Investigation Of Disease Outbreaks Research Articles

Analysis of Mpox by Occupation and Industry in Seven U.S. Jurisdictions, May 2022-March 2023.

During responses to outbreaks, the collection and analysis of data on employed case patients' industry and occupation are necessary to better understand the relationship between work and health outcomes. The occurrence of mpox by occupation and industry has not previously been assessed in the context of the 2022 outbreak. We analyzed employment data from 2548 mpox cases reported to the U.S. Centers for Disease Control and Prevention from surveillance systems in seven U.S. jurisdictions and population-based reference data on employment patterns from the U.S. Bureau of Labor Statistics to describe the differential proportionate distribution of cases across occupation and industry groups using the proportionate morbidity ratio. In gender-specific analyses, we found that men employed in certain occupations and industries had a higher relative risk of mpox than others. While occupational transmission cannot be ruled out, it is more likely that individuals with personal and behavioral risk factors for mpox were more likely to work in these occupations and industries. This analysis provides an example of collecting and analyzing occupation and industry data in case reports to understand possible differences in risk by occupation and industry in infectious disease outbreak investigation and help inform resource allocation, messaging, and response.

Epidemiological Consequences of Individual Centrality on Wild Chimpanzees.

Disease outbreaks are one of the key threats to great apes and other wildlife. Because the spread of some pathogens (e.g., respiratory viruses, sexually transmitted diseases, ectoparasites) are mediated by social interactions, there is a growing interest in understanding how social networks predict the chain of pathogen transmission. In this study, we built a party network from wild chimpanzees (Pan troglodytes), and used agent-based modeling to test: (i) whether individual attributes (sex, age) predict individual centrality (i.e., whether it is more or less socially connected); (ii) whether individual centrality affects an individual's role in the chain of pathogen transmission; and, (iii) whether the basic reproduction number (R0) and infectious period modulate the influence of centrality on pathogen transmission. We show that sex and age predict individual centrality, with older males presenting many (degree centrality) and strong (strength centrality) relationships. As expected, males are more central than females within their network, and their centrality determines their probability of getting infected during simulated outbreaks. We then demonstrate that direct measures of social interaction (strength centrality), as well as eigenvector centrality, strongly predict disease dynamics in the chimpanzee community. Finally, we show that this predictive power depends on the pathogen's R0 and infectious period: individual centrality was most predictive in simulations with the most transmissible pathogens and long-lasting diseases. These findings highlight the importance of considering animal social networks when investigating disease outbreaks.

Identifying Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data.

Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has not been investigated in the molecular epidemiology field. To understand how contact tracing influences a recovered phylogeny, we developed a new simulation tool called SEEPS (Sequence Evolution and Epidemiological Process Simulator) that allows for the simulation of contact tracing and the resulting transmission tree, pathogen phylogeny, and corresponding virus genetic sequences. Importantly, SEEPS takes within-host evolution into account when generating pathogen phylogenies and sequences from transmission histories. Using SEEPS, we demonstrate that contact tracing can significantly impact the structure of the resulting tree, as described by popular tree statistics. Contact tracing generates phylogenies that are less balanced than the underlying transmission process, less representative of the larger epidemiological process, and affects the internal/external branch length ratios that characterize specific epidemiological scenarios. We also examined real data from a 2007-2008 Swedish HIV-1 outbreak and the broader 1998-2010 European HIV-1 epidemic to highlight the differences in contact tracing and expected phylogenies. Aided by SEEPS, we show that the data collection of the Swedish outbreak was strongly influenced by contact tracing even after downsampling, while the broader European Union epidemic showed little evidence of universal contact tracing, agreeing with the known epidemiological information about sampling and spread. Overall, our results highlight the importance of including possible non-uniform sampling schemes when examining phylogenetic trees. For that, SEEPS serves as a useful tool to evaluate such impacts, thereby facilitating better phylogenetic inferences of the characteristics of a disease outbreak. SEEPS is available at github.com/MolEvolEpid/SEEPS.

Collaborative wildlife disease outbreak investigation and response at Bells Swamp Victoria, February 2023.

