Whole genome sequencing and identification of Bacillus endophyticus and B. anthracis isolated from anthrax outbreaks in South Africa

Abstract Background Bacillus endophyticus is a soil plant-endophytic bacterium, while B. anthracis is the causative agent of anthrax. The virulence factors of B. anthracis are the plasmid encoded tripartite toxins (pXO1) and poly-γ-glutamic acid (PGA) capsule (pXO2). B. endophyticus isolated alongside B. anthracis from animals that died of anthrax in Northern Cape Province (NCP), South Africa, harbored polyglutamate genes. The study compared the characteristics of B. anthracis and B. endophyticus with other Bacillus species with a focus on the presence of the PGA capsule or/and unbound PGA. The morphology and whole genome sequence analysis of B. endophyticus strains and B. anthracis were compared. Results In conventional microbiology, B. endophyticus showed gram-positive round-shaped rods in single/short chains, which were endospore-forming, non-motile, non-haemolytic with white and dry colonies, and γ-phage resistant. B. anthracis was differentiated from B. endophyticus based on the latter’s box-shaped rods in pairs/long chains, white-grey and slimy colonies, encapsulated and γ-phage susceptible. The study identified a PGA polyglutamate synthase operon that consisted of pgsBCA, γ-glutamyltranspeptidase (ggt) and pgsE in B. endophyticus genomes. Conclusions PGA regions of B. anthracis contain capBCADE genes located in the pXO2 required for capsulation formation, while B. endophyticus contain the pgsBCAE genes in the chromosome. Whole genome and microbiology analysis identified B. endophyticus, as a non-capsuled endospore-forming bacterium that consists of PGA required for biosynthesis. B. endophyticus strains do not synthesize surface associated PGA, therefore capsule visualization of B. anthracis is a key diagnostic characteristic. The study highlights the significance of using whole genome shotgun sequencing to identify virulence and other important genes that might be present amongst unknown samples from natural outbreaks. None of the B. anthracis related plasmids or virulence genes were found in the B. endophyticus genomes

Occurrence, Antimicrobial Resistance, and Virulence Profiles of Salmonella Serovars Isolated from Wild Reptiles in South Africa

Reptiles are carriers of an array of microorganisms, including signifcant zoonotic bacteria of the genus Salmonella, which cause a disease referred to as salmonellosis that afects both animals and humans. Tis study investigated the occurrence of Salmonella serovars in wild reptiles at Timbavati Private Game Reserve in Limpopo Province, South Africa, and examined their virulence and antimicrobial resistance gene profles. A total of 19 wild reptiles were sampled, which resulted in 30 presumptive Salmonella isolates. Te isolates were identifed using polymerase chain reaction (PCR) by amplifying the invA gene and were further confrmed by 16S rRNA gene sequencing. Salmonella serovars were detected in chameleons (36.8%), lizards (31.6%), snakes (15.8%), and tortoises (15.8%). Te use of 16S rRNA gene sequencing revealed that Salmonella enterica subsp. enterica serovar Salamae (30%), S. enterica subsp. enterica (16.7%), S. enterica subsp. enterica serovar Typhimurium (13.3%), and S. enterica subsp. enterica serovar Indiana (13.3%) were the four most common subspecies among the investigated 30 isolates. Detected virulence genes included pagN (100%), hilA (96.7%), ssrB (96.7%), prgH (86.7%), and marT (86.7%). Te isolates exhibited resistance to nalidixic acid (43.3%) and kanamycin (43.3%), followed by streptomycin (16.7%) and ciprofoxacin (3.3%). Antibiotic-resistant genes were detected as follows: strA, strB, qnrA, qnrS, parC, aadA, aac(6′)-Ib, and aac(6′)-Ib-cr at 33.3%, 6.7%, 16.7, 13.3%, 10%, 23.3%, 6.7%, and 10%, respectively. Te fndings highlight the necessity of educational initiatives aimed at reducing reptile-related infections. Efective antibiotic treatment appears promising for infection, given the minimal drug resistance observed in reptile Salmonella serovars in the current stud

Molecular detection of Coxiella burnetii and Coxiella species in rats and chickens from poultry farms in North West Province, South Africa

Abstract Background Coxiella burnetii is a bacterial pathogen that causes query fever and coxiellosis in humans and animals, respectively. There is a scarcity of studies on the prevalence of C. burnetii infections in rats and chickens in South Africa. Objective The aim of this study was to determine the occurrence of C. burnetii in rats and chickens sampled from poultry farms in the North West Province of South Africa. Methods DNA was extracted from rodent kidneys (n = 68) and chicken faeces (n = 52). Two rodent pest species, namely Rattus rattus and Rattus tanezumi, were identified by analysis of CO1 gene sequences. Detection of C. burnetii was carried out using polymerase chain reaction assays targeting 23S rRNA, 16S rRNA and IS111 markers. Results C. burnetii was detected in 16.2%, 8.8% and 25% of R. rattus, R. tanezumi and chickens, respectively. Conclusions The findings in this study demonstrate that rodents and chickens are harbouring C. burnetii at sampled poultry farms. There should be frequent screening for C. burnetii in poultry operations. The likelihood of future transmission between rodents and chickens, including humans, also needs to be investigated

The phylogenomic landscape of extended-spectrum β-lactamase producing Citrobacter species isolated from surface water

