Laboratory Diagnostic Capacity for Fungal Infections in Nigerian Tertiary Hospitals: A Gap Analysis Survey

BACKGROUND

An estimated 11.8% of Nigerians suffer from invasive fungal infections (IFIs) yearly. Laboratory capacity to diagnose IFIs in Nigeria has not been objectively assessed.

OBJECTIVE

To identify the gaps in laboratory capacity for diagnosis of IFIs in Nigerian tertiary hospitals.

METHODS

Clinical microbiologists in Nigerian tertiary hospitals were invited to partake in a 21-item online survey via a professional chat group and email. A descriptive crosssectional study of survey responses was conducted. Frequencies were computed for microscopy, culture, antifungal sensitivity, and non-culture based diagnostic modalities.

FINDINGS

Respondents were from 22 tertiary hospitals spread across the six geo-political zones of Nigeria. Gaps identified include absence of mycology laboratory/bench in 5/22 (22.7%), no access to a biosafety cabinet in 5/22 (22.7%), lack of laboratory scientists formally trained in mycology in 9/22 (40.9%), lack of participation in external quality assurance in all (100%), lack of automated blood culture facilities in 9/22 (40.9%), no yeast identification beyond germ tube test in12/22 (54.5%), and no anti-fungal sensitivity testing in 17/22 (77.3%). Galactomannan, cryptococcal antigen lateral flow assay and latex agglutination tests are used in 1(4.5%), 3 (13.6%) and 5 (22.7%) centres respectively; antigen/antibody based non-culture diagnostics were totally absent in 12/22 (54.5%) hospitals.

CONCLUSION

Nigerian tertiary hospitals have gaps in the laboratory capacity to diagnose invasive fungal infections despite the significant size of the population at risk of these life-threatening infections in the country. Economically feasible diagnostic solutions and models as well as capacity building are urgently required.

Descriptive epidemiology of coronavirus disease 2019 in Nigeria, 27 February-6 June 2020

The objective of this study was to describe the epidemiology of COVID-19 in Nigeria with a view of generating evidence to enhance planning and response strategies. A national surveillance dataset between 27 February and 6 June 2020 was retrospectively analysed, with confirmatory testing for COVID-19 done by real-time polymerase chain reaction (RT-PCR). The primary outcomes were cumulative incidence (CI) and case fatality (CF). A total of 40 926 persons (67% of total 60 839) had complete records of RT-PCR test across 35 states and the Federal Capital Territory, 12 289 (30.0%) of whom were confirmed COVID-19 cases. Of those confirmed cases, 3467 (28.2%) had complete records of clinical outcome (alive or dead), 342 (9.9%) of which died. The overall CI and CF were 5.6 per 100 000 population and 2.8%, respectively. The highest proportion of COVID-19 cases and deaths were recorded in persons aged 31-40 years (25.5%) and 61-70 years (26.6%), respectively; and males accounted for a higher proportion of confirmed cases (65.8%) and deaths (79.0%). Sixty-six per cent of confirmed COVID-19 cases were asymptomatic at diagnosis. In conclusion, this paper has provided an insight into the early epidemiology of COVID-19 in Nigeria, which could be useful for contextualising public health planning.

A participatory and systemic training approach for IPC improvement in Nigerian health facilities

Background

Health care-associated infections (HAI) are one of the most common adverse events in care delivery and a major public health problem. A large percentage of HAI in hospitals are preventable through effective infection prevention and control (IPC) measures. IPC trainings for health care personnel based only on technical content do not lead to sustainable improvement of IPC standard precautions. To address this problem, the Nigeria Centre for Disease Control (NCDC) in collaboration with the Robert Koch Institute (RKI) developed a multimodal training approach to facilitate the transfer of IPC competences into working routine in Nigerian health facilities.

Objectives

The training should foster the ability of health care workers to act and communicate participatory, analyze IPC problems systemically and to develop and perform tailored IPC activities in their health facilities. It should empower health care workers to initiate and promote sustainable IPC improvement locally.

Results

We developed a participatory training approach which focusses on the relational and organizational dimension of IPC. It addresses the human and infrastructural factors for IPC compliance in daily working routine. A variety of training methods offers practice tools in communication, systemic thinking and team work, and allows experiencing a participatory attitude. The training program consists of two face to face workshops and an interjacent field project. 28 Health care workers of 14 health facilities in Lagos State participated the first implementation of the training program in 2018. The training evaluation showed the high relevance of the training to the HCW. The field projects showed that the participants could apply the participatory approach for IPC improvement.

