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PubMed2026

Recent Advances in Surveillance Strategies for Nasopharyngeal Carcinoma.

PURPOSE OF REVIEW: Nasopharyngeal carcinoma (NPC) is a malignant tumor characterized by a distinct geographical distribution. Effective surveillance is crucial for the early detection of recurrence or metastasis and for improving patient prognosis.This review systematically examines current NPC follow-up protocols and recent developments to inform individualized precision surveillance. RECENT FINDINGS: This review focuses on two main aspects. 1) We compare and analyze current major NPC follow-up guidelines, with key discussions covering follow-up frequency, imaging modalities (including magnetic resonance imaging [MRI] and positron emission tomography [PET]), plasma Epstein-Barr virus DNA (EBV-DNA) monitoring, and functional assessments. 2)We elaborate on the application prospects and research progress of genomics, radiomics, and artificial intelligence in NPC surveillance. Studies suggest that risk-stratified, individualized follow-up strategies, such as those based on conditional survival models, can enhance the cost-effectiveness of surveillance. Additionally, emerging technologies, including radiomics and artificial intelligence, show promise for improving recurrence risk assessment, prognostic stratification, and individualized surveillance in NPC. Concurrently, advances in genomics and radiomics offer new opportunities for predicting complications and guiding treatment adjustments. Future efforts should focus on integrating multidisciplinary expertise to develop dynamic monitoring systems that enable precise follow-up and ultimately improve patient survival outcomes.

Humans↗

PubMed2026

Artificial intelligence-assisted detection and optical differentiation of colorectal lesions in Lynch syndrome surveillance (CADLY2): a multicentre, open-label, randomised controlled superiority trial.

BACKGROUND: Artificial intelligence (AI)-based computer-aided detection (CADe) systems improve adenoma detection in average-risk colorectal cancer screening. Meanwhile, evidence in Lynch syndrome surveillance is sparse and inconsistent. We assessed the effect of CADe on adenoma detection during Lynch syndrome surveillance. Computer-aided optical diagnosis (CADx) performance for optical differentiation of colorectal lesions was evaluated as a secondary aim. METHODS: CADLY2 was an international, multicentre, open-label, randomised controlled superiority trial at nine specialised hereditary cancer surveillance centres in Belgium, Germany, the Netherlands, and Spain. Adults aged 18 years or older with genetically confirmed Lynch syndrome scheduled for surveillance colonoscopy were randomly assigned (1:1) to high-definition white-light (HD-WL) colonoscopy alone or to HD-WL colonoscopy with computer-aided assistance from CAD EYE (Fujifilm, Tokyo, Japan). CAD EYE was used for CADe during withdrawal and for CADx after lesion detection. Randomisation was done centrally through a secure web-based system using Pocock's minimisation algorithm with a stochastic component and was stratified by centre, sex, previous colorectal cancer, underlying pathogenic variant, and interval since previous colonoscopy. Allocation concealment was ensured through the centralised web-based system. Patients were masked to group allocation until the start of withdrawal in procedures with mild sedation, or until completion of the procedure in procedures with propofol-based sedation. Endoscopists were not masked. The primary outcome was adenoma detection rate, defined as the proportion of patients with at least one histopathologically confirmed adenoma, analysed in the full analysis set (defined as all randomly allocated patients with available data for the primary outcome). The diagnostic performance of the CADx system was evaluated as a secondary outcome. The safety analysis set comprised all randomly allocated patients who underwent a study colonoscopy. This study is registered with the German Clinical Trials Register, DRKS00030695, and is completed. FINDINGS: Between May 9, 2023, and Oct 30, 2025, 757 patients were randomly allocated to HD-WL colonoscopy (377 patients) or to AI-assisted colonoscopy (380 patients); 733 patients were included in the full analysis set (369 HD-WL and 364 AI-assisted). The median age was 49 years (IQR 38-59) in the HD-WL group and 50 years (38-59) in the AI-assisted group; 213 (58%) were female and 156 (42%) male in the HD-WL group, and 207 (57%) were female and 157 (43%) male in the AI-assisted group. The adenoma detection rate was 30·9% (114 of 369 patients) with HD-WL versus 33·8% (123 of 364 patients) with CADe assistance (odds ratio 1·14 [95% CI 0·83-1·57], p=0·41). For CADx differentiation of neoplastic versus non-neoplastic lesions in the paired lesion-level analysis, with histopathology as the reference standard and sessile serrated lesions and traditional serrated adenomas classified as non-neoplastic, CADx sensitivity was 85·9% (95% CI 82·0-89·1) and specificity was 91·4% (89·4-93·0). Three adverse events occurred in the AI-assisted group: two mild post-polypectomy bleedings and one serious pulmonary embolism or deep venous thrombosis unrelated to the procedure. No adverse events occurred in the HD-WL group. INTERPRETATION: CADe-assisted colonoscopy did not show the absolute improvement in adenoma detection rate that was assumed in the prespecified sample-size calculation. CADx did not clearly improve lesion differentiation beyond expert optical diagnosis in expert Lynch syndrome surveillance settings. FUNDING: Third-party research funding of the National Center for Hereditary Tumor Syndromes, University Hospital Bonn.

