Systematic review of Integrated Disease Surveillance and Response (IDSR) implementation in the African region.

BACKGROUND: The WHO African region frequently experiences outbreaks and epidemics of infectious diseases often exacerbated by weak health systems and infrastructure, late detection, and ineffective outbreak response. To address this, the WHO Regional Office for Africa developed and began implementing the Integrated Disease Surveillance and Response strategy in 1998. OBJECTIVES: This systematic review aims to document the identified successes and challenges surrounding the implementation of IDSR in the region available in published literature to highlight areas for prioritization, further research, and to inform further strengthening of IDSR implementation. METHODS: A systematic review of peer-reviewed literature published in English and French from 1 July 2012 to 13 November 2019 was conducted using PubMed and Web of Science. Included articles focused on the WHO African region and discussed the use of IDSR strategies and implementation, assessment of IDSR strategies, or surveillance of diseases covered in the IDSR framework. Data were analyzed descriptively using Microsoft Excel and Tableau Desktop 2019. RESULTS: The number of peer-reviewed articles discussing IDSR remained low, with 47 included articles focused on 17 countries and regional level systems. Most commonly discussed topics were data reporting (n = 39) and challenges with IDSR implementation (n = 38). Barriers to effective implementation were identified across all IDSR core and support functions assessed in this review: priority disease detection; data reporting, management, and analysis; information dissemination; laboratory functionality; and staff training. Successful implementation was noted where existing surveillance systems and infrastructure were utilized and streamlined with efforts to increase access to healthcare. CONCLUSIONS AND IMPLICATIONS OF FINDINGS: These findings highlighted areas where IDSR is performing well and where implementation remains weak. While challenges related to IDSR implementation since the first edition of the technical guidelines were released are not novel, adequately addressing them requires sustained investments in stronger national public health capabilities, infrastructure, and surveillance processes.

Salmonella enterica serovar Typhi H58 clone has been endemic in Zimbabwe from 2012 to 2019.

BACKGROUND: Typhoid fever, caused by S. enterica ser. Typhi, continues to be a substantial health burden in developing countries. Little is known of the genotypic diversity of S. enterica ser. Typhi in Zimbabwe, but this is key for understanding the emergence and spread of this pathogen and devising interventions for its control. OBJECTIVES: To report the molecular epidemiology of S. enterica ser. Typhi outbreak strains circulating from 2012 to 2019 in Zimbabwe, using comparative genomics. METHODS: A review of typhoid cases records from 2012 to 2019 in Zimbabwe was performed. The phylogenetic relationship of outbreak isolates from 2012 to 2019 and emergence of antibiotic resistance was investigated by whole-genome sequence analysis. RESULTS: A total 22 479 suspected typhoid cases, 760 confirmed cases were reported from 2012 to 2019 and 29 isolates were sequenced. The majority of the sequenced isolates were predicted to confer resistance to aminoglycosides, ß-lactams, phenicols, sulphonamides, tetracycline and fluoroquinolones (including qnrS detection). The qnrS1 gene was associated with an IncN (subtype PST3) plasmid in 79% of the isolates. Whole-genome SNP analysis, SNP-based haplotyping and resistance determinant analysis showed that 93% of the isolates belonged to a single clade represented by multidrug-resistant H58 lineage I (4.3.1.1), with a maximum pair-wise distance of 22 SNPs. CONCLUSIONS: This study has provided detailed genotypic characterization of the outbreak strain, identified as S. Typhi 4.3.1.1 (H58). The strain has reduced susceptibility to ciprofloxacin due to qnrS carried by an IncN (subtype PST3) plasmid resulting from ongoing evolution to full resistance.

Measuring Timeliness of Outbreak Response in the World Health Organization African Region, 2017-2019.

Large-scale protracted outbreaks can be prevented through early detection, notification, and rapid control. We assessed trends in timeliness of detecting and responding to outbreaks in the African Region reported to the World Health Organization during 2017-2019. We computed the median time to each outbreak milestone and assessed the rates of change over time using univariable and multivariable Cox proportional hazard regression analyses. We selected 296 outbreaks from 348 public reported health events and evaluated 184 for time to detection, 232 for time to notification, and 201 for time to end. Time to detection and end decreased over time, whereas time to notification increased. Multiple factors can account for these findings, including scaling up support to member states after the World Health Organization established its Health Emergencies Programme and support given to countries from donors and partners to strengthen their core capacities for meeting International Health Regulations.

Novel Approach to Support Rapid Data Collection, Management, and Visualization During the COVID-19 Outbreak Response in the World Health Organization African Region: Development of a Data Summarization and Visualization Tool.

