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Sydney M Gambushe,1 Oliver T Zishiri,1 Mohamed E El Zowalaty2 1School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa; 2Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE 75 123, SwedenCorrespondence: Mohamed E El Zowalaty, Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE 75 123, Sweden, Email elzow005@gmail.comAbstract: Escherichia coli O157:H7 is an important food-borne and water-borne pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome in humans and may cause serious morbidity and large outbreaks worldwide. People with bloody diarrhea have an increased risk of developing serious complications such as acute renal failure and neurological damage. The hemolytic-uremic syndrome (HUS) is a serious condition, and up to 50% of HUS patients can develop long-term renal dysfunction or blood pressure-related complications. Children aged two to six years have an increased risk of developing HUS. Clinical enteropathogenic Escherichia coli (EPEC) infections show fever, vomiting, and diarrhea. The EPEC reservoir is unknown but is suggested to be an asymptomatic or symptomatic child or an asymptomatic adult carrier. Spreading is often through the fecal-oral route. The prevalence of EPEC in infants is low, and EPEC is highly contagious in children. EPEC disease in children tends to be clinically more severe than other diarrheal infections. Some children experience persistent diarrhea that lasts for more than 14 days. Enterotoxigenic Escherichia coli (ETEC) strains are a compelling cause of the problem of diarrheal disease. ETEC strains are a global concern as the bacteria are the leading cause of acute watery diarrhea in children and the leading cause of traveler’s diarrhea. It is contagious to children and can cause chronic diarrhea that can affect the development and well-being of children. Infections with diarrheagenic E. coli are more common in African countries. Antimicrobial agents should be avoided in the acute phase of the disease since studies showed that antimicrobial agents may increase the risk of HUS in children. The South African National Veterinary Surveillance and Monitoring Programme for Resistance to Antimicrobial Drugs has reported increased antimicrobial resistance in E. coli. Pathogenic bacterial strains have developed resistance to a variety of antimicrobial agents due to antimicrobial misuse. The induced heavy metal tolerance may also enhance antimicrobial resistance. The prevalence of antimicrobial resistance depends on the type of the antimicrobial agent, bacterial strain, dose, time, and mode of administration. Developing countries are severely affected by increased resistance to antimicrobial agents due to poverty, lack of proper hygiene, and clean water, which can lead to bacterial infections with limited treatment options due to resistance.Keywords: Escherichia coli, O157:H, Shiga-toxins, hemolysin, LEE, metagenomic, PhiG17, verotoxin, zoonosis, One health, antimicrobial resistance, acid resistance

Thobeka P Mthembu,1 Oliver T Zishiri,1 Mohamed E El Zowalaty2,3 1School of Life Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa; 2Virology and Microbiology Research Group, School of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa; 3Infectious Diseases and Anti-Infective Research Group, College of Pharmacy, University of Sharjah, Sharjah, 27272, UAECorrespondence: Mohamed E El ZowalatyDepartment of Pharmacy, City University College of Ajman, Ajman 18484, UAEEmail elzow001@gmail.comBackground: Antibiotic-resistant bacterial pathogens associated with livestock remain a major concern worldwide as they get transmitted from animals to humans and cause foodborne and zoonotic diseases.Methods: Antimicrobial resistance in livestock-associated Salmonella spp in South Africa was investigated using molecular DNA methods. Three hundred and sixty-one environmental faecal samples were randomly collected from avian (chicken and ducks), cows, pigs, goats, and sheep. Salmonella spp. were isolated on selective media and were confirmed using the polymerase chain reaction. Antimicrobial susceptibility testing against ampicillin, chloramphenicol, ciprofloxacin, ceftriaxone, azithromycin, tetracycline, amoxicillin-clavulanate and trimethoprim-sulfamethoxazole was determined using the Kirby–Bauer disk diffusion method. Isolates were screened for the presence of blaTEM-1, blaCMY-2, tetA, tetC, sul2 and dfrA7 resistance genes by PCR.Results: Most of the isolates were resistant to ampicillin (64%), tetracycline (63%), amoxicillin-clavulanate (49%), trimethoprim-sulfamethoxazole (38%), and ceftriaxone (20%). Eight percent of the tested isolates were ciprofloxacin-resistant Salmonella spp. Multidrug resistance was observed with the mean multiple antibiotic resistance (MAR) index of 0.31. The study demonstrated that 43% of the isolates were multiple drug resistant. The prevalence rates of resistance genes were 44% for blaTEM-1, 35% for blaCMY-2, 21% for sul2, 18% for tetC, 14% for dfrA7 and 8% for tetA.Conclusion: Resistance to ceftriaxone, detection of blaCMY-2 gene and the high level of intermediate susceptibility (33%) against ciprofloxacin suggested that livestock carry problematic Salmonella spp. This study used the global one-health initiative to report the potential public health risks of livestock-associated pathogens and highlights the importance of monitoring the trends of antimicrobial resistance for sustainability of antibiotics.Keywords: Salmonella, food-borne pathogens, zoonotic, animals, antimicrobial, resistance, blaTEM-1, blaCMY-2, bacteria, ciprofloxacin