Humans↗

PubMed2026

Clinical Validation of a Multiplex Urine Biomarker Assay for Surveillance of Recurrent Bladder Cancer.

PURPOSE: More than 50% of patients with non-muscle-invasive bladder cancer experience recurrence, requiring lifelong surveillance with repeated cystoscopy. Given the invasive nature and cost of cystoscopy, accurate noninvasive tools are needed to support risk-adapted monitoring. We evaluated the ability of Oncuria-Monitor, a multiplex urine biomarker assay, to detect recurrent bladder cancer during surveillance. PATIENTS AND METHODS: Between February 2017 and August 2020, six medical centers in the United States and Japan prospectively enrolled 300 patients with a history of bladder cancer, generating 1,248 serial urine samples. Participants were divided into training and validation cohorts. At each surveillance visit over 2 years, urine samples were analyzed in a blinded manner using Oncuria-Monitor and BladderChek, alongside urine cytology. Test performance was compared with cystoscopy and histopathology-confirmed recurrence. RESULTS: Recurrent bladder cancer was identified in 31% (93/300) of participants, with 143 total recurrences during follow-up, including 90 tumors in the validation cohort. In the validation cohort, Oncuria-Monitor achieved a sensitivity of 85.6% [95% confidence interval (CI), 78.1%-92.2%] and a negative predictive value (NPV) of 93% (95% CI, 89.2%-96.4%). In comparison, BladderChek demonstrated a sensitivity of 20.0% and an NPV of 88%, whereas urine cytology showed a sensitivity of 36.9% and an NPV of 91.6%. The number needed to evaluate to detect one recurrence was 3 for both cystoscopy and Oncuria-Monitor, compared with 15 for BladderChek and 8 for cytology. CONCLUSIONS: In this large prospective longitudinal study, Oncuria-Monitor demonstrated clinically actionable performance, enabling a rule-out strategy that could safely reduce cystoscopy in approximately 25% of surveillance visits. These findings support a paradigm shift toward biomarker-guided, risk-adapted surveillance in bladder cancer that reduces unnecessary invasive procedures while maintaining oncologic safety.

Humans↗

PubMed2025

Oropouche Virus Importation in Southern Brazil and Emerging Concern Calling for Enhanced Public Health Surveillance.

Oropouche virus (OROV), an arthropod-borne virus transmitted by Culicoides paraensis, is an endemic arbovirus that historically circulates mostly in the Amazon basin. Between 2022 and 2024, it reemerged as a more widespread public health concern in South America. We conducted a pooled-sample molecular surveillance study to understand the prevalence of Oropouche fever in Brazil's southernmost state. Over 18 months, we analyzed 4060 samples to monitor the virus emergence in the Rio Grande do Sul state. We detected the first human case of OROV in the state, and our phylogenetic reconstruction indicated a travel-related introduction from the Amazon region into Rio Grande do Sul. Despite the absence of local transmission, the invasion of Culicoides paraensis and enzootic circulation of the OROV in Rio Grande do Sul highlight the risk of Oropouche fever outbreaks in the region. We demonstrated that pooled-sample surveillance effectively monitors virus introduction during periods of low endemic circulation, serving as an essential active surveillance tool for the timely detection of virus emergence and enhancing public health preparedness. The multiple introductions of distinct OROV lineages into southern Brazil underscore the importance of genomic surveillance and public health strategies to monitor and mitigate arbovirus spread in the region.