In February 2023, a report of morbidity and mortality in waterbirds triggered a collaborative regional wildlife disease outbreak investigation and response, led by Parks Victoria. Triage, rehabilitation and diagnosis of sick and dead birds were undertaken by Zoos Victoria (ZV), Agriculture Victoria, Vets for Compassion, Wildlife Victoria and Melbourne Veterinary School (MVS). The field response focused on collection of sick and dead birds for wildlife welfare, for diagnosis, and to reduce environmental contamination. Botulism was suspected, based on clinical signs and lack of significant gross pathology, and this diagnosis was confirmed by PCR testing. Low pathogenicity avian influenza (LPAI) viruses non H5 or H7 were detected in two birds and ruled out in all in others tested. These incidental, non-clinical LPAI detections are considered part of the natural wild bird virus community in Australia. A number of elements contributed to the collaborative effort. Regional individuals had the necessary connections for reporting, collecting and transporting birds. There was rapid determination by the Victorian Department of Energy, Environment and Climate Action (DEECA) that Parks Victoria, as the land managers, should lead the response. Zoos Victoria provided capacity and expertise in wildlife triage and rehabilitation, and Agriculture Victoria, ZV and MVS were responsible for veterinary management of the response and diagnosis. Field investigation and response were conducted by Parks Victoria, Agriculture Victoria, MVS and veterinary teams from Vets for Compassion and Wildlife Victoria. Wildlife Health Australia (WHA) provided guidance and information, approved National Significant Disease Investigation Program funding and captured the event in the national wildlife health information database. Communication and media were important for community understanding of the event.

Impact of the COVID-19 Pandemic on the State Enteric Disease Public Health Workforce in the Western United States, March-April 2022.

To assess the impact of the COVID-19 pandemic on the state-level enteric disease workforce and routine enteric disease surveillance and outbreak investigation activities in the western United States. Key informant interviews conducted using bidirectional video from March to April 2022. Enteric disease epidemiologists at state public health agencies in the western states served by the Colorado and Washington Integrated Food Safety Centers of Excellence. Key themes were identified using grounded theory. Nine themes were identified including excessive workload, shifts in local and state responsibilities, challenges with retention and hiring, importance of student teams, laboratory supplies shortages, changes to case and outbreak investigation priorities, transitioning back to enterics, adoption of new methods and technology, and current and future needs. The COVID-19 pandemic response had a substantial impact on state-level enteric disease activities in western states, with many staff members diverted from routine responsibilities and a de-prioritization of enteric disease work. There is a need for sustainable solutions to address staffing shortages, prioritize employee mental health, and effectively manage routine workloads when responding to emergencies.

The Veterinarian’s Role in Biocontainment Research Animal Facilities and Prevention of Spread of Pathogens: A Case of Nigeria and South Africa

Infections acquired in research laboratories and unintentional pathogen escapes from breaches in biocontainment pose risks to humans and the environment, necessitating the need for effective biosafety and biosecurity management frameworks in biocontainment research animal facilities (BRAFs). We examine key biosafety issues associated with BRAFs, including inadequate decontamination procedures for wastewater and experimental samples, handling high biosafety level pathogens in lower-level laboratories, risks of animal bites and sharps injuries, contamination of bedding and enrichment materials, and improper management and transportation of biohazard samples. Additionally, we discuss the role of veterinarians in research animal facilities and the challenges they encounter in maintaining biocontainment standards. We emphasise the importance of routine monitoring of effluent water to detect possible disease outbreaks. We recommend a thorough investigation of disease outbreaks to identify potential sources of pathogen release from BRAFs, which could serve as hotspots for future disease outbreaks. Findings from such investigations will inform the development of policies aimed at safeguarding human populations from future pandemics and preventing BRAFs from becoming sources of infectious disease outbreaks.