Conclusions

A participatory and systemic approach for IPC trainings enables health care workers to take action for IPC improvement locally.

Key messages

We developed and implemented a participatory training approach that addresses the relational and organizational dimension of IPC. Health care workers took tailored actions for IPC improvement locally.

Mobile-based and open-source infectious disease surveillance and outbreak management in Tanzania

Introduction

The PANDORA-ID-NET consortium aims to build capacity for effective outbreak response in sub-Saharan Africa. Part of this mission is to develop a real-time data sharing platform for disease outbreaks that leverages centralised data management and uses mobile technologies for data gathering and feedback. We have committed to using open-source technologies, so that the platform can be deployed on regional IT infrastructure and further developed by local staff, and collected data can be stored and processed in the region of origin. This abstract aims to describe how we identified a state of the art open-source system that fulfils these criteria, and the process of how we are extending it to function within the current infectious disease control framework in Tanzania, under our partnership with the Ifakara Health Institute (IHI).

Methods

To find state of the art open-source systems matching our criteria, we performed a rapid review of the literature. We screened 1022 articles and found 15 candidate systems, out of which only SORMAS satisfied the criteria. SORMAS was developed jointly by the Helmholtz Centre for Infection Research (HZI) and the Nigeria CDC, and was modeled on Nigeria's successful response to the Ebola outbreak. The system can be used for case management, contact tracing, surveillance, and laboratory sample management. Data is collected and synchronised using Android mobile devices (both online and offline) and data aggregation and analysis are performed in real-time via a web application

Results

Having chosen SORMAS, we established a collaboration between the SORMAS developer team and the PANDORA team. IHI are guiding ongoing work on adapting SORMAS to the Tanzanian health facility geography and the country's case definition guidelines for notifiable diseases.

Conclusions

Once adapted for Tanzania, SORMAS will fill an unoccupied niche in infectious disease control, improving the quality of collected case data and enabling better outbreak response

Key messages

A state of the art, mobile-based, open-source outbreak management and infectious disease surveillance system (SORMAS) is being deployed in Tanzania. We outline our experience with piloting SORMAS in Tanzania, building on the experience of our Nigerian and German partners, who rolled out this system nationally in Nigeria and other African countries.

The response to re-emergence of yellow fever in Nigeria, 2017

Yellow fever (YF) is an acute viral hemorrhagic disease caused by the YF virus (arbovirus) which continues to cause severe morbidity and mortality in Africa. A case of YF was confirmed in Nigeria on the 12th of September 2017, 21 years after the last confirmed case. The patient belongs to a nomadic population with a history of low YF vaccination uptake, in the Ifelodun Local Government Area (LGA) of Kwara State, Nigeria. An active case search in Ifelodun and its five contiguous LGAs led to the listing of 55 additional suspect cases of YF within the period of the outbreak investigation between September 18 to October 6, 2017. The median age of cases was 15 years, and 54.4% were males. Of these, blood samples were collected from 30 cases; nine tested positive in laboratories in Nigeria and six were confirmed positive for YF by the WHO reference laboratory in the region; Institut Pasteur, Dakar. A rapid YF vaccination coverage assessment was carried out, resulting in a coverage of 46% in the LGAs, with 25% of cases able to produce their vaccination cards. All stages of the yellow fever vector, Aedes mosquito were identified in the area, with high larval indices (House and Breteau) observed. In response to the outbreak, YF surveillance was intensified across all States in Nigeria, as well as reactive vaccination and social mobilisation campaigns carried out in the affected LGAs in Kwara State. A state-wide YF preventive campaign was also initiated.

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.

Social marketing approaches to nutrition and physical activity interventions in early care and education centres: a systematic review

INTRODUCTION

Social marketing is a promising planning approach for influencing voluntary lifestyle behaviours, but its application to nutrition and physical activity interventions in the early care and education setting remains unknown.

METHODS

PubMed, ISI Web of Science, PsycInfo and the Cumulative Index of Nursing and Allied Health were systematically searched to identify interventions targeting nutrition and/or physical activity behaviours of children enrolled in early care centres between 1994 and 2016. Content analysis methods were used to capture information reflecting eight social marketing benchmark criteria.