Brazil↗

PubMed2026

Comparative genomic epidemiology of food- and patient-derived diarrheagenic Escherichia coli from sentinel surveillance in Southeast China.

Diarrheagenic Escherichia coli (DEC) remains an important foodborne pathogen, yet long-term comparative genomic surveillance data jointly characterizing food-derived and patient-derived isolates remain limited. This surveillance-based comparative study integrated antimicrobial susceptibility testing and whole-genome sequencing to characterize diarrheagenic Escherichia coli isolates recovered from food and patient sources in Lishui, Southeast China, during 2018-2025, with emphasis on occurrence, resistance profiles, genomic backgrounds, and plasmid replicon-associated features. Antimicrobial susceptibility testing was performed for 258 selected isolates, and whole-genome sequencing was conducted for a curated analytical subset of 204 isolates. The sequenced subset was used for diversity-oriented comparative genomic analysis rather than for unbiased prevalence estimation of the entire DEC collection. EAEC predominated in both sources, although food-associated occurrence was heterogeneous across categories, with the highest recovery rate observed in raw meat. Patient-derived isolates showed a broader overall resistance burden, whereas food-derived isolates retained substantial resistance to tetracycline, chloramphenicol, and florfenicol. Phylogenetic analysis showed partial overlap in genomic backgrounds between food-derived and patient-derived isolates, while representative resistance determinants displayed both broadly distributed and lineage-enriched patterns. Replicon-based plasmid profiling identified 42 plasmid types, including 12 detected in both sources, with IncF-related replicons predominating among these shared profiles. Several food-derived isolates carried multiple plasmid replicon types that were also observed in patient-derived isolates. Overall, food-derived and patient-derived DEC showed partial overlap in genomic backgrounds, resistance determinants, and replicon-defined plasmid profiles within this surveillance setting, while retaining source-associated heterogeneity. These findings should be interpreted as surveillance-based comparative evidence rather than as evidence of direct source attribution or transmission.

Humans↗

PubMed2026

Parental Perspectives and Experiences with Genetic Testing and Surveillance for Cancer Predisposition in Healthy Young Children.

OBJECTIVES: To evaluate parental experiences following diagnosis of a cancer predisposition syndrome (CPS) in childhood and to assess parental perspectives on population-based genomic newborn screening (gNBS) for CPS. STUDY DESIGN: Participants were guardians of children diagnosed with a CPS by age 8, for whom cancer surveillance was recommended, and who had no history of cancer before the CPS diagnosis. Participants completed a demographic survey, genetic knowledge assessment, and a semistructured qualitative interview. Thematic analysis was performed on interview transcripts. Clinical data were abstracted from medical records. RESULTS: We enrolled 25 parents of children with 7 different CPS, including Li-Fraumeni syndrome (43%), familial adenomatous polyposis (14%), nevoid basal cell carcinoma syndrome (11%), and Beckwith-Wiedemann syndrome (11%). Parents characterized receiving a CPS diagnosis as emotionally challenging but also felt empowered by engagement in proactive cancer surveillance. They identified logistical, emotional, physical, and financial burdens of surveillance; however, most perceived that these burdens were outweighed by the medical and emotional advantages. The majority endorsed implementation of gNBS for pediatric cancer risk. CONCLUSIONS: Parents of presymptomatic children with a CPS experience both psychological distress and benefits following a genetic diagnosis. Despite the burdens of surveillance, parents express support for early genomic identification of cancer risk. These findings have implications for the care of children with CPS and inform implementation of population-based gNBS for CPS.

Humans↗

PubMed2027

Global Genomic Surveillance.

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.

Humans↗

PubMed2026

National Antimicrobial Resistance Monitoring System: Three Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance.