BACKGROUND: The COVID-19 pandemic has created unprecedented challenges to the systematic and timely sharing of COVID-19 field data collection and management. The World Health Organization (WHO) is working with health partners on the rollout and implementation of a robust electronic field data collection platform. The delay in the deployment and rollout of this electronic platform in the WHO African Region, as a consequence of the application of large-scale public health and social measures including movement restrictions and geographical area quarantine, left a gap between data collection and management. This lead to the need to develop interim data management solutions to accurately monitor the evolution of the pandemic and support the deployment of appropriate public health interventions. OBJECTIVE: The aim of this study is to review the design, development, and implementation of the COVID-19 Data Summarization and Visualization (DSV) tool as a rapidly deployable solution to fill this critical data collection gap as an interim solution. METHODS: This paper reviews the processes undertaken to research and develop a tool to bridge the data collection gap between the onset of a COVID-19 outbreak and the start of data collection using a prioritized electronic platform such as Go.Data in the WHO African Region. RESULTS: In anticipation of the implementation of a prioritized tool for field data collection, the DSV tool was deployed in 18 member states for COVID-19 outbreak data management. We highlight preliminary findings and lessons learned from the DSV tool deployment in the WHO African Region. CONCLUSIONS: We developed a rapidly deployable tool for COVID-19 data collection and visualization in the WHO African Region. The lessons drawn on this experience offer an opportunity to learn and apply these to improve future similar public health informatics initiatives in an outbreak or similar humanitarian setting, particularly in low- and middle-income countries.

Ebola Virus Infection Associated with Transmission from Survivors.

Ebola virus (EBOV) can persist in immunologically protected body sites in survivors of Ebola virus disease, creating the potential to initiate new chains of transmission. From the outbreak in West Africa during 2014-2016, we identified 13 possible events of viral persistence-derived transmission of EBOV (VPDTe) and applied predefined criteria to classify transmission events based on the strength of evidence for VPDTe and source and route of transmission. For 8 events, a recipient case was identified; possible source cases were identified for 5 of these 8. For 5 events, a recipient case or chain of transmission could not be confidently determined. Five events met our criteria for sexual transmission (male-to-female). One VPDTe event led to at least 4 generations of cases; transmission was limited after the other events. VPDTe has increased the importance of Ebola survivor services and sustained surveillance and response capacity in regions with previously widespread transmission.

Contact tracing performance during the Ebola epidemic in Liberia, 2014-2015.

BACKGROUND: During the Ebola virus disease (EVD) epidemic in Liberia, contact tracing was implemented to rapidly detect new cases and prevent further transmission. We describe the scope and characteristics of contact tracing in Liberia and assess its performance during the 2014-2015 EVD epidemic. METHODOLOGY/PRINCIPAL FINDINGS: We performed a retrospective descriptive analysis of data collection forms for contact tracing conducted in six counties during June 2014-July 2015. EVD case counts from situation reports in the same counties were used to assess contact tracing coverage and sensitivity. Contacts who presented with symptoms and/or died, and monitoring was stopped, were classified as "potential cases". Positive predictive value (PPV) was defined as the proportion of traced contacts who were identified as potential cases. Bivariate and multivariate logistic regression models were used to identify characteristics among potential cases. We analyzed 25,830 contact tracing records for contacts who had monitoring initiated or were last exposed between June 4, 2014 and July 13, 2015. Contact tracing was initiated for 26.7% of total EVD cases and detected 3.6% of all new cases during this period. Eighty-eight percent of contacts completed monitoring, and 334 contacts were identified as potential cases (PPV = 1.4%). Potential cases were more likely to be detected early in the outbreak; hail from rural areas; report multiple exposures and symptoms; have household contact or direct bodily or fluid contact; and report nausea, fever, or weakness compared to contacts who completed monitoring. CONCLUSIONS/SIGNIFICANCE: Contact tracing was a critical intervention in Liberia and represented one of the largest contact tracing efforts during an epidemic in history. While there were notable improvements in implementation over time, these data suggest there were limitations to its performance-particularly in urban districts and during peak transmission. Recommendations for improving performance include integrated surveillance, decentralized management of multidisciplinary teams, comprehensive protocols, and community-led strategies.

Persistence of Ebola virus after the end of widespread transmission in Liberia: an outbreak report.

