Browsing by Author "Kaba, Mamadou"

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    Open Access
    Association of Faecalibacterium, Lachnospira, Veillonella, and Rothia with childhood wheezing
    (2019) Kanyemba, Saara; Kaba, Mamadou; Tow, Lemese Ah
    Wheezing symptoms among children, present major health and economic problems globally. A recent study conducted in Canada observed a reduction in stool bacterial genera Faecalibacterium, Lachnospira, Veillonella and Rothia (FLVR) in three-month old infants with atopy-wheeze symptoms. It is not known whether this is true in different human populations worldwide. The overall aim of this dissertation was to investigate the contribution of any of the FLVR bacteria or their combination in the occurrence of infant wheezing within the Drakenstein Child Health Study (DCHS), South Africa. To address this aim, I began my thesis's project by conducting a systematic literature review which investigated the association of FLVR bacteria with the occurrence of different respiratory diseases in humans. My review provided evidence for the possible involvement of FLVR bacteria in human respiratory diseases, including asthma, pulmonary tuberculosis and pneumonia. Furthermore, this review highlighted the need for a well-designed and large study to investigate the contribution of the FLVR bacteria in respiratory diseases, in an African setting. Secondly, I optimized SYBR Green based real-time quantitative polymerase chain reaction (qPCR) as well as conventional PCR assays for the detection of FLVR bacteria. Using the optimized assays, I screened 533 stool samples collected from 140 wheezing and 140 nonwheezing infants. The optimized assays demonstrated good performance in the detection of FLVR bacteria from human stool samples. Using qPCR, Rothia, Veillonella, Faecalibacterium and Lachnospira were detected in 90% (479/533), 73% (388/533), 51% (274/533) and 14% (77/533) of the samples, respectively. Conventional PCR permitted the detection of Rothia, Veillonella, Faecalibacterium and Lachnospira in 55% (263/479), 74% (289/388), 53% (145/274) and 0% (0/77) of the qPCR positive samples, respectively. I also determined the factors associated with faecal colonization by FLVR bacteria in the first year of life. I showed that reduced colonisation by Faecalibacterium was associated with male gender (adjusted OR = 0.65, 95%CI: 0.42 - 0.98) and TC-Newman residence (adjusted OR = 0.52, 95%CI: 0.29 - 0.91). Breastfeeding was associated with less colonisation by both Lachnospira, (adjusted OR = 0.17, 95%CI: 0.05 - 0.49) and Veilonella (adjusted OR = 0.32, 95%CI: 0.10 - 0.91). Mother's tertiary education was significantly associated with high Rothia colonisation (adjusted OR = 11.73, 95%CI: 1.36 - 2.58). In the last section of my thesis, I assessed the association of FLVR bacteria with infant wheezing using logistic regression models. I found a significant association of Rothia with reduced risk of infant wheezing (adjusted odds ratio (aOR)=0.54, 95%CI: 0.28-0.93) and recurrent wheezing (aOR=0.29, 95%CI: 0.05-0.88). Using receiver operating characteristic curves (ROC), I showed that among all FLVR bacteria, Lachnospira (AUROC = 0.833, 95%CI: 0.64-1.00) and Rothia (AUC=0.707, 95%CI: 0.62-0.79) could serve as biomarkers for early prediction of infant wheezing. Overall, this is the first study on FLVR bacteria and infant wheezing to be conducted in Africa. Its findings encourage more research to be conducted in order to elucidate the potential protective role of Rothia against childhood wheeze and asthma, as well as the contribution of Lachnospira in asthma development.
