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Molecular detection, genetic diversity and phylogenetic analysis of anaplasma marginale infecting cattle in South Africa
No full textBovine anaplasmosis caused by Anaplasma marginale is endemic in South Africa. This
endemicity is due to presence of tick vectors that transmit A. marginale the causal agent
of the disease and the high seroprevalence in Limpopo, Free State and North West
provinces. To date, the genetic diversity of A. marginale isolates infecting cattle in all
South African provinces, except Free State, are generally unknown. Recently, vaccines
based on the A. marginale major surface protein 1 a (MSP1 a) has been proposed as a
strategy for controlling bovine anaplasmosis. However, characterization of genetic
diversities of the A. marginale isolates in these regions is still needed before this protein
can be used for vaccine development. Therefore, the aim of this study was to determine
the prevalence, genetic diversity and phylogenetic relationship of A. marginale infecting
cattle in all South African provinces except the Free State.
A total of 280 whole blood samples were collected from cattle in all provinces with
exception of the Free State. Twenty six districts and municipalities were included in this
sampling. Anaplasma marginale genomic DNA was then extracted from the blood
sample using ZR Genomic DNA 1M Tissue Miniprep (Zymo Research, CA, USA). A
polymerase chain reaction (PCR) was done with primers targeting msp1a and msp4
genes and the PCR products were sequenced using genetic analyser (ABI, Life
technologies, CA, USA). The generated sequences were analysed by bioinformatics
and their phylogeny as well as genetic diversity index (GDI) was determined based on
the sequences of msp1a and msp4 genes.
Overall, the prevalence of A. marginale infection in cattle was 76% in all provinces
except for Northern Cape Province where the prevalence was zero. The prevalence per
province was as follows: Eastern Cape 19.1 %, Gauteng 9.6%, KwaZulu-Natal 23.0%,
Limpopo 15.3%, Mpumalanga 10.1%, North West 12.4% and Western Cape 10.5%.
The msp1 a revealed genetic variability with regions of different types of tandem repeats.
Some repeats were conserved amongst the A. marginale strains and revealed low
variable peptides in the MSP1 a tandem repeats. A polynomial correlation (R2=0. 76)
was observed between the GDI and anaplasmosis prevalence per province.
Interestingly, provinces with the highest prevalence were not the ones with highest or
lowest GDI.
The analysis of msp4 gene sequences, which provided evolutionary information about
geographically distinct A. marginale strains, was used in the present study for
phylogenetic analysis of samples from Limpopo (LP), Mpumalanga (MP), North West
(NW), Gauteng (GP), KwaZulu-Natal (KZN), Eastern Cape (EC) and Western Cape
(WC) provinces of South Africa. Two clades were observed which consisted of first
clade (LP, NW, GP, KZN and WC) and second clade (MP and EC) isolates.
In addition when DNA sequence variation of msp4 gene was analysed in combination
with isolates from other countries outside South Africa, important phylogeographic
information was observed. The South African strains had 100% identity with isola tes
from Kenya, Zimbabwe and Australia. Good representation of the Southern and
Northern Hemispheres was observed and demonstrated that the msp4 gene was a
good phylogeographic marker. These results indicated that A. marginale is widespread
in South Africa, and suggested that the analysis of msp1a and msp4 gene sequences
provided an understanding of the phylogeny and epidemiology of A. marginale in South
Africa.National Research Foundation (NRF
In-vitro bioactivity of fractions from a local medicinal plant on HIV-1 replication, and selected fungal and bacterial pathogens
No full textMSc (Microbiology)Department of Microbiolog
Evaluation of single nucleotide polymorphisms in virulence genes of Mycobacterium tuberculosis as markers of lineages and sub-lineages in Tshwane region
Get PDFDissertation (MSc)--University of Pretoria, 2020.The thesis/Dissertation is under embargo until September 2023.Tuberculosis (TB) is one of the top ten leading causes of death worldwide with millions of new
TB cases reported every year. Understanding the genetic diversity of Mycobacterium tuberculosis
(M. tuberculosis) is very crucial for rapid diagnosis and to reduce transmission of TB. Various
diagnostic techniques, anti-tuberculosis reagents and vaccination are available, however, the
disease is far from being eradicated (Brudey et al., 2006).
