022. We conducted a comprehensive outbreak investigation after a confirmed CCHF human case in Podor. This included sample collections from humans, animals, and ticks from the household and surrounding area. Human and animal samples were tested by ELISA for antibodies to CCHF virus and by reverse transcription polymerase chain reaction (RT-PCR) for CCHF virus RNA, whereas tick samples underwent CCHF RT-PCR only. Positive RT-PCR samples underwent viral genome sequencing for genetic characterization. We determined three CCHF human cases, with two deaths, as well as virus circulation in 11 ticks and in livestock, with an overall seroprevalence of 42.5%. CCHF IgG antibodies were detected in human contact cases, showing its prior prevalence in the area. Phylogenetic analyses revealed high genetic diversity within CCHF genotypes, with existence of reassortants and cocirculation of two different isolates from various origins in Mboyo and Nenette villages, where human cases were detected. The data showed a correlation between the strains identified in humans and ticks in each village, showing two independent emergences in Podor. The outbreak in Podor was probably because of the high abundance of animal hosts in this sylvopastoral area, the diversity of tick populations with the presence of the main CCHF vectors, and the increasing prevalence of CCHF virus. The surveillance in this area needs to be strengthened.

Humans↗
PubMed2026

H5N1 Clade 2.3.4.4b Infections in Domestic Cats During an Avian Influenza Outbreak in Italy: Implications for One Health Surveillance.

BACKGROUND: H5Nx goose/Guangdong (Gs/GD) lineage highly pathogenic avian influenza (HPAI) viruses pose a significant public health threat due to their global spread, mutation accumulation, and expanding host range. The descendant clade 2.3.4.4b has been causing widespread infections in birds and increasing spillover events in mammals. METHODS: This report documents the first fatal case of highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b infection in a domestic cat in Italy, detected in early January 2025. The cat (CAT 1) resided on a backyard poultry farm experiencing a high pathogenicity avian influenza outbreak and succumbed rapidly following the onset of respiratory signs. A second exposed cat (CAT 2) developed clinical disease without fatal outcome. Comprehensive outbreak investigations were conducted, including pathological, serological, molecular analyses, and genomic characterization. RESULTS: Pathological examination of CAT 1 revealed acute necrotizing bronchointerstitial pneumonia, non-suppurative meningoencephalitis, and disseminated foci of hepatic necrosis. Interestingly, the PB2-E627K mutation associated with mammalian virus adaptation was observed in the feline viral isolate compared to avian isolates. Such polymerase complex mutations are key determinants of host range and increase pathogenicity in mammals. CAT 2 from the same farm tested negative for AIV genome detection but subsequently seroconverted for antibodies against NPA, H5, and N1. CONCLUSION: Sharing these findings is crucial for surveillance aimed at enabling early identification of increased risks to human and animal health, preventing cross-species viral transmission and mitigating the risk of potential spillover events.

Animals↗
PubMed2027

Workflow for Long-Read Amplicon Sequencing of Chikungunya Virus Using Oxford Nanopore Technology.

This protocol provides a comprehensive, step-by-step workflow for whole-genome sequencing of Chikungunya virus (CHIKV) using an amplicon-based strategy optimized for Oxford Nanopore Technologies (ONT) platforms. The procedure includes detailed instructions for sample handling, viral RNA extraction, quality control, cDNA synthesis, multiplex PCR amplification, library preparation, sequencing, and primary bioinformatic processing. The protocol is designed to maximize reproducibility across laboratories and is suitable for genomic surveillance applications, including outbreak investigation and molecular epidemiology, even when working with low-to-moderate viral loads.

Chikungunya virus↗
PubMed2026

From commensal to pathobiont: The emergence of virulence-enhanced Escherichia coli in China's food-animal systems - insights with future implications.

