Papers by Tonney Nyirenda
Elsevier eBooks, 2020
Nontyphoidal Salmonella (NTS) typically causes self-limiting enterocolitis in high-income setting... more Nontyphoidal Salmonella (NTS) typically causes self-limiting enterocolitis in high-income settings. In sub-Saharan Africa (SSA), however, NTS is a major cause of bloodstream infections, termed invasive nontyphoidal Salmonella (iNTS) disease, causing an estimated 1.9 million cases and 388,000 deaths annually. In SSA, specific clades of Salmonella Typhimurium and Salmonella Enteritidis associated with genomic degradation and multi-drug resistance have emerged. iNTS disease disproportionately affects adults with advanced HIV infection and young children with immature immunity, HIV, and malaria. Children in SSA bear two-thirds of the burden of disease. The non-specific nature of iNTS disease makes it difficult to differentiate from other causes of non-focal febrile illness, and the widespread emergence of multi-drug resistance and emerging cephalosporin resistance presents increasing treatment challenges. iNTS disease causes a large burden of morbidity and mortality in SSA, and there is much that is still unknown about environmental and host reservoirs and transmission of the pathogen and about optimal therapy for this condition. iNTS is also a problem in other resource-limited areas among individuals with HIV, malaria, and compromised or immature immune systems, although SSA accounts for the largest global burden. Vaccine acceleration is a high priority
BioTech
Nontyphoidal Salmonella (NTS) is a leading cause of morbidity and mortality caused by enteric pat... more Nontyphoidal Salmonella (NTS) is a leading cause of morbidity and mortality caused by enteric pathogens worldwide in both children and adults, and vaccines are not yet available. The measurement of antigen-specific antibodies in the sera of vaccinated or convalescent individuals is crucial to understand the incidence of disease and the immunogenicity of vaccine candidates. A solid and standardized assay used to determine the level of specific anti-antigens IgG is therefore of paramount importance. In this work, we presented the characterization of a customized enzyme-linked immunosorbent assay (ELISA) with continuous readouts and a standardized definition of EU/mL. We assessed various performance parameters: standard curve accuracy, dilutional linearity, intermediate precision, specificity, limits of blanks, and quantification. The simplicity of the assay, its high sensitivity and specificity coupled with its low cost and the use of basic consumables and instruments without the need...
PLOS Global Public Health
Economic consequences of COVID-19 illness and healthcare use for households in low income countri... more Economic consequences of COVID-19 illness and healthcare use for households in low income countries are not well known. We estimated costs associated with COVID-19 care-seeking and treatment from a household perspective and assessed determinants of treatment costs. A cross-sectional household survey was conducted between December 2020 and November 2021 in urban and peri-urban areas of Blantyre district. Adults (age ≥18 years) with confirmed COVID-19 were asked to report the symptoms they experienced or prompted them to seek COVID-19 tests as well as healthcare seeking behaviors preceding and following COVID-19 diagnosis. For individuals who sought healthcare, information on out-of-pocket expenditures incurred while seeking and receiving care including on transport, food etc. by both the patients and their guardians was collected. Finally, data on time use seeking, receiving care and during convalesces was recorded. Multivariate Generalized Linear Models were used to evaluate associa...
Open Forum Infectious Diseases
Nontyphoidal Salmonella are a leading cause of community-onset bacteremia and other serious infec... more Nontyphoidal Salmonella are a leading cause of community-onset bacteremia and other serious infections in sub-Saharan African countries where large studies indicate that they are an uncommon cause of moderate-to-severe diarrhea. Approximately 535 000 nontyphoidal Salmonella invasive disease illnesses and 77 500 deaths were estimated to occur in 2017; 422 000 (78.9%) illnesses and 66 500 (85.9%) deaths in countries in sub-Saharan Africa. Lineages of Salmonella enterica serovar Typhimurium sequence type (ST) 313 and lineages of Salmonella enterica serovar Enteritidis ST11 dominate as causes of invasive disease. A major reservoir for these specific strains outside of humans has not been identified to date. Human fecal shedding of such strains is common in areas where nontyphoidal Salmonella invasive disease incidence is high. The case-fatality ratio of nontyphoidal Salmonella invasive disease is approximately 15%. Early diagnosis and treatment are needed to avert fatal outcomes. Antimi...
