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PubMed2026

The 2026 Bundibugyo Ebola Outbreak: A Warning for Global Preparedness for Future Epidemics.

Dear Editor, The 2026 Bundibugyo Ebolavirus (BDBV) outbreak has once again demonstrated that the threat of emerging diseases remains a major global health challenge. The outbreak, first detected in the Democratic Republic of Congo (DRC) and spread to Uganda, is not only a regional crisis but also a test of the world's preparedness for pathogens with epidemic potential. Unlike Zaire Ebolavirus (EBOV), which has benefited from effective vaccines and treatments in recent years, BDBV still lacks a licensed vaccine or specific treatment[1]. As of June 6, a total of 515 laboratory-confirmed cases and 91 deaths have been reported in DRC, while Uganda has reported 19 laboratory-confirmed cases and two deaths. The occurrence of unexplained deaths among both the community and healthcare workers, along with prior reports of an unidentified hemorrhagic fever, suggest that the outbreak has been likely originated in March 2026 or even earlier. Accordingly, the virus is believed to have spread unnoticed for several weeks before being identified through genomic sequencing in mid-May 2026[2]. The resurgence of Ebola in Africa results from a complex interaction of environmental, social, and political factors. Deforestation, the development of mining activities, the expansion of agriculture, and increased human contact with wildlife have elevated the likelihood of spillovers from wildlife reservoirs, particularly fruit bats, which are considered the most likely natural hosts of ebolaviruses. Moreover, weak disease surveillance systems and limited access to health services have delayed the identification of early cases. The similarity of the initial symptoms of Ebola to other endemic diseases in the region, such as malaria, makes early diagnosis difficult and provides ample opportunity for transmission to spread. Insecurity, misinformation, attacks on healthcare facilities, and armed conflict in the region have also posed serious challenges to the implementation of contact tracing programs and rapid response to the epidemic[3,4]. One of the most critical challenges highlighted by this outbreak is the weakness of diagnostic capacities in the affected areas. The initial 2007 outbreak of BDBV proved that delayed lab confirmation paralyzes public health responses[5]. Now, dealing with a much larger outbreak in 2026, the persistence of this challenge highlights a dangerous failure to invest in diagnostic infrastructure over the last 19 years. Many health facilities do not have access to molecular laboratories, rapid sample transport systems, and biosafety infrastructure[6]. These limitations delay the diagnosis and isolation of patients, thus perpetuating disease transmission. Investment in the development of mobile laboratories, rapid point-of-care diagnostic tests, and digital reporting systems can dramatically reduce the time to diagnosis and response to an outbreak. The BDBV outbreak shows that laboratory preparedness must be considered an essential part of global health security. Furthermore, the early detection of emerging pathogens depends not only on diagnostic technologies but also on the expertise of local scientists who are able to recognize unusual epidemiological and laboratory patterns. During the current outbreak, suspected Ebola cases initially tested negative using common diagnostic tests (designed for Zaire Ebola Virus), which delayed the identification of the BDBV. Specifically, field-based diagnostics in Bunia were calibrated exclusively to detect the EBOV responsible for recent Congolese outbreaks. Consequently, patient samples collected throughout late April and early May yielded negative results, requiring cross-country transport to Kinshasa for genomic confirmation[2]. This experience revealed a major vulnerability in outbreak preparedness: diagnostic tools designed for known threats may be ineffective in detecting less common or unexpected pathogens. Therefore, strengthening local scientific capacities, developing genomic surveillance, and expanding access to flexible and adaptable diagnostic platforms should be considered as a top priority for global health security. The lack of a licensed vaccine for BDBV was one of the most significant challenges of this epidemic. While the rVSV-ZEBOV vaccine has played a significant role in controlling Zaire ebolavirus, there is no licensed vaccine for BDBV. In response to this outbreak, efforts to develop mRNA-based vaccines, adenoviral vectors, rVSV-based vaccines, and multipotent vaccines have been accelerated[7]. However, the experience of this epidemic has shown that the development of medical products for rare diseases continues to face financial and investment constraints. This challenge highlights the need for sustained support from governments and international institutions for research and development of pathogens with epidemic potential. The 2026 Bundibugyo outbreak provides several key lessons for the global community. First, early detection and rapid diagnosis are the most important factors in containing the epidemic. The 19-year interval between the 2007 BDBV outbreak and the 2026 outbreak underscores persistent shortcomings in investment toward decentralized, pan-ebolavirus diagnostic infrastructure, with diagnostic delays hindering timely outbreak identification in both instances. Second, the trust and active participation of local communities are as important as medical interventions. Additionally, the rapid cross-border transmission dynamics between the DRC and Uganda demonstrate that blanket travel restrictions and border closures are impractical. As communities in the Great Lakes region routinely cross national borders for trade and healthcare, coordinated regional surveillance and timely information sharing are likely to be more effective than broad border closures in mitigating disease transmission[8]. Third, the protection of health workers must be a priority in preparedness plans. Fourth, a "One Health" approach is essential for simultaneous monitoring of humans, animals, and the environment. Although BDBV is not a new pathogen, the lack of licensed medical interventions and limited investment in research reflect many of the vulnerabilities associated with the concept of "Disease X."[9]. Unlike Zaire Ebola Virus, for which licensed vaccines and monoclonal antibody therapies are available, BDBV forces public health responses to rely almost entirely on non-pharmaceutical interventions such as isolation and infection control[10]. This gap reflects the structural inequity in global health research and development funding, with pathogens affecting resource-limited regions receiving insufficient attention until they spark an international emergency[2]. The BDBV outbreak proves that global epidemic preparedness cannot be pathogen-selective; it requires proactive investment in broad-spectrum countermeasures and resilient frontline health systems[8]. In conclusion, the 2026 BDBV outbreak is a serious wake-up call for the global health system. The epidemic revealed that gaps in surveillance systems, diagnostic capacities, vaccine development, and preparedness for emerging diseases persist. Investing in health infrastructure, developing Pan-Ebolavirus vaccines, strengthening laboratories, expanding the One-Health approach, and supporting research on emerging zoonotic pathogens must be at the top of global health security priorities. Otherwise, the BDBV outbreak may be just a prelude to larger crises to come.