Mycobacterium tuberculosis is classified into seven major lineages that are key to the most
research areas. Recently, multidrug M. tuberculosis have been reported as the most dangerous
strains that cause a life-threatening TB. However, the M. tuberculosis with modified virulence and
transmissibility, particularly those that are caused by mutations leading to genetic variation and
increased pathogenicity are highly reported (Zaychikova et al., 2015). Genetic markers such as
variable number tandem repeats, insertion sequence element and direct repeats have been used to
identify lineages. However, the techniques (such as spoligotyping, IS6110-RLFP and MIRU-
VNTR) that use these genetic markers have a lot of drawbacks and some have low discriminatory
power (Mikheecheva et al., 2017).
Recently, single nucleotide polymorphisms (SNPs) are regarded as the most promising genetic
markers for genotyping M. tuberculosis because they have low-level homoplasy and high
discriminatory power (Zaychikova et al., 2015). The present study proposed that genotyping M.
tuberculosis using polymorphisms in virulence genes may be an alternative approach to determine
lineages and may help to detect the M. tuberculosis strains that are epidemiologically dangerous
and have adapted to specific geographic regions. This study aimed to identify and evaluate a set
of virulence gene SNPs as markers of M. tuberculosis strains circulating in the Tshwane region.
A total of 150 susceptible and resistant M. tuberculosis cultures stored in Mycobacteria growth
indicator tubes (MGIT) tubes were collected from May to October 2018 at the National Health
Laboratory Service, Tshwane Academic Division (NHLS/TAD) to conduct this study. The DNA
was extracted using hexadecyltrimethylammonium bromide (CTAB) method and spoligotyping
was done to screen for M. tuberculosis lineages. The Beijing and LAM genotypes detected by
spoligotyping were sequenced using the Illumina Miseq platform. The bioinformatic analysis of virulence genes in 56 genomes of M. tuberculosis belonging to Beijing and LAM genotypes was
performed to detect lineage-specific SNPs markers.
Of the 150 M. tuberculosis collected, 57.3% were susceptible M. tuberculosis strains while 42.7%
were drug-resistant TB. Spoligotyping of 150 isolates resulted to 86.7% previously shared type
(ST) and 13.3% orphans yielding a clustering rate of 63.3%. The Beijing family was found to be
the most predominant lineage by 26.7%, followed by T family (16%), LAM (13.3%), East Africa
Indian (EAI) (8.7%), S (6%), Manu (4.7%), H (4.7%), CAS (4.0%) and X3 (2.7%).
The number of susceptible M. tuberculosis isolates per lineages was higher than drug-resistant TB
with isolates detected as Beijing contributing 17.3% of all susceptible isolates, followed by isolates
classified as orphans (10%), T family (9.3%), LAM family (8%) and CAS (2.67%). The
association between anti-tuberculosis drug-resistant TB and lineages was found in EAI lineage
(6.7%), Manu (4%) and S family (3.3%). The family with a high number of isolates which were
drug-resistant TB was the EAI1-SOM sub-lineage belonging to the EAI family.
This study successfully identified 29 Beijing and 6 LAM signature SNPs that can be used to
classify clinical M. tuberculosis isolates. Within these signature SNPs, fadD28 (1521 C>T),
eccCb1 (1479 G>A), pks5 (6210 G>A), and ponA2 (372 G>T) were identified in the Beijing strains
and fadD28 (1392 C>G) within the LAM strains that were not reported in previous studies.
Furthermore, this study detected the lineage-specific SNPs: mce3B (145 T>G), eccCb1 (1556
G>T), vapC12 (95 A>G) in Beijing BO/W148 and cyp125 (1076 T>C), mce3B (44 T>C), vapC25
(221 A>C), vapB34 (140 C>A) F15/LAM4/KZN sub-lineages which have been reported to be
virulent and associated with drug resistance.
This study showed a high genetic diversity of M. tuberculosis strains circulating within the
Tshwane region. The Beijing lineage identified in this study was found to be more predominant
than the rest of the identified genotypes. This study proposed the alternative method for genotyping
M. tuberculosis strains using SNPs in virulence genes of M. tuberculosis. Observations from this
study also highlight the advantage of using WGS technique over other genotyping methods such
as IS6110-RFLP that has more drawbacks, as most genotypic methods discriminate M.
tuberculosis strains using specific genes or regions in the genome of M. tuberculosis while WGS
uses the complete genome of M. tuberculosis to determine different M. tuberculosis lineage.National Research Foundation (NRF)The thesis is under embargo until September 2022.Medical MicrobiologyMScUnrestricte
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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