A fundamental shift in Escherichia coli epidemiology is being driven by convergence of virulence determinants and antimicrobial resistance within linked human-animal-environment systems. In China, the rapid growth of food-animal production, extensive antimicrobial use, and complex food networks are accelerating the emergence and dissemination of virulence-enhanced E. coli pathobionts. This review synthesizes recent epidemiological, genomics, and outbreak data to characterize China's evolving landscape of food-animal-associated E. coli. We highlight a significant shift from classical pathotypes to hybrid lineages that simultaneously carry virulence factors and last-resort antibiotic resistance determinants, including mcr-1, tet(X4), and blaNDM. These traits disseminate rapidly via plasmid-mediated horizontal gene transfer, facilitating rapid adaptation and enabling cross-sectoral One Health transmission. National surveillance, foodborne outbreak investigations, and whole-genome sequencing data show that food-animal reservoirs are active evolutionary niches that drive pathogen diversity and fitness, rather than serving merely as contamination sources. Whole-genome sequencing also pinpoints high-risk clones (e.g., ST394) and plasmid-mediated co-selection of virulence and AMR. The emergence of hybrid pathotypes (e.g., STEC/ETEC) and AMR-virulence co-selection challenges traditional classification and limits the effectiveness of conventional surveillance approaches. The 2017 colistin ban reduced mcr-1, yet ongoing resistance and emerging tet(X4) demand integrated surveillance. Collectively, these findings call for reconceptualizing E. coli as a dynamic genomic entity embedded within a unified ecological network. Addressing this threat requires an integrated One Health strategy including genomic surveillance, agricultural antimicrobial stewardship, and coordinated food-environment-clinical monitoring to prevent high-risk clone emergence and global spread.

Animals↗
PubMed2025

Whole-genome automated assembly pipeline for Chlamydia trachomatis strains from reference, in vitro and clinical samples using the integrated CtGAP pipeline.

Whole genome sequencing (WGS) is pivotal for the molecular characterization of Chlamydia trachomatis (Ct)-the leading bacterial cause of sexually transmitted infections and infectious blindness worldwide. Ct WGS can inform epidemiologic, public health and outbreak investigations of these human-restricted pathogens. However, challenges persist in generating high-quality genomes for downstream analyses given its obligate intracellular nature and difficulty with in vitro propagation. No single tool exists for the entirety of Ct genome assembly, necessitating the adaptation of multiple programs with varying success. Compounding this issue is the absence of reliable Ct reference strain genomes. We, therefore, developed CtGAP-Chlamydia trachomatisGenome Assembly Pipeline-as an integrated 'one-stop-shop' pipeline for assembly and characterization of Ct genome sequencing data from various sources including isolates, in vitro samples, clinical swabs and urine. CtGAP, written in Snakemake, enables read quality statistics output, adapter and quality trimming, host read removal, de novo and reference-guided assembly, contig scaffolding, selective ompA, multi-locus-sequence and plasmid typing, phylogenetic tree construction, and recombinant genome identification. Twenty Ct reference genomes were also generated. Successfully validated on a diverse collection of 363 samples containing Ct, CtGAP represents a novel pipeline requiring minimal bioinformatics expertise with easy adaptation for use with other bacterial species.

Chlamydia trachomatis↗
PubMed2026

Comparative evaluation of three high-molecular-weight DNA extraction kits for Oxford Nanopore sequencing of Clostridioides difficile and Clostridium perfringens.