Ebolavirus↗

PubMed2026

Waterborne norovirus outbreaks in China, 2000-2022: a systematic review.

In China, waterborne transmission is a relatively rare route for norovirus outbreaks; however, once it occurs, the outbreaks tend to be large in scale, prolonged in duration, and difficult to control. This systematic review characterizes the epidemiological features of such outbreaks in China. We searched the WANFANG, CNKI, PubMed, and Web of Science databases for literature on waterborne norovirus outbreaks published up to November 2023. From 2000 to 2022, a total of 112 outbreaks were reported in China among the 97 articles included. These outbreaks involved approximately 19,796 cases and 565,485 exposures, median of 98 cases per outbreak, with a median attack rate of 6.09 %. Most outbreaks occurred in southern regions, particularly in coastal provinces, with schools (59, 52.68 %) and towns or villages (25, 22.52 %) being the most common settings. The highest number of outbreaks was reported in February and the lowest in July, with an average of 8.25 outbreaks per month. Higher attack rates were associated with outbreaks occurring in winter, in primary schools, and in southern regions of the Qinling-Huaihe line. Contamination of barreled water and self-provided wells was the primary risk factor for waterborne norovirus outbreaks. Although waterborne transmission is a relatively rare route for norovirus outbreaks in China, it can cause large-scale outbreaks in a short period. Consequently, it is still necessary to enhance protection of water sources, rigorous water quality monitoring, and public health education on water sanitation.

Humans↗

PubMed2026

Mapping High-Rate Clusters of Animal Contact-Related Human Salmonella enterica Single-State Outbreaks in the United States, 2009-2022: A Spatial Epidemiological Approach to Inform Public Health Surveillance.

