Seasonal trends in epidemiological and entomological profiles of malaria transmission in North Central Nigeria

Comparison of bacterial culture with BioFire® FilmArray® multiplex PCR screening of archived cerebrospinal fluid specimens from children with suspected bacterial meningitis in Nigeria

BACKGROUND

Diagnosis of bacterial meningitis remains a challenge in most developing countries due to low yield from bacterial culture, widespread use of non-prescription antibiotics, and weak microbiology laboratories. The objective of this study was to compare the yield from standard bacterial culture with the multiplex nested PCR platform, the BioFire® FilmArray® Meningitis/Encephalitis Panel (BioFire ME Panel), for cases with suspected acute bacterial meningitis.

METHODS

Following Gram stain and bacterial culture on cerebrospinal fluid (CSF) collected from children aged less than 5 years with a clinical suspicion of acute bacterial meningitis (ABM) as defined by the WHO guidelines, residual CSF specimens were frozen and later tested by BioFire ME Panel.

RESULTS

A total of 400 samples were analyzed. Thirty-two [32/400 (8%)] of the specimens were culture positive, consisting of; three Salmonella spp. (2 Typhi and 1 non-typhi), three alpha hemolytic Streptococcus, one Staphylococcus aureus, six Neisseria meningitidis, seven Hemophilus influenzae, 11 Streptococcus pneumoniae and 368 were culture negative. Of the 368 culture-negative specimens, the BioFire ME Panel detected at least one bacterial pathogen in 90 (24.5%) samples, consisting of S. pneumoniae, N. meningitidis and H. influenzae, predominantly. All culture positive specimens for H. influenzae, N. meningitidis and S. pneumoniae also tested positive with the BioFire ME Panel. In addition, 12 specimens had mixed bacterial pathogens identified. For the first time in this setting, we have data on the viral agents associated with meningitis. Single viral agents were detected in 11 (2.8%) samples while co-detections with bacterial agents or other viruses occurred in 23 (5.8%) of the samples.

CONCLUSIONS

The BioFire® ME Panel was more sensitive and rapid than culture for detecting bacterial pathogens in CSF. The BioFire® ME Panel also provided for the first time, the diagnosis of viral etiologic agents that are associated with meningoencephalitis in this setting. Institution of PCR diagnostics is recommended as a routine test for suspected cases of ABM to enhance early diagnosis and optimal treatment.

Seasonality influences key physiological components contributing to Culex pipiens vector competence

Mosquitoes are the most important animal vector of disease on the planet, transmitting a variety of pathogens of both medical and veterinary importance. Mosquito-borne diseases display distinct seasonal patterns driven by both environmental and biological variables. However, an important, yet unexplored component of these patterns is the potential for seasonal influences on mosquito physiology that may ultimately influence vector competence. To address this question, we selected Culex pipiens, a primary vector of the West Nile virus (WNV) in the temperate United States, to examine the seasonal impacts on mosquito physiology by examining known immune and bacterial components implicated in mosquito arbovirus infection. Semi-field experiments were performed under spring, summer, and late-summer conditions, corresponding to historically low-, medium-, and high-intensity periods of WNV transmission, respectively. Through these experiments, we observed differences in the expression of immune genes and RNA interference (RNAi) pathway components, as well as changes in the distribution and abundance of Wolbachia in the mosquitoes across seasonal cohorts. Together, these findings support the conclusion that seasonal changes significantly influence mosquito physiology and components of the mosquito microbiome, suggesting that seasonality may impact mosquito susceptibility to pathogen infection, which could account for the temporal patterns in mosquito-borne disease transmission.

Time to recovery and its predictors among children 6-59 months with acute malnutrition admitted to community inpatient therapeutic feeding centers in Katsina State, Northwest Nigeria: a retrospective review of health records (2010-2016)

BACKGROUND

Severe acute malnutrition (SAM) among children under five years of age remains a huge public health and economic burden in Sub-Saharan Africa. We investigated time to recovery and its predictors among children aged 6 to 59 months admitted into Community-based Management of Acute Malnutrition (CMAM) stabilisation centres for complicated severe acute malnutrition and whether the outcomes met the minimum Sphere standards.

METHODS

The study was a retrospective cross sectional quantitative review of data recorded in six CMAM stabilization centres registers in four Local Government Areas, Katsina state, Nigeria from September 2010 to November 2016. Records of 6925 children, aged 6-59 months with complicated SAM were reviewed. Descriptive analysis was used to compare performance indicators with Sphere project reference standards. Cox proportional hazard regression analysis was used to estimate the predictors of recovery rate at p < 0.05 and Kaplan-Meier curve to predict the probability of surviving different forms of SAM.

