Cellular immune responses against Streptococcus pneumoniae in the human lung

Background Streptococcus pneumoniae is the leading cause of community-acquired pneumonia in all ages, with the greatest incidence occurring in children, the elderly and HIV-infected individuals. HIV-infected adults are at least 25-fold at risk of bacterial pneumonia compared to age-matched HIV-uninfected individuals, but the immunological mechanisms for this risk are still unclear. Alveolar macrophages (AMs) are the major sentinel phagocytic population found in the airway responsible for the early clearance and control of respiratory pathogens. I hypothesise that HIV infection is associated with impaired airway alveolar phagocyte killing function, leading to survival and propagation of pneumococci. Methods Three groups of participants aged between 18 to 60 years were recruited, consisting of asymptomatic HIV-uninfected adults, HIV-infected adults on shortterm or long-term antiretroviral therapy (ART) residing in Blantyre, Malawi. Lower airway samples (bronchoalveolar lavage fluid) were collected from the participants and used to investigate airway mediated defence immunity against S. pneumoniae in an ex vivo model. The airway cells were infected with pneumococci (serotype 3 strain) and the number of alveolar phagocytes associated with bacteria were measured and phenotyped using flow cytometry. Intracellular and extracellular bacterial killing was measured using quantitative culture in a gentamicin protection assay (GPA) and bacterial outgrowth assay, respectively. Confocal microscopy was used to visualise pneumococci within AMs following infection. Results Alveolar macrophages were the principal phagocytic cells associated with IgGopsonised pneumococcal-ST3 following ex vivo infection, irrespective of HIV status. AM from HIV-infected adults did not exhibit impaired binding and internalisation of IgG-opsonised pneumococcal-ST3, irrespective of ART duration. Furthermore, airway cell-mediated control of extracellular S. pneumoniae outgrowth during early infection was also not impaired in HIV-infected adults on ART. However, HIV-infected adults on ART demonstrated reduced AMs-mediated intracellular killing capacity of S. pneumoniae during the late killing phase (24-hours post infection) with pneumococci persisting in CD206+AMs. The presence of extracellular S. pneumoniae 24-hours post infection in a bacterial outgrowth assay was propagated by intracellular bacterial persistence. Conclusion In summary, the data from this thesis demonstrates that AMs from HIV-infected adults on ART have impaired late bacterial killing capacity, leading to intracellular bacterial persistence and propagation of extracellular pneumococcal outgrowth. Persistence of the pneumococci within CD206+AMs could serve as a reservoir for pneumococcal infection in the lung, potentially contributing to increased susceptibility to pneumococcal pneumonia in HIV-infected individuals

Inappropriate antibiotic use in Zimbabwe in the COVID-19 era : a perfect recipe for antimicrobial resistance

The global COVID-19 pandemic has resulted in an upsurge in antimicrobial use. The increase in use is multifactorial, and is particularly related to the empirical treatment of SARSCoV-2 and suspected coinfections with antimicrobials and the limited quality of diagnostics to differentiate viral and bacterial pneumonia. The lack of clear clinical guidelines across a wide range of settings, and the inadequacy of public health sectors in many countries, have contributed to this pattern. The increased use of antimicrobials has the potential to increase incidences of antimicrobial resistance, especially in low-resource countries such as Zimbabwe already grappling with multidrugresistant micro-organism strains. By adopting the antimicrobial stewardship principles of the correct prescription and optimised use of antimicrobials, as well as diagnostic stewardship, revamping regulatory oversight of antimicrobial surveillance may help limit the occurrence of antimicrobial resistance during this pandemic.http://www.mdpi.com/journal/antibioticsSchool of Health Systems and Public Health (SHSPH

Inappropriate Antibiotic Use in Zimbabwe in the COVID-19 Era: A Perfect Recipe for Antimicrobial Resistance

