Background Stool is an important diagnostic specimen for tuberculosis in populations who struggle... more Background Stool is an important diagnostic specimen for tuberculosis in populations who struggle to provide sputum, such as children or people living with HIV. However, the culture of Mycobacterium tuberculosis (M. tuberculosis) complex strains from stool perform poorly. This limits the opportunity for phenotypic drug resistance testing with this specimen. Therefore, reliable molecular methods are urgently needed for comprehensive drug resistance testing on stool specimens. Methods We evaluated the performance of targeted next-generation sequencing (tNGS, Deeplex® Myc-TB) for the detection of mutations associated with M. tuberculosis complex drug resistance on DNA isolated from stool specimens provided by participants from a prospective cohort of patients treated for tuberculosis in Eswatini (n = 66; 56 with and 10 participants without M. tuberculosis complex DNA detected in stool by real-time quantitative PCR), and an independent German validation cohort of participants with cultu...
SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-... more SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al . curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA
Xpert MTB/RIF rapidly detects resistance to rifampicin (RR); however, this test misses I491F-RR c... more Xpert MTB/RIF rapidly detects resistance to rifampicin (RR); however, this test misses I491F-RR conferring the rpoB mutation, common in southern Africa. In addition, Xpert MTB/RIF does not distinguish between viable and dead Mycobacterium tuberculosis (MTB).
Additional file 3: Fig. S1. Phylogenetic diversity and drug susceptibility of the 412 M. tubercul... more Additional file 3: Fig. S1. Phylogenetic diversity and drug susceptibility of the 412 M. tuberculosis complex isolates from Eswatini. Fig. S2. Lineage distribution across Eswatini. Fig. S3. Isolates selected for further whole-genome sequencing analysis.
Additional file 1: Table S1. Origin of Rv0678 mutant isolates included in homoplastic analysis. T... more Additional file 1: Table S1. Origin of Rv0678 mutant isolates included in homoplastic analysis. Table S2. Drug resistance mutations and cluster analysis of collection 2 strains and EMBL-EBI ENA sequence read archive numbers. Table S3. BDQ and CFZ Minimum inhibitory concentration of 25 Rv0678 mutant and 12 wild type strains. Table S4. WGS of 273 isolates submitted to the EMBL-EBI ENA sequence read archive. Table S5. Epidemiological and genotyping data of 412 Mtbc-strains. Table S6. Phenotypic DST data of 412 Mtbc-strains, resistance mediating mutations for 273 whole genome sequenced isolates. Table S7. Drug resistance mediating mutations of all MDR clusters.
Multivariable penalized maximum likelihood logistic regression models of risk factors associated ... more Multivariable penalized maximum likelihood logistic regression models of risk factors associated with misclassification. (PDF 181 kb)
Directed acyclic graph (DAG) presenting possible relationships between Biocentric laboratory (LAB... more Directed acyclic graph (DAG) presenting possible relationships between Biocentric laboratory (LAB-1/LAB-2) and the probability of VL misclassification. (PDF 194 kb)
Additional file 1. Urine colour scale designed to assess the degree of haemoglobinuria. Dark-colo... more Additional file 1. Urine colour scale designed to assess the degree of haemoglobinuria. Dark-coloured urine with a colourimetric of 5 or above was considered evidence of haemoglobinuria [18]. With permission from the NEJM.
In resource-limited settings where antiretroviral treatment (ART) is being scaled-up, the World H... more In resource-limited settings where antiretroviral treatment (ART) is being scaled-up, the World Health Organization (WHO) recommends the surveillance of transmitted HIV drug resistance (HIVDR). We used the WHO's HIVDR threshold survey method to assess transmitted HIVDR in three antenatal clinic (ANC) sites along the corridor between the two most populous cities in Swaziland, where ART was introduced in 2003. From July-August 2006, remnant sera were aliquoted from HIV serosurvey specimens collected from 70 primagravidas <25 years old attending ANC during the national HIV serosurvey. Genotyping was performed at the National Institute for Communicable Diseases, South Africa. Transmitted resistance was defined by the WHO's surveillance list of mutations. HIVDR prevalence was categorized using the WHO's threshold survey binomial sequential sampling method. Among the 70 eligible specimens, 61 were sequenced--60 (98%) were identified as subtype C and one as subtype B. No maj...