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    The contribution of respiratory pathogens to Sudden Unexpected Death in Infancy
    (2016) Ishimirwe, Elyse Sandrine; Kaba, Mamadou; Heyns, Marise
    Background: Sudden unexpected death in infancy (SUDI) is among the most frequent causes of mortality in infants less than one year of age. Respiratory infections have been identified as the most frequent cause of death in these infants. Yet, the broad range of respiratory pathogen that might be involved in SUDI is poorly studied. This study aimed to investigate the incidence of the respiratory pathogens in SUDI. Methods: A prospective study was carried out on SUDI cases admitted to Salt River Forensic Pathology Laboratory from February 2015 through May 2015. Cerebrospinal fluid, pericardial fluid and lung biopsy were collected from each study participant during post-mortem examination. Total nucleic acids were extracted on the automated QIAsymphony platform. The microbial diversity was investigated using a commercialized multiplex real-time PCR assay, the "FTD Respiratory pathogens 33" kit. This assay is able to detect 21 viruses, 11 bacteria and one fungus. In each real-time PCR run, a positive and non-template sterile water were included as controls. Results: Thirty SUDI cases (median age, 3 (interquartile range (IQR): 2 - 8 months) were included in the study. Twenty participants were males. Positive microbiological results from at least one of the three samples were obtained in 28 cases (93%). According to the type of sample, respiratory pathogens were detected in almost all the lung biopsies (93%), while it was only detected in 60% and 50% of the cerebrospinal and the pericardial fluids, respectively. The median cycle threshold value was lower in lung biopsies (30 (IQR: 28 ‒ 35)) compared to both cerebrospinal (34 (IQR: 30 ‒ 36)) and pericardial fluids (35 (IQR: 33 ‒ 35)) (p= 0.039). In lung biopsies, the most commonly detected bacteria were K. pneumoniae (47%, 14/30) and M. catarrhalis (20%, 6/30). H. influenza (7%, 2/30) and M. pneumoniae (7%, 2/30) were the bacteria often detected in pericardial fluid and cerebrospinal fluid, respectively. Human Metapneumovirus was the most frequently virus detected in all three sample types assessed, accounting for 33% (10/30) in cerebrospinal fluid, 37% (11 /30) in pericardial fluid and 57% (17/30) in lung biopsy samples, respectively. A single type of pathogen was detected n seven of the 28 positive cases. Conclusion: This study highlights the potential implication of respiratory infection in SUDI and it reports one of the highest incidences of respiratory pathogens in SUDI cases. In addition, it is the first to report the high incidence rate of Human Metapneumovirus in SUDI cases. The findings also showed that the majority of SUDI cases are associated with synergetic interaction of multiple respiratory infections. However, data related to histopathology and bacterial culture were not available. A broad range of respiratory pathogens should be included in the routine investigation of SUDI cases with more sensitive diagnostic methods.
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    Detection of Streptococcus pneumoniae from different types of nasopharyngeal swabs in children
    (Public Library of Science, 2013) Dube, Felix S; Kaba, Mamadou; Whittaker, Elizabeth; Zar, Heather J; Nicol, Mark P
    BACKGROUND: A better understanding of the epidemiology of nasopharyngeal carriage of Streptococcus pneumoniae is important to assess the impact of vaccination and the pathogenesis of pneumococcal disease. We compared the recovery of S. pneumoniae from nylon flocked, Dacron and rayon swabs. METHODS: The recovery of S. pneumoniae from mocked specimens using flocked, Dacron and rayon swabs were compared by culture. The yield from paired nasopharyngeal (NP) samples obtained from healthy children sampled with flocked and Dacron swabs was also determined using culture and lytA -targeted real-time polymerase chain reaction (qPCR). RESULTS: Using mock specimen, the percentage recovery of S. pneumoniae ATCC 49619 (serotype 19F) strain from the flocked swabs was 100%, while it was 41% from Dacron swabs and 7% from rayon swabs. Similar results were observed for S. pneumoniae serotypes 1 and 5. S. pneumoniae was cultured from 18 of 42 (43%) paired NP samples from the healthy children (median age 8 [interquartile range (IQR) 5-16] months). The median number of colony-forming units (CFU) recovered from flocked swabs was two-fold higher (8.8×10 4 CFU/mL [IQR, 2.0×10 2 - 4.0×10 5 CFU/mL]) than Dacron swabs (3.7×10 4 CFU/mL [IQR, 4.0×10 2 -3.2×10 5 CFU/mL], p  = 0.17). Using lytA -targeted qPCR from paired NP samples, the median copy number of S. pneumoniae detected from flocked swabs was significantly higher than from Dacron swabs (3.0×10 5 genome copies/mL [IQR, 1.3×10 2 −1.8×10 6 ] vs. 9.3×10 4 genome copies/mL [IQR, 7.0×10 1 −1.1×10 6 ]; p  = 0.005). CONCLUSION: Flocked swabs released more S. pneumoniae compared to both Dacron and rayon swabs from mock specimens. Similarly, higher bacterial loads were detected by qPCR from flocked swabs compared with Dacron swabs from healthy children.
