Molecular characterisation and immunological analysis of clinical and environmental isolates of Mycobacterium kansasii from South African gold mines

PhD, Faculty of Health Sciences, University of the WitwatersrandThe South African gold-mining workforce has an unusually high incidence of Mycobacterium kansasii disease, yet little is known about the possible sources of M. kansasii infection, genetic diversity and the basis for this organism’s pathogenicity. The purpose of this study was to investigate these issues in a gold-mining environment. Five M. kansasii isolates and 10 other potentially pathogenic mycobacteria were cultured mainly from showerhead biofilms. PCR-restriction analysis (PRA) of the hsp65 gene on 191 clinical and on the 5 environmental M. kansasii isolates revealed 160 subtype I (157 clinical and 3 environmental), 8 subtype II (clinical) and 6 subtype IV (5 clinical and 1 environmental) strains. Twenty-two isolates (21 clinical and 1 environmental) did not show the typical M. kansasii PRA patterns. After confirmation by DNA sequencing as belonging to the M. kansasii species, the results suggested that these isolates were probably new subtypes of M. kansasii. In contrast to the clonal population structure found amongst the subtype I isolates from studies in other countries, DNA fingerprinting of 114 subtype I clinical and environmental isolates showed genetic diversity amongst the isolates. One of the 2 environmental isolates showed 100% identity with a clinical isolate, suggesting that water distribution systems are the possible sources of M. kansasii infection for the miners. An investigation into the genetic differences between clinical (subtype I) and environmental (III, IV and V) isolates, using Hybridisation Monitored Differential Analysis (HMDA), identified 45 open reading frames (ORFs) encoding predominantly membrane-associated proteins that include six potential virulence factors, two family members of transcription regulators for drug and xenobiotic metabolism, three family members of multidrug efflux systems, a number of proteins associated with lipid and carbohydrate metabolism and transport, and a number of hypothetical proteins with unknown function. Immunological analysis of M. kansasii isolates, using the Lymphocyte Transformation and Cytometric Bead Array assays, showed that M. kansasii modulates immune responses through suppression of lymphocyte blastogenesis and by altering the expression of Th1/Th2/Th17 cytokines by human lymphocytes in vivo for its own survival. This study demonstrated for the first time that water distribution systems in South Africa are possible sources of M. kansasii infection, and showed that subtype I strains of M. kansasii from the study region display genetic diversity and have unique or divergent genes not found in other subtypes. It also demonstrated that immunosuppression is one of the pathogenic mechanisms employed by M. kansasii

Evidence of EBV infection in lymphomas diagnosed in Lusaka, Zambia

Introduction: Epstein-Barr virus (EBV) is a ubiquitous virus that infects more than 90% of the world's population, and is implicated in lymphoma pathogenesis. However, in Zambia during the diagnosis of these lymphomas, the association of the virus with the lymphomas is not established. Since most patients with lymphomas have poor prognosis, the identification of the virus within the lymphoma lesion will allow for more targeted therapy. The aim of this study was to provide evidence of the presence of the EBV in lymphomas diagnosed at the University Teaching Hospital (UTH) in Lusaka, Zambia.Methods: one hundred and fifty archival formalin-fixed paraffin embedded suspected lymphoma tissues stored over a 4-year period in the Histopathology Laboratory at the UTH in Lusaka, Zambia, were analysed. Histological methods were used to identify the lymphomas, and the virus was detected using Polymerase Chain Reaction (PCR). Subtyping of the virus was achieved through DNA sequencing of the EBNA-2 region of the viral genome. Chi square or fisher's exact test was used to evaluate the association between EBV status, type of lymphoma and gender.Results: the majority of the lymphomas identified were non-Hodgkin's lymphoma (NHL) (80%) followed by Hodgkin's lymphoma (HL) (20%). EBV was detected in 51.8% of the cases, 54.5% of which were associated with NHL cases, while 40.9% associated with HL cases. The predominant subtype of the virus in both types of lymphomas was subtype 1. One of the lymphoma cases harboured both subtype 1 and 2 of the virus.Conclusion: this study showed that EBV is closely associated with lymphomas. Therefore, providing evidence of the presence of the virus in lymphoma tissues will aid in targeted therapy. To our knowledge this is the first time such data has been generated in Zambia