Automated cooling tower detection through deep learning for Legionnaires’ disease outbreak investigations: a model development and validation study

Cooling towers containing Legionella spp are a high-risk source of Legionnaires' disease outbreaks. Manually locating cooling towers from aerial imagery during outbreak investigations requires expertise, is labour intensive, and can be prone to errors. We aimed to train a deep learning computer vision model to automatically detect cooling towers that are aerially visible. Between Jan 1 and 31, 2021, we extracted satellite view images of Philadelphia (PN, USA) and New York state (NY, USA) from Google Maps and annotated cooling towers to create training datasets. We augmented training data with synthetic data and model-assisted labelling of additional cities. Using 2051 images containing 7292 cooling towers, we trained a two-stage model using YOLOv5, a model that detects objects in images, and EfficientNet-b5, a model that classifies images. We assessed the primary outcomes of sensitivity and positive predictive value (PPV) of the model against manual labelling on test datasets of 548 images, including from two cities not seen in training (Boston [MA, USA] and Athens [GA, USA]). We compared the search speed of the model with that of manual searching by four epidemiologists. The model identified visible cooling towers with 95·1% sensitivity (95% CI 94·0-96·1) and a PPV of 90·1% (95% CI 90·0-90·2) in New York City and Philadelphia. In Boston, sensitivity was 91·6% (89·2-93·7) and PPV was 80·8% (80·5-81·2). In Athens, sensitivity was 86·9% (75·8-94·2) and PPV was 85·5% (84·2-86·7). For an area of New York City encompassing 45 blocks (0·26 square miles), the model searched more than 600 times faster (7·6 s; 351 potential cooling towers identified) than did human investigators (mean 83·75 min [SD 29·5]; mean 310·8 cooling towers [42·2]). The model could be used to accelerate investigation and source control during outbreaks of Legionnaires' disease through the identification of cooling towers from aerial imagery, potentially preventing additional disease spread. The model has already been used by public health teams for outbreak investigations and to initialise cooling tower registries, which are considered best practice for preventing and responding to outbreaks of Legionnaires' disease. None.

The usefulness of nanopore sequencing in whole-genome sequencing-based genotyping of Listeria monocytogenes and Salmonella enterica serovar Enteritidis.

This study unveils that Oxford Nanopore Technologies sequencing, by itself, holds the potential to serve as a whole-genome sequencing-based genotyping tool in public health laboratories, enabling routine subtyping of bacterial isolates for disease surveillance and outbreak investigations.

Salmonella Hadar linked to two distinct transmission vehicles highlights challenges to enteric disease outbreak investigations.

In 2020, an outbreak of Salmonella Hadar illnesses was linked to contact with non-commercial, privately owned (backyard) poultry including live chickens, turkeys, and ducks, resulting in 848 illnesses. From late 2020 to 2021, this Salmonella Hadar strain caused an outbreak that was linked to ground turkey consumption. Core genome multilocus sequence typing (cgMLST) analysis determined that the Salmonella Hadar isolates detected during the outbreak linked to backyard poultry and the outbreak linked to ground turkey were closely related genetically (within 0-16 alleles). Epidemiological and traceback investigations were unable to determine how Salmonella Hadar detected in backyard poultry and ground turkey were linked, despite this genetic relatedness. Enhanced molecular characterization methods, such as analysis of the pangenome of Salmonella isolates, might be necessary to understand the relationship between these two outbreaks. Similarly, enhanced data collection during outbreak investigations and further research could potentially aid in determining whether these transmission vehicles are truly linked by a common source and what reservoirs exist across the poultry industries that allow Salmonella Hadar to persist. Further work combining epidemiological data collection, more detailed traceback information, and genomic analysis tools will be important for monitoring and investigating future enteric disease outbreaks.

Pathogenic characteristics of an aggregated diarrhea event caused by Plesiomonas shigelloides from stream.