BACKGROUND: Outbreak response efforts for the 2014-15 Ebola virus disease epidemic in west Africa brought widespread transmission to an end. However, subsequent clusters of infection have occurred in the region. An Ebola virus disease cluster in Liberia in November, 2015, that was identified after a 15-year-old boy tested positive for Ebola virus infection in Monrovia, raised the possibility of transmission from a persistently infected individual. METHODS: Case investigations were done to ascertain previous contact with cases of Ebola virus disease or infection with Ebola virus. Molecular investigations on blood samples explored a potential linkage between Ebola virus isolated from cases in this November, 2015, cluster and epidemiologically linked cases from the 2014-15 west African outbreak, according to the national case database. FINDINGS: The cluster investigated was the family of the index case (mother, father, three siblings). Ebola virus genomes assembled from two cases in the November, 2015, cluster, and an epidemiologically linked Ebola virus disease case in July, 2014, were phylogenetically related within the LB5 sublineage that circulated in Liberia starting around August, 2014. Partial genomes from two additional individuals, one from each cluster, were also consistent with placement in the LB5 sublineage. Sequencing data indicate infection with a lineage of the virus from a former transmission chain in the country. Based on serology and epidemiological and genomic data, the most plausible scenario is that a female case in the November, 2015, cluster survived Ebola virus disease in 2014, had viral persistence or recurrent disease, and transmitted the virus to three family members a year later. INTERPRETATION: Investigation of the source of infection for the November, 2015, cluster provides evidence of Ebola virus persistence and highlights the risk for outbreaks after interruption of active transmission. These findings underscore the need for focused prevention efforts among survivors and sustained capacity to rapidly detect and respond to new Ebola virus disease cases to prevent recurrence of a widespread outbreak. FUNDING: US Centers for Disease Control and Prevention, Defense Threat Reduction Agency, and WHO.

Tracking and responding to an outbreak of tuberculosis using MIRU-VNTR genotyping and whole genome sequencing as epidemiological tools.

Background: We describe an outbreak that contributed to a near doubling of the incidence of tuberculosis in Southampton, UK. We examine the importance of 24 locus mycobacterial interspersed repetitive unit variable number tandem repeat (MIRU-VNTR) genotyping in its identification and management and the role of whole genome sequencing (WGS) in tracing the spread of the strain. Methods: Outbreak cases were defined as those diagnosed between January and December 2011 with indistinguishable 24 locus-MIRU-VNTR genotypes or, cases linked epidemiologically. A cluster questionnaire was administered by TB nurses to identify contacts and social settings. Results: Overall, 25 patients fulfilled the case definition. No cases with this MIRU-VNTR genotype had been detected in the UK previously. Connections were found between all cases through household contacts or social venues including a football club, Internet cafe and barber's shop. Public health actions included extended contact tracing, venue screening and TB awareness-raising. The outbreak resulted in a high rate of transmission and high incidence of clinical disease among contacts. Conclusions: This outbreak illustrates the value of combining active case-finding with prospective MIRU-VNTR genotyping to identify settings to undertake public health action. In addition WGS revealed that the VNTR-defined cluster was a single outbreak and that active TB transmission not reactivation was responsible for this outbreak in non-UK born individuals.

Ebola virus disease contact tracing activities, lessons learned and best practices during the Duport Road outbreak in Monrovia, Liberia, November 2015.

BACKGROUND: Contact tracing is one of the key response activities necessary for halting Ebola Virus Disease (EVD) transmission. Key elements of contact tracing include identification of persons who have been in contact with confirmed EVD cases and careful monitoring for EVD symptoms, but the details of implementation likely influence their effectiveness. In November 2015, several months after a major Ebola outbreak was controlled in Liberia, three members of a family were confirmed positive for EVD in the Duport Road area of Monrovia. The cluster provided an opportunity to implement and evaluate modified approaches to contact tracing. METHODS: The approaches employed for improved contact tracing included classification and risk-based management of identified contacts (including facility based isolation of some high risk contacts, provision of support to persons being monitored, and school-based surveillance for some persons with potential exposure but not listed as contacts), use of phone records to help locate missing contacts, and modifications to data management tools. We recorded details about the implementation of these approaches, report the overall outcomes of the contact tracing efforts and the challenges encountered, and provide recommendations for management of future outbreaks. RESULTS: 165 contacts were identified (with over 150 identified within 48 hours of confirmation of the EVD cases) and all initially missing contacts were located. Contacts were closely monitored and promptly tested if symptomatic; no contacts developed disease. Encountered challenges related to knowledge gaps among contact tracing staff, data management, and coordination of contact tracing activities with efforts to offer Ebola vaccine. CONCLUSIONS: The Duport Road EVD cluster was promptly controlled. Missing contacts were effectively identified, and identified contacts were effectively monitored and rapidly tested. There is a persistent risk of EVD reemergence in Liberia; the experience controlling each cluster can help inform future Ebola control efforts in Liberia and elsewhere.