Pigs as a potential source of emerging livestock-associated Staphylococcus aureus in Africa: a systematic review

Objective: To assess the emergence of livestock-associated Staphylococcus aureus including methicillin-resistant S. aureus (MRSA) in the pig and pork production systems in Africa for the past two decades. Methods: PubMed and African Journals OnLine were searched for relevant primary studies from 2000 to 2019 using standardized key words. In total, 19 eligible articles were included in this review. Results: The prevalence of S. aureus including MRSA ranged from 0% to 55% among live pigs and raw pork, and from 9.4% to 30.8% among pig farm and abattoir workers. Risk factors associated with S. aureus carriage among workers were: male gender, working in an abattoir, and medical-related occupation of a household member. S. aureus and MRSA from pigs and pork production systems in Africa are potentially pathogenic with diverse spa types and clonal complexes, with genes encoding antimicrobial resistance, heavy metal resistance, and virulence factors including secreted and enterotoxins, proteases and immune evasion cluster. The typical livestock-associated S. aureus CC398 and mecC genes were reported in two studies. Conclusion: Pigs are a potential source of the emerging livestock-associated S. aureus in Africa. Continued monitoring using a 'One Health' approach is recommended for effective infection prevention and control of these infections in Africa

Whole Genome Sequence Analysis Reveals Lower Diversity and Frequency of Acquired Antimicrobial Resistance (AMR) Genes in E. coli From Dairy Herds Compared With Human Isolates From the Same Region of Central Zambia

Antibiotic treatment of sick dairy cattle is critical for the sustainability of this production system which is vital for food security and societal prosperity in many low and middle-income countries. Given the increasingly high levels of antibiotic resistance worldwide and the challenge this presents for the treatment of bacterial infections, the rational use of antibiotics in humans and animals has been emphatically recommended in the spirit of a “One Health” approach. The aim of this study was to characterize antimicrobial resistance (AMR) genes and their frequencies from whole genome sequences of Escherichia coli isolated from both dairy cattle and human patients in central Zambia. Whole genome sequences of E. coli isolates from dairy cattle (n = 224) and from patients at a local hospital (n = 73) were compared for the presence of acquired AMR genes. In addition we analyzed the publicly available genomes of 317 human E. coli isolates from over the wider African continent. Both acquired antibiotic resistance genes and phylogroups were identified from de novo assemblies and SNP based phylogenetic analyses were used to visualize the distribution of resistance genes in E. coli isolates from the two hosts. Greater acquired AMR gene diversity was detected in human compared to bovine E. coli isolates across multiple classes of antibiotics with particular resistance genes for extended-spectrum beta lactamases (ESBL), quinolones, macrolides and fosfomycin only detected in E. coli genomes of human origin. The striking difference was that the Zambian or wider African human isolates were significantly more likely to possess multiple acquired AMR genes compared to the Zambian dairy cattle isolates. The median number of resistance genes in the Zambian cattle cohort was 0 (0–1 interquartile range), while in the Zambian human and wider African cohorts the medians and interquartile ranges were 6 (4–9) and 6 (0–8), respectively. The lower frequency and reduced diversity of acquired AMR genes in the dairy cattle isolates is concordant with relatively limited antibiotic use that we have documented in this region, especially among smallholder farmers. The relatively distinct resistant profiles in the two host populations also indicates limited sharing of strains or genes

HIV-positive demonstrate more salt sensitivity and nocturnal non-dipping blood pressure than HIV-negative individuals

