Papers by zamantungwa Khumalo
Frontiers in tropical diseases, May 28, 2024
Veterinary Sciences, Oct 10, 2023
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
To my parents and siblings who understood the value of studying. To my fiancé for his sustained s... more To my parents and siblings who understood the value of studying. To my fiancé for his sustained support at all times. To my unborn baby who kept his calm spirit and accepted that mom is a hard worker.
Viruses, Jul 5, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Research Square (Research Square), Nov 18, 2022
Background: Mastitis is an important disease in dairy industry causing major economic burden. Sub... more Background: Mastitis is an important disease in dairy industry causing major economic burden. Subclinical mastitis (SCM) is regarded as one of the most economically important diseases affecting the dairy industry due to the nancial constraints incurred by it. Subclinical mastitis as compared to clinical mastitis does not cause visible changes in the udder or physical changes of the milk hence the need for routine testing and surveillance. Materials and methods: The aim of this study was to assess the prevalence of subclinical mastitis in dairy cows of smallholder farms in the Free State province using California mastitis test (CMT) and somatic cell counts (SCC) and further characterise staphylococcal species isolated by using Matrix-assisted laser desorption/ionization-time of ight mass spectrometry (MALDI-TOF MS) and Polymerase chain reaction (PCR). Results: The CMT results revealed that out of 166 cows, only 55 (33%) were positive for intramammary infection. The quarter level prevalence based on SCC was 87 (54%) for intramammary infections. Out of 50 bacterial culture isolates, 48 (96%) were identi ed as S. aureus (76%), S. epidermidis (4%), S. chromogenes (12%) and S. haemolyticus (4%) by MALDI-TOF MS. The 16S rDNA PCR products and obtained sequences indicated that S. aureus was the dominant species infecting tested cows at 76%, followed by S. chromogenes, S. agnetis, S. argenteus and S. devriesei at 10%, 4%, 4%) and 1% respectively. Conclusions: This study has shown the presence of diverse Staphylococcusspecies infecting subclinical mastitis cows in sampled areas of the Free State province. It further indicated the importance of using various diagnostic tools for bacterial infection surveillance involved in subclinical mastitis to ensure accurate species identi cation.
Background: Mastitis is an important disease in dairy industry causing major economic burden. Sub... more Background: Mastitis is an important disease in dairy industry causing major economic burden. Subclinical mastitis (SCM) is regarded as one of the most economically important diseases affecting the dairy industry due to the financial constraints incurred by it. Subclinical mastitis as compared to clinical mastitis does not cause visible changes in the udder or physical changes of the milk hence the need for routine testing and surveillance. Materials and methods: The aim of this study was to assess the prevalence of subclinical mastitis in dairy cows of small-holder farms in the Free State province using California mastitis test (CMT) and somatic cell counts (SCC) and further characterise staphylococcal species isolated by using Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and Polymerase chain reaction (PCR). Results: The CMT results revealed that out of 166 cows, only 55 (33%) were positive for intramammary infection. The quarter level...
Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massiv... more Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.
BackgroundInfants suffering from lower respiratory tract infections (LRTIs) have distinct nasopha... more BackgroundInfants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or a consequence of it, is unknown. In order to answer this question, longitudinal studies are needed.MethodsWe conducted an analysis of a longitudinal prospective cohort study of 1,981 Zambian mother-infant pairs who underwent NP sampling from 1-week through 14-weeks of age at 2-3-week intervals. Ten of the infants in the cohort developed LRTI and were matched 3:1 with healthy comparators. We completed 16S rRNA gene sequencing on the samples each of these infants contributed, as well as from baseline samples of the infants’ mothers, and characterized the normal maturation of the healthy infant NP microbiome, compared to infants who developed LRTI.ResultsThe infant NP microbiome maturation was characterized by transitioning from Staphylococcus dominant to respiratory-gen...
PLOS ONE
Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to ... more Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most a...
Scientific Reports, 2022
The gut microbiota of mosquitoes plays a critical role in the life history of the animal. There i... more The gut microbiota of mosquitoes plays a critical role in the life history of the animal. There is a growing body of research characterising the gut microbiota of a range of mosquito species, but there is still a paucity of information on some members of the Anopheles gambiae complex. In this study, the gut microbiota of four laboratory strains were characterised. SENN (Anopheles arabiensis—insecticide susceptible major vector), SENN DDT (Anopheles arabiensis—insecticide resistant major vector), MAFUS (Anopheles merus—minor vector) and SANGWE (Anopheles quadriannulatus—non-vector) were used in this study. The microbiota of fourth instar larvae, 3-day old, 15-day old non-blood fed and 15-day old blood fed females were characterised by MALDI-TOF mass spectroscopy and 16 s rRNA gene sequencing by next generation sequencing. The four strains differed in species richness but not diversity. The major vectors differ in β-diversity from that of the minor and non-vectors. There was no differ...