Antimicrobial resistance (AMR) occurs when bacteria and other microorganisms adapt in ways that make medicines less effective, causing infections that are harder to treat and more likely to spread. According to the Centers for Disease Control and Prevention (CDC), AMR infections affect millions of Americans each year and contribute to thousands of deaths (CDC, 2019). After three decades of operation, the U.S. National Antimicrobial Resistance Monitoring System (NARMS) stands as a model of sustained, collaborative public health surveillance. What began in 1996 as an effort to track resistance in Salmonella and E. coli O157 has evolved into a One Health surveillance network monitoring AMR across the farm-to-fork continuum. Through a partnership among CDC, the Food and Drug Administration (FDA), the U.S. Department of Agriculture (USDA), state and local health departments, and universities, NARMS has become the backbone of foodborne AMR surveillance in the United States. The past decade has been particularly transformative. NARMS explored new sampling to include companion animals, minor livestock, aquaculture, surface water, and wildlife. Whole-genome sequencing (WGS) revolutionized the program's capabilities, enabling timely identification of emerging pathogens and revealing how resistance genes spread. Near real-time public dashboards make NARMS data accessible to researchers, clinicians, regulators, and policymakers. NARMS data shape decisions about new animal drug approvals, guide stewardship programs, and inform clinical treatment guidelines nationwide. As NARMS enters its fourth decade with a 2026-2030 strategic plan, the program will leverage artificial intelligence and metagenomics while expanding surveillance to fill remaining gaps ensuring this vital system continues to protect the food supply and both human and animal health from AMR.

Antimicrobial Resistance (AMR)↗

PubMed2026

Re-emerging Marburg virus disease in Africa: spillover ecology, geographic expansion, and surveillance vulnerabilities.

Marburg virus disease (MVD) is re-emerging across Africa as a high-consequence zoonosis shaped by expanding ecological suitability, repeated spillover, and uneven surveillance capacity. This review synthesizes current evidence on the ecological, epidemiological, and operational determinants of contemporary Marburg virus (MARV) emergence. We conceptualize MVD as an ecological-emergence system produced by interactions among reservoir-host biology, environmental change, human exposure, health-system readiness, and mobility, rather than as a series of isolated outbreaks. Recent detections in multiple African regions indicate wider enzootic circulation than previously recognized and support repeated, reservoir-associated introductions from distributed ecological foci. Spillover risk is heightened where mining, land-use change, agricultural encroachment, settlement growth, climate-sensitive habitat disruption, and population movement increase contact with Egyptian rousette bats (Rousettus aegyptiacus) and contaminated roost environments. Following primary spillover, diagnostic delays, fragmented surveillance, limited laboratory decentralization, healthcare-associated transmission, and mobility-linked exposure can enable outbreak amplification and delayed recognition. Serological findings further suggest possible "shadow epidemiology," with unrecognized or mild MARV infections occurring outside confirmed outbreak chains. Critical preparedness gaps persist in ecological risk mapping, longitudinal reservoir surveillance, decentralized molecular diagnostics, genomic sequencing, data integration, and cross-border early warning. Future preparedness should move beyond reactive containment toward integrated One Health approach combining predictive ecological surveillance, rapid community-level detection, real-time genomics, infection prevention, risk communication, and regional coordination to identify spillover early and prevent human transmission.

Animals↗

PubMed2025

Whole genome sequencing and phylogenetic classification accelerate the implementation of respiratory syncytial virus genomic surveillance in Canada: a pilot study.

UNLABELLED: Whole genome sequencing (WGS) has emerged as a powerful tool to facilitate the study of existing and emerging infectious diseases. WGS-based genomic surveillance provides information on the genetic diversity and tracks the evolution of important viral pathogens, including respiratory syncytial virus (RSV). Multiplex tiling polymerase chain reaction (PCR) assays have been used to facilitate sequencing of a variety of pathogens in support of genomics-based surveillance initiatives. We developed, optimized, and implemented multiplex tiling PCR assays for RSVA and RSVB capable of generating near-complete genomes in the majority of contemporaneous specimens tested. A pilot data set comprising 52 RSVA and 37 RSVB genomes derived from Canadian clinical specimens during the 2022-2023 respiratory virus season was used to perform phylogenetic analyses using both near-complete genome and glycoprotein (G) sequences. Overall, the RSV phylogenetic tree built with whole genomes showed identical lineage clusters as compared to the G gene but was more discriminatory. Moreover, the availability of complete genomes enables the identification of a broader range of mutations. For instance, mutations identified in the fusion protein among Canadian isolates tested here, including S377N, K272M, S276N, S211N, S206I, and S209Q, could affect the efficacy of current vaccines or antiviral-based therapeutics. In conclusion, our work reinforces other recent studies demonstrating the utility of multiplex tiling PCR assays to facilitate high-throughput WGS of RSV, which is capable of supporting enhanced genomic surveillance initiatives, as well as the more comprehensive genomic analyses required to inform public health strategies for the development and usage of vaccines and antiviral drugs. IMPORTANCE: We present assays to efficiently sequence genomes of RSVA and RSVB. This enables researchers and public health agencies to acquire high-quality genomic data using rapid and cost-effective approaches. Genomic data-based comparative analysis can be used to conduct surveillance and monitor circulating isolates for efficacy of vaccines and antiviral therapeutics.