INTRODUCTION: Nontyphoidal Salmonella enterica (NTS) is a major zoonotic enteric pathogen. Animal contact-related NTS outbreaks have increased in the United States over the last decade. Geospatial analysis can identify locations with elevated risk of NTS outbreaks where public health authorities can focus their NTS prevention and intervention efforts. METHODS: We analysed NTS outbreak data reported from individual states to the Centers for Disease Control via the National Outbreak Reporting System between 2009 and 2022 across the continental contiguous United States. A geospatial analytical framework that included disease mapping, spatial interpolation, and global and local clustering methods was applied to identify regions with high NTS outbreak rates. Given that the study period (2009-2022) included the COVID-19 pandemic, an interrupted time series negative binomial model was used to assess changes in NTS incidence before and after 2020. RESULTS: A total of 104 NTS single-state outbreaks were reported to the National Outbreak Reporting System (NORS) during the study period. The mean annual incidence rate was 0.02 NTS outbreaks per million person-years. The primary animal contact categories associated with outbreaks were mammals (cattle, pigs, sheep, and horses), birds (backyard chickens, ducklings, and turkeys), and reptiles (turtles and lizards). Exposure settings included farms, fairgrounds, agricultural feed stores, veterinary clinics, dairy/agricultural settings, and residential settings. The local cluster detection methods consistently identified areas with significantly high NTS animal contact-related outbreak rates in the Mountain West, Midwest, and Northeast of the US. The interrupted time series analysis indicated a reduction in incidence following the onset of the COVID-19 pandemic (IRR = 0.03; p = 0.06). CONCLUSION: NTS animal contact-related single-state outbreaks revealed distinct spatial clustering across the United States, with higher risks in the Mountain West, Midwest, and Northeast. Diversity of animal-contact sources and exposure settings depicted complex transmission dynamics of NTS. A decline in reported NTS outbreaks was observed after the COVID-19 pandemic. Focused prevention and control programs are needed in high-risk areas to mitigate the burden of NTS outbreaks.

United States↗

PubMed2026

Applicability of Nanopore-only whole-genome sequencing for Pseudomonas aeruginosa outbreak investigation in the ICU setting: a multicentric study.

UNLABELLED: Pseudomonas aeruginosa outbreaks frequently occur in intensive care units (ICUs). In particular, ICU patients requiring mechanical ventilation are vulnerable to P. aeruginosa ventilator-associated pneumonia, which is associated with high morbidity and mortality. Fast and accurate genotyping during the early stage is crucial to document and manage P. aeruginosa outbreaks at the ICU. In this study, we have evaluated the applicability of Oxford Nanopore whole-genome sequencing (WGS) for outbreak investigation and antimicrobial resistance (AMR) prediction. To evaluate whether a Nanopore-only WGS workflow was able to reproduce Illumina-confirmed transmission clusters, 19 P. aeruginosa isolates from ICUs at UZ Brussels (Belgium) that were previously sequenced with Illumina were sequenced using a Nanopore-only workflow based on the latest V14 chemistry, followed by bioinformatic analysis via BugSeq and MBioSEQ Ridom Typer. Although both bioinformatic platforms showed high concordance between Illumina and Nanopore data, MBioSEQ Ridom Typer yielded the lowest allelic distance (maximum one cgMLST allele), confirming all outbreak clusters. When applying the Nanopore-only workflow to longitudinally collected isolates, low genetic heterogeneity (maximum three cgMLST alleles) was observed between isolates from the same patient. WGS and subsequent outbreak analysis of 65 respiratory P. aeruginosa isolates collected from 38 different ICU patients across six Belgian hospitals during a 9-month period showed no intra- or inter-hospital transmission. When the Nanopore-only WGS data were used to predict AMR, there was high categorical agreement (95%) between AMR genotype and phenotype. These findings highlight the potential of Nanopore WGS as a rapid and accurate tool for outbreak investigation of P. aeruginosa. IMPORTANCE: In recent years, Nanopore sequencing has found its way to clinical laboratories because of its affordability, scalability, and, most importantly, its ability to obtain sequencing results in near-real time. However, despite improved raw read accuracies with the latest generation R10.4.1 flow cells, the question remains whether the achieved accuracy is sufficient for accurate bacterial outbreak investigation, particularly in high-risk settings such as intensive care units (ICUs). In this study, we show that Nanopore-only whole-genome sequencing (WGS) is able to match Illumina-only WGS in terms of accuracy for Pseudomonas aeruginosa outbreak investigation in the ICU setting, although important sequence type-dependent and even strain-specific methylation issues need to be resolved in order to guarantee this accuracy. By providing a fast and accurate workflow for reliable P. aeruginosa outbreak investigation, this study could pave the way for large-scale implementation of Nanopore-only WGS, leading to faster outbreak response times.

Humans↗

PubMed2022

A deep learning approach to real-time HIV outbreak detection using genetic data.