The global COVID-19 pandemic has resulted in an upsurge in antimicrobial use. The increase in use is multifactorial, and is particularly related to the empirical treatment of SARS-CoV-2 and suspected coinfections with antimicrobials and the limited quality of diagnostics to differentiate viral and bacterial pneumonia. The lack of clear clinical guidelines across a wide range of settings, and the inadequacy of public health sectors in many countries, have contributed to this pattern. The increased use of antimicrobials has the potential to increase incidences of antimicrobial resistance, especially in low-resource countries such as Zimbabwe already grappling with multidrug-resistant micro-organism strains. By adopting the antimicrobial stewardship principles of the correct prescription and optimised use of antimicrobials, as well as diagnostic stewardship, revamping regulatory oversight of antimicrobial surveillance may help limit the occurrence of antimicrobial resistance during this pandemic

Sepsis in cancer patients residing in Zimbabwe: Spectrum of bacterial and fungal aetiologies and their antimicrobial susceptibility patterns.

Background Cancer and sepsis comorbidity is a major public health problem in most parts of the world including Zimbabwe. The microbial aetiologies of sepsis and their antibiograms vary with time and locations. Knowledge on local microbial aetiologies of sepsis and their susceptibility patterns is critical in guiding empirical antimicrobial treatment choices. Methods This was a descriptive cross-sectional study which determined the microbial aetiologies of sepsis from blood cultures of paediatric and adult cancer patients obtained between July 2016 and June 2017. The TDR-X120 blood culture system and TDR 300B auto identification machine were used for incubation of blood culture bottles and identification plus antimicrobial susceptibility testing, respectively. Results A total of 142 participants were enrolled; 50 (35.2%) had positive blood cultures, with 56.0% Gram positive, 42.0% Gram-negative bacteria and 2.0% yeast isolated. Common species isolated included coagulase negative Staphylococcus spp. (CoNS) (22.0%), E. coli (16.0%), K. pneumoniae (14.0%), E. faecalis (14.0%) and S. aureus (8.0%). Gram-negative isolates exhibited high resistance to gentamicin (61.9%) and ceftriaxone (71.4%) which are the empiric antimicrobial agents used in our setting. Amikacin and meropenem showed 85.7 and 95.2% activity respectively against all Gram-negative isolates, whilst vancomycin and linezolid were effective against 96.2 and 100.0% of all Gram-positive isolates respectively. We isolated 10 (66.7%) extended spectrum β-lactamase (ESBL) amongst the E. coli and K. pneumoniae isolates. Ten (66.7%) of the Staphylococcus spp. were methicillin resistant. Conclusions CoNS, E. coli, K. pneumoniae, E. faecalis and S. aureus were the major microbial drivers of sepsis amongst cancer patients in Zimbabwe. Most isolates were found to be resistant to commonly used empirical antibiotics, with isolates exhibiting high levels of ESBL and methicillin resistance carriage. A nationwide survey on microbial aetiologies of sepsis and their susceptibility patterns would assist in the guidance of effective sepsis empiric antimicrobial treatment among patients with cancer

Fungal CNS Infections in Africa: The Neuroimmunology of Cryptococcal Meningitis

Cryptococcal meningitis (CM) is the leading cause of central nervous system (CNS) fungal infections in humans, with the majority of cases reported from the African continent. This is partly due to the high burden of HIV infection in the region and reduced access to standard-of-care including optimal sterilising antifungal drug treatments. As such, CM is responsible for 10-15% of all HIV-related mortality, with a large proportion being preventable. Immunity to the causative agent of CM, Cryptococcus neoformans, is only partially understood. IFNγ producing CD4+ T-cells are required for the activation of myeloid cells, especially macrophages, to enable fungal killing and clearance. However, macrophages may also act as a reservoir of the fungal yeast cells, shielding them from host immune detection thus promoting latent infection or persistent chronic inflammation. In this chapter, we review the epidemiology and pathogenesis of CNS fungal infections in Africa, with a major focus on CM, and the antifungal immune pathways operating to protect against C. neoformans infection. We also highlight the areas of research and policy that require prioritisation to help reduce the burden of CNS fungal diseases in Africa

