Taxonomy and population genetics of Fusarium subglutinans sensu lato on pine and mango

Fusarium subglutinans sensu lato is a complex of fungi, which are the causal agents of important diseases on a wide variety of plants. Two important diseases caused by F. subglutinans sensu lato are pitch canker and mango malformation. F. subglutinans sensu lato isolates causing pitch canker on pine trees have been described as a separate species, F. circinatum. whereas F. subglutinans sensu lato isolates associated with mango malformation have not been formally described. The objective of study was to clarify the taxonomy and population genetics of the pitch canker and mango malformation fungi residing in the Gibberellafujikuroi complex. The introductory chapter of this thesis provides a review of the taxonomic classifications used for Fusarium spp. in the G. fujikuroi complex. In addition, the current knowledge pertaining to the population structure of the pitch canker and mango malformation fungi is discussed. In the second chapter the occurrence of F. circinatum was investigated in Mexico. Fusarium isolates were collected from pine trees in Mexico and identified as F. circinatum. Morphology, sexual compatibility studies, pathogenicity tests and histone H3-RFLPs were used to identify and characterize this fungus. The pitch canker fungus, F. circinatum and its teleomorph, G. circinata has been recently described. However, the name G. circinata is invalid, because insufficient information was provided to characterize the type specimen in the description. Additional information and a selection of F. circinatum isolates were, therefore, obtained and studies were undertaken in order to validate the description of G. circinata. The teleomorph G. circinata was validated and morphological criteria were shown to clearly distinguish F. circinatum from other F. subglutinans sensu lato isolates. Chapter four presents a study aimed at better understanding relationships between populations of F. circinatum from different geographical areas. For this study co¬dominant molecular markers were developed. These were then used to determine the genetic diversity, genetic distance and migration between different F. circinatum populations. Analysis revealed a high diversity in the Florida population and a low diversity in the South African population. Genetic analysis also indicated that the South African F. circinatum population originated in Mexico. In chapter five, the influence of sexual reproduction on the F. circinatum populations sampled over ten years in South Africa were studied. Sexual compatibility, vegetative compatibility and allelic diversity that were determined using polymorphic markers, developed in chapter four, were used. These results suggested that sexual reproduction is occurring more frequently in the more recently collected populations than in the initial population. Mango malformation is an important disease in mango growing areas. The study presented in chapter six indicated that this disease is associated with two distinct Fusarium spp. in the section Liseola. The two new Fusarium spp. are thus described as F. mangiferae and F. sterilihyphosum using morphological criteria In chapter seven, the distribution and vegetative compatibility of both F. mangiferae and F. sterilihyphosum was determined for the South Africa populations. Results revealed that each of these species differ in their distribution in South Africa. Vegetative compatibility tests also suggest that both species represent single genets in South Africa. Fusarium subglutinans sensu lato isolates associated with pme and mango are economically important fungi. The focus of the studies presented in this thesis has been on the taxonomy and population genetics of these fungi, with special reference to their occurrence in South Africa. Each of the chapters will contributes towards a better understanding of the taxonomy, population genetics and biology of these fungi.Thesis (PhD)--University of Pretoria, 2006.Microbiology and Plant PathologyUnrestricte

Genome sequences of Brucella abortus and Brucella suis strains isolated from bovine in Zimbabwe

This is a report of whole-genome sequences of a Brucella abortus strain and two Brucella suis strains isolated from bovine in Zimbabwe. These strains were selected based on their origin and data obtained when using multiplex PCR assays, then sequenced using next-generation sequencing technologies.The Institutional Research Theme funding through the Genomics Research Institute (GRI) at the University of Pretoria, South Africa.http://genomea.asm.orghb201

Genomic sequence data and single nucleotide polymorphism genotyping of Bacillus anthracis strains isolated from animal anthrax outbreaks in Northern Cape Province, South Africa