Pathogen genomic sequence data are increasingly made available for epidemiological monitoring. A main interest is to identify and assess the potential of infectious disease outbreaks. While popular methods to analyze sequence data often involve phylogenetic tree inference, they are vulnerable to errors from recombination and impose a high computational cost, making it difficult to obtain real-time results when the number of sequences is in or above the thousands. Here, we propose an alternative strategy to outbreak detection using genomic data based on deep learning methods developed for image classification. The key idea is to use a pairwise genetic distance matrix calculated from viral sequences as an image, and develop convolutional neutral network (CNN) models to classify areas of the images that show signatures of active outbreak, leading to identification of subsets of sequences taken from an active outbreak. We showed that our method is efficient in finding HIV-1 outbreaks with R0 ≥ 2.5, and overall a specificity exceeding 98% and sensitivity better than 92%. We validated our approach using data from HIV-1 CRF01 in Europe, containing both endemic sequences and a well-known dual outbreak in intravenous drug users. Our model accurately identified known outbreak sequences in the background of slower spreading HIV. Importantly, we detected both outbreaks early on, before they were over, implying that had this method been applied in real-time as data became available, one would have been able to intervene and possibly prevent the extent of these outbreaks. This approach is scalable to processing hundreds of thousands of sequences, making it useful for current and future real-time epidemiological investigations, including public health monitoring using large databases and especially for rapid outbreak identification.

Humans↗

PubMed2026

Whole-genome sequencing links a Salmonella Newport ST164 outbreak on Fernando de Noronha to prior circulation in the Brazilian poultry supply chain.

Foodborne outbreaks at geographically isolated tourist destinations pose distinctive One Health challenges, combining limited local surveillance capacity, complex intercontinental supply chains, and high visitor turnover. In May 2021, a diarrheal outbreak linked to a gastronomic festival in Fernando de Noronha, that is a remote UNESCO World Heritage island off northeastern Brazil, was attributed to Salmonella enterica serovar Newport ST164. We applied an integrated genomic approach and epidemiological investigation to propose a transmission chain contextualizing and refining case definition of the S. Newport epidemic clone within national and international diversity. Whole-genome sequencing (WGS), SNP-based phylogenomic, pangenome analysis, Salmonella pathogenicity island (SPI) profiling, and resistome characterization was performed on 17 epidemiologically attributed outbreak isolates and 68 contextual genomes from Brazil, France, the United Kingdom, and the United States. The SNP analysis identified a 13 genome clonal core with less than 20 different SNPs demonstrating the possible connection between 9 patient isolates, 2 food isolates, and 2 food handler isolates, consistent with the involvement of colonised kitchen staff in cross-contamination of the ready-to-eat mussel dish. Three poultry isolates in 2020 from a mainland producer, ∼2180 km from Fernando de Noronha, differed only 13 to 17 Core-SNPs from the outbreak core, suggesting prior lineage circulation in the supply chain. Pangenome analysis also supports this evidence revealing near-complete genomic overlap of 4544 shared genes within the 5745 gene clusters (99.9%) between outbreak and non-outbreak backgrounds that mostly differentiate by a defense/prophage-associated accessory module. The resistome comprised intrinsic efflux determinants without acquired resistance and showed 35.3% of intermediate ciprofloxacin susceptibility. This One Health based study provides a WGS genomic reconstruction of a S. Newport ST164 outbreak at a remote tourist island, supporting the possibility of circulation from poultry-associated mainland reservoirs and findings consistent with cross-contamination at a gastronomic seafood festival.

Brazil↗

PubMed2026

Responding to a protracted tuberculosis outbreak: lessons from multiple rounds of investigation in a Chinese boarding school.

PURPOSE: This study analysed a multi-semester pulmonary tuberculosis (PTB) cluster outbreak in a Chinese boarding school to provide evidence for future epidemic control. METHODS: Contacts were screened via symptoms, infection tests and chest radiography. Screening expanded progressively from close contacts to same-floor contacts, then all students and staff. Whole-genome sequencing (WGS) with single nucleotide polymorphism (SNP) and bioinformatics analysis was used for lineage classification, transmission clustering (≤12 SNPs defining a cluster) and drug resistance prediction. RESULTS: From 2020 to 2022, 20 students were diagnosed with PTB, half laboratory-confirmed. Most cases clustered in class 16 and were epidemiologically linked to the primary case (case 0), who had household PTB exposure. Case 0 and case 1 had diagnostic delays exceeding 3 and 6 months, respectively. WGS of five isolates (case 1, 3, 4, 9 and 10) collected over three semesters showed all belonged to lineage 2 and differed by ≤12 SNPs, confirming the same transmission chain. The infection rate in class 16 (46.34%) was significantly higher than other case classes (19.05%) and classes without cases (8.27%) (χ2 = 61.169, p < 0.001). No new cases were detected during a one-year follow-up of students involved in the outbreak after the final round of screening, nor among household contacts of all cases followed up to the present. CONCLUSIONS: Lack of entry health examinations facilitated the outbreak. Delayed diagnosis, incomplete contact screening and absence of preventive treatment led to cross-semester persistence. The infection rate disparity confirms class 16 as the outbreak epicentre. Improving community case management, extending contact follow-up and enhancing cluster outbreak measures are recommended to prevent future outbreaks.

