Preliminary Outbreak Investigation and Spatial Epidemiology of Rabbit Hemorrhagic Disease Outbreak in Nigeria

The outbreak of highly contagious transboundary rabbit hemorrhagic disease (RHD) in Nigeria has a severe socio-economic impact on the rabbit industry. We present the outbreak investigation and spatial epidemiology of the first confirmed RHD outbreak in Nigeria from a field survey of 28 stochastic outbreaks in Kwara State, north-central Nigeria. A total of 1,639 rabbits died from 2,053 susceptible rabbits. The serotype “RHDV-2” was detected in tissue samples from some of the outbreaks. The case fatality rate of the RHDV-2 outbreak was 79.8%. The source of the outbreak is still unknown. Most (71.4%) of the farmers had introduced new rabbits into their farms 1–2 weeks before the outbreak. Most of the farmers practiced biosecurity measures such as farm fencing (83.1%) and routine disinfection of the farm materials (53.6%). However, only 17.8% of the farmers enforced movement restrictions into their farms. Some of the farmers (42.8%) had restocked their farms after being affected by the RHD outbreak and 75% of all those farmers that have restocked had used the RHD vaccine. There was no statistically significant association between adherence to biosecurity measures and the RHD outbreak in affected farms (p = 0.408). However, the introduction of new rabbits into rabbit farms significantly pre-disposed farms to the RHD outbreak (p < 0.001). There is a need for active surveillance of RHD across the country to ensure efficient and effective tracking, monitoring, and control of the disease. Equally, understanding the genetic diversity of the Lagoviruses in Nigeria that cause RHD to aid vaccine development is of utmost importance to prevent future RHD outbreaks.

Healthcare-associated links in transmission of nontuberculous mycobacteria among people with cystic fibrosis (HALT NTM) study: Rationale and study design

Background Healthcare-associated transmission of nontuberculous mycobacteria (NTM) among people with cystic fibrosis (pwCF) has been reported and is of increasing concern. No standardized epidemiologic investigation tool has been published for healthcare-associated NTM outbreak investigations. This report describes the design of an ongoing observational study to standardize the approach to NTM outbreak investigation among pwCF. Methods This is a parallel multi-site study of pwCF within a single Center who have respiratory NTM isolates identified as being highly-similar. Participants have a history of positive airway cultures for NTM, receive care within a single Center, and have been identified as part of a possible outbreak based on genomic analysis of NTM isolates. Participants are enrolled in the study over a 3-year period. Primary endpoints are identification of a shared healthcare-associated encounter(s) among patients in a Center and identification of environmental isolates that are genetically highly-similar to respiratory isolates recovered from pwCF. Secondary endpoints include characterization of potential transmission modes and settings, as well as incidence and prevalence of healthcare-associated environmental NTM species/subspecies by geographical region. Discussion We hypothesize that genetically highly-similar strains of NTM among pwCF cared for at the same Center may arise from healthcare sources including patient-to-patient transmission and/or acquisition from environmental sources. This novel study design will establish a standardized, evidence-based epidemiologic investigation tool for healthcare-associated NTM outbreak investigation within CF Care Centers, will broaden the scope of independent outbreak investigations and demonstrate the frequency and nature of healthcare-associated NTM transmission in CF Care Centers nationwide. Furthermore, it will provide valuable insights into modeling risk factors associated with healthcare-associated NTM transmission and better inform future infection prevention and control guidelines. This study will systematically characterize clinically-relevant NTM isolates of CF healthcare environmental dust and water biofilms and set the stage to describe the most common environmental sources within the healthcare setting harboring clinically-relevant NTM isolates. Trial registration ClinicalTrials.gov NCT04024423. Date of registry July 18, 2019.

An outbreak investigation of dengue in medical students and health care workers in a tertiary care hospital, Pune

Dengue is fast emerging mosquito borne viral disease. There was sudden outbreak of dengue cases among Medical students and Health Care Workers in tertiary care hospital from September to November 2019. Therefore, outbreak investigation carried out and corrective actions taken to halt the outbreak. Study Objectives are to investigate outbreak of dengue cases in medical students and Health Care Workers and to take corrective actions to halt the outbreak.The outbreak investigations of Dengue cases was done as 28 cases were admitted which includes medical students and Health Care Workers in tertiary care hospital from September to November 2019. A thorough search for breeding sites of Aedes mosquito was done in premises of hospital, college and residential area. 5 teams were made consisting of Sanitary Inspector, interns, resident doctors and lecturer. House to house surveys were done for container index in Resident quarters and employees quarters. Health education on prevention of dengue was given to Medical students and Health Care Workers including interns, resident doctors, undergraduate students. Antilarval measures like abating, fogging and spraying of oildone.The mean age was 27.2 years, ranged for 14-68 years. Males 15(53.5%) and Females 13(46.4%). Out of 28,12(42.8%) Undergraduate students, 9(32.1%) Resident doctors and 7(25%) employees. 22(78.5%) NS-1positivecases and 16(57.1%) IgM dengue positive cases. The most common symptom found in this was fever (100%). Thrombocytopenia was most common abnormal laboratory finding which was present in 22(79%) patients out of 28 patients. Out of 22 patients having thrombocytopenia, platelet transfusion was done to 4 patients. Mean duration of stay in the hospital was 4 days.With the corrective measures taken, no new case of dengue was notified in November 2019 among Medical Students and Health Care Workers.

Genomics-informed outbreak investigations of SARS-CoV-2 using civet

The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 5 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different 'catchments' and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health.