Pneumococcal pneumonia and carriage in Africa before and after introduction of pneumococcal conjugate vaccines, 2000-2019:protocol for systematic review

INTRODUCTION:Africa harbours a high burden of pneumococcal disease, with associated high mortality rates. Despite 34 countries introducing the pneumococcal conjugate vaccine, which reduces the risk of pneumococcal carriage (a prerequisite for disease) of some of the most pathogenic pneumococcal serotypes, it remains uncertain whether they will achieve the sustained direct or indirect protection necessary to reduce pneumococcal carriage to levels sufficient to interrupt transmission and disease. We will therefore summarise the available data on the impact of the pneumococcal conjugate vaccine in reducing vaccine serotype carriage and pneumococcal pneumonia in Africa between 2000 and 2019. METHODS AND ANALYSIS:Using a predetermined search strategy, we will conduct a comprehensive search of PubMed, MEDLINE database, the Excerpta Medica Database, the ISI Web of Science (Science Citation Index), Scopus and the African Index Medicus to identify published studies reporting the prevalence of Streptococcus pneumoniae carriage (vaccine type and non-vaccine type), incidence rates of pneumococcal pneumonia and mortality among children, adults and HIV-infected (all-ages) pre-pneumococcal conjugate vaccine (PCV) and post-PCV introduction (published between 1st January 2000 and 31st December 2019) in African countries that have introduced PCVs (PCV7/PCV10/PCV13) in their routine national immunisation programme. The studies retained and data extracted will be assessed for bias using prevalidated tools and checklists. Heterogeneity across studies will be assessed using the χ2 test on Cochrane Q statistic. A random effect meta-analysis will be used to estimate the overall prevalence of pneumococcal carriage and incidence of pneumococcal pneumonia across studies with similar characteristics. Results will be reported in compliance with the Meta-Analysis Of Observational Studies in Epidemiology guidelines. The protocol has been prepared in accordance to the 2015 guidelines on Preferred Reporting Items for Systematic Reviews and Meta-Analyses. ETHICS AND DISSEMINATION:This systematic review will not require ethical approval as we will be using already published data. The final manuscript will be submitted for publication in a peer-reviewed journal and presented at conferences. PROSPERO REGISTRATION NUMBER:CRD42019130976

Influenza-like illness is associated with high pneumococcal carriage density in Malawian children.

Background High pneumococcal carriage density is a risk factor for invasive pneumococcal disease (IPD) and transmission, but factors that increase pneumococcal carriage density are still unclear. Methods We undertook a cross-sectional study to evaluate the microbial composition, cytokine levels and pneumococcal carriage densities in samples from children presenting with an influenza-like illness (ILI) and asymptomatic healthy controls (HC). Results The proportion of children harbouring viral organisms (Relative risk (RR) 1.4, p=0.0222) or ≥4 microbes at a time (RR 1.9, p<0.0001), was higher in ILI patients than HC. ILI patients had higher IL-8 levels in nasal aspirates than HC (median [IQR], 265.7 [0 – 452.3] vs. 0 [0 – 127.3] pg/ml; p = 0.0154). Having an ILI was associated with higher pneumococcal carriage densities compared to HC (RR 4.2, p<0.0001). Conclusion These findings suggest that children with an ILI have an increased propensity for high pneumococcal carriage density. This could in part contribute to increased susceptibility to IPD and transmission in the community

Implementation of Antibody Rapid Diagnostic Testing versus Real-Time Reverse Transcription-PCR Sample Pooling in the Screening of COVID-19: a Case of Different Testing Strategies in Africa

COVID-19 has wreaked havoc across the globe, although cases in Africa remain lower than 50 other regions but they are gradually on an upward trajectory. To date, COVID-19 cases have 51 been reported in 54 countries. However, due to limited SARS-COV-2 rRT-PCR testing 52 capacity and scarcity of testing reagents, it is probable that the total number of cases could 53 far exceed published statistics. In this viewpoint, using Ghana, Malawi, South Africa and 54 Zimbabwe as examples of countries that have implemented different testing strategies, we 55 argue that the implementation of sample pooling for rRT-PCR over antibody rapid diagnostic 56 testing could have a greater impact in assessing disease burden. Sample pooling offers huge 57 advantages compared to single test rRT-PCR, as it lowers experimental costs, personnel 58 time, reduces burnout and analytical run-times. Africa is already strained in terms of testing 59 resources for COVID-19, hence cheaper alternative ways need to be implemented to 60 conserve resources, maximise on mass testing and reduce transmission in the wider 61 population