Humans↗

PubMed2025

Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks.

Pathogen genomic data are increasingly being used to investigate transmission dynamics in infectious disease outbreaks. Combining genomic data with epidemiological data should substantially increase our understanding of outbreaks, but this is highly challenging when the outbreak under study is only partially sampled, so that both genomic and epidemiological data are missing for intermediate links in the transmission chains. Here, we present a new dynamic programming algorithm to perform this task efficiently. We implement this methodology into the well-established TransPhylo framework to reconstruct partially sampled outbreaks using a combination of genomic and epidemiological data. We use simulated datasets to show that including epidemiological data can improve the accuracy of the inferred transmission links compared with inference based on genomic data only. This also allows us to estimate parameters specific to the epidemiological data (such as transmission rates between particular groups), which would otherwise not be possible. We then apply these methods to two real-world examples. First, we use genomic data from an outbreak of tuberculosis in Argentina, for which data was also available on the HIV status of sampled individuals, in order to investigate the role of HIV coinfection in the spread of this tuberculosis outbreak. Second, we use genomic and geographical data from the 2003 epidemic of avian influenza H7N7 in the Netherlands to reconstruct its spatial epidemiology. In both cases, we show that incorporating epidemiological data into the genomic analysis allows us to investigate the role of epidemiological properties in the spread of infectious diseases.

Humans↗

PubMed2025

Temporal reconstruction of a Salmonella Enteritidis ST11 outbreak in New Zealand.

Outbreaks caused by Salmonella Enteritidis are commonly linked to eggs and poultry meat internationally, but this serovar had never been detected in Aotearoa New Zealand (NZ) poultry prior to 2021. Locally designated genomic cluster Salmonella Enteritidis_2019_C_01, was implicated in a 2019 outbreak associated with a restaurant in Auckland. Four Enteritidis_2019_C_01 sub-clusters have since been identified, two retrospectively, in the Auckland region. Authorities initiated a formal outbreak investigation after genomically indistinguishable S. Enteritidis was isolated from the NZ poultry production environment. This study analysed 231 S. Enteritidis genomes obtained from the outbreak using Bayesian phylodynamic tools to gain insight into the outbreak's dynamics and origin. We used Bayesian integrated coalescent epoch plots to estimate the change of the Enteritidis ST11 population size over time and marginal structured coalescent approximation to estimate transmission between poultry producers. We investigated human and poultry isolates to elucidate the time and location of the most recent common ancestor of the outbreak and transmission pathways. The median most recent common ancestor was estimated to be February 2019. We found evidence of amplification and spread of strain Enteritidis_2019_C_01 within the poultry industry, as well as transmission events throughout the production chain. The intervention by the public health and food safety authorities coincided with a drop in the effective population size of the S. Enteritidis ST11 as well as notified human cases. This information is crucial for understanding and preventing the transmission of S. Enteritidis in NZ poultry to ensure poultry meat and eggs are safe for consumption.

Salmonella enteritidis↗

PubMed2026

Interspecies Exchange of Mobile Genetic Elements During a Plant Disease Outbreak.