Recent household transmission of tuberculosis in England, 2010-2012: retrospective national cohort study combining epidemiological and molecular strain typing data.

BACKGROUND: We estimate the proportion of tuberculosis (TB) in England due to recent household transmission, identify factors associated with being a household transmitter, and investigate the impact that identification of a case has on time to treatment of subsequent cases. METHODS: TB cases notified between 2010 and 2012 in England in the same household as another case were identified; 24 locus MIRU-VNTR strain typing (ST) was used to identify household cases with likely recent transmission. Treatment delay in index and subsequent cases was compared. Risk factors for being a household transmitter were identified in univariable and multivariable analyses. RESULTS: Overall, 7.7% (1849/24,060) of TB cases lived in a household with another case. We estimate that 3.9% were due to recent household transmission. ST data was unavailable for 67% (1242) of household pairs. For those with ST data, 64% (386) had confirmed, 11% probable (66) and 25% (155) refuted household transmission. The median treatment delay was 65 days for index cases and 37 days for subsequent asymptomatic cases. Risk factors for being a household transmitter included being under 25 years old, UK-born with Black African, Indian or Pakistani ethnicity, or born in Somalia or Romania. CONCLUSIONS: This study has a number of implications for household TB contact tracing in low incidence countries, including the potential to reduce the diagnostic delay for subsequent household cases and the benefit of using ST to identify when to conduct source contact tracing outside the household. As 25% of TB cases in households had discordant strains, households with multiple TB cases do not necessarily represent household transmission. The additional fact that 25% of index cases within households only had extra-pulmonary TB demonstrates that, if household contact tracing is limited to pulmonary TB cases (as recently recommended in UK guidelines), additional cases of active TB in households will be missed. Our finding that no lineage of TB was associated with recent household transmission and with no increased transmissibility in the Beijing lineage compared to others, suggests that the lineage need not impact contact tracing efforts. Improvements in contact tracing have the potential to reduce transmission of TB in low incidence countries.

Recent TB transmission, clustering and predictors of large clusters in London, 2010-2012: results from first 3†years of universal MIRU-VNTR strain typing.

BACKGROUND: The incidence of TB has doubled in the last 20 years in London. A better understanding of risk groups for recent transmission is required to effectively target interventions. We investigated the molecular epidemiological characteristics of TB cases to estimate the proportion of cases due to recent transmission, and identify predictors for belonging to a cluster. METHODS: The study population included all culture-positive TB cases in London residents, notified between January 2010 and December 2012, strain typed using 24-loci multiple interspersed repetitive units-variable number tandem repeats. Multivariable logistic regression analysis was performed to assess the risk factors for clustering using sociodemographic and clinical characteristics of cases and for cluster size based on the characteristics of the first two cases. RESULTS: There were 10 147 cases of which 5728 (57%) were culture confirmed and 4790 isolates (84%) were typed. 2194 (46%) were clustered in 570 clusters, and the estimated proportion attributable to recent transmission was 34%. Clustered cases were more likely to be UK born, have pulmonary TB, a previous diagnosis, a history of substance abuse or alcohol abuse and imprisonment, be of white, Indian, black-African or Caribbean ethnicity. The time between notification of the first two cases was more likely to be <90 days in large clusters. CONCLUSIONS: Up to a third of TB cases in London may be due to recent transmission. Resources should be directed to the timely investigation of clusters involving cases with risk factors, particularly those with a short period between the first two cases, to interrupt onward transmission of TB.

Achieving compliance with the International Health Regulations by overseas territories of the United Kingdom of Great Britain and Northern Ireland.

The 2005 International Health Regulations (IHR) came into force for all Member States of the World Health Organization (WHO) in June 2007 and the deadline for achieving compliance was June 2012. The purpose of the IHR is to prevent, protect against, control - and provide a public health response to - international spread of disease. The territory of the United Kingdom of Great Britain and Northern Ireland and that of several other Member States, such as China, Denmark, France, the Netherlands and the United States of America, include overseas territories, which cover a total population of approximately 15 million people. Member States have a responsibility to ensure that all parts of their territory comply with the IHR. Since WHO has not provided specific guidance on compliance in the special circumstances of the overseas territories of Member States, compliance by these territories is an issue for self-assessment by Member States themselves. To date, no reports have been published on the assessment of IHR compliance in countries with overseas territories. We describe a gap analysis done in the United Kingdom to assess IHR compliance of its overseas territories. The findings and conclusions are broadly applicable to other countries with overseas territories which may have yet to assess their compliance with the IHR. Such assessments are needed to ensure compliance across all parts of a Member States' territory and to increase global health security.