Comparison of non-invasive methods of assessing liver fibrosis in combination ART-experienced Zimbabweans

Background: The prevalence of morbidity and mortality associated with liver disease among HIV-infected individuals on combination antiretroviral therapy (ART) is high. Early screening of liver disease is essential, as it provides an opportunity for successful treatment. Hence, there is a need for reliable, inexpensive and non-invasive early markers of hepatic damage. Objectives: Non-invasive algorithms are available for assessing the extent of liver fibrosis as markers of ongoing inflammatory damage. This study compared the use of the FibroTest, Fibrosis-4 (FIB-4) index, APRI test and AST:ALT ratio in assessing liver fibrosis in combination ART-experienced individuals. Methods: In a comparative cross-sectional study, 79 participants between the ages of 8 and 62 years were recruited. The performance of each fibrosis algorithm was determined using established cut-off scores for clinically significant liver fibrosis. Results: The prevalence of liver fibrosis as determined by the FibroTest, FIB-4 index, APRI test and AST: ALT ratio were 19.0%, 21.5%, 12.7% and 79.7%, respectively. For individual biomarkers, A-2M concentration (p < 0.001) and AST activity (p = 0.003) remained significantly elevated in participants with fibrosis than those without as defined by FibroTest and APRI test, respectively, after adjustments for multiple comparisons. Conclusion: Our data demonstrate a high prevalence of asymptomatic liver fibrosis among combination ART-experienced individuals in Zimbabwe, and this warrants adequate monitoring of liver fibrosis in individuals on ART. Discordance of fibrosis results among the algorithms and individual biomarkers and calls for further work in identifying optimal biomarkers for detection of asymptomatic fibrosis

Epidemiology and aetiologies of cryptococcal meningitis in Africa, 1950-2017: protocol for a systematic review.

IntroductionCryptococcal meningitis is a neglected disease and an AIDS-defining illness, responsible for 15% of all AIDS-related deaths globally. In 2014, the estimated number of incident cryptococcal meningitis cases was 223 100, with 73% of them occurring in Africa. Currently available data on the prevalence, incidence, aetiologies and mortality of cryptococcal meningitis across Africa are sparse and of limited quality. We propose to conduct the first systematic review to summarise the epidemiological data available on cryptococcal meningitis and its aetiological causes in Africa.Methods and analysisWe will search PubMed, MEDLINE, Excerpta Medica Database, ISI Web of Science, Africa Index Medicus, Cumulative Index to Nursing and Allied Health for studies on cryptococcal meningitis published between 1st January 1950 and 31st December 2017, involving adults and/or children residing in Africa. After study selection, full text paper acquisition and data extraction, we will use validated tools and checklists to assess the quality of reporting and risk of bias for each study. Heterogeneity across studies will be assessed using the χ2 test on Cochrane's Q statistic and a random effect meta-analysis will be used to estimate the overall prevalence, incidence density and mortality of cryptococcal meningitis across studies with similar characteristics. This protocol is prepared and presented in accordance with the 2015 Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols guidelines. Reporting of the results will be compliant with the Meta-Analysis Of Observational Studies in Epidemiology (MOOSE) guidelines.Ethics and disseminationThere is no requirement for ethical approval since we will be using data from published studies. The final report will be published in a peer-reviewed journal and further presented at conferences. This study is expected to provide useful contextual estimates needed to inform treatment policies on the African continent and assess the impact of diagnostic and prevention strategies on the burden of cryptococcal meningitis in the post antiretroviral therapy era.Prospero registration numberCRD42017081312