Outbreak sequencing provides insight into the origin and evolutionary processes acting on emerging pathogens. Sequencing a historic multihost outbreak of Ralstonia spp. in Martinique shows the outbreak was caused by two lineages that diverged at separate times from mainland populations. One lineage (Ralstonia pseudosolanacearum I-18) was originally introduced from Asia to South America, where it became well established prior to its dissemination to Martinique, where it retains a signature of specialization on solanaceous hosts. The novel lineage first identified during the outbreak (Ralstonia solanacearum IIB-4NPB) arose from a mainland population endemic to the Americas prior to its arrival in Martinique, where host-range expansion was observed. In contrast to minor changes in secreted effector protein repertoires, the emergent R. solanacearum IIB-4NPB acquired a novel integrative and conjugative element (ICERsoRUN1145). After identifying all Ralstonia spp. ICEs and mapping their spatial and phylogenetic distribution among Ralstonia spp. sampled during the outbreak, we found closely related ICEs circulating in mainland populations of R. pseudosolanacearum, indicating likely exchange between introduced and endemic Ralstonia spp. The family of ICEs in Ralstonia (ICERs) has a conserved bipartite structure and display a striking pattern of functional specialization in each cargo gene insertion hotspot: the first hotspot is a target for metabolic gene acquisition, and the second is a target for defense element acquisition. This work provides unparalleled phylogenetic and spatial resolution of an unusual outbreak and highlights the role of horizontal transfer in shaping the ecological success of an emerging pathogen.

Plant Diseases↗

PubMed2026

Genomic characteristics and tracing analysis of an acute gastroenteritis outbreak associated with rotavirus C in a boarding high school.

BACKGROUND: Rotaviruses are major pathogens of childhood acute gastroenteritis, dominated by rotavirus A (RVA). Outbreaks caused by human rotavirus C (RVC) are rarely reported, and relevant genomic data remain scarce. This genomic investigation of an RVC outbreak improves our understanding of viral diversity and transmission dynamics. METHODS: We performed epidemiological surveys, nucleic acid testing and whole-genome sequencing (WGS) on specimens from a 2025 RVC-associated gastroenteritis outbreak at a Chinese boarding high school. Sequence alignment, phylogenetic and molecular tracing analyses were conducted to explore RVC evolution via point mutation, segment reassortment and genomic recombination. RESULTS: This typical point-source campus outbreak was linked to an indoor student gathering matching the incubation period of RVC. Thirteen RVC FX strains were recovered from 11 rectal swabs and two vomitus samples. Their viral protein (VP) 4 and VP7 sequences shared high homology with Russian reference strains, carrying distinct amino acid variations. No segment reassortment or recombination was detected in VP4/VP7 genes. CONCLUSIONS: Dense, closed campus settings facilitate RVC clustered transmission. Limitations included absent screening of asymptomatic canteen staff. Rapid nucleic acid testing enabled timely pathogen identification for outbreak control. Greater attention should be paid to the public health risk of RVC. These whole-genome sequencing data enrich resources for studying RVC evolution and vaccine development.

Acute gastroenteritis outbreak↗

PubMed2025

Investigation of a Mycobacterium fortuitum prosthetic joint infection outbreak at two ambulatory surgery centers in Tennessee.

OBJECTIVE: This study outlines the investigation into an outbreak of Mycobacterium fortuitum infections involving 17 cases undergoing hip or knee surgeries at two ambulatory surgery centers (ASCs) in Tennessee from January 2023 to November 2024. Notably, the outbreak could not be attributed to contaminated water sources, which are typically associated with non-tuberculous mycobacteria (NTM) outbreaks, presenting a unique challenge. METHODS: Outbreak investigation steps included Infection Prevention (IP) assessments, case-control study, environmental sampling, whole genome sequencing, and a healthcare personnel (HCP) exposure questionnaire. RESULTS: IP assessment highlighted several concerns, including no formal facility water management program (WMP), a lack of dedicated IP personnel and certified sterile processing staff, the absence of a formalized system for tracking surgical site infections, and a notable gap in understanding the requirements for reporting diseases. The case-control findings revealed a significant association between the presence of a surgical technologist in the operating room during the procedures and the occurrence of NTM infections, indicated by an odds ratio of 55.77 (95% CI [3.16-985.44]; P = 0.0097). Thirteen clinical isolates collected at one ASC and three additional isolates collected at a second ASC were highly related by whole genome sequencing. CONCLUSION: The study further elucidates valuable insights gained from the outbreak response, including the gaps in surveillance within the ambulatory surgical setting and systematic collection of cultures from environmental sources. It emphasizes the importance of thorough vetting, onboarding, continuing education, and practice monitoring for HCP.

Humans↗

PubMed2026

Emergence of a Bundibugyo virus variant in the 2026 outbreak in the Democratic Republic of the Congo and Uganda.