This study aimed to investigate the cause of a foodborne disease outbreak in Huzhou on August 14, 2023. Multiple enteropathogens were detected using FilmArray, and the pathogen was subsequently isolated and cultured from anal swabs of the cases and stream water. The isolated strains were identified using VITEK MS, and antimicrobial susceptibility test, pulsed field gel electrophoresis (PFGE) molecular typing, and whole genome sequencing (WGS) were performed on the isolates of Plesiomonas shigelloides. Gene annotation and sequence alignment were used to analyze the virulence genes and drug resistance genes of the strains. A phylogenetic tree was constructed based on single nucleotide polymorphism (SNP), and homology analysis was conducted to trace the origin of P. shigelloides. A total of 7 strains of P.shigelloides were isolated, with 3 from stream water and 4 from anal swabs. All 7 strains exhibited the same PFGE pattern and showed resistance to amikacin, trimethoprim-sulfamethoxazole, chloramphenicol, tetracycline, cefazolin, streptomycin, and florfenicol. The isolated strains carried the same resistance genes and virulence factors. In the sequences of the isolated strains from this outbreak, 11 mutation sites were detected. The phylogenetic tree based on SNP sites showed that these strains were homologous. This foodborne disease outbreak caused by P.shigelloides was the first reported in Huzhou. WGS can be used as a complementary method to PFGE for epidemiological investigations of disease outbreaks.

Subclinical infection caused by a recombinant vaccine-like strain poses high risks of lumpy skin disease virus transmission.

Lumpy skin disease (LSD) is a transboundary viral infection, affecting cattle with characteristic manifestations involving multiple body systems. A distinctive characteristic of lumpy skin disease is the subclinical disease manifestation wherein animals have viremia and shed the virus through nasal and ocular discharges, while exhibiting no nodules but enlarged lymph nodes that are easily oversighted by inexperienced vets. Further research on the role of subclinically ill animals in the transmission of LSD virus (LSDV) can contribute to the development of more effective tools to control the disease worldwide. Thus, this study aims to determine the potential role of subclinical infection in virus transmission in a non-vector-borne manner. To achieve this, we inoculated animals with the recombinant vaccine-like strain (RVLS) Udmurtiya/2019 to cause clinical and subclinical LSDV infection. After the disease manifestation, we relocated the subclinically ill animals to a new clean facility followed by the introduction of another five animals to determine the role of RVLS-induced subclinical infection in the virus transmission via direct/indirect contact. After the introduction of the naïve animals to the relocated subclinically ill ones in a shared airspace, two introduced animals contracted the virus (clinically and subclinically), showing symptoms of fever, viremia, and seroconversion in one animal, while three other introduced animals remained healthy and PCR-negative until the end of the study. In general, the findings of this study suggest the importance of considering LSDV subclinical infection as a high-risk condition in disease management and outbreak investigations.

Investigation of outbreaks and risk factors for brucellosis in goat and sheep farms in central Thailand

Background and Aim: Brucellosis is a harmful disease that affects a wide range of animals and adversely affects both animal and human health. Brucella melitensis is a zoonotic disease that causes brucellosis in sheep and goats. This study aimed to identify human index cases, identify risk factors for brucellosis in goat and sheep farms, and establish recommendations for farmers. Materials and Methods: An unmatched case-control study was conducted on goat or sheep farms in central Thailand. We utilized animal disease reports and outbreak investigation data extracted from the Department of Livestock Development, Thailand, and assessed these secondary data. A questionnaire was used to collect data. Serum samples were parallel tested for brucellosis using the modified Rose Bengal test and indirect enzyme-linked immunosorbent assay. Univariate and multivariate logistic regression analyses were performed. Results: An index case of human brucellosis was reported in the province of Chai Nat. Patients who were goat farmers or had previous experience of goat farming were included. Bacteria were introduced into the patient's farms by purchasing goats, grazing in public grassland, and insufficient biosecurity. Multivariable logistic regression analysis identified a higher risk of brucellosis positivity in the large herd than in the small herd (adjusted odds ratio = 8.61; 95% confidence interval = 1.62-45.71). Conclusion: These results suggest that goat or sheep farms with 50 heads should take further measures to prevent disease transmission, such as increasing the frequency of disease testing within the herd and strengthening the biosecurity system. Keywords: brucellosis, goat farms, outbreak investigation, risk factor, sheep farms.

Outbreak Linked to Morel Mushroom Exposure - Montana, 2023.