Abstract Background Citrobacter species are Gram-negative opportunistic pathogens commonly reported in nosocomial-acquired infections. This study characterised four Citrobacter species that were isolated from surface water in the North West Province, South Africa. Results Phenotypic antimicrobial susceptibility profiles of the isolates demonstrated their ability to produce the extended-spectrum β-lactamase (ESBL). Whole genomes were sequenced to profile antibiotic resistance and virulence genes, as well as mobile genetic elements. In silico taxonomic identification was conducted by using multi-locus sequence typing and average nucleotide identity. A pangenome was used to determine the phylogenomic landscape of the Citrobacter species by using 109 publicly available genomes. The strains S21 and S23 were identified as C. braakii, while strains S24 and S25 were C. murliniae and C. portucalensis, respectively. Comparative genomics and sequenced genomes of the ESBL-producing isolates consisted of n = 91; 83% Citrobacter species in which bla- CMY−101 (n = 19; 32,2%) and bla- CMY−59 (n = 12; 38,7%) were prevalent in C. braakii, and C. portucalensis strains, respectively. Macrolide (acrAB-TolC, and mdtG) and aminoglycoside (acrD) efflux pumps genes were identified in the four sequenced Citrobacter spp. isolates. The quinolone resistance gene, qnrB13, was exclusive to the C. portucalensis S25 strain. In silico analysis detected plasmid replicon types IncHI1A, IncP, and Col(VCM04) in C. murliniae S24 and C. portucalensis S25, respectively. These potentially facilitate the T4SS secretion system in Citrobacter species. In this study, the C. braakii genomes could be distinguished from C. murliniae and C. portucalensis on the basis of gene encoding for cell surface localisation of the CPS (vexC) and identification of genes involved in capsule polymer synthesis (tviB and tviE). A cluster for the salmochelin siderophore system (iro-BCDEN) was found in C. murliniae S24. This is important when it comes to the pathogenicity pathway that confers an advantage in colonisation. Conclusions The emerging and genomic landscapes of these ESBL-producing Citrobacter species are of significant concern due to their dissemination potential in freshwater systems. The presence of these ESBL and multidrug-resistant (MDR) pathogens in aquatic environments is of One Health importance, since they potentially impact the clinical domain, that is, in terms of human health and the agricultural domain, that is, in terms of animal health and food production as well as the environmental domain

Molecular Detection of Integrons, Colistin and β-lactamase Resistant Genes in Salmonella enterica Serovars Enteritidis and Typhimurium Isolated from Chickens and Rats Inhabiting Poultry Farms

The rapid growth of multidrug-resistant Salmonella is a global public health concern. The aim of this study was to detect integrons, colistin and β-lactamase resistance genes in Salmonella enteritidis and typhimurium. A total of 63 isolates of S. enteritidis (n = 18) and S. typhimurium (n = 45) from fecal samples of layers and rats at chicken farms were screened for antibiotic resistant genes. Conventional PCR was performed for the detection of integrons (classes 1, 2, and 3), colistin (mcr-1-5) and β-lactamase (blaCTX-M, blaCTX-M-1, blaCTX-M-2, blaCTX-M-9, blaCTX-M-15, blaTEM, blaSHV, and blaOXA) resistant genes. Of these isolates, 77% and 27% of S. typhimurium and S. enteritidis harboured the mcr-4 encoded gene for colistin, respectively. The prevalence of class 1 integrons for S. typhimurium and S. enteritidis was 100% for each serovar, while for class 2 integrons of S. typhimurium and S. enteritidis it was 49% and 33% respectively, while class 3 integron genes was not detected. Our study also detected high levels of β-lactamase encoding genes (bla gene), namely blaCTX-M, blaCTX-M-1, blaCTX-M-9 and blaTEM from both S. typhimurium and S. enteritidis. This, to our knowledge, is the first report of mcr-4 resistance gene detection in Salmonella serovars in South Africa. This study also highlights the importance of controlling rats at poultry farms in order to reduce the risk of transmission of antibiotic resistance to chickens and eventually to humans

Prevalence and antimicrobial resistance profiles of Campylobacter species in South Africa: a “One Health” approach using systematic review and meta-analysis

Objectives: This study investigated the prevalence and antibiotic resistance (AR) profiles of Campylobacter spp. isolated from animals, humans, and the environment in South Africa based on available published data. Methods: Original articles published from January 1, 1990 to January 1, 2021 were searched from PubMed, ScienceDirect, Google Scholar, Africa Index Medicus, Scopus, and African Journal Online databases. Data were analyzed with Comprehensive Meta-Analysis (version 3.0). Results: After screening, articles on animals (n = 25), humans (n = 7), environment (n = 3), animals/environment (n = 2), and a (n = 1) study on animals, humans, and the environment were included in this review. The pooled prevalence estimates (PPEs) were 28.8%, 16.4%, and 28.4% in animals, humans, and the environment, respectively. The Campylobacter jejuni and Campylobacter coli species were commonly isolated from humans, animals, and the environment in South Africa. The AR profiles were screened from 2032 Campylobacter spp., with the highest PPE of AR observed against clindamycin (76.9%) and clarithromycin (76.5%). Campylobacter isolates tested with the disk diffusion assay and minimum inhibitory concentration methods recorded an overall AR prevalence of 35.3% and 37.1%, respectively, whereas multidrug resistance PPE was 35.3%. Conclusion: Regular surveillance of Campylobacter spp. prevalence and its antimicrobial resistance strains is recommended, as well as the formulation of a “One Health” approach for better management and control of Campylobacter spp. infection in South Africa