Modelling the Contributions of Malaria, HIV, Malnutrition and Rainfall to the Decline in Paediatric Invasive Non-typhoidal Salmonella Disease in Malawi

Introduction Nontyphoidal Salmonellae (NTS) are responsible for a huge burden of bloodstream infection in Sub-Saharan African children. Recent reports of a decline in invasive NTS (iNTS) disease from Kenya and The Gambia have emphasised an association with malaria control. Following a similar decline in iNTS disease in Malawi, we have used 9 years of continuous longitudinal data to model the interrelationships between iNTS disease, malaria, HIV and malnutrition. Methods Trends in monthly numbers of childhood iNTS disease presenting at Queen’s Hospital, Blantyre, Malawi from 2002 to 2010 were reviewed in the context of longitudinal monthly data describing malaria slide-positivity among paediatric febrile admissions, paediatric HIV prevalence, nutritional rehabilitation unit admissions and monthly rainfall over the same 9 years, using structural equation models (SEM). Results Analysis of 3,105 iNTS episodes identified from 49,093 blood cultures, showed an 11.8% annual decline in iNTS (p < 0.001). SEM analysis produced a stable model with good fit, revealing direct and statistically significant seasonal effects of malaria and malnutrition on the prevalence of iNTS disease. When these data were smoothed to eliminate seasonal cyclic changes, these associations remained strong and there were additional significant effects of HIV prevalence. Conclusions These data suggest that the overall decline in iNTS disease observed in Malawi is attributable to multiple public health interventions leading to reductions in malaria, HIV and acute malnutrition. Understanding the impacts of public health programmes on iNTS disease is essential to plan and evaluate interventions

Domestic river water use and risk of typhoid fever: results from a case-control study in Blantyre, Malawi.

BACKGROUND Typhoid fever remains a major cause of morbidity and mortality in low and middle-income settings. In the last 10 years, several reports have described the re-emergence of typhoid fever in southern and eastern Africa, associated with multidrug-resistant H58 Salmonella Typhi. Here, we identify risk factors for pediatric typhoid fever in a large epidemic in Blantyre, Malawi. METHODS A case-control study was conducted between April 2015 and November 2016. Cases were recruited at a large teaching hospital, while controls were recruited from the community, matched by residential ward. Stepwise variable selection and likelihood ratio testing were used to select candidate risk factors for a final logistic regression model. RESULTS Use of river water for cooking and cleaning was highly associated with risk of typhoid fever (OR 4.6 [CI: 1.6-12.5]). Additional risk factors included protective effects of soap in the household (OR 0.6 [CI: 0.4-0.98]) and more than one water sources used in the previous 3 weeks (OR 3.2 [CI: 1.6-6.2]). Attendance at school or other daycare was also identified as a risk factor (OR 2.7 [CI: 1.4-5.3]) and was associated with the highest attributable risk (51.3%). CONCLUSIONS These results highlight diverse risk factors for typhoid fever in Malawi, with implications for control in addition to the provision of safe drinking water. There is an urgent need to improve our understanding of transmission pathways of typhoid fever, both to develop tools for detecting S. Typhi in the environment, and inform water, sanitation, and hygiene interventions

An investigation into clinical, epidemiological and genomic changes in epidemic Salmonella blood stream infection in Malawi