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    Dynamics of faecal bacterial populations in early infancy as determined by massively parallel sequencing
    (2015) Claassen, Shantelle; Nicol, Mark; Kaba, Mamadou
    Background: Meconium microbiota have recently gained great interest; however very few studies have included meconium specimens when longitudinally characterizing the infant GIT microbiota. This study therefore aimed to longitudinally characterize meconium microbiota profiles during the first seven months of life and to compare these profiles with those from maternal faecal specimens using quality controlled Illumina MiSeq sequencing data. Methods: We sampled infant meconium and maternal faecal specimens at birth, as well as two subsets of infant faecal specimens at 4-12 and 20-28 weeks of life. We extracted nucleic acid from faecal specimens using the automated QIAsymphony ® SP instrument. Using Illumina MiSeq technology, we sequenced the V4 region of the bacterial 16S rRNA gene. We determined whether sufficient reads were sequenced using accumulation curves; whether any contamination occurred; and whether our sequencing approach was reproducible. The relative abundances of taxonomically classified operational taxonomic units (OTUs), and the Shannon diversity and Bray Curtis dissimilarity indices served to characterize faecal specimens from participants. Log ratio biplots and generalized linear mixed models served to statistically determine differences between faecal bacterial profiles. Results: Faecal specimens were collected from 90 mothers and 107 infants at birth, 72 infants at 4-12 and 36 infants at 20 28 weeks of age. We classified OTUs from two non-template controls which were indicative of potential contamination. Correcting for contamination resulted in a loss of 10 % of OTUs classified. Our reproducibility analysis correlated with increased concentrations of template used during library preparation. Based on diversity measures, meconium specimens harboured the most diverse bacterial profiles. The highest proportions of OTUs classified from meconium belonged to the phylum Proteobacteria (60 %), while the phylum Firmicutes was most abundant at 4-12 weeks (49 %) and 20-28 weeks (64 %) of life. The phylum Actinobacteria was at its highest at 4-12 weeks of age (26 %) and its increased proportions were associated with breastfeeding at 6-10 weeks of life. Firmicutes constituted the majority (79 %) of bacteria from maternal faecal specimens. No mother- infant pairs clustered at any of the time points studied, but infant bacterial profiles became more adult-like with increased age. An increase in infant age significantly affected bacterial proportions of 87 OTUs. Interestingly, we observed that infants exposed to HIV had higher proportions of the genus Leuconostoc and higher diversity indices compared to HIV unexposed infants at 4-12 weeks of age. Conclusion: Our study highlights that reproducibility may be worsened by the use of low template concentrations during library preparation, which may also skew diversity measures. We conclude that meconium is not sterile and that infant faecal bacterial profiles become more adult-like with increased age.
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    Epidemiology of extended spectrum beta-lactamase and carbapenemase-producing bacteria in stool from apparently healthy children, South Africa
    (2015) Manenzhe, Rendani Innocent; Nicol, Mark; Kaba, Mamadou
    Background: The prevalence of extended-spectrum beta-lactamase (ESBL) - and carbapenemase-producing Enterobacteriaceae in healthy humans in the community is largely unknown. We aimed to determine the prevalence and genetic characteristics of ESBL- and carbapenemase-producing Enterobacteriaceae in stools from healthy infants and their mothers, and to determine the risk factors associated with their carriage. Methods: This study was nested within the Drakenstein Child Health Study, a birth cohort in a semi-rural region of Western Cape Province, South Africa. Maternal and infants faecal samples (including the meconium) were collected at birth and at two additional time-points (5-12 and 20-28 weeks) from the infants only. Samples were screened for ESBLs and carbapenemase-producing organisms using ChromID ESBL and ChromID CARBA media, respectively. Identification of suspect ESBL/carbapenemase-producing isolates and antibiotic susceptibility were determined using the Vitek 2 system. ESBL production was confirmed using the combination disc test, and that of carbapenemase using the modified hodge test. Selected ESBL and carbapenemase genes were evaluated by the singleplex conventional polymerase chain reaction and Sanger sequencing. Risk factors were assessed by univariate analysis using the EPI Info version 7 software.
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    Longitudinal colonisation by Streptococcus pneumoniae and nasopharyngeal microbial interactions in health and disease: a South African birth cohort study
    (2016) Dube, Felix Sizwe; Mulder, Nicola; Kaba, Mamadou
    Streptococcus pneumoniae (the pneumococcus) is the most common cause of childhood pneumonia. Nasopharyngeal (NP) colonization by the pneumococcus is a necessary first step in the pathogenesis of pneumonia and yet the dynamic nature of pneumococcal colonization remains incompletely understood. In children, asymptomatic colonization of the nasopharynx by the pneumococcus is common and also serves as a reservoir for person-to-person transmission. We aimed to investigate in detail, the dynamics of pneumococcal nasopharyngeal carriage over the first year of life, in a cohort of South African children, particularly after implementation of the 13-valent pneumococcal conjugate vaccine (PCV-13). The study will further elucidate the interaction of S. pneumoniae with other respiratory pathogens and how such interactions may contribute development of severe disease.