Le Règlement sanitaire international de 2005 (RSI) est entré en vigueur pour tous les États membres de l'Organisation mondiale de la Santé en juin 2007, et la date limite pour sa mise en conformité était juin 2012. L'objectif du RSI est de prévenir, de protéger, de contrôler ­ et d'apporter une réponse de santé publique ­ à la propagation internationale des maladies. Le territoire du Royaume-Uni de Grande-Bretagne et d'Irlande du Nord et celui d'autres États membres, comme la Chine, le Danemark, la France, les Pays-Bas et les États-Unis d'Amérique, se composent de territoires d'outre-mer, lesquels couvrent une population totale d'environ 15 millions d'habitants. Les États membres ont la responsabilité de veiller à ce que toutes les parties de leur territoire se conforment au RSI. Étant donné que l'OMS ne fournit pas d'orientation spécifique concernant la conformité dans les circonstances spéciales des territoires d'outre-mer des États membres, leur conformité est une question d'auto-évaluation par les États membres eux-mêmes. À ce jour, aucun rapport n'a été publié sur l'évaluation de la conformité au RSI dans les pays possédant des territoires d'outre-mer. Nous décrivons une analyse des lacunes effectuée au Royaume-Uni pour évaluer la conformité au RSI de ses territoires d'outre-mer. Les résultats et les conclusions sont largement applicables aux autres pays possédant des territoires d'outre-mer, qui peuvent cependant évaluer leur propre conformité au RSI. Ces évaluations sont nécessaires pour veiller à la conformité dans toutes les parties du territoire d'un État membre et pour augmenter la sécurité sanitaire mondiale.

El Reglamento Sanitario Internacional 2005 (RSI) entró en vigor para todos los Estados miembros de la Organización Mundial de la Salud (OMS) en junio de 2007 con junio de 2012 como fecha límite para lograr el cumplimiento. El objetivo del RSI es prevenir, proteger, controlar y proporcionar una respuesta de salud pública a la propagación internacional de enfermedades. El territorio del Reino Unido de Gran Bretaña e Irlanda del Norte y otros Estados miembros como China, Dinamarca, Francia, los Países Bajos y los Estados Unidos de América cuentan con territorios de ultramar que abarcan una población total de aproximadamente 15 millones de personas. Los Estados miembros tienen la responsabilidad de garantizar que todos sus territorios cumplan con el RSI. Puesto que la OMS no ha proporcionado orientación específica sobre el cumplimiento para las circunstancias especiales de los territorios de ultramar de los Estados miembros, el cumplimiento por parte de estos territorios es un problema que los propios Estados miembros tienen que evaluar. Hasta la fecha no se han publicado informes sobre la evaluación del cumplimiento del RSI en los países con territorios de ultramar. Describimos un análisis de las deficiencias realizado en el Reino Unido con objeto de evaluar el cumplimiento del RSI de sus territorios de ultramar. Los resultados y conclusiones son ampliamente aplicables a otros países con territorios de ultramar que quizá aún tengan que evaluar su cumplimiento con el RSI. Dichas evaluaciones son necesarias para asegurar el cumplimiento en todos los territorios de los Estados miembros y para aumentar la seguridad sanitaria mundial.

Incidence and patterns of detection and management of childhood-onset hereditary retinal disorders in the UK.

BACKGROUND: A prospective, national population-based cross-sectional study to enable understanding of the burden and management in the UK of hereditary retinal disorders presenting in childhood. METHODS: Children aged <16 years with a new diagnosis of an inherited retinal disorder made between September 2006 and February 2008 in the UK were identified through two national active surveillance schemes. Clinical and socio-demographic information was collected on each child at diagnosis and 9 months later using standardised questionnaires. RESULTS: 241 patients were reported with 24 distinct diagnoses. 14% had additional systemic disorders and 13% had dual sensory impairment. Annual incidence was 1.4/100,000 children (aged 0-15 years) and the cumulative incidence by age 16 years was 22.3/100,000 children. The most common mode of inheritance was autosomal recessive. A significantly higher rate was seen in males than females (relative rate (RR) 1.53), in children of Asian compared with White ethnicity (RR 7.12) and in those in the worst quintile of socio-economic deprivation compared with those in the best (RR 1.43). Parents most commonly detected a problem with their child's vision. Up to seven different health professionals were involved in a child's early management, and variations were noted in the proportion of eligible children having assessments for low vision aids, statement of educational needs and certification as sight-impaired. CONCLUSIONS: These findings illustrate the highly heterogeneous nature of childhood retinal dystrophies and provide previously unavailable data on disease incidence, distributions and management, which are important for service provision and for planning future treatment programmes, particularly as novel therapies become available.