Bloodstream infection (BSI) caused by nontyphoidal serotypes of Salmonella is one of the most important causes of morbidity and mortality in sub-Saharan Africa (SSA). Invasive nontyphoidal Salmonella disease (iNTS) is especially associated with HIV in adults and HIV, malaria and malnutrition in children in this setting. HIV-infected subjects are at particular risk of recurrent disease, both from recrudescence from a sanctuary site and re-infection. Whole- genome sequencing has revealed a novel sequence type (ST) of S. Typhimurium, ST313, is particularly associated with iNTS in SSA and that ST313 display the genomic signature of differential host adaptation. Little is known about African strains of S. Enteritidis. The Malawi Liverpool Wellcome Trust Clinical Research Programme (MLW) has conducted BSI surveillance in adult and paediatric medical patients in Blantyre, Malawi since 1998, enabling long term trends in iNTS to be described. Paediatric iNTS disease has been placed in the context of malaria, malnutrition and seasonality using structural equation modelling. An observational cohort was recruited to describe changes in adult BSI cases following the roll-out of ART in Blantyre. A longitudinal cohort study with enhanced microbiological surveillance was undertaken to investigate the site of persistence of NTS in HIV infected adults and the effect of recurrence upon the emergence of antimicrobial resistance. Lastly whole-genome sequencing was undertaken to compare invasive, African strains of S. Enteritidis with a reference isolate and to construct a global phylogeny of this serotype. There have been three epidemics of invasive Salmonella disease in Blantyre, all of which were preceded by the emergence of a multidrug resistant (MDR) strain. These were caused initially by S. Enteritidis which was then followed by S. Typhimurium, but most recently an epidemic of MDR S. Typhi has started. NTS has declined from epidemic levels, but remains an important cause of BSI in Blantyre and has been demonstrated to acquire cephalosporin iv and fluoroquinolone resistance just once through an IncHI2 plasmid. The decline in paediatric malaria is complex and multi-factorial. It cannot be attributed solely to malaria control interventions as has been the case in other settings. All causes of BSI are falling in adults and this is likely to be attributable in part to the hugely successful HIV treatment programme in Blantyre. The rapid initiation of ART appears to rapidly confer protection against recurrence of iNTS and even though more adult patients are surviving into convalescence, in this cohort, no further emergence of extended resistance was seen. Just as there is a distinct African clade of S. Typhimurium, a distinct clade of S. Enteritidis has emerged in SSA, which also possess the genomic signature of differential host adaptation, a novel prophage repertoire and a novel, MDR plasmid. In Blantyre, iNTS disease has declined from its epidemic peaks, but remains an important cause of BSI. The epidemiology of iNTS is more complex in Blantyre than other settings, but it seems likely that improved in-patient care and measures to control the HIV-pandemic impact on survival and recurrence. Two clades of NTS have emerged from host promiscuous serotypes, both of which have genomic degradation in genes governing potential host range and there is a critical need to understand the environmental niches and transmission pathways of these differentially adapted, invasive clades

Aetiology and outcomes of sepsis in adults in sub-Saharan Africa: a systematic review and meta-analysis

Background Aetiology and outcomes of sepsis in sub-Saharan Africa (sSA) are poorly described; we performed a systematic review and meta-analysis to summarise the available data. Methods Systematic searches of PubMed and Scopus were undertaken to identify prospective studies recruiting adults (> 13 years) with community-acquired sepsis in sSA post-2000. Random effects meta-analysis of in-hospital and 30-day mortality was undertaken and available aetiology data also summarised by random effects meta-analysis. Results Fifteen studies of 2800 participants were identified. Inclusion criteria were heterogeneous. The majority of patients were HIV-infected, and Mycobacterium tuberculosis was the most common cause of blood stream infection where sought. Pooled in-hospital mortality for Sepsis-2-defined sepsis and severe sepsis was 19% (95% CI 12–29%) and 39% (95% CI 30–47%) respectively, and sepsis mortality was associated with the proportion of HIV-infected participants. Mortality and morbidity data beyond 30 days were absent. Conclusions Sepsis in sSA is dominated by HIV and tuberculosis, with poor outcomes. Optimal antimicrobial strategies, including the role of tuberculosis treatment, are unclear. Long-term outcome data are lacking. Standardised sepsis diagnostic criteria that are easily applied in low-resource settings are needed to establish an evidence base for sepsis management in sSA

Cost-effectiveness of using environmental surveillance to target the roll-out typhoid conjugate vaccine

Typhoid conjugate vaccine (TCV) has been shown to be costeffective in some settings, but to make the most of limited healthcare funds, the WHO recommends that decisions about when and where to introduce TCV should be based on local evidence of transmission. Further, Gavi, The Vaccine Alliance, recommends that countries request TCV funding based on epidemiological data from within-country. Since few countries have reliable case reporting, we considered environmental surveillance as a decision-support tool for vaccine introduction choices. Environmental surveillance methods are still in development and this analysis assesses its potential as a decision support tool. We combined a disease transmission simulation model with an economic model, to quantify the value of surveillance. The disease transmission model is fit to historical case reporting from Blantyre, Malawi. The economic model takes a social perspective and incorporates the cost of environmental surveillance, vaccination, and both direct and indirect cost of care for acute typhoid cases. We find that the use of time-limited environmental surveillance to differentiate low- from high-endemicity areas is low cost relative to potential savings, especially if it is paired with a locally targeted vaccination campaign. These findings are robust to the uncertainty of cost model parameters and underlying endemicity

Development of a protocol for assessing the role of WASH in AMR distribution in the environment