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    Mupirocin-resistant Staphylococcus aureus in Africa: a systematic review and meta-analysis
    (BioMed Central, 2018-08-15) Shittu, Adebayo O; Kaba, Mamadou; Abdulgader, Shima M; Ajao, Yewande O; Abiola, Mujibat O; Olatimehin, Ayodele O
    Background Mupirocin is widely used for nasal decolonization of Staphylococcus aureus to prevent subsequent staphylococcal infection in patients and healthcare personnel. However, the prolonged and unrestricted use has led to the emergence of mupirocin-resistant (mupR) S. aureus. The aim of this systematic review was to investigate the prevalence, phenotypic and molecular characteristics, and geographic spread of mupR S. aureus in Africa. Methods We examined five electronic databases (EBSCOhost, Google Scholar, ISI Web of Science, MEDLINE, and Scopus) for relevant English articles on screening for mupR S. aureus from various samples in Africa. In addition, we performed random effects meta-analysis of proportions to determine the pooled prevalence of mupR S. aureus in Africa. The search was conducted until 3 August 2016. Results We identified 43 eligible studies of which 11 (26%) were obtained only through Google Scholar. Most of the eligible studies (28/43; 65%) were conducted in Nigeria (10/43; 23%), Egypt (7/43; 16%), South Africa (6/43; 14%) and Tunisia (5/43; 12%). Overall, screening for mupR S. aureus was described in only 12 of 54 (22%) African countries. The disk diffusion method was the widely used technique (67%; 29/43) for the detection of mupR S. aureus in Africa. The mupA-positive S. aureus isolates were identified in five studies conducted in Egypt (n = 2), South Africa (n = 2), and Nigeria (n = 1). Low-level resistance (LmupR) and high-level resistance (HmupR) were both reported in six human studies from South Africa (n = 3), Egypt (n = 2) and Libya (n = 1). Data on mupR-MRSA was available in 11 studies from five countries, including Egypt, Ghana, Libya, Nigeria and South Africa. The pooled prevalence (based on 11 human studies) of mupR S. aureus in Africa was 14% (95% CI =6.8 to 23.2%). The proportion of mupA-positive S. aureus in Africa ranged between 0.5 and 8%. Furthermore, the frequency of S. aureus isolates that exhibited LmupR, HmupR and mupR-MRSA in Africa were 4 and 47%, 0.5 and 38%, 5 and 50%, respectively. Conclusions The prevalence of mupR S. aureus in Africa (14%) is worrisome and there is a need for data on administration and use of mupirocin. The disk diffusion method which is widely utilized in Africa could be an important method for the screening and identification of mupR S. aureus. Moreover, we advocate for surveillance studies with appropriate guidelines for screening mupR S. aureus in Africa.
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    Respiratory microbes present in the nasopharynx of children hospitalised with suspected pulmonary tuberculosis in Cape Town, South Africa
    (BioMed Central, 2016-10-24) Dube, Felix S; Kaba, Mamadou; Robberts, F J Lourens; Tow, Lemese A; Lubbe, Sugnet; Zar, Heather J; Nicol, Mark P
    Background: Lower respiratory tract infection in children is increasingly thought to be polymicrobial in origin. Children with symptoms suggestive of pulmonary tuberculosis (PTB) may have tuberculosis, other respiratory tract infections or co-infection with Mycobacterium tuberculosis and other pathogens. We aimed to identify the presence of potential respiratory pathogens in nasopharyngeal (NP) samples from children with suspected PTB. Method: NP samples collected from consecutive children presenting with suspected PTB at Red Cross Children’s Hospital (Cape Town, South Africa) were tested by multiplex real-time RT-PCR. Mycobacterial liquid culture and Xpert MTB/RIF was performed on 2 induced sputa obtained from each participant. Children were categorised as definite-TB (culture or qPCR [Xpert MTB/RIF] confirmed), unlikely-TB (improvement of symptoms without TB treatment on follow-up) and unconfirmed-TB (all other children). Results: Amongst 214 children with a median age of 36 months (interquartile range, [IQR] 19–66 months), 34 (16 %) had definite-TB, 86 (40 %) had unconfirmed-TB and 94 (44 %) were classified as unlikely-TB. Moraxella catarrhalis (64 %), Streptococcus pneumoniae (42 %), Haemophilus influenzae spp (29 %) and Staphylococcus aureus (22 %) were the most common bacteria detected in NP samples. Other bacteria detected included Mycoplasma pneumoniae (9 %), Bordetella pertussis (7 %) and Chlamydophila pneumoniae (4 %). The most common viruses detected included metapneumovirus (19 %), rhinovirus (15 %), influenza virus C (9 %), adenovirus (7 %), cytomegalovirus (7 %) and coronavirus O43 (5.6 %). Both bacteria and viruses were detected in 73, 55 and 56 % of the definite, unconfirmed and unlikely-TB groups, respectively. There were no significant differences in the distribution of respiratory microbes between children with and without TB. Using quadratic discriminant analysis, human metapneumovirus, C. pneumoniae, coronavirus 043, influenza virus C virus, rhinovirus and cytomegalovirus best discriminated children with definite-TB from the other groups of children. Conclusions: A broad range of potential respiratory pathogens was detected in children with suspected TB. There was no clear association between TB categorisation and detection of a specific pathogen. Further work is needed to explore potential pathogen interactions and their role in the pathogenesis of PTB.