RESULTS

Marasmus was the most common form of severe acute malnutrition (86%). Overall, the outcomes met the minimum sphere standards for inpatient management of SAM. Children with oedematous SAM (13.9%) had the lowest survival rate on Kaplan-Meier graph. The mortality rate was significantly higher during the 'lean season'-May to August (Adjusted Hazard Ratio (AHR) = 0.491, 95% CI = 0.288-0.838). MUAC at Exit (AHR = 0.521, 95% CI = 0.306-0.890), marasmus (AHR = 2.144, 95% CI = 1.079-4.260), transfers from OTP (AHR = 1.105, 95% CI = 0.558-2.190) and average weight gain (AHR = 0.239, 95% CI = 0.169-0.340) were found to be significant predictors of time-to-recovery with p values < 0.05.

CONCLUSION

The study showed that, despite a high turnover of complicated SAM cases in the stabilization centres, the community approach to inpatient management of acute malnutrition enabled early detection and reduced delays in access to care of complicated SAM cases. In the face of health workforce shortage in rural communities to provide pediatric specialist care for SAM children, we recommend task shifting to community health care workers through in service training could bridge the gap and save more lives of children dying from the complication of SAM in rural communities in Nigeria.

Urban malaria in sub-Saharan Africa: dynamic of the vectorial system and the entomological inoculation rate

Sub-Saharan Africa is registering one of the highest urban population growth across the world. It is estimated that over 75% of the population in this region will be living in urban settings by 2050. However, it is not known how this rapid urbanization will affect vector populations and disease transmission. The present study summarizes findings from studies conducted in urban settings between the 1970s and 2020 to assess the effects of urbanization on the entomological inoculation rate pattern and anopheline species distribution. Different online databases such as PubMed, ResearchGate, Google Scholar, Google were screened. A total of 90 publications were selected out of 1527. Besides, over 200 additional publications were consulted to collate information on anopheline breeding habitats and species distribution in urban settings. The study confirms high malaria transmission in rural compared to urban settings. The study also suggests that there had been an increase in malaria transmission in most cities after 2003, which could also be associated with an increase in sampling, resources and reporting. Species of the Anopheles gambiae complex were the predominant vectors in most urban settings. Anopheline larvae were reported to have adapted to different aquatic habitats. The study provides updated information on the distribution of the vector population and the dynamic of malaria transmission in urban settings. The study also highlights the need for implementing integrated control strategies in urban settings.

Analyses of case-based surveillance data on malaria in pregnancy in Plateau State, Nigeria 2013–2017

Background:

Malaria in pregnancy accounts for 11% of maternal death in Nigeria. Plateau State has a low uptake of intermittent preventive treatment of malaria among women attending antenatal care.

Objectives:

This study examined the trend and made projections of reported cases of malaria in pregnancy in Plateau State.

Methods:

Data were extracted from the state disease surveillance system from January 2013 to December 2017. Reported cases of malaria in pregnancy within the 5 years under investigation were retrieved, merged and sorted by month of reporting and Local Government Area (LGA). Prevalence was calculated yearly for each LGA in Plateau State using Geographic Information System. Seasonal variation and projection were based on a multiplicative time series model.

Results:

In total, 62,997 cases of malaria in pregnancy were retrieved. Prevalence was 6.9% in 2013 and increased to 15.1% in 2017. Higher prevalence was observed in Wase, Kanam and Shendam LGAs. A cyclical trend with highest number of malaria in pregnancy cases was found within the third quarter of all the years. Within the 5 years, there was higher seasonal variation for quarters three (1.209834) and one (1.099711). The highest number of cases of malaria in pregnancy was likely to occur in the third quarter, while the least was found in the second quarter. The projected numbers of malaria in pregnancy cases are 20,121, 22,593 and 25,064 for year 2018, 2019 and 2020, respectively, and the highest number of cases occurs in the third quarter.

Conclusion:

Malaria in pregnancy follows an increasing trend in Plateau State, with greatest severity in the third quarter of the year. An effective intervention strategy against malaria among pregnant women is advocated.

Acute Kidney Injuries in Children with Severe Malaria: A comparative study of diagnostic criteria based on serum cystatin C and creatinine levels

Objectives

Serum creatinine levels are often used to diagnose acute kidney injury (AKI), but may not necessarily accurately reflect changes in glomerular filtration rate (GFR). This study aimed to compare the prevalence of AKI in children with severe malaria using diagnostic criteria based on creatinine values in contrast to cystatin C.