The Journal of Infectious Diseases, 2014
Background. Salmonella Typhimurium (STm) remain a prominent cause of bacteremia in sub-Saharan Af... more Background. Salmonella Typhimurium (STm) remain a prominent cause of bacteremia in sub-Saharan Africa. Complement-fixing antibodies to STm develop by 2 years of age. We hypothesized that STm-specific CD4 + T cells develop alongside this process. Methods. Eighty healthy Malawian children aged 0-60 months were recruited. STm-specific CD4 + T cells producing interferon γ, tumor necrosis factor α, and interleukin 2 were quantified using intracellular cytokine staining. Antibodies to STm were measured by serum bactericidal activity (SBA) assay, and anti-STm immunoglobulin G antibodies by enzyme-linked immunosorbent assay. Results. Between 2006 and 2011, STm bacteremias were detected in 449 children <5 years old. STm-specific CD4 + T cells were acquired in infancy, peaked at 14 months, and then declined. STm-specific SBA was detectable in newborns, declined in the first 8 months, and then increased to a peak at age 35 months. Acquisition of SBA correlated with acquisition of anti-STm-lipopolysaccharide (LPS) immunoglobulin G (r = 0.329 [95% confidence interval, .552-.062]; P = .01) but not anti-STm-outer membrane protein or anti-STm-flagellar protein (FliC). Conclusions. Acquisition of STm-specific CD4 + T cells in early childhood is consistent with early exposure to STm or cross-reactive protein antigens priming this T-cell development. STm-specific CD4 + T cells seem insufficient to protect against invasive nontyphoidal Salmonella disease, but sequential acquisition of SBA to STm LPS is associated with a decline in its incidence.
The COVID-19 pandemic continues to impact health systems globally and robust surveillance is crit... more The COVID-19 pandemic continues to impact health systems globally and robust surveillance is critical for pandemic control, however not all countries can sustain community surveillance programs. Wastewater surveillance has proven valuable in high-income settings, but little is known about how river and informal sewage in low-income countries can be used for environmental surveillance of SARS-CoV-2. In Malawi, a country with limited community-based COVID-19 testing capacity, we explored the utility of rivers and wastewater for SARS-CoV-2 surveillance. From May 2020 – January 2022, we collected water from up to 112 river or informal sewage sites/month, detecting SARS-CoV-2 in 8.3% of samples. Peak SARS-CoV-2 detection in water samples predated peaks in clinical cases. Sequencing of water samples identified the Beta, Delta, and Omicron variants, with Delta and Omicron detected well in advance of detection in patients. Our work highlights wastewater can be used for detecting emerging wa...
Methods and Protocols
Salmonella Typhimurium and Salmonella Enteritidis are leading causative agents of invasive nontyp... more Salmonella Typhimurium and Salmonella Enteritidis are leading causative agents of invasive nontyphoidal Salmonella (iNTS) disease, which represents one of the major causes of death and morbidity in sub-Saharan Africa, still partially underestimated. Large sero-epidemiological studies are necessary to unravel the burden of disease and guide the introduction of vaccines that are not yet available. Even if no correlate of protection has been determined so far for iNTS, the evaluation of complement-mediated functionality of antibodies generated towards natural infection or elicited upon vaccination may represent a big step towards this achievement. Here we present the setup and the intra-laboratory characterization in terms of repeatability, intermediate precision, linearity, and specificity of a high-throughput luminescence-based serum bactericidal assay (L-SBA). This method could be useful to perform sero-epidemiological studies across iNTS endemic countries and for evaluation of anti...