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    The stool microbiota and infant wheezing illness - the Drakenstein child health study, South Africa
    (2019) Ngwarai, Michelle Rudo; Kaba, Mamadou; Tow, Lemese Ah
    Background: Wheezing is one of the leading respiratory symptoms in childhood, which with recurrent occurrence can lead to asthma at school age. Few studies, with conflicting findings, have investigated the contribution of stool bacteria in childhood wheezing illness. Additionally, most of the published studies were conducted in high-income countries using small sample sizes and targeted bacterial detection techniques. To address these limitations, we conducted this study to determine the association of the infant stool bacterial diversity and composition with wheezing development. Methods: We conducted a longitudinal case-control study nested within the Drakenstein Child Health Study, Western Cape, South Africa. We included 140 infants with wheeze (cases) and 140 age-matched controls. Passed faecal samples were collected from infants at birth, whilst aspirated or passed faecal samples were collected at six weeks, six months and 12 months. Deoxyribonucleic acid (DNA) was extracted from all the samples using the manual ZR Fecal DNA MiniPrep™ Kit. Sequencing of the hypervariable V4 region of the 16S rRNA gene was performed using the Illumina MiSeq technique. The resulting sequencing data was subjected to bioinformatic quality control checks and statistical analysis. Results: One of the main findings from the systematic review of wheezing data was the observed association between the development of atopic wheezing and four bacteria namely Faecalibacterium, Lachnospira, Veillonella and Rothia. This study included 280 children (n=123 female and n=157 male) recruited from TC Newman (38.5%) and Mbekweni (61.5%) areas. Stool samples were collected from 159 infants at birth, 114 infants at six weeks, 141 infants at six months and 98 infants at 12 months of age. Aspirate and passed stool samples were found to be similar and comparable in terms of the bacterial composition. At age six weeks, 16% (23/140) of the infants included had wheezed once. During the first year, the proportion of infants with recurrent wheezing (≥ 2 wheezing episodes) was 56% (78/140). Independent factors influencing the composition and diversity of the infants faecal bacteria were feeding practices, age of mothers and living conditions (all p0.05). In addition, we did not find significant difference between infants with and without wheeze for selected bacteria reported to be associated with wheezing. However, we observed an increased relative abundance of Proteobacteria at 12 months of age in infants who had previously wheezed. Additionally, Lactobacillales was in apparently significantly higher proportions in recurrent wheezers as compared to infants who wheezed once (p< 0.05). We did not observe distinct faecal bacterial profiles between infants with and without wheeze at any taxonomic level analysis (all p> 0.05). In addition, we did not find significant difference between infants with and without wheeze for selected bacteria reported to be associated with wheezing. However, we observed an increased relative abundance of Proteobacteria at 12 months of age in infants who had previously wheezed. Additionally, Lactobacillales was in apparently significantly higher proportions in recurrent wheezers as compared to infants who wheezed once (p< 0.05). Conclusion: This study shows that aspirated stool is a good alternative for passed stool in microbiome studies. Furthermore, it revealed the complex and dynamic nature of the faecal bacteria, as well as factors influencing the faecal bacterial profile during the first year of life. More studies in this cohort, including the use of metagenomic and metabolomic approaches are required to demonstrate the role played by bacterial types and their metabolites in the development of wheezing illness. Finally, because recurrent wheezing is one of the precursors of asthma, there is a need for an additional follow-up of these infants in order to investigate the contribution of the early faecal microbiome in the development of asthma at school age.