Humans↗

PubMed1978

Statistical principles of monitoring and surveillance in public health.

Monitoring and surveillance are seen as statistical procedures that will help health authorities to achieve better health services with the existing resources-monitoring being an integrated system of making observations on health and environmental factors and of scrutinizing, storing, and retrieving those data, and surveillance being a closely associated system for collating and interpreting the data.Monitoring should be an action oriented activity and may encompass a wide range of health activities, for example, communicable and noncommunicable diseases, environmental pollutants, and specific problems in health care delivery systems. Both monitoring and surveillance systems have to be related to control measures, and, since the available resources are usually limited, a scale of priorities has to be developed by the statistician in cooperation with the competent authorities.MONITORING MAY BE PERFORMED ON EITHER THE INDIVIDUAL OR AGGREGATE LEVEL AND SHOULD BE PLANNED TO TAKE INTO ACCOUNT THE COURSE OF THE DISEASE UNDER CONSIDERATION: it is concerned with monitoring stimuli and events. Collection of data, for example, on exposure to a pollutant, may be continuous and automatically recorded, or regular or irregular through population sampling or registries. The statistical requirements of monitoring and surveillance systems are discussed and a checklist of features to be considered is given in an annex.

Electronic Data Processing↗

PubMed1978

[Present situation and future prospects for epidemiological surveillance within the framework of Quebec new health system (author's transl)].

Epidemiological surveillance in Quebec is part of the integral system of this activity throughout the whole of Canada and the United States. Since surveillance is aimed mainly at the ecosystem of the disease rather than just the cases, the activities are insured from the horizontal point of view by several organisations, aided by various Ministeries (health, agriculture, industry and commerce). The vertical structure (besides the Center for Disease Control in Atlanta as coordinator) includes the federal Laboratory Centre for Disease Control, its epidemiology and surveillance bureaus, as well as its territorial epidemiologists, provincial epidemiologists and their teams. Quebec has recently been given a new health structure, introduced in conjunction with the traditional organisations by the new Departments of Community Health, and the Social Centres of Community Services. This structure which is new to North America is characterised mostly by its close integration with community health. Moreover, it represents an excellent opportunity for developing an epidemiological surveillance complementary to local problems and for heightening their responsibility.

Communicable Disease Control↗

PubMed2026

Surveilled subjectivation: narratives of drug policing among people who use prohibited drugs in Sweden.

In Sweden, possession and personal use of drugs are criminalized since 1988, resulting in police work being directed towards minor drug offenses. Despite this, police and other authorities are encouraged to protect the health and wellbeing of people who use prohibited drugs (PWUPD). Knowledge is scarce on how this drug policy plays out in practice. This study therefore analyzes interviews with 20 PWUPD who visited harm reduction services and interacted with policing agents in Stockholm, Sweden. The analysis is based on the participants' narratives of drug policing, and it concerns how they produced themselves as subjects through relations between materiality and discourse. We utilize the concept of surveilled subjectivation to elucidate what the participants could do, what they knew and who they could be or become under drug policing. Four themes were identified illustrating the link between discourse and materiality in PWUPD's surveilled subjectivation: "Material aspects of surveillance"; "Resisting the 'drug abuser' identity"; "Fighting power with power"; and "Crossing boundaries and becoming-other". The participants described nonstop efforts to prevent their bodies, activities, belongings and environments from being enfolded by drug law enforcement, which otherwise would fuel even more surveillance. They therefore disassociated themselves from the "drug abuser" identity, and managed encounters with policing agents by keeping a low profile or acting compliantly. While the study highlights the skills and knowledges the participants deployed to navigate omnipresent drug policing, we conclude that their production of autonomous and empowered subjectivities would be facilitated if possession and use of drugs were no longer criminalized.

Humans↗

PubMed2025

Prospective characterisation of drug-resistant bloodstream infections in Africa and Asia (ACORN2): a surveillance network assessment.