During March-April 2023, a total of 51 persons reported mild to severe gastrointestinal illness after eating at restaurant A in Bozeman, Montana. The outbreak resulted in multiple severe outcomes, including three hospitalizations and two deaths. After an inspection and temporary restaurant closure, the Montana Department of Public Health and Human Services and Montana's Gallatin City-County Health Department collaborated with CDC to conduct a matched case-control study among restaurant patrons to help identify the source of the outbreak. Consumption of morel mushrooms, which are generally considered edible, was strongly associated with gastrointestinal illness. A dose-response relationship was identified, and consumption of raw morel mushrooms was more strongly associated with illness than was consumption of those that were at least partially cooked. In response to the outbreak, educational public messaging regarding morel mushroom preparation and safety was shared through multiple media sources. The investigation highlights the importance of prompt cross-agency communication and collaboration, the utility of epidemiologic studies in foodborne disease outbreak investigations, and the need for additional research about the impact of morel mushroom consumption on human health. Although the toxins in morel mushrooms that might cause illness are not fully understood, proper preparation procedures, including thorough cooking, might help to limit adverse health effects.

Investigating the workforce capacity and needs for animal disease surveillance and outbreak investigation: a mixed-methods study of veterinary services in Vietnam.

The need for strengthening national capacities for disease prevention, preparedness, and response is increasingly becoming urgent. Central to this is strengthening existing systems and workforce capacity for disease surveillance and disease outbreak response. This study aimed to evaluate the national capacity and needs of veterinary services in Vietnam in animal disease surveillance and outbreak investigation skills. A cross-sectional, convergent, mixed-methods study was conducted between November 2020 and April 2021. An online questionnaire was administered to government field veterinarians, followed by descriptive and multivariable analyses to understand field capacity, specifically levels of experience in outbreak investigation and animal health surveillance. Semi-structured interviews were conducted with various stakeholders in veterinary services and interview transcripts were coded and thematically analyzed. Qualitative results were used to contextualize quantitative findings from the survey. Overall, 178 field veterinary staff completed the online survey, and 25 stakeholders were interviewed. Eighty percent of respondents reported a high priority for further training in both animal disease surveillance and outbreak investigation. Training and competence were more limited at the district and commune levels, highlighting a gap in capacity at the subnational level. Reasons included a lack of in-depth training opportunities, limited access to resources and high staff turnover. Respondents who completed postgraduate qualifications in epidemiology or Field Epidemiology Training Programs were more likely to have higher levels of experience in animal health surveillance and outbreak investigation. This study identified gaps in knowledge and adoption of practices most often related to local-level or less experienced veterinary staff with limited training opportunities in epidemiology. Findings inform the prioritization of training and planning activities to further enhance the national capacity of veterinary services in Vietnam. Underlying explanations for existing gaps in capacity include inequities in skill development and training opportunities across levels of veterinary staff, gaps in the chain of command and unequal funding across provinces.

Mentorship of the next generation of One Health workers through experiential learning: A case of students of Makerere University

Abstract Multiple zoonotic disease outbreaks occurred in Uganda over the past two decades and have needed operationalization of the One Health (OH) Approach to respond effectively. Between 2016 and 2018, the African One Health University Network (AFROHUN) supported 61 students (25 females, 36 males) to join multisectoral and multidisciplinary government national and district task force disease response teams. The goal of joining these teams was to build and strengthen the students’ disease investigation and response skills in real time using a One Health approach. Qualitative methods were used to collect student and partner responses on their field experiences. The AFROHUN project identified the experiential knowledge and skills that the students gained. Student project reports were reviewed by the joint technical teams from the university and the national/district task forces. These included training materials and disease outbreak investigation and response reports. Partnerships and collaboration between the university One Health networks and the government enabled 35 graduate and 26 undergraduate students to receive joint mentorship from the national or district task force outbreak response teams. Most participants were from degree programs in Public Health, Epidemiology, Environmental Health, Veterinary, Wildlife Sciences, and Infectious Disease Management, while few students were from social sciences. Students were mentored in seven competency-based areas of disease management: (1) biorisk management, (2) community engagement and coordination, (3) epidemiology, (4) leadership, (5) outbreak investigation and response, (6) risk communication, and (7) surveillance. In conclusion, zoonotic outbreaks provided real-life learning opportunities for students in disease outbreak investigation and response using a multidisciplinary and multisectoral approach. The identified skills can be incorporated into educational materials such as curricula and present an ideal opportunity to build partnerships for workforce development. One Health impact statement The next generation of One Health workers, those capable of working across sectors and disciplines to improve the health of animals, humans, plants, and the environment, need soft and technical skills to guarantee optimal preparedness, prevention, and response to disease outbreaks and understand the animal to human transmission dynamics of disease. In countries where emerging, re-emerging, and endemic zoonoses and hemorrhagic fevers are prevalent, it is crucial to provide these real-life or experiential training opportunities for university students, working closely in multidisciplinary teams. The “real-time” joint mentorship by the government’s multidisciplinary and multisectoral outbreak response teams, during disease outbreaks, provides an opportunity to build and strengthen student skills in biorisk management, community engagement and coordination, epidemiology, leadership, outbreak investigation and response, risk communication, and surveillance.