Frontiers in Immunology
People Living with HIV (PLHIV) are at an increased risk of pneumococcal pneumonia than HIV-uninfe... more People Living with HIV (PLHIV) are at an increased risk of pneumococcal pneumonia than HIV-uninfected adults, but the reasons for this are still not well understood. We investigated whether alveolar macrophages (AM) mediated control of pneumococcal infection is impaired in PLHIV compared to HIV-uninfected adults. We assessed anti-bactericidal activity against Streptococcus pneumoniae of primary human AM obtained from PLHIV and HIV-uninfected adults. We found that pneumococcus survived intracellularly in AMs at least 24 hours post ex vivo infection, and this was more frequent in PLHIV than HIV-uninfected adults. Corroborating these findings, in vivo evidence showed that PLHIV had a higher propensity for harboring S. pneumoniae within their AMs than HIV-uninfected adults. Moreover, bacterial intracellular survival in AMs was associated with extracellular propagation of pneumococcal infection. Our data suggest that failure of AMs to eliminate S. pneumoniae intracellularly could contrib...
Background To retain the spread of SARS-CoV-2, fast, sensitive and cost-effective testing is esse... more Background To retain the spread of SARS-CoV-2, fast, sensitive and cost-effective testing is essential, particularly in resource limited settings (RLS). Current standard nucleic acid-based RT-PCR assays, although highly sensitive and specific, require transportation of samples to specialised laboratories, trained staff and expensive reagents. The latter are often not readily available in low- and middle-income countries and this may significantly impact on the successful disease management in these settings. Various studies have suggested a SARS-CoV-2 loop mediated isothermal amplification (LAMP) assay as an alternative method to RT-PCR. Methods Four previously published primer pairs were used for detection of SARS-CoV-2 in the LAMP assay. To determine optimal conditions, different temperatures, sample input and incubation times were tested. Ninety-two extracted RNA samples from St. George's Hospital, London, 10 non-extracted nasopharyngeal swab samples from Great Ormond Street ...
This is data from multiple diagnostic tests (4 qPCR assays, 1 stool culture) for Salmonella infec... more This is data from multiple diagnostic tests (4 qPCR assays, 1 stool culture) for Salmonella infection as well as JAGS / R code to analyse the data. Each test returns a positive / negative result. The software implements a latent Markov model.<br>Data provided under a CC BY 4.0 license, software under an MIT license.<br>Data files used by the uploaded software code:* salexpoLIMSDataSetComplete.csv* TAC Results_4Marc TAC TTR TAC InvA Ct For Correlation.csv* TTR & InvA master file Ct for correlation.csv<br>* TTRInvASensitivity20170724_corrected.csv<br><br>Raw data:* TAC Results_TAC-TTR_TAC-InvA_I_Ct ValuesTAC Results_TAC-TTR_TAC-InvA_IC_Ct-values.csv* Salmonella_Detection_Stool_TTR_InvA_raw_data.xlsx<br>
BackgroundInvasiveSalmonellainfections cause significant morbidity and mortality in Sub-Saharan A... more BackgroundInvasiveSalmonellainfections cause significant morbidity and mortality in Sub-Saharan Africa. However, the routes of transmission are uncertain. We conducted a case-control study of index-case and geographically-matched control households in Blantyre, Malawi, samplingSalmonellaisolates from index cases, healthy people, animals, and the household environment.MethodologySixty index cases of human invasiveSalmonellainfection were recruited (March 2015-Oct 2016). Twenty-eight invasive Non-TyphoidalSalmonella(iNTS) disease and 32 typhoid patients consented to household sampling. Each index-case household was geographically matched to a control household. Extensive microbiological sampling included stool sampling from healthy household members, stool or rectal swabs from household-associated animals and boot-sock sampling of the household environment.Findings1203 samples from 120 households, yielded 43 non-TyphoidalSalmonella(NTS) isolates from 25 households (overall sample posi...