ABSTRACT. Ticks carry and transmit a remarkable array of pathogens including bacteria, protozoa a... more ABSTRACT. Ticks carry and transmit a remarkable array of pathogens including bacteria, protozoa and viruses, which may be of veterinary and/or of medical significance. With little to no information regarding the presence of tick-borne zoonotic pathogens or their known vectors in southern Africa, the aim of our study was to screen for Anaplasma phagocytophilum, Borrelia burgdorferi, Coxiella burnetii, Rickettsia species and Ehrlichia ruminantium in ticks collected and identified from ruminants in the Eastern Cape, Free State, KwaZulu-Natal and Mpumalanga Provinces of South Africa. The most abundant tick species identified in this study were Rhipicephalus evertsi evertsi (40%), Rhipicephalus species (35%), Amblyomma hebraeum (10%) and Rhipicephalus decoloratus (14%). A total of 1634 ticks were collected. DNA was extracted, and samples were subjected to PCR amplification and sequencing. The overall infection rates of ticks with the target pathogens in the four Provinces were as follows...
The Beta variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in S... more The Beta variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in South Africa in late 2020 and rapidly became the dominant variant, causing over 95% of infections in the country during and after the second epidemic wave. Here we show rapid replacement of the Beta variant by the Delta variant, a highly transmissible variant of concern (VOC) that emerged in India and subsequently spread around the world. The Delta variant was imported to South Africa primarily from India, spread rapidly in large monophyletic clusters to all provinces, and became dominant within three months of introduction. This was associated with a resurgence in community transmission, leading to a third wave which was associated with a high number of deaths. We estimated a growth advantage for the Delta variant in South Africa of 0.089 (95% confidence interval [CI] 0.084-0.093) per day which corresponds to a transmission advantage of 46% (95% CI 44-48) compared to the Beta variant. Th...
Background: Subclinical mastitis (SCM) is one of the most economically important diseases affecti... more Background: Subclinical mastitis (SCM) is one of the most economically important diseases affecting the dairy industry. The SCM does not cause visible changes in the udder or physical changes of the milk as compared to clinical mastitis, and a clear overview of the prevalence and risk factors in the different regions of Africa is still lacking. The objective of this study was to investigate the prevalence of SCM and assess the associated risk factors and dominant bacterial pathogens among cattle in Africa. Materials and methods: Using a systematic review and meta-analysis approach, we gathered literature concerning SCM among cattle in Africa, published from 2020 through 2021in five databases. Results: A total of 1,560 records were retrieved and at the end of the screening, 38 studies were eligible for inclusion in the meta-analysis. The random-effects meta-analysis model showed that the weighted pooled prevalence of SCM in cattle in Africa was 51.5% (95% CI: 44.0-58.9%). Heterogenei...
Bovine anaplasmosis caused by the intraerythrocytic rickettsial pathogen Anaplasma marginale is e... more Bovine anaplasmosis caused by the intraerythrocytic rickettsial pathogen Anaplasma marginale is endemic in South Africa. Anaplasma marginale subspecies centrale also infects cattle; however, it causes a milder form of anaplasmosis and is used as a live vaccine against A. marginale. There has been less interest in the epidemiology of A. marginale subsp. centrale, and, as a result, there are few reports detecting natural infections of this organism. When detected in cattle, it is often assumed that it is due to vaccination, and in most cases, it is reported as coinfection with A. marginale without characterization of the strain. A total of 380 blood samples from wild ruminant species and cattle collected from biobanks, national parks, and other regions of South Africa were used in duplex real-time PCR assays to simultaneously detect A. marginale and A. marginale subsp. centrale. PCR results indicated high occurrence of A. marginale subsp. centrale infections, ranging from 25 to 100% in national parks. Samples positive for A. marginale subsp. centrale were further characterized using the msp1aS gene, a homolog of msp1␣ of A. mar-ginale, which contains repeats at the 5= ends that are useful for genotyping strains. A total of 47 Msp1aS repeats were identified, which corresponded to 32 A. marginale subsp. centrale genotypes detected in cattle, buffalo, and wildebeest. RepeatAnalyzer was used to examine strain diversity. Our results demonstrate a diversity of A. marginale subsp. centrale strains from cattle and wildlife hosts from South Africa and indicate the utility of msp1aS as a genotypic marker for A. marginale subsp. centrale strain diversity.
Uploads
Papers by zamantungwa Khumalo