Background: High dietary salt and a lack of reduced blood pressure (BP) at night (non-dipping) are risk factors for the development of hypertension which may result in end-organ damage and death. The effect of high dietary salt on BP in black people of sub-Saharan Africa living with HIV is not well established. The goal of this study was to explore the associations between salt sensitivity and nocturnal blood pressure dipping according to HIV and hypertension status in a cohort of adult Zambian population. Methods: We conducted an interventional study among 43 HIV-positive and 42 HIV-negative adults matched for age and sex. Study participants were instructed to consume a low (4 g) dietary salt intake for a week followed by high (9 g) dietary salt intake for a week. Salt resistance and salt sensitivity were defined by a mean arterial pressure difference of ≤5 mmHg and ≥ 8 mmHg, respectively, between the last day of low and high dietary salt intervention. Nocturnal dipping was defined as a 10–15% decrease in night-time blood pressure measured with an ambulatory blood pressure monitor. Results: The median age was 40 years for both the HIV-positive and the HIV-negative group with 1:1 male to female ratio. HIV positive individuals with hypertension exhibited a higher BP sensitivity to salt (95%) and nondipping BP (86%) prevalence compared with the HIV negative hypertensive (71 and 67%), HIV positive (10 and 24%) and HIV-negative normotensive (29 and 52%) groups, respectively (p < 0.05). Salt sensitivity was associated with non-dipping BP and hypertension in both the HIV-positive and HIV-negative groups even after adjustment in multivariate logistic regression (< 0.001). Conclusions: The results of the present study suggest that high dietary salt intake raises blood pressure and worsens nocturnal BP dipping to a greater extent in hypertensive than normotensive individuals and that hypertensive individuals have higher dietary salt intake than their normotensive counterparts. Regarding HIV status, BP of HIV-positive hypertensive patients may be more sensitive to salt intake and demonstrate more non-dipping pattern compared to HIV-negative hypertensive group. However, further studies with a larger sample size are required to validate this

Three transmission events of Vibrio cholerae O1 into Lusaka, Zambia

Cholera has been present and recurring in Zambia since 1977. However, there is a paucity of data on genetic relatedness and diversity of the Vibrio cholerae isolates responsible for these outbreaks. Understanding whether the outbreaks are seeded from existing local isolates or if the outbreaks represent separate transmission events can inform public health decisions. Seventy-two V. cholerae isolates from outbreaks in 2009/2010, 2016, and 2017/2018 in Zambia were characterized using multilocus variable number tandem repeat analysis (MLVA) and whole genome sequencing (WGS). The isolates had eight distinct MLVA genotypes that clustered into three MLVA clonal complexes (CCs). Each CC contained isolates from only one outbreak. The results from WGS revealed both clustered and dispersed single nucleotide variants. The genetic relatedness of isolates based on WGS was consistent with the MLVA, each CC was a distinct genetic lineage and had nearest neighbors from other East African countries. In Lusaka, isolates from the same outbreak were more closely related to themselves and isolates from other countries than to isolates from other outbreaks in other years. Our observations are consistent with i) the presence of random mutation and alternative mechanisms of nucleotide variation, and ii) three separate transmission events of V. cholerae into Lusaka, Zambia. We suggest that locally, case-area targeted invention strategies and regionally, well-coordinated plans be in place to effectively control future cholera outbreaks.https://doi.org/10.1186/s12879-021-06259-

Towards a competency-based doctoral curriculum at the University of Zambia: lessons from practice