Short reports on cutaneous leishmaniasis outbreak investigation in Ankesha-Guagsa district, Amhara region, Northwest Ethiopia

Cutaneous leishmaniasis is spreading in Ethiopia and outbreaks have been recorded at new foci. In the Ankesha-Guagsa district, from September 24 to 28, 2020, 39 suspected cases were screened, and amastigote stages were identified in lesion samples of 34 (87.2%) cases.

Data collection for outbreak investigations: process for defining a minimal data set using a Delphi approach

Background Timely but accurate data collection is needed during health emergencies to inform public health responses. Often, an abundance of data is collected but not used. When outbreaks and other health events occur in remote and complex settings, operatives on the ground are often required to cover multiple tasks whilst working with limited resources. Tools that facilitate the collection of essential data during the early investigations of a potential public health event can support effective public health decision-making. We proposed to define the minimum set of quantitative information to collect whilst using electronic device or not. Here we present the process used to select the minimum information required to describe an outbreak of any cause during its initial stages and occurring in remote settings. Methods A working group of epidemiologists took part in two rounds of a Delphi process to categorise the variables to be included in an initial outbreak investigation form. This took place between January–June 2019 using an online survey. Results At a threshold of 75 %, consensus was reached for nineteen (23.2%) variables which were all classified as ‘essential’. This increased to twenty-six (31.7%) variables when the threshold was reduced to 60% with all but one variable classified as ‘essential’. Twenty-five of these variables were included in the ‘Time zero initial case investigation’ ‘(T0)’ form which was shared with the members of the Rapid Response Team Knowledge Network for field testing and feedback. The form has been readily available online by WHO since September 2019. Conclusion This is the first known Delphi process used to determine the minimum variables needed for an outbreak investigation. The subsequent development of the T0 form should help to improve the efficiency and standardisation of data collection during emergencies and ultimately the quality of the data collected during field investigation.

Case Study of an Outbreak: Resident, Staff, and Community Indicators

Outbreak investigation is not infection control. We present a self-study of factors influencing outcomes inside a single nursing home during the early stage of the outbreak - February to May 2020. We examine 3 sources of influence: Practice / Operations; Local, State & Federal Policies; Uncontrollable operational factors. Outcomes of interest include: mortality and resident / staff health. Data consists of clinical records, review of communications, and interviews with staff present during the critical period. Infection control is different from outbreak investigation. There must be a balance between staff empowerment and adherence to guidelines. In an outbreak, staff need the confidence to make decisions based on incomplete knowledge. The presentation concludes with lessons learned – what worked and what actions need improvement. There are areas requiring further analyses of policy and ethics.

Descriptive analysis of a tuberculosis outbreak from a northern Saskatchewan First Nations community—December 2018 to May 2019

Background: The tuberculosis (TB) incidence rate for northern Saskatchewan First Nations on-reserve is 1.5 higher than the national average. In December 2018 a member of one of these communities was diagnosed with 4+ smear-positive TB, spurring an outbreak investigation. Objectives: To describe the public health response to TB outbreak investigation and highlight the risk factors associated with TB transmission in northern Saskatchewan; and to highlight the relevance of social network contact investigation tool in outbreak management. Methods: Descriptive analysis included active TB cases and latent TB infection (LTBI) cases linked by contact investigation to the index case. Data were collected from active TB case files. Statistical analyses were performed and social network analysis conducted using household locations as points of contact between cases. Results: A total of eight active TB cases and 41 LTBI cases were identified as part of the outbreak between December 2018 and May 2019. Half of the cases (4/8) were 25 to 34 years old, and five were smear negative. One-third of the people with LTBI were 15 to 24 years old, and about a half tested positive to the new tuberculin skin test (TST). The commonly reported risk factors for TB and LTBI cases were alcohol use, cigarette use, marijuana use, previous TB infection and homelessness. Social network analysis indicated a relationship between increased node centrality and becoming an active case. Conclusion: Real-time social network contact investigation used in active-case finding was very successful in identifying cases, and enhanced nursing support, mobile clinics and mobile X-ray worked well as a means of confirming cases and offering treatment. TB outbreaks in northern Saskatchewan First Nations on-reserve communities are facilitated by population-specific factors. Efforts to implement context-specific interventions are paramount in managing TB outbreaks and preventing future transmission.

An Official Outbreak Investigation of Acute Haemorrhagic Diarrhoea in Dogs in Norway Points to Providencia alcalifaciens as a Likely Cause

An outbreak investigation was initiated in September 2019, following a notification to the Norwegian Food Safety Authority (NFSA) of an unusually high number of dogs with acute haemorrhagic diarrhoea (AHD) in Oslo. Diagnostic testing by reporting veterinarians had not detected a cause. The official investigation sought to identify a possible common cause, the extent of the outbreak and prevent spread. Epidemiological data were collected through a survey to veterinarians and interviews with dog owners. Diagnostic investigations included necropsies and microbiological, parasitological and toxicological analysis of faecal samples and food. In total, 511 dogs with acute haemorrhagic diarrhoea were registered between 1 August and 1 October. Results indicated a common point source for affected dogs, but were inconclusive with regard to common exposures. A notable finding was that 134 of 325 faecal samples (41%) cultured positive for Providencia alcalifaciens. Whole genome sequencing (WGS) of 75 P. alcalifaciens isolates from 73 dogs revealed that strains from 51 dogs belonged to the same WGS clone. Findings point to P. alcalifaciens as implicated in the outbreak, but investigations are needed to reveal the pathogenic potential of P. alcalifaciens in dogs and its epidemiology.