This report presents genomic data on sequence reads and draft genomes of Bacillus anthracis isolates from anthrax outbreaks in animals in an endemic region of South Africa as well as genotyping of the strains using canonical single nucleotide polymorphisms (canSNPs). It is derived from an article entitle “Phylogenomic structure of B. anthracis strains in the Northern Cape Province, South Africa revealed novel single nucleotide polymorphisms”. Whole genome sequencing (WGS) of twenty-three B. anthracis strains isolated during 1998 and 2009 anthrax outbreaks in the Northern Cape Province (NCP), as well as a strain from Botswana (6102_6B) and one from Namibia-South Africa transfrontier conservation area (Sendlingsdrift, 6461_SP2) were obtained using both the HiSeq 2500 and MiSeq Illumina platforms. Mismatch amplification mutation assay (melt-MAMA) qPCR were used to identify the canSNP genotypes within the global population of B. anthracis. DNA sequencing data is available at NCBI Sequence Read Archive and GenBank database under accession N0. PRJNA580142 and PRJNA510736 respectively. A phylogenetic tree and CanSNP typing profiles of the isolates are presented within this article.The Institute of Tropical Medicine (ITM), Belgium, National Research Foundation and AgriSETA (Agriculture Sector Education Training Authority) in South Africa.http://www.elsevier.com/locate/dibam2020Veterinary Tropical Disease

Ecological suitability modeling for anthrax in the Kruger National Park, South Africa

The spores of the soil-borne bacterium, Bacillus anthracis, which causes anthrax are highly resistant to adverse environmental conditions. Under ideal conditions, anthrax spores can survive for many years in the soil. Anthrax is known to be endemic in the northern part of Kruger National Park (KNP) in South Africa (SA), with occasional epidemics spreading southward. The aim of this study was to identify and map areas that are ecologically suitable for the harboring of B. anthracis spores within the KNP. Anthrax surveillance data and selected environmental variables were used as inputs to the maximum entropy (Maxent) species distribution modeling method. Anthrax positive carcasses from 1988±2011 in KNP (n = 597) and a total of 40 environmental variables were used to predict and evaluate their relative contribution to suitability for anthrax occurrence in KNP. The environmental variables that contributed the most to the occurrence of anthrax were soil type, normalized difference vegetation index (NDVI) and precipitation. Apart from the endemic Pafuri region, several other areas within KNP were classified as ecologically suitable. The outputs of this study could guide future surveillance efforts to focus on predicted suitable areas for anthrax, since the KNP currently uses passive surveillance to detect anthrax outbreaks.S1 Table. Worldclim variables used in Maxent model.S2 Table. Overview of environmental data used in Maxent indicating the variables, type of data and source.S1 Fig. Spatially unique cases of Bacillus anthracis and the predicted suitability for B. anthracis occurrence.S2 Fig. Twelve environmental variables used in the final Maxent model.http://www.plosone.orgam2018Production Animal StudiesVeterinary Tropical Disease

Molecular characterisation of two homoeologous elicitor-responsive lipin genes in cotton

The identification and molecular characterisation of two lipin-like gene copies (GhLIPN) in cotton, Gossypium hirsutum, an allotetraploid derived from two progenitor diploid Gossypium species, is described. Sequence analyses of the GhLIPN copies, designated GhLIPN-1 and -2, revealed that they contain 11 exons, separated by ten introns. They each have a 2,643 bp open reading frame that encodes 880 aa proteins, and share a 97.7 and 95.5 % sequence similarity at the translated nucleotide and amino acid level, respectively. The GhLIPN genes have a distinct domain architecture consisting of an archetypical N-terminal lipin domain, followed by a haloacid dehalogenase (HAD) domain towards the C-terminus. A Southern blot did not distinguish between the two gene copies, which suggests that they may be homoeologs rather than paralogs. GhLIPN-2 is more similar to a homoeologous sequence from G. raimondii, representing the ancestral D-genome, compared to GhLIPN-1 that matches G. herbaceum and that represents the A-genome. Our data indicate that GhLIPN-1 and GhLIPN-2 are homoeologs that derive from the A- and the D-diploid genomes, respectively. The promoter sequences of GhLIPN-1 and -2 differ by 56 %, as a result of multiple indels. In silico analysis of the promoter regions revealed that both genes contain numerous putative defence-related and elicitor-responsive cis-elements that support a role for GhLIPN in defence responses. Relative quantification real-time PCR confirmed the up-regulation in response to a cell-wall-derived V. dahliae elicitor, which supported the association of GhLIPN with defence signalling. The results add a new dimension to the proposed roles of lipins in plants by suggesting that lipins may have a role in defence signalling.The South African National Research Foundation and the University of Johannesburg.http://link.springer.com/journal/438hb2013ab201