Methods

This prospective cross-sectional study was performed between June 2016 and May 2017 at the University of Ilorin Teaching Hospital, Ilorin, Nigeria. A total of 170 children aged 0.5–14 years old with severe malaria were included. Serum cystatin C levels were determined using a particle-enhanced immunoturbidmetric assay method, while creatinine levels were measured using the Jaffe reaction. Renal function assessed using cystatin C-derived estimated GFR (eGFR) was compared to that measured using three sets of criteria based on creatinine values including the Kidney Disease: Improved Global Outcomes (KDIGO) and World Health Organization (WHO) criteria as well as an absolute creatinine cut-off value of >1.5 mg/dL.

Results

Mean serum cystatin C and creatinine levels were 1.77 ± 1.37 mg/L and 1.23 ± 1.80 mg/dL, respectively (P = 0.002). According to the KDIGO, WHO and absolute creatinine criteria, the frequency of AKI was 32.4%, 7.6% and 16.5%, respectively. In contrast, the incidence of AKI based on cystatin C-derived eGFR was 51.8%. Overall, the rate of detection of AKI was significantly higher using cystatin C compared to the KDIGO, WHO and absolute creatinine criteria (P = 0.003, <0.001 and <0.001, respectively).

Conclusion

Diagnostic criteria for AKI based on creatinine values may not indicate the actual burden of disease in children with severe malaria.

Predicting lymphatic filariasis elimination in data-limited settings: A reconstructive computational framework for combining data generation and model discovery

Although there is increasing importance placed on the use of mathematical models for the effective design and management of long-term parasite elimination, it is becoming clear that transmission models are most useful when they reflect the processes pertaining to local infection dynamics as opposed to generalized dynamics. Such localized models must also be developed even when the data required for characterizing local transmission processes are limited or incomplete, as is often the case for neglected tropical diseases, including the disease system studied in this work, viz. lymphatic filariasis (LF). Here, we draw on progress made in the field of computational knowledge discovery to present a reconstructive simulation framework that addresses these challenges by facilitating the discovery of both data and models concurrently in areas where we have insufficient observational data. Using available data from eight sites from Nigeria and elsewhere, we demonstrate that our data-model discovery system is able to estimate local transmission models and missing pre-control infection information using generalized knowledge of filarial transmission dynamics, monitoring survey data, and details of historical interventions. Forecasts of the impacts of interventions carried out in each site made by the models estimated using the reconstructed baseline data matched temporal infection observations and provided useful information regarding when transmission interruption is likely to have occurred. Assessments of elimination and resurgence probabilities based on the models also suggest a protective effect of vector control against the reemergence of LF transmission after stopping drug treatments. The reconstructive computational framework for model and data discovery developed here highlights how coupling models with available data can generate new knowledge about complex, data-limited systems, and support the effective management of disease programs in the face of critical data gaps.

As modelling becomes commonly used in the design and evaluation of parasite elimination programs, the need for well-defined models and datasets describing the nature of transmission processes in local settings is becoming pronounced. For many neglected tropical diseases, however, data for site-specific model identification are typically sparse or incomplete. In this study, we present a new data-model computational discovery system that couples data-assimilation methods based on existing monitoring survey data with model-generated data about baseline conditions to discover the local transmission models required for simulating the impacts of interventions in typical endemic locations for the macroparasitic disease, lymphatic filariasis (LF). Using data from eight study sites in Nigeria and elsewhere, we show that our reconstructive computational framework is able to combine information contained within partially-available site-specific monitoring data with knowledge of parasite transmission dynamics embedded in process-based models to generate the missing data required for inducing reliable locally applicable LF models. We also show that the models so discovered are able to generate the intervention forecasts required for supporting management-relevant decisions in parasite elimination.

Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa

Background

The burden of typhoid in sub-Saharan African (SSA) countries has been difficult to estimate, in part, due to suboptimal laboratory diagnostics. However, surveillance blood cultures at two sites in Nigeria have identified typhoid associated with Salmonella enterica serovar Typhi (S. Typhi) as an important cause of bacteremia in children.

Methods

A total of 128 S. Typhi isolates from these studies in Nigeria were whole-genome sequenced, and the resulting data was used to place these Nigerian isolates into a worldwide context based on their phylogeny and carriage of molecular determinants of antibiotic resistance.