Background Stool is an important diagnostic specimen for tuberculosis in populations who struggle... more Background Stool is an important diagnostic specimen for tuberculosis in populations who struggle to provide sputum, such as children or people living with HIV. However, the culture of Mycobacterium tuberculosis (M. tuberculosis) complex strains from stool perform poorly. This limits the opportunity for phenotypic drug resistance testing with this specimen. Therefore, reliable molecular methods are urgently needed for comprehensive drug resistance testing on stool specimens. Methods We evaluated the performance of targeted next-generation sequencing (tNGS, Deeplex® Myc-TB) for the detection of mutations associated with M. tuberculosis complex drug resistance on DNA isolated from stool specimens provided by participants from a prospective cohort of patients treated for tuberculosis in Eswatini (n = 66; 56 with and 10 participants without M. tuberculosis complex DNA detected in stool by real-time quantitative PCR), and an independent German validation cohort of participants with cultu...
SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-... more SARS-CoV-2 across Africa The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al . curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA
Xpert MTB/RIF rapidly detects resistance to rifampicin (RR); however, this test misses I491F-RR c... more Xpert MTB/RIF rapidly detects resistance to rifampicin (RR); however, this test misses I491F-RR conferring the rpoB mutation, common in southern Africa. In addition, Xpert MTB/RIF does not distinguish between viable and dead Mycobacterium tuberculosis (MTB).
Additional file 3: Fig. S1. Phylogenetic diversity and drug susceptibility of the 412 M. tubercul... more Additional file 3: Fig. S1. Phylogenetic diversity and drug susceptibility of the 412 M. tuberculosis complex isolates from Eswatini. Fig. S2. Lineage distribution across Eswatini. Fig. S3. Isolates selected for further whole-genome sequencing analysis.
Additional file 1: Table S1. Origin of Rv0678 mutant isolates included in homoplastic analysis. T... more Additional file 1: Table S1. Origin of Rv0678 mutant isolates included in homoplastic analysis. Table S2. Drug resistance mutations and cluster analysis of collection 2 strains and EMBL-EBI ENA sequence read archive numbers. Table S3. BDQ and CFZ Minimum inhibitory concentration of 25 Rv0678 mutant and 12 wild type strains. Table S4. WGS of 273 isolates submitted to the EMBL-EBI ENA sequence read archive. Table S5. Epidemiological and genotyping data of 412 Mtbc-strains. Table S6. Phenotypic DST data of 412 Mtbc-strains, resistance mediating mutations for 273 whole genome sequenced isolates. Table S7. Drug resistance mediating mutations of all MDR clusters.
Multivariable penalized maximum likelihood logistic regression models of risk factors associated ... more Multivariable penalized maximum likelihood logistic regression models of risk factors associated with misclassification. (PDF 181 kb)
Directed acyclic graph (DAG) presenting possible relationships between Biocentric laboratory (LAB... more Directed acyclic graph (DAG) presenting possible relationships between Biocentric laboratory (LAB-1/LAB-2) and the probability of VL misclassification. (PDF 194 kb)
Additional file 1. Urine colour scale designed to assess the degree of haemoglobinuria. Dark-colo... more Additional file 1. Urine colour scale designed to assess the degree of haemoglobinuria. Dark-coloured urine with a colourimetric of 5 or above was considered evidence of haemoglobinuria [18]. With permission from the NEJM.
In resource-limited settings where antiretroviral treatment (ART) is being scaled-up, the World H... more In resource-limited settings where antiretroviral treatment (ART) is being scaled-up, the World Health Organization (WHO) recommends the surveillance of transmitted HIV drug resistance (HIVDR). We used the WHO's HIVDR threshold survey method to assess transmitted HIVDR in three antenatal clinic (ANC) sites along the corridor between the two most populous cities in Swaziland, where ART was introduced in 2003. From July-August 2006, remnant sera were aliquoted from HIV serosurvey specimens collected from 70 primagravidas <25 years old attending ANC during the national HIV serosurvey. Genotyping was performed at the National Institute for Communicable Diseases, South Africa. Transmitted resistance was defined by the WHO's surveillance list of mutations. HIVDR prevalence was categorized using the WHO's threshold survey binomial sequential sampling method. Among the 70 eligible specimens, 61 were sequenced--60 (98%) were identified as subtype C and one as subtype B. No maj...
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Papers by Gugu Maphalala