Epidemiological and Molecular Genetic Analysis of Outbreaks of Acute Intestinal Infections in the Khabarovsk Krai in 2022

Introduction: Acute intestinal infections are amongst the most important health concerns worldwide. The majority of them are caused by viruses spread through environmental objects contaminated with feces. A high incidence of intestinal infections is registered annually in the Far Eastern Federal District of the Russian Federation. Over 50 % of cases of established etiology are induced by rota- and noroviruses. Moreover, outbreaks of viral intestinal infections are registered annually in almost all regions of the Far Eastern Federal District, including the Khabarovsk Krai. Objective: To analyze the incidence of acute intestinal infections and the results of molecular genetics testing of intestinal viruses that caused the outbreaks in the Khabarovsk Krai in the year 2022. Materials and methods: We used epidemiological and statistical methods to analyze the incidence and conducted molecular genetics testing of samples obtained from patients with acute intestinal infections and their contacts in the foci of the disease in the Khabarovsk Krai. Results: The acute intestinal infection situation in the Khabarovsk Krai in 2022 was unfavorable. The regional incidence rate was 20.6 % higher than that in the Far Eastern Federal District, with most diseases induced by intestinal viruses and numerous outbreaks registered. Our epidemiological investigation of six outbreaks revealed the fecal-oral transmission route of infection through contaminated food, household contacts and, probably, water. Molecular genetics testing of the causes of outbreaks showed circulation of norovirus genotypes GII.4Sydney[P16], GII.4Sydney[P31], GII.17[P17], and GII.6[P7] as well as rotavirus A genotypes G9P[8], G4P[8] and G3P[8] in the Khabarovsk Krai. Some of the identified norovirus genotypes had already caused outbreaks in the Khabarovsk Krai: GII.17[P17] – back in 2015 among the population of the Mnogovershinny village, GII.6[P7] – in the years 2018 and 2019 in the city of Khabarovsk, thus indicating long-term circulation of these genotypes. Conclusion: Surveillance over changes in genetic diversity of the viral population is required to evaluate contribution of various gene variants of rota- and noroviruses to the incidence of acute intestinal infections. In this regard, molecular typing of rota- and noroviruses should be performed not only when investigating disease outbreaks, but also when sporadic cases are registered.

Validating the Utility of Multilocus Variable Number Tandem-repeat Analysis (MLVA) as a Subtyping Strategy to Monitor Listeria monocytogenes In-built Food Processing Environments

Listeria monocytogenes is a serious human pathogen and an enduring challenge to control for the ready-to-eat food processing industry. Cost-effective tools that can be deployed by commercial or in-house laboratories to rapidly investigate and resolve contamination events in the built food processing environment are of value to the food industry. Multilocus variable number tandem-repeat analysis (MLVA) is a molecular subtyping method, which along with other same-generation methods such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) is being superseded in disease tracking and outbreak investigations by whole-genome sequencing (WGS). In this paper, it is demonstrated that MLVA can continue to play a valuable role as a valid, fast, simple, and cost-effective method to identify and track Listeria monocytogenes subtypes in factory environments, with the method being highly congruent with MLST. Although MLVA does not have the discriminatory power of WGS to identify truly persistent clones, with careful interpretation of results alongside isolate metadata, it remains a powerful tool in situations and locations where WGS may not be readily available to food business operators.