In May 2026, an outbreak of Ebola disease caused by Bundibugyo virus (BDBV, species Orthoebolavirus bundibugyoense) was declared in the Democratic Republic of the Congo (DRC), with cases originating from DRC and locally transmitted cases reported in Uganda. Bundibugyo virus disease (BVD) outbreaks were previously recorded in 2007-2008 in Bundibugyo District, Uganda, and in 2012 in Isiro, DRC. Here, we generated 22 genomes from samples obtained from individuals with BVD in DRC and Uganda. These genomes form a well-supported phylogenetic cluster separate from BDBV variants associated with the 2007 and 2012 outbreaks, together with evidence for sustained human transmission. This is consistent with the emergence of a new zoonotic spillover event rather than resurgence from previously reported variants. Besides ongoing efforts in strengthening surveillance systems, community engagement, establishing Ebola treatment centers, and developing targeted medical countermeasures; our report advocates to specifically increase decentralized laboratory diagnostics capacity, with pan-Orthoebolavirus assays, including genomic sequencing capacity, for limiting further outbreak expansion, timely detection and control of future outbreaks.

Journal Article↗

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

Outbreaks of fluconazole-resistant Candida parapsilosis are driven by low-biofilm-producing isolates that emerge under host selection.

Candida parapsilosis is a major human fungal pathogen, with recent global outbreaks driven by fluconazole-resistant (FLCR-Cp) isolates that are difficult to eradicate and associated with poor clinical outcomes. However, the microbial traits enabling persistence of these outbreak lineages remain poorly defined. Here, we show that FLCR-Cp isolates responsible for prolonged, multi-country outbreaks consistently exhibit a striking low-biofilm-producing (LBP) phenotype. Contrary to the prevailing view that robust biofilm formation promotes persistence, LBP strains displayed enhanced stress tolerance, increased cell wall masking, and reduced immune recognition. These traits conferred resistance to neutrophil and macrophage killing and enhanced survival in immune cell-rich organs during systemic infection. Genome-wide transcriptomic profiling revealed extensive metabolic and regulatory rewiring in LBP strains. Whole-genome sequencing (WGS) of a global isolate collection further demonstrated that the LBP phenotype has emerged independently multiple times, supporting convergent evolution under host selection. Functional genomic analyses suggest that biofilm attenuation arises through multigenic changes, and disruption of key biofilm-associated transcriptional regulators enhanced fitness during immune interactions. Together, our findings overturn the assumption that robust biofilm formation drives outbreak persistence and instead identify biofilm attenuation as an adaptive tradeoff that promotes immune evasion and long-term survival. These results redefine our understanding of C. parapsilosis adaptation during healthcare-associated outbreaks and shift attention toward host-driven evolutionary processes than environmental persistence alone.

Biofilms↗

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↗

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↗

PubMed2025

Candida auris outbreak in a cardiothoracic transplant intensive care unit: implications for infection prevention practices and keeping pace with an evolving landscape.

OBJECTIVE: To describe the mitigation strategies for a Candida auris outbreak in a cardiothoracic transplant intensive care unit (CTICU) and its implications for infection prevention practices. DESIGN: Retrospective cohort study from July 2023 to February 2024. SETTING: A large academic medical center. METHODS: A multidisciplinary team convened to conduct the outbreak investigation and develop mitigation strategies in the CTICU. RESULTS: From July 2023 to February 2024, 34 possible hospital-onset cases of C. auris were identified in our CTICU. Whole-genome sequencing and phylogenetic analysis based on pairwise single nucleotide polymorphism (WG-SNP) distance revealed two distinct outbreak clusters. Of the 34 patients, 11 (32.3%) were solid organ transplant recipients and 12 (35.3%) had a mechanical circulatory support device. Of the cohort, only 11/34 (32.3%) had prior exposure to high-risk healthcare facilities within six months prior to admission, as follows: acute inpatient rehabilitation facilities (AIRs) (n = 5, 14.7%), skilled nursing facilities (SNFs) (n = 3, 8.8%), and long-term acute care hospitals (LTACHs) (n = 3, 8.8%). The cohort had a median of 22.0 antibiotic-days prior to their positive results. Five (14.7%) patients had C. auris candidemia, three of whom expired likely due to infection. Infection Prevention (IP) interventions addressed several modes of transmission, including healthcare personnel hands, shared patient equipment, and the environment. CONCLUSION: Our experience suggests that the epidemiology of C. auris may be changing, pointing towards a rising prevalence in acute care settings. IP interventions targeting hand hygiene behavior and promoting centralizing cleaning and disinfection of shared patient equipment may have contributed to outbreak resolution.

Humans↗