We describe a collaborative, iterative, and participatory process that we undertook to develop and adopt a competency-based doctoral curriculum framework at the University of Zambia. There needs to be more than the traditional unstructured apprenticeship of PhD training in a knowledge-based economy where PhD graduates are expected to contribute to industry problem-solving. The lack of industry-driven competencies and, to some extent, limited skills possessed by PhD graduates relative to the demands of employers has led to the misclassification of doctoral degrees as mere paper certificates. Further, under traditional PhD training without specific core competencies, it has led to criticisms of such PhD studies as a waste of resources. The calls to rethink doctoral development in broader employment contexts led many countries to redesign their PhD programs. Training has increasingly introduced industrial linkages and industry-defined research projects to increase the attractiveness of doctoral students. Whereas developed countries have made significant reforms towards competency-based PhD training, little or nothing has been done in developing countries, especially in sub-Saharan Africa. This against the demands that Africa needs more than 100,000 PhDs in the next decade to spur economic development. Against this background, the University of Zambia has developed an industry-driven structured competency-based PhD curriculum framework. The framework will guide and support the development of standardized program-specific PhD curricula, delivery, and assessment of competencies at the University of Zambia, ensuring that doctoral students acquire skills and demonstrate core competencies that are transferable and applicable in industry settings. This framework focuses on the development of specific competencies that are necessary for successful PhD completion. The competencies are divided into three main categories: research, teaching, and professional development. Each category is then broken down into ten core competencies from which respective doctoral programs will develop sub-competencies. It is from these core competencies and sub-competencies that learning outcomes, assessment methods, and teaching activities are developed. It is envisioned that this new competency-based doctoral curriculum framework will be a helpful tool in training a cadre of professionals and researchers who benefit the industry and contribute to economic and societal development

Microscopic Analysis and Quality Assessment of Induced Sputum From Children With Pneumonia in the PERCH Study.

BACKGROUND.: It is standard practice for laboratories to assess the cellular quality of expectorated sputum specimens to check that they originated from the lower respiratory tract. The presence of low numbers of squamous epithelial cells (SECs) and high numbers of polymorphonuclear (PMN) cells are regarded as indicative of a lower respiratory tract specimen. However, these quality ratings have never been evaluated for induced sputum specimens from children with suspected pneumonia. METHODS.: We evaluated induced sputum Gram stain smears and cultures from hospitalized children aged 1-59 months enrolled in a large study of community-acquired pneumonia. We hypothesized that a specimen representative of the lower respiratory tract will contain smaller quantities of oropharyngeal flora and be more likely to have a predominance of potential pathogens compared to a specimen containing mainly saliva. The prevalence of potential pathogens cultured from induced sputum specimens and quantity of oropharyngeal flora were compared for different quantities of SECs and PMNs. RESULTS.: Of 3772 induced sputum specimens, 2608 (69%) had 25 PMNs per LPF, measures traditionally associated with specimens from the lower respiratory tract in adults. Using isolation of low quantities of oropharyngeal flora and higher prevalence of potential pathogens as markers of higher quality, 25 PMNs per LPF) was the microscopic variable most associated with high quality of induced sputum. CONCLUSIONS.: Quantity of SECs may be a useful quality measure of induced sputum from young children with pneumonia

The Diagnostic Utility of Induced Sputum Microscopy and Culture in Childhood Pneumonia.

BACKGROUND.: Sputum microscopy and culture are commonly used for diagnosing the cause of pneumonia in adults but are rarely performed in children due to difficulties in obtaining specimens. Induced sputum is occasionally used to investigate lower respiratory infections in children but has not been widely used in pneumonia etiology studies. METHODS.: We evaluated the diagnostic utility of induced sputum microscopy and culture in patients enrolled in the Pneumonia Etiology Research for Child Health (PERCH) study, a large study of community-acquired pneumonia in children aged 1-59 months. Comparisons were made between induced sputum samples from hospitalized children with radiographically confirmed pneumonia and children categorized as nonpneumonia (due to the absence of prespecified clinical and laboratory signs and absence of infiltrate on chest radiograph). RESULTS.: One induced sputum sample was available for analysis from 3772 (89.1%) of 4232 suspected pneumonia cases enrolled in PERCH. Of these, sputum from 2608 (69.1%) met the quality criterion of <10 squamous epithelial cells per low-power field, and 1162 (44.6%) had radiographic pneumonia. Induced sputum microscopy and culture results were not associated with radiographic pneumonia, regardless of prior antibiotic use, stratification by specific bacteria, or interpretative criteria used. CONCLUSIONS.: The findings of this study do not support the culture of induced sputum specimens as a diagnostic tool for pneumonia in young children as part of routine clinical practice