BACKGROUND: Antimicrobial resistance (AMR) is a major global health threat, but there is scarcity of laboratory surveillance data linked to clinical information to determine burden and inform interventions, especially from low-income and middle-income countries. The ACORN2 study sought to address this through prospective case-based surveillance in 19 hospitals across Africa and Asia to characterise drug-resistant infections by origin, clinical syndrome, patient age, outcome, and geographical location. METHODS: Patients were enrolled on selected wards and clinical data were collected daily for community-acquired infections (CAIs). Point prevalence surveys for hospital-acquired infections (HAIs) were conducted weekly. Mortality was assessed at discharge and after 28 days. Linked microbiology data were extracted from local laboratory databases. Primary descriptive analyses focused on WHO Global Antimicrobial Resistance and Use Surveillance System pathogen (target organism) bloodstream infections (BSIs). Comparisons were adjusted for clustering by site using random effects models. FINDINGS: Over 31 months, 41 907 infections were characterised from 41 032 admissions. Two-thirds were children (19 351; 47·2%) or neonates (6649; 16·2%). There were marked differences in pathogen incidence and antibiotic resistance when clinical infections were stratified by patient age category and infection origin (CAI/HAI). The highest rates of target organism AMR BSI were third-generation cephalosporin-resistant (3GC-R) Escherichia coli (718·56/100 000 blood cultured infection episodes), meticillin-resistant Staphylococcus aureus (586·89/100 000 blood cultured infection episodes), and 3GC-R Klebsiella pneumoniae (364·92/100 000 blood cultured infection episodes). In-hospital mortality was 13·1% (166/1265) in patients with target organism BSI versus 6·2% (1357/21 845) in those with negative blood cultures, p<0·0001. INTERPRETATION: ACORN2 has shown practical implementation of collecting linked clinical-laboratory AMR data in low-income and middle-income countries and identified a significant burden of WHO GLASS BSI. Adoption of the ACORN2 approach at scale might enhance use of diagnostic microbiology and improve the volume of clinical data included in national and global AMR surveillance datasets. FUNDING: Wellcome.

Humans↗

PubMed2026

Antimicrobial resistance surveillance through wastewater: methodological considerations for metagenomic approaches and public health perspectives.

Antimicrobial resistance (AMR) is a recognised global threat with substantial predicted impact on lives, agriculture, and the economy. Metagenomic sequencing is being increasingly used for AMR surveillance and detection, given its capacity for community-level AMR profiling with high-level resolution. This technology has seen an explosion of surveillance efforts and data generation; however, the variation between workflows has direct implications on the sequencing results and their interpretation. In this Personal View, we summarise aspects of the sequencing workflow that need to be considered during metagenomic study design, for meaningful and reliable population-based surveillance. We reflect on the vital role of standardisation for capturing the ground truth of AMR and data comparability and reproducibility, and in addition, review the limitations of the various phenotypic and genotypic methods of AMR detection. We further highlight complex mechanisms of resistance to antimicrobials that could hinder our ability to confidently assess the true AMR burden in the environment and those that are often overlooked during surveillance.

Metagenomics↗

PubMed2026

Evaluation of Oxford nanopore sequencing for antimicrobial resistance surveillance in Salmonella: comparison with phenotypic antimicrobial susceptibility in a large-scale study.