UNLABELLED: Clostridioides difficile and Clostridium perfringens are Gram-positive, spore-forming anaerobic pathogens affecting humans and animals, for which genomic data have been mainly generated using short-read or hybrid sequencing approaches. In this study, we evaluated three commercial non-bead-beating DNA extraction kits designed for high-molecular-weight DNA recovery for Oxford Nanopore long-read whole-genome sequencing of two C. difficile and two C. perfringens strains, including one reference strain and one clinical or environmental isolate per species. Based on sequencing performance and kit ease of use, one kit was selected for additional sequencing of plasmid-carrying strains of both species. All three kits allowed correct identification of sequence types, toxin-encoding genes, and antimicrobial resistance determinants, confirming their suitability for clinical and epidemiological applications. However, the BT MasterPure Kit provided the highest DNA concentrations, longest fragment sizes, and superior read lengths and N50 values, particularly for C. difficile, achieving >100× coverage and enabling reliable circularization of chromosomes and plasmids, including a C. difficile metronidazole resistance plasmid and C. perfringens plasmids carrying toxin and antibiotic resistance genes. The other kits produced slightly lower DNA yields, resulting in shorter reads and reduced genome coverage for C. difficile, highlighting the challenge of extracting high-quality DNA from Gram-positive, spore-forming bacteria. Overall, this study provides practical guidance for selecting DNA extraction protocols optimized for Oxford Nanopore sequencing of C. difficile and C. perfringens, supporting high-quality genome assemblies and plasmid characterization and facilitating the routine genomic surveillance of clinically relevant spore-forming pathogens. IMPORTANCE: High-quality genomic data are essential for accurate characterization of Clostridioides difficile and Clostridium perfringens, two clinically and epidemiologically important Gram-positive, spore-forming pathogens. However, long-read sequencing performance can be strongly influenced by the choice of DNA extraction method, particularly for organisms with robust cell walls, where commonly used methods can lead to fragmented DNA. In this work, DNA of four strains was extracted using three commercial high-molecular-weight DNA extraction kits and sequenced using Oxford Nanopore Technologies. The best-performing kit was also evaluated using three additional strains known to harbor plasmids in order to assess its plasmid recovery efficiency. The results demonstrated successful plasmid recovery, circularization, and characterization. DNA extraction protocols optimized for Oxford Nanopore sequencing enable the rapid and cost-effective characterization of C. difficile and C. perfringens for genomic surveillance or outbreak investigations.

Clostridioides difficile↗
PubMed2022

Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study.

BACKGROUND: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. METHODS: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data collection period, followed by intervention periods comprising 8 weeks of 'rapid' (<48 hr) and 4 weeks of 'longer-turnaround' (5-10 days) sequencing using a sequence reporting tool (SRT). Data were collected on all hospital-onset COVID-19 infections (HOCIs; detected &#x2265;48 hr from admission). The impact of the sequencing intervention on IPC knowledge and actions, and on the incidence of probable/definite hospital-acquired infections (HAIs), was evaluated. RESULTS: A total of 2170 HOCI cases were recorded from October 2020 to April 2021, corresponding to a period of extreme strain on the health service, with sequence reports returned for 650/1320 (49.2%) during intervention phases. We did not detect a statistically significant change in weekly incidence of HAIs in longer-turnaround (incidence rate ratio 1.60, 95% CI 0.85-3.01; p=0.14) or rapid (0.85, 0.48-1.50; p=0.54) intervention phases compared to baseline phase. However, IPC practice was changed in 7.8 and 7.4% of all HOCI cases in rapid and longer-turnaround phases, respectively, and 17.2 and 11.6% of cases where the report was returned. In a 'per-protocol' sensitivity analysis, there was an impact on IPC actions in 20.7% of HOCI cases when the SRT report was returned within 5 days. Capacity to respond effectively to insights from sequencing was breached in most sites by the volume of cases and limited resources. CONCLUSIONS: While we did not demonstrate a direct impact of sequencing on the incidence of nosocomial transmission, our results suggest that sequencing can inform IPC response to HOCIs, particularly when returned within 5 days. FUNDING: COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) (grant code: MC_PC_19027), and Genome Research Limited, operating as the Wellcome Sanger Institute. CLINICAL TRIAL NUMBER: NCT04405934.

Humans↗
PubMedDate not supplied

Inclusion body hepatitis in broiler chickens in Iraq.

Eighteen outbreaks of inclusion body hepatitis (IBH) were identified in broiler chickens in Baghdad in 1977 and 1978. The disease was seen mainly in 4-to-6-week-old broiler chickens. The mortality rate did not exceed 1% in any outbreak investigated. The most common gross findings were stellate or punctiform hemorrhagic areas in markedly fatty livers. Noticed in many cases were enlarged and pale kidneys, hemorrhagic lesions in the skeletal muscles, and pale fattened bone marrow. Histological examination of tissues revealed fat droplets and intranuclear inclusion bodies in degenerated liver cells. Eosinophilic inclusion bodies were seen in all cases. Only five cases had basophilic inclusions along with the eosinophilic ones. The etiologic agent was isolated on chorioallantoic membrane (CAM) of 12-day-old embryonated chicken eggs. The disease was produced experimentally in 4-week-old chicks using infected CAM suspension.

Animals↗