Results

Several distinct S. Typhi genotypes were identified in Nigeria that were related to other clusters of S. Typhi isolates from north, west and central regions of Africa. The rapidly expanding S. Typhi clade 4.3.1 (H58) previously associated with multiple antimicrobial resistances in Asia and in east, central and southern Africa, was not detected in this study. However, antimicrobial resistance was common amongst the Nigerian isolates and was associated with several plasmids, including the IncHI1 plasmid commonly associated with S. Typhi.

Conclusions

These data indicate that typhoid in Nigeria was established through multiple independent introductions into the country, with evidence of regional spread. MDR typhoid appears to be evolving independently of the haplotype H58 found in other typhoid endemic countries. This study highlights an urgent need for routine surveillance to monitor the epidemiology of typhoid and evolution of antimicrobial resistance within the bacterial population as a means to facilitate public health interventions to reduce the substantial morbidity and mortality of typhoid.

Typhoid fever, a serious bloodstream infection caused by the bacterium Salmonella Typhi, is a major cause of disease and death around the world. There have been limited data on the epidemiology of typhoid in many countries in sub-Saharan African, including Nigeria. Recent evidence, however, showed that typhoid was an important cause of bacteraemia in children residing in two regions of Nigeria. Here, we analyzed the whole genome sequences of 128 S. Typhi isolates from two studies in order to elucidate the population structure and characterize the genetic components of antimicrobial resistance. We found that the multiple S. Typhi genotypes identified were closely related to other S. Typhi from neighboring regions of Africa and that multidrug resistance (MDR) was common among these isolates, and in many cases was associated with the IncHI1 plasmid known to cause MDR typhoid. These results provide evidence that typhoid was established in Nigeria as a result of several independent introductions into the country and that there has been extensive exchange of S. Typhi in and around the region of West Africa. This study emphasizes the importance of surveillance to improve our understanding of the epidemiology of typhoid, which is needed to underpin public health measures to reduce the spread of disease and facilitate patient management.

Salmonella Bacteremia Among Children in Central and Northwest Nigeria, 2008-2015

BACKGROUND

Etiologic agents of childhood bacteremia remain poorly defined in Nigeria. The absence of such data promotes indiscriminate use of antibiotics and delays implementation of appropriate preventive strategies.

METHODS

We established diagnostic laboratories for bacteremia surveillance at regional sites in central and northwest Nigeria. Acutely ill children aged <5 years with clinically suspected bacteremia were evaluated at rural and urban clinical facilities in the Federal Capital Territory, central region and in Kano, northwest Nigeria. Blood was cultured using the automated Bactec incubator system.

RESULTS

Between September 2008 and April 2015, we screened 10,133 children. Clinically significant bacteremia was detected in 609 of 4051 (15%) in the northwest and 457 of 6082 (7.5%) in the central region. Across both regions, Salmonella species account for 24%-59.8% of bacteremias and are the commonest cause of childhood bacteremia, with a predominance of Salmonella enterica serovar Typhi. The prevalence of resistance to ampicillin, chloramphenicol, and cotrimoxazole was 38.11%, with regional differences in susceptibility to different antibiotics but high prevalence of resistance to readily available oral antibiotics.

CONCLUSIONS

Salmonella Typhi is the leading cause of childhood bacteremia in central Nigeria. Expanded surveillance is planned to define the dynamics of transmission. The high prevalence of multidrug-resistant strains calls for improvement in environmental sanitation in the long term and vaccination in the short term.

Malariometric Indices among Nigerian Children in a Rural Setting

Malaria contributes to high childhood morbidity and mortality in Nigeria. To determine its endemicity in a rural farming community in the south-south of Nigeria, the following malariometric indices, namely, malaria parasitaemia, spleen rates, and anaemia were evaluated in children aged 2-10 years. This was a descriptive cross-sectional survey among school-age children residing in a rubber plantation settlement. The children were selected from six primary schools using a multistaged stratified cluster sampling technique. They were all examined for pallor, enlarged spleen, or liver among other clinical parameters and had blood films for malaria parasites. Of the 461 children recruited, 329 (71.4%) had malaria parasites. The prevalence of malaria parasitaemia was slightly higher in the under fives than that of those ≥5 years, 76.2% and 70.3%, respectively. Splenic enlargement was present in 133 children (28.9%). The overall prevalence of anaemia was 35.7%. Anaemia was more common in the under-fives (48.8%) than in those ≥5 years (32.8%). The odds of anaemia in the under fives were significantly higher than the odds of those ≥5 years (OR = 1.95 [1.19-3.18]). Malaria is highly endemic in this farming community and calls for intensification of control interventions in the area with special attention to school-age children.