UNLABELLED: Salmonella is a major zoonotic foodborne pathogen, and antimicrobial resistance (AMR) in Salmonella presents a significant public health challenge. Compared with conventional antimicrobial susceptibility testing (AST), whole-genome sequencing (WGS) provides a more rapid and comprehensive approach to AMR characterization, thereby informing antimicrobial selection and supporting public health surveillance. In this study, Oxford Nanopore Technology (ONT)-based WGS was performed on 1,490 Salmonella isolates collected through nationwide surveillance in Taiwan in 2025. Genotypic resistance inferred from WGS data was compared with phenotypic AST results to assess the performance of ONT-WGS. Overall, WGS-inferred resistance showed high concordance with phenotypic resistance for most antimicrobials. However, major genotype-phenotype discordance was observed, attributed to four categories: (i) breakpoint-dependent classification, (ii) reduced or absent phenotypic expression of resistance genes, (iii) minimum inhibitory concentration (MIC) modulation by ramAp, and (iv) absence of known AMR determinants. Notable discrepancies included tigecycline resistance without known genetic determinants, nalidixic acid resistance linked to ramAp-mediated MIC elevation, and a high prevalence of colistin resistance (35.7%) in S. Enteritidis, with most resistant isolates lacking identifiable AMR determinants. Additionally, a significant proportion of ESBL- and AmpC-producing isolates were classified as susceptible or intermediate to cefotaxime and ceftazidime under CLSI criteria, highlighting the potential for misclassification and treatment failure. These findings demonstrate that ONT-WGS enables accurate and comprehensive AMR characterization by directly identifying resistance determinants and avoiding potential misclassification associated with breakpoint-based AST interpretations. When interpreted appropriately, WGS can support better antimicrobial selection and serve as a valuable alternative to conventional susceptibility testing. IMPORTANCE: Accurate prediction of antimicrobial resistance is essential for appropriate therapy and effective surveillance of Salmonella. However, discordance between genotype-based predictions and phenotypic antimicrobial susceptibility testing (AST) can complicate clinical interpretation. In this nationwide study of 1,490 Salmonella isolates, we show that Oxford Nanopore Technology-based whole-genome sequencing (ONT-WGS) provides rapid and comprehensive detection of antimicrobial resistance determinants with high concordance to phenotypic AST. We further identify four major mechanisms underlying genotype-phenotype discordance, including breakpoint-dependent classification, reduced or absent phenotypic expression of resistance genes, minimum inhibitory concentration (MIC) modulation by ramAp, and the absence of known AMR determinants. These findings demonstrate how WGS can complement conventional AST, improve interpretation of challenging susceptibility results, and strengthen genomic surveillance of emerging antimicrobial-resistant Salmonella.

Microbial Sensitivity Tests↗

PubMed2026

Methods for cost-efficient, whole genome sequencing surveillance for enhanced detection of outbreaks in a hospital setting.

INTRODUCTION: Outbreaks of healthcare-associated infections (HAI) result in substantial patient morbidity and mortality; mitigation efforts by infection prevention teams have the potential to curb outbreaks and prevent transmission to additional patients. The incorporation of whole genome sequencing (WGS) surveillance of suspected high-risk pathogens often identifies outbreaks that are not detected by traditional infection prevention methods and provides evidence for transmission. Our approach to real-time WGS surveillance, the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), has 1) identified serious outbreaks that were otherwise undetected and 2) shown the potential to be cost saving. METHODS: We describe our cost-efficient methods to perform WGS surveillance and data analysis of pathogens for institutions that are interested in expanding infection prevention surveillance. We provide an overview of the weekly workflow of EDS-HAT during two distinct phases over three years. RESULTS: In an average week at our tertiary healthcare system, we sequenced 60 samples at a cost of less than $100 each during Phase 1, and 80 samples for less than $70 each in Phase 2, inclusive of laboratory reagents and staff salaries. The average turnaround time, from sample collection to reporting data to infection prevention, was nine days. CONCLUSIONS: Performing EDS-HAT in real-time can be both feasible and time-efficient. Providing such timely information to aid in outbreak detection could identify transmission events sooner and thus could increase patient safety.

Disease Outbreaks↗

PubMed1975

Surveillance of Iowa swine herds for influenza-like illness: combined serologic and virus isolation method.

Five Iowa swine herds (involving about 7,000 swine) were placed under surveillance for signs of influenza-like illness. Blood samples for hemagglutination-inhibition (HI) tests of serums and nasal secretions on swabs for viral isolation were collected from 20 feeder swine in each herd at the outset of surveillance. On the basis of results of HI tests, 6 swine in each herd tested were chosen to be resampled 6 weeks after the first blood sample was collected if swine influenza virus (SIV) was not isolated, but 3 weeks after the first blood sample was collected if SIV was isolated at the outset of surveillance. The swine chosen for resampling were considered sentinels in a herd for the duration of surveillance. Swine influenza virus was isolated from 20 of 20 swine in each of 2 herds that had signs of influenza-like illness. The initial HI titer of each of the 20 swine in the 2 herds was less than 10. However, serum samples prepared from blood collected from sentinel swine in the 2 herds 3 weeks after isolation of SIV had HI geometric mean titers (GMT) of 23 and 34. One herd had an initial HI GMT of 21. A SIV was not isolated from this herd, and serum samples obtained from 3 of the 6 sentinel seine 6 weeks after the first blood sample was collected still had demonstrable HI antibody.

Animals↗