PLOS ONE, 2021
Efficient and effective viral detection methodologies are a critical piece in the global response... more Efficient and effective viral detection methodologies are a critical piece in the global response to COVID-19, with PCR-based nasopharyngeal and oropharyngeal swab testing serving as the current gold standard. With over 100 million confirmed cases globally, the supply chains supporting these PCR testing efforts are under a tremendous amount of stress, driving the need for innovative and accurate diagnostic solutions. Herein, the utility of a direct-to-PCR method of SARS-CoV-2 detection grounded in mechanical homogenization is examined for reducing resources needed for testing while maintaining a comparable sensitivity to the current gold standard workflow of nasopharyngeal and oropharyngeal swab testing. In a head-to-head comparison of 30 patient samples, this initial clinical validation study of the proposed homogenization-based workflow demonstrated significant agreeability with the current extraction-based method utilized while cutting the total resources needed in half.
Background: Salmonella bacteraemia is an important public health problem in children from sub Sah... more Background: Salmonella bacteraemia is an important public health problem in children from sub Saharan Africa (SSA). Understanding what constitutes natural acquired immunity to Salmonella is crucial for the development of Salmonella vaccine. It was hypothesized that natural Salmonella exposure within the GIT and peripheral blood induces the generation of specific-antibodies and T cells and these might provide protection to subsequent Salmonella infection. Methods: Natural acquisition of antibody and T cell immunity to Salmonella was investigated in healthy and Salmonella infected Malawian children. Acquisition of typhoid vaccine induced T cell immunity in healthy adults from the United Kingdom (UK) was investigated to model natural immunizing events occurring within the gut associated lymphoid tissues (GALTs) following Salmonella infection. Acquisition of immunity was examined using immunological tools including the intra-cellular cytokine staining assay (ICS), serum bactericidal act...
Wellcome Open Research, 2020
Background: The relationship between asymptomatic Salmonella exposure within the gastrointestinal... more Background: The relationship between asymptomatic Salmonella exposure within the gastrointestinal tract and Salmonella bacteraemia is poorly understood, in part due to the low sensitivity of stool culture, and the lack of validated molecular diagnostic tests for the detection of Salmonella in stool. The study aimed to determine a reliable molecular diagnostic test for Salmonella in stool specimens. Methods: We optimized an in-house monoplex real time polymerase chain reaction (PCR) for the detection of Salmonella TTR and InvA genes in stool by including a selenite broth pre-culture step for Salmonella before DNA extraction, and validated their specificity against other local common pathogens. Then we assessed their performance against a well-validated multiplex PCR targeting the same TTR and InvA genes, and against stool culture using clinical stool specimens collected from a cohort of 50 asymptomatic healthy Malawian children that were sampled at 1-month intervals over a period of...
Journal of Blood Medicine, 2018
Aim: Although malaria and HIV infections independently affect the electrolyte and hematologic pro... more Aim: Although malaria and HIV infections independently affect the electrolyte and hematologic profiles, little is known of how these profiles are affected in individuals coinfected with malaria and HIV. We therefore conducted this study to investigate the electrolyte and hematologic profiles of Malawian adults presenting with either uncomplicated malaria (UM), severe malaria (SM), and those presenting with HIV and UM or HIV and SM. Methods: Study participants were recruited at Queen Elizabeth Central Hospital, and malaria infection was confirmed by rapid diagnostic test and malaria slides, and full blood count, HIV, and wet chemistries were analyzed. Results: Sodium, potassium, calcium, and chloride levels of all 4 study groups were similar to those of healthy controls. Both HIV-infected groups (UM and SM) had lower red blood cell counts and lower hemoglobin concentration than the reference range. Platelet counts were lower in both HIV-uninfected SM cases (64×10 9 /L) and in the HIV-infected SM cases (66×10 9 /L) compared to the reference range (115-290×10 9 /L). HIV-UM cases had higher proportion and absolute counts of neutrophils and white blood cell counts compared to the HIV+ UM cases. Conclusion: HIV infection did not affect the electrolyte profile of Malawian adults presenting with UM or SM but had an effect on red blood cells, Hb concentration, neutrophils, and platelet counts.
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Papers by Tonney Nyirenda