A5089110165- Pneumonia and Respiratory Infections
- Respiratory viral infections research
- Influenza Virus Research Studies
- Antibiotic Resistance in Bacteria
- Pneumocystis jirovecii pneumonia detection and treatment
- SARS-CoV-2 detection and testing
- Escherichia coli research studies
- Viral gastroenteritis research and epidemiology
- Genomics and Phylogenetic Studies
- Biosensors and Analytical Detection
- Bacterial Infections and Vaccines
- Otolaryngology and Infectious Diseases
- Pediatric health and respiratory diseases
- SARS-CoV-2 and COVID-19 Research
- Dental Research and COVID-19
- Streptococcal Infections and Treatments
- Gallbladder and Bile Duct Disorders
- Viral Infections and Immunology Research
- Vaccine Coverage and Hesitancy
- Animal Virus Infections Studies
- Gut microbiota and health
- Bacterial Identification and Susceptibility Testing
- Clostridium difficile and Clostridium perfringens research
- Probiotics and Fermented Foods
- Pediatric Hepatobiliary Diseases and Treatments
Centre for Inflammation Research
2018-2025
University of Edinburgh
2018-2025
Queen's Medical Centre
2020-2025
Yale University
2022-2024
Malawi-Liverpool-Wellcome Trust Clinical Research Programme
2017-2023
University of Liverpool
2017-2023
Yale New Haven Health System
2023
Queen Elizabeth Central Hospital
2017-2023
University of Malawi
2017-2021
The Queen's Medical Research Institute
2021
To combat the high burden of rotavirus gastroenteritis, multiple African countries have introduced vaccines into their childhood immunization programs. Malawi incorporated a G1P[8] vaccine (Rotarix) its schedule in 2012. Utilizing surveillance platform hospitalized gastroenteritis cases, we examined phylodynamics strains that circulated before (1998 to 2012) and after (2013 2014) introduction. Analysis whole genomes obtained through next-generation sequencing revealed all randomly selected...
Abstract We have developed an efficient and inexpensive pipeline for streamlining large-scale collection genome sequencing of bacterial isolates. Evaluation this method involved a worldwide research collaboration focused on the model organism Salmonella enterica , 10KSG consortium. Following optimization logistics that shipping isolates as thermolysates in ambient conditions, project assembled diverse 10,419 from low- middle-income countries. The genomes were sequenced using LITE library...
Efforts to treat Escherichia coli infections are increasingly being compromised by the rapid, global spread of antimicrobial resistance (AMR). Whilst AMR in E. has been extensively investigated resource-rich settings, sub-Saharan Africa molecular patterns not well described. In this study, we have begun explore population structure and determinants amongst isolates from Malawi.Ninety-four patients admitted Queen's Hospital, Malawi, were whole-genome sequenced. The selected on basis diversity...
Abstract Objectives ESBL-producing Klebsiella pneumoniae (KPN) pose a major threat to human health globally. We carried out WGS study understand the genetic background of KPN in Malawi and place them context other global isolates. Methods sequenced genomes 72 invasive carriage isolates collected from patients admitted Queen Elizabeth Central Hospital, Blantyre, Malawi. performed phylogenetic population structure analyses on these previously published Kenya (n = 66) outside sub-Saharan Africa...
Predicting individual vaccine responses remains a significant challenge due to the complexity and variability of immune processes. To address this gap, we developed immunaut , an open-source, data-driven framework implemented as R package specifically designed for all systems vaccinologists seeking analyze predict immunological outcomes across diverse vaccination settings. Leveraging one most comprehensive live attenuated influenza (LAIV) datasets date - 244 Gambian children enrolled in...
Pneumococcal infections cause a high death toll in Sub Saharan Africa (SSA) but the recently rolled out pneumococcal conjugate vaccines (PCV) will reduce disease burden. To better understand population impact of these vaccines, comprehensive analysis large collections isolates sampled prior to vaccination is required. Here we present genomic study invasive before implementation PCV13 Malawi.
Abstract Background Immunity to Streptococcus pyogenes in high burden settings is poorly understood. We explored S. nasopharyngeal colonization after intranasal live attenuated influenza vaccine (LAIV) among Gambian children aged 24–59 months, and resulting serological response 7 antigens. Methods A post hoc analysis was performed 320 randomized receive LAIV at baseline (LAIV group) or not (control). determined by quantitative polymerase chain reaction (qPCR) on swabs from (day 0), day 7,...
Abstract Hyper-virulent Streptococcus pneumoniae serotype 1 strains are endemic in Sub-Saharan Africa and frequently cause lethal meningitis outbreaks. It remains unknown whether genetic variation modulates tropism into cerebrospinal fluid to central nervous system (CNS) infections, particularly meningitis. Here, we address this question through a large-scale linear mixed model genome-wide association study of 909 African pneumococcal isolates collected from CNS non-CNS human samples. By...