Contamination of the environment by pathogenic bacteria in a livestock farm in Limpopo Province, South Africa

The aim of this study was to investigate the occurrence and diversity of pathogenic bacteria in the environment at a livestock farm in Limpopo Province. Environmental samples were collected from three sampling locations: cattle camp (CC), sheep camp (SHC), and goat camp (GC). Samples were processed and analysed for total bacterial counts in the Biotechnology Laboratory, University of Limpopo, South Africa. Identifications were done with Matrix Assisted Laser Disorption Ionisation Time of Flight Mass Spectometry (MALDI-TOF MS) using the simplified on plate technique. The colony forming unit formula per gram of environmental sample (CFU/g) was used to determine total bacterial counts. High counts were observed in CC and low counts in SHC for both soil and faecal samples. Bacillus species were the most dominant across the sampling locations for soil samples. Bacillus cereus occurred in 36 samples (33%), however, the frequency of isolation dominated in the CC with (44.4%), GC (22.2%) and SHC (13%). Staphylococcus aureus had the least frequency (2.2%) followed by Listeria monocytogenes (4.4%). In faecal samples, the occurrence and level of contamination with bacterial species varied across sampling locations with Escherichia coli dominating in the CC with 20% frequency, and abscent from SHC and GC.http://www.aloki.huam2020Veterinary Tropical Disease

Investigation of Brucella melitensis in sable antelope (Hippotragus niger) in South Africa

Supplementary Data 1: Mitigation plan for Farm 1.In this study, Brucella melitensis infection in sable antelope (Hippotragus niger) was investigated on two wildlife ranches in South Africa over a 12-year period in order to determine the origin of the outbreaks and the role of livestock in maintaining the disease. Retrospective data were obtained from farm records and interviews as well as samples tested from di erent disease scenarios and clinical settings. On one ranch, 10 of 74 sable tested seropositive for B. melitensis in 2004 but were certified clear of infection after no further brucellosis cases were detected following repeated serological tests and culling over a five-year period. Recrudescence occurred in 2013 (7 of 187 brucellosis positives) and in 2014 (one positive), with persistent, latent infection being the most reasonable explanation. In a second case study, linked to the first one through a common vendor, 15 of 80 sable tested positive in 2016, some five years after the acquisition of the animals from a putative source. Brucella melitensis biovar 1 and/or 3 were isolated from each outbreak on both ranches. Both outbreaks resulted in substantial losses for the owners, arising from testing and culling and significant resource expenditure by the state. The study identified the diagnostic challenges for identifying and resolving disease outbreaks in wildlife, the persistence of B. melitensis in sable, the risks associated with animal movements, and the need for a wildlife-sensitive disease control scheme. Although the actual source of infection could not be identified, the investigation points away from local livestock as a source of ongoing infection while the persistent infection is consistent with the disease circulating within small, ranched populations and being spread through the keeping and trading of high-value animals. The implications of the study findings to disease control in wildlife are discussed.The ARC-Onderstepoort Veterinary Research (OVR); the Department of Agriculture, Land Reform and Rural Development; National Research Foundation (NRF) and the University of Pretoria.http://www.mdpi.com/journal/microorganismsam2021Centre for Veterinary Wildlife StudiesParaclinical SciencesProduction Animal StudiesVeterinary Tropical Disease

Sero-prevalence of brucellosis among clinically suspect human cases presenting at health facilities in Namibia from 2012 to 2017

OBJECTIVE : This study estimated seroprevalence among human patients presenting with brucellosis-like symptoms in Namibia using serological test results from 2012-2017. METHODS : Presumptive cases were screened using a brucellosis commercial agglutination test kit. RESULTS : Apparent prevalence of human brucellosis was 11.64% (113/971, 95% CI: 9.77-13.81), while active infections were estimated at 6.90% (67/971, 95% CI: 5.47-8.67). Seropositive cases were clustered in the 30-40 year age group, and in females (64%) than males (36%) (z = -5.24, p < 0.01). Age (RR: 0.980 95% CI: 0.907-1.05) and gender (RR: 0.800, 95% CI: 0.598-1.069) were not risk factors for Brucella infection.http://www.elsevier.com/journals/biomedical-and-environmental-sciences/0895-3988hj2022Veterinary Tropical Disease

Assessment of knowledge, attitudes and practices relating to brucellosis among cattle farmers, meat handlers and medical professionals in Namibia