RESULTS

The review included 135 articles representing 77 interventions. Two interventions incorporated all eight benchmark criteria, but the majority included fewer than four. Each intervention included behaviour and methods mix criteria, and more than half identified audience segments. Only one-third of interventions incorporated customer orientation, theory, exchange and insight. Only six interventions addressed competing behaviours. We did not find statistical significance for the effectiveness of interventions on child-level diet, physical activity or anthropometric outcomes based on the number of benchmark criteria used.

CONCLUSION

This review highlights opportunities to apply social marketing to obesity prevention interventions in early care centres. Social marketing could be an important strategy for early childhood obesity prevention efforts, and future research investigations into its effects are warranted.

Group A streptococcal infections during the seasonal influenza outbreak 2010/11 in South East England

We present a series of 19 cases of invasive Group A streptococcal (iGAS) infection reported to the Thames Valley Health Protection Unit from 1 December 2010 to 15 January 2011. Ten patients died and a prodrome of influenza-like illness was reported in 14 cases. Influenza B co-infection was confirmed in four cases, three of which were fatal. Our report provides further evidence that influenza B co-infection with iGAS has the potential to cause significant morbidity and mortality.

Group A streptococcal infections during the seasonal influenza outbreak 2010/11 in South East England

We present a series of 19 cases of invasive Group A streptococcal (iGAS) infection reported to the Thames Valley Health Protection Unit from 1 December 2010 to 15 January 2011. Ten patients died and a prodrome of influenza-like illness was reported in 14 cases.Influenza B co-infection was confirmed in four cases,three of which were fatal. Our report provides further evidence that influenza B co-infection with iGAS has the potential to cause significant morbidity and mortality.

Verbal autopsy can consistently measure AIDS mortality: a validation study in Tanzania and Zimbabwe

BACKGROUND

Verbal autopsy is currently the only option for obtaining cause of death information in most populations with a widespread HIV/AIDS epidemic.

METHODS

With the use of a data-driven algorithm, a set of criteria for classifying AIDS mortality was trained. Data from two longitudinal community studies in Tanzania and Zimbabwe were used, both of which have collected information on the HIV status of the population over a prolonged period and maintained a demographic surveillance system that collects information on cause of death through verbal autopsy. The algorithm was then tested in different times (two phases of the Zimbabwe study) and different places (Tanzania and Zimbabwe).

RESULTS

The trained algorithm, including nine signs and symptoms, performed consistently based on sensitivity and specificity on verbal autopsy data for deaths in 15-44-year-olds from Zimbabwe phase I (sensitivity 79%; specificity 79%), phase II (sensitivity 83%; specificity 75%) and Tanzania (sensitivity 75%; specificity 74%) studies. The sensitivity dropped markedly for classifying deaths in 45-59-year-olds.

CONCLUSIONS

Verbal autopsy can consistently measure AIDS mortality with a set of nine criteria. Surveillance should focus on deaths that occur in the 15-44-year age group for which the method performs reliably. Addition of a handful of questions related to opportunistic infections would enable other widely used verbal autopsy tools to apply this validated method in areas for which HIV testing and hospital records are unavailable or incomplete.

An outbreak of influenza A(H1N1)v in a boarding school in South East England, May-June 2009

An outbreak of influenza A(H1N1)v was confirmed in May and June 2009 in a boarding school in South East England involving 102 symptomatic cases with influenza-like illness. Influenza A(H1N1)v infection was laboratory-confirmed by PCR in 62 pupils and one member of staff.

Is STI surveillance in England meeting the requirements of the 21st century? An evaluation of data from the South West Region

Binary file ES_Abstracts_Final_ECDC.txt matches

Unacceptably high mortality related to measles epidemics in Niger, Nigeria, and Chad

BACKGROUND

Despite the comprehensive World Health Organization (WHO)/United Nations Children's Fund (UNICEF) measles mortality-reduction strategy and the Measles Initiative, a partnership of international organizations supporting measles mortality reduction in Africa, certain high-burden countries continue to face recurrent epidemics. To our knowledge, few recent studies have documented measles mortality in sub-Saharan Africa. The objective of our study was to investigate measles mortality in three recent epidemics in Niamey (Niger), N'Djamena (Chad), and Adamawa State (Nigeria).