Resistance in Malawi and Uganda (DRUM) consortium to measure the role of WASH in the transmission and control of AMR Abstract In Low and Middle Income countries (LMICs), there is a high incidence of severe bacterial infection, a critically inadequate health system infrastructure to diagnose and treat bacterial infections and widespread and uncontrolled availability of antimicrobials. This situation causes both a huge burden of morbidity and mortality, and is increasing selective pressure for the emergence of antimicrobial resistance (AMR) in pathogens. As LMICs will be the last to benefit from new classes of antimicrobials it is therefore urgent to undertake research addressing AMR in LMICs that aims to identify drivers and interrupt transmission of AMR determinants responsible. Exposures associated with WASH are integral to enteric bacteria and AMR transmission. AMR elements have been found in water, faeces and wastewater in LMICs, and this is compounded by a lack of faecal management (e.g. open defaecation, lack of access to faecal sludge management) and multiple uses of water (e.g. washing, irrigation, animal management and drinking). These factors contribute to community borne AMR transmission, and must be considered across multiple exposure pathways within the community. Focused in urban, peri-urban and rural settings in Malawi and Uganda, the Drivers of Antimicrobial Resistance in Uganda and Malawi (DRUM) consortium is an interdisciplinary programme funded by the Medical Research Council (2018 – 2021). The study aims to address three key questions (1) What are the drivers of ESBL E. coli and ESBL Klebsiella pneumoniae transmission in Uganda and Malawi?; (2) What are the critical points at which efforts to interrupt human AMR acquisition are likely to have the greatest impact?; and (3) Which strategies are likely to be most affordable and feasible to societies and how far is this specific to context? The research will develop agent-based models to enable us to predict how these transmission pathways can be interrupted. Data will be collated on a range of issues including: antibiotic use; antibiotic availability; illness; household demographics; and environmental contamination using both qualitative and quantitative methods. Key to this model will be the under researched area of AMR and WASH. This will develop a clear understanding of water, sanitation and hygiene (WASH) infrastructure and practices both domestically and institutionally [transect walks n=8; observations and checklists at household n=255; institutions n=50], identify the underlying influences on current practices [in depth interviews n=75; key informant interviews n=50; behavioral determinant questionnaires n=500; focus group discussions n=25] and identify drivers which may be amenable to change. These methods will be described in detail. Data will be collected with extensive environmental sampling to identify the transmission routes, support the design of the model and inform interventions. Existing national and international policies in the WASH sector do not currently consider AMR, and the production of evidence in this area is key to supporting and driving policy integration and uptake

rPinecone : Define sub-lineages of a clonal expansion via a phylogenetic tree

The ability to distinguish different circulating pathogen clones from each other is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low-variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this software was demonstrated using both simulated outbreaks and real genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.Peer reviewe

Gut mucosal colonisation with extended-spectrum beta-lactamase producing Enterobacteriaceae in sub-Saharan Africa: a systematic review and meta-analysis.

Background: Extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) threaten human health; and, in areas of sub-Saharan Africa (sSA) where carbapenems are not available, may render ESBL-E infections untreatable. Gut mucosal colonisation probably occurs before infection, making prevention of colonisation an attractive target for intervention, but the epidemiology of ESBL-E in sSA is poorly described. Objectives: Describe ESBL-E colonisation prevalence in sSA and risk factors associated with colonisation. Methods: Studies included were prospective cross-sectional or cohort studies reporting gut mucosal ESBL-E colonisation in any population in sSA. We searched PubMed and Scopus on 18 December 2018. We summarise the range of prevalence across sites and tabulated risk factors for colonisation. The protocol was registered (Prospero ID CRD42019123559). Results: From 2975 abstracts we identified 32 studies including a total of 8619 participants from a range of countries and settings. Six studies were longitudinal; no longitudinal studies followed patients beyond hospital discharge.  Prevalence varied between 5 and 84% with a median of 31%, with a relationship to setting: pooled ESBL-E colonisation in community studies was 18% (95% CI 12 to 28, 12 studies); in studies recruiting people at admission to hospital colonisation was 32% (95% CI 24 to 41% 8 studies); and for inpatients, colonisation was 55% (95% CI 49 to 60%, 7 studies). Antimicrobial use was associated with increased risk of ESBL-E colonisation, and protected water sources or water treatment by boiling may reduce risk. Conclusions: ESBL-E colonisation is common in sSA, but how people become carriers and why is not well understood. To inform the design of interventions to interrupt transmission in this setting requires longitudinal, community studies