BACKGROUND : Brucellosis is a re-emerging zoonosis of significant socio-economic, animal and public health importance. It is principally a foodborne or occupation-associated infection of humans, whose effective control depends on maximum cooperation of high-risk populations. OBJECTIVES : The study assessed knowledge, attitudes and practices relating to brucellosis among cattle farmers (communal and commercial), meat handlers (abattoir and butchery workers) and medical professionals (nurses and doctors) in Namibia. METHODS : Between June 2019 and September 2020, self-administered questionnaires and questionnaire interviews were carried out in cattle farmers (n = 264), meat handlers (n = 143) and medical professionals (n = 124) in Namibia. RESULTS : Overall, 43.50% (231/531) of respondents were aware of brucellosis, with the highest awareness among medical professionals (73.39%, 91/124) and the least in meat handlers (13.99%, 20/143). Awareness of brucellosis was associated with tertiary education (p < 0.001) and the medical profession (p < 0.001). However, most medical professionals (98.39%, 122/124) did not consider brucellosis as a differential diagnosis in cases of persistent febrile illness. A proportion of communal (85.60%) and commercial (71.00%) farmers; abattoir workers (44.40%); butchers (53.50%); nurses (55.60%); and medical doctors (28.00%) consumed raw milk. CONCLUSIONS : The study identified the purchase of animals of unknown health status; assisting cow delivery; handling of aborted fetuses with no protective wear; consumption of raw milk, homemade cheese, cattle testes and undercooked livers, as risk factors for Brucella infection in cattle and humans. Thus, intensified risk communication, including public health education, is recommended, in particular, among meat handlers and communal farmers, to promote awareness and discourage risky practices.https://wileyonlinelibrary.com/journal/vms3hj2023Veterinary Tropical Disease

The significance of viral, bacterial and protozoan infections in zebra : a systematic review and meta-analysis of prevalence

TABLE S1 : PRISMA Checklists.TABLE S2 : Checklists based on Migliavaca et al. (2020).TABLE S3 : JBI critical appraisal checklists.TABLE S4 : Clinical signs, influencing factors and genotype/serotypes associated with microbial infections in zebra.Wild equids can harbour multi-host infectious agents that are able to affect other wildlife species, but also domestic animals and humans. The direct and indirect contact between wild and domestic equids is constantly increasing due to global movement of horses and equine products, the depletion of natural areas and climate and land-usage changes, which could result in burdensome epidemics. Nevertheless, currently there is a lack of adequate epidemiological data from zebra. Three electronic databases were searched from 10 to 20 March 2021 for publications reporting bacterial, viral and protozoan infections in zebra. Data for a total of 12 relevant variables were extracted from reviewed papers to undergo a qualitative analysis. Prevalence-reporting studies were subjected to meta-analysis for estimating the pooled prevalence and seroprevalence of microbials in wild zebra populations. We identified 30 pathogen species and the most represented were equine Herpesvirus 1 and 9, Bacillus anthracis, African horse sickness virus and Theileria equi. They were reported from all the three zebra species, both in captivity and wilderness. Pooled seroprevalences were estimated for the equine Orbiviruses AHSV (70%; 95% CI: 35–96%) and EEV (21%; 95% CI: 8–38%) and for the equine α-Herpesviruses EHV-1 (72%; 95% CI: 43–93%), EHV-4 (40%; 95% CI: 0–100%) and EHV-9 (58%; 95% CI: 9-98%), and pooled prevalences for the equine piroplasms T. equi (100%; 95% CI: 94–100%) and B. caballi (8%; 95% CI: 0–28%). Zebra is most probably a component of the reservoir from which AHSV, EHV-1 and T. equi can be directly or indirectly transmitted to horse populations, potentially causing disastrous epidemics. Zebra can also harbour zoonotic pathogens like B. anthracis, Brucella spp., A. phagocytophylum, CCHFV and T. brucei. Other agents like EHV-9, BPV-1 and BPV-2 have the potential to spread from zebra to other wild endangered animal species. We conclude that zebra is an important host of multiple and dangerous pathogens for both animals and humans. Comprehensive studies focused on the prevalence of infectious agents present in zebra populations and the associated risk factors are required.http://www.italian-journal-of-mammalogy.ithj2023Veterinary Tropical Disease