While considerable attention was placed on SARS-CoV-2 testing and surveillance programs in the K-12 setting, younger age groups childcare centers were largely overlooked. Childcare facilities are vital to communities, allowing parents/guardians remain at work providing safe environments for both children staff. Therefore, early COVID-19 pandemic (October 2020), we established a PCR-based program facilities, staff with goal of collecting actionable public health data aiding communities...
Otitis media with effusion (OME) is a common inflammatory disease that primarily affects children. OME defined as chronic low-grade inflammation of the middle ear (ME), without any signs infection and persisting in ME for more than 3 months. The precise pathogenesis is, however, not fully understood. Here, we comprehensively characterized compared host immune responses (inflammatory cells mediators) overall microbial community composition (microbiota) present matched (MEE) samples, external...
A special-care neonatal unit from a large public hospital in Malawi was noted as having more frequent, difficult-to-treat infections, and suspected outbreak of multi-drug-resistant Klebsiella pneumoniae investigated using genomic characterisation. All K. bloodstream infections (BSIs) patients the ward (n=62), subset BSI isolates (n=38) other paediatric wards hospital, collected over 4 year period were studied. After whole genome sequencing, strain sequence types (STs), plasmid types,...
ABSTRACT Molecular methods have improved the sensitivity of detection pneumococcal carriage in saliva. However, they typically require sample culture enrichment and nucleic acid extraction prior to performing assay may limit scalability for extensive surveillance pneumococcus, particularly low-resource settings. We evaluated performance a DNA-extraction-free method pneumococcus developed streamlined qPCR-based protocol omitting DNA extraction. Using saliva samples collected from children...
Influenza and other respiratory viruses promote
Abstract Background Pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal diseases globally. genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden. Methods We undertook whole-genome sequencing (WGS) of 660 isolates collected through from healthy carriers 2 years 13-valent (PCV13) introduction and 1 year after rollout northern Malawi. investigated changes structure, within-lineage serotype...
Abstract Background Molecular methods have improved the sensitivity of detection pneumococcal carriage in saliva. However, they typically require sample culture-enrichment and nucleic acid extraction, prior to performing assay. These factors may limit scalability for extensive surveillance pneumococcus, particularly low-resource settings. In this study, we evaluated performance a DNA-extraction-free method pneumococcus Methods We developed streamlined qPCR-based protocol omitting DNA...
ABSTRACT A suspected outbreak of multi-drug resistant (MDR) Klebsiella pneumoniae in a Malawian neonatal unit was investigated using whole-genome sequencing. Strain-types, virulence and resistance genes K. isolated from patients the hospital over four-year period were identified. MDR ST340 clone implicated as likely cause.
Abstract Background While considerable attention was placed on SARS-CoV-2 testing and surveillance programs in the K-12 setting, younger age groups childcare centers were largely overlooked. Childcare facilities are vital to communities, allowing parents/guardians remain at work providing safe environments for both children staff. Therefore, early COVID-19 pandemic, we established a PCR-based program facilities, staff with goal of collecting actionable public health data aiding communities...
Increasing antimicrobial resistance and limited alternative treatments have led to fluoroquinolone-resistant Shigella strain inclusion on the WHO global priority pathogens list. In this study we characterized multiple isolates from Malawi with whole genome sequence analysis, identifying acquirable fluoroquinolone determinant qnrS1 .
Highlights•Pneumococcal-specific Th17 responses in HIV-infected adults are preserved.•The frequency of pneumococcal-specific cells is increased ART-treated adults.•Depletion unlikely the reason behind susceptibility to pneumonia adults.SummaryObjectiveWe explored if HIV infection associated with impaired T-Helper 17 against Streptococcus pneumoniae lung.MethodsWe recruited 30 HIV-uninfected healthy controls, 23 asymptomatic not on ART, and 40 ART (Median time 3.5yrs), whom we collected...
Background: Live attenuated influenza vaccine (LAIV) alters nasopharyngeal microbial community structures in adults. Additionally, LAIV immunogenicity varies across populations for reasons poorly understood, but may be linked to the microbiome. We investigated impact of on microbiota, and microbiota an open label randomised controlled trial Gambian children.Methods: conducted a phase IV clinically well children aged 24-59 months The Gambia (NCT02972957). Participants (n=330) were 2:1 receive...
Background: Influenza and other respiratory viruses promote Streptococcus pneumoniae proliferation in the upper tract. We investigated effect of intranasal live attenuated influenza vaccine (LAIV) on nasopharyngeal S. density Gambian children, to study LAIV-pneumococcal interactions for first time a low middle-income country (LMIC) with high pneumococcal carriage rates.Methods: In an open-label, randomised controlled trial (NCT02972957) The Gambia, 330 healthy children aged 24-59 months were...
Abstract Background Important questions remain about the role of older adults in driving transmission pneumococcus community. This is a critical question for understanding potential indirect effects using pneumococcal conjugate vaccines (PCVs) adults. For non-institutionalized individuals, most likely source adult-to-adult household. The goal this study was to characterize dynamics and risk factors acquisition Methods We designed longitudinal sample > 60 years age living same...