A Bayesian Method for Exposure Prevalence Comparison During Foodborne Disease Outbreak Investigations.

CDC and health departments investigate foodborne disease outbreaks to identify a source. To generate and test hypotheses about vehicles, investigators typically compare exposure prevalence among case-patients with the general population using a one-sample binomial test. We propose a Bayesian alternative that also accounts for uncertainty in the estimate of exposure prevalence in the reference population. We compared exposure prevalence in a 2020 outbreak of Escherichia coli O157:H7 illnesses linked to leafy greens with 2018-2019 FoodNet Population Survey estimates. We ran prospective simulations using our Bayesian approach at three time points during the investigation. The posterior probability that leafy green consumption prevalence was higher than the general population prevalence increased as additional case-patients were interviewed. Probabilities were >0.70 for multiple leafy green items 2 weeks before the exact binomial p-value was statistically significant. A Bayesian approach to assessing exposure prevalence among cases could be superior to the one-sample binomial test typically used during foodborne outbreak investigations.

Wildlife nidoviruses: biology, epidemiology, and disease associations of selected nidoviruses of mammals and reptiles.

Wildlife is the source of many emerging infectious diseases. Several viruses from the order Nidovirales have recently emerged in wildlife, sometimes with severe consequences for endangered species. The order Nidovirales is currently classified into eight suborders, three of which contain viruses of vertebrates. Vertebrate coronaviruses (suborder Cornidovirineae) have been extensively studied, yet the other major suborders have received less attention. The aim of this minireview was to summarize the key findings from the published literature on nidoviruses of vertebrate wildlife from two suborders: Arnidovirineae and Tornidovirineae. These viruses were identified either during investigations of disease outbreaks or through molecular surveys of wildlife viromes, and include pathogens of reptiles and mammals. The available data on key biological features, disease associations, and pathology are presented, in addition to data on the frequency of infections among various host populations, and putative routes of transmission. While nidoviruses discussed here appear to have a restricted in vivo host range, little is known about their natural life cycle. Observational field-based studies outside of the mortality events are needed to facilitate an understanding of the virus-host-environment interactions that lead to the outbreaks. Laboratory-based studies are needed to understand the pathogenesis of diseases caused by novel nidoviruses and their evolutionary histories. Barriers preventing research progress include limited funding and the unavailability of virus- and host-specific reagents. To reduce mortalities in wildlife and further population declines, proactive development of expertise, technologies, and networks should be developed. These steps would enable effective management of future outbreaks and support wildlife conservation.

Multidrug Resistance and Plasmid Profiles of Escherichia coli Isolated from Lebanese Broiler Farms.

The present study was undertaken to determine the antimicrobial resistance patterns and plasmid fingerprints of commensal Escherichia coli isolated from Lebanese broiler chickens. To that end, a total of 30 E. coli isolates were collected from 15 semi-open broiler farms from North Lebanon and Bekaa Valley. Results showed that all the isolates were resistant to at least nine out of 18 evaluated antimicrobial agents. The best-performing antibiotic families were Carbapenems (Imipenem) and Quinolones (Ciprofloxacin and Norfloxacin) to which only 0.0 and 8.3% of the isolates were resistant, respectively. Fifteen various plasmid profiles were depicted, and all the isolates were found to possess one or multiple plasmids. The plasmid sizes varied from 1.2 to 21.0 kbp, and the most commonly detected plasmid had a size of 5.7 kbp (23.3% of the isolates). There was no significant association between the number of plasmids per isolate and resistance to a particular drug. Nevertheless, the presence of specific plasmids, namely, the 2.2 or 7.7 kbp sized ones, was strongly correlated to Quinolones or Trimethoprim resistance, respectively. Both the 7.7 and 6.8 kbp plasmids showed mild correlation to Amikacin resistance, and the 5.7 kbp plasmid was mildly correlated to Piperacillin-Tazobactam resistance. Our findings highlight the need to revise the list of antimicrobials currently used in Lebanese poultry and associate the presence of specific plasmids to antimicrobial resistance patterns in E. coli isolates. The revealed plasmid profiles could also serve any future epidemiological investigation of poultry disease outbreaks in the country.