METHODS AND FINDINGS

We conducted three exhaustive household retrospective mortality surveys in one neighbourhood of each of the three affected areas: Boukoki, Niamey, Niger (April 2004, n = 26,795); Moursal, N'Djamena, Chad (June 2005, n = 21,812); and Dong District, Adamawa State, Nigeria (April 2005, n = 16,249), where n is the total surveyed population in each of the respective areas. Study populations included all persons resident for at least 2 wk prior to the study, a duration encompassing the measles incubation period. Heads of households provided information on measles cases, clinical outcomes up to 30 d after rash onset, and health-seeking behaviour during the epidemic. Measles cases and deaths were ascertained using standard WHO surveillance-case definitions. Our main outcome measures were measles attack rates (ARs) and case fatality ratios (CFRs) by age group, and descriptions of measles complications and health-seeking behaviour. Measles ARs were the highest in children under 5 y old (under 5 y): 17.1% in Boukoki, 17.2% in Moursal, and 24.3% in Dong District. CFRs in under 5-y-olds were 4.6%, 4.0%, and 10.8% in Boukoki, Moursal, and Dong District, respectively. In all sites, more than half of measles cases in children aged under 5 y experienced acute respiratory infection and/or diarrhoea in the 30 d following rash onset. Of measles cases, it was reported that 85.7% (979/1,142) of patients visited a health-care facility within 30 d after rash onset in Boukoki, 73.5% (519/706) in Moursal, and 52.8% (603/1,142) in Dong District.

CONCLUSIONS

Children in these countries still face unacceptably high mortality from a completely preventable disease. While the successes of measles mortality-reduction strategies and progress observed in measles control in other countries of the region are laudable and evident, they should not overshadow the need for intensive efforts in countries that have just begun implementation of the WHO/UNICEF comprehensive strategy.

Outbreak of E. coli O157 infection in the south west of the UK: risks from streams crossing seaside beaches

In August 2004 seven cases of Escherichia coli O157 infection were identified in children on holiday in Cornwall, southwest England, all of whom had stayed at different sites in the area. Isolates from all seven cases were confirmed as E. coli serogroup O157 phage type 21/28. We carried out a case-control study among holidaymakers who visited the beach. A standardised questionnaire was administered by telephone to parents. They were asked where on the beach the children had played, whether they had had contact with the stream that flowed across the beach, and about their use of food outlets and sources of food eaten. Cases were more likely to have played in the stream than controls (OR [1.72- undefined]). The time spent in the stream by cases was twice spent there by controls. Cases and controls were equally exposed to other suspected risk factors. PFGE profiles for all the cases were indistinguishable. Increased numbers of coliforms were found in the stream prior to the outbreak. Cattle were found grazing upstream. We suggest that the vehicle of infection for an outbreak of acute gastrointestinal illness caused by E. coli O157 was a contaminated freshwater stream flowing across a seaside beach. The onset dates were consistent with a point source. Heavy rainfall in the days preceding the outbreak might have lead to faeces from the cattle potentially contaminated by E. coli O157 contaminating the stream, thereby leading to the outbreak. Control measures included fencing off the part of the stream in which children played, and putting up warning signs around the beach.

Worldwide distribution of HPV types in women with normal cervical cytology and in women with cervical adenocarcinoma

Two recently published international studies have advanced knowledge of the worldwide distribution of human papillomavirus types and of the cause of cervical adenocarcinomas – a category of disease that forms a small but important and increasing proportion of all cervical cancers

Outbreak of E. coli O157 infection in the south west of the UK: risks from streams crossing seaside beaches

In August 2004 seven cases of Escherichia coli O157 infection were identified in children on holiday in Cornwall, southwest England, all of whom had stayed at different sites in the area. Isolates from all seven cases were confirmed as E. coli serogroup O157 phage type 21/28. We carried out a case-control study among holidaymakers who visited the beach. A standardised questionnaire was administered by telephone to parents. They were asked where on the beach the children had played, whether they had had contact with the stream that flowed across the beach, and about their use of food outlets and sources of food eaten. Cases were more likely to have played in the stream than controls (OR [1.72- undefined]). The time spent in the stream by cases was twice spent there by controls. Cases and controls were equally exposed to other suspected risk factors. PFGE profiles for all the cases were indistinguishable. Increased numbers of coliforms were found in the stream prior to the outbreak. Cattle were found grazing upstream. We suggest that the vehicle of infection for an outbreak of acute gastrointestinal illness caused by E. coli O157 was a contaminated freshwater stream flowing across a seaside beach. The onset dates were consistent with a point source. Heavy rainfall in the days preceding the outbreak might have lead to faeces from the cattle potentially contaminated by E. coli O157 contaminating the stream, thereby leading to the outbreak. Control measures included fencing off the part of the stream in which children played, and putting up warning signs around the beach.