Cwengile C Dweba,1 Oliver T Zishiri,1 Mohamed E El Zowalaty2 1Discipline of Genetics, School of Life Sciences, College of Agriculture Engineering and Sciences, University of KwaZulu-Natal, Durban, South Africa; 2Microbiology and Virology Research Group, School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa Abstract: Staphylococcus aureus is an opportunistic pathogen of human and other mammals that is of increasing clinical and veterinary importance due to its ability to rapidly develop antimicrobial resistance. The injudicious use of antibiotics has given rise to the emergence of antibiotic resistant S. aureus strains, most importantly methicillin-resistant Staphylococcus aureus (MRSA). The emergence of livestock-associated MRSA (LA-MRSA) has highlighted the importance of directed research toward its prevention, as well as the need for the discovery and development of more efficient treatment than is currently available. Furthermore, the treatment of MRSA is complicated by the co-selection of heavy metal and antibiotic resistance genes by microorganisms. Livestock and livestock production systems are large reservoirs of heavy metals due to their use in feed as well as environmental contaminant, which has allowed for the selection of LA-MRSA isolates with heavy metal resistance. The World Health Organization reported that Africa has the largest gaps in data on the prevalence of antimicrobial resistance, with no reports on rates for LA-MRSA harboring heavy metal resistance in South Africa. This review aimed to report the emergence of LA-MRSA in South Africa, specifically the most frequent sequence type ST398, globally. Furthermore, we aimed to highlight the importance of LA-MRSA in clinical and food security, as well as this research gap in South Africa. This review sheds light on the prevalence of heavy metals in livestock farms and abattoirs, and focuses on the phenomenon of the co-selection of heavy metal and antibiotic resistance genes in MRSA, emphasizing the importance of a focused direction for research in humans, animals as well as environment using one-health approach. Keywords: Staphylococcus aureus, methicillin resistance, livestock, MRSA, humans, antimicrobial resistance, antibiotics, resistance, virulence, heavy metals, LA-MRSA, one health

Background: Mannose-binding lectin (MBL) is a key component of the innate immune system that plays a crucial role in binding to the microbial sugar surface to recognize and eliminate pathogens by activating the complement system., Objective: To detect and quantify the MBL protein concentration and chicken MBL expression in selected chicken breeds in South Africa., Methods: Forty-five blood samples from three indigenous chicken breeds, Ovambo (OV = 9), Venda (VD = 9) and Potchefstroom Koekoek (PK = 9), and two exotic chicken breeds, Rhode Island Red (RIR = 9) and Lohmann Brown (LB = 9), were used for MBL protein concentration using enzyme-linked immunosorbent assay (ELISA) techniques. Also 20 liver samples from symptomatic two indigenous chicken breeds, OV (5) and PK (5), and two exotic chicken breeds, RIR (5) and LB (5), were used for MBL expression using quantitative polymerase chain reaction (qPCR) techniques. A general linear model was done using Tukey's multiple comparison post hoc test., Results: The findings revealed MBL protein concentration from 5.26 to 18.56 µg/mL. The LB breed had the lowest mean 6.40 ± 0.80 µg/mL, whereas the PK breed had the highest mean MBL concentration of 17.70 ± 0.24 µg/mL of MBL protein concentration. At 12, 25 and 35 weeks, the MBL proteins of OV, VD, PK, RIR and LB varied significantly at p ≤ 0.05. The mRNA MBL expression of OV and LB breeds showed a 1-fold decrease in MBL expression, while RIR showed a 2-fold increase in MBL expression, and the PK showed more than a 3-fold increase in MBL expression relative to the control. The least-squares means for OV, LB, PK and RIR mRNA MBL expression were 0.54 ± 0.19, 0.68 ± 0.30, 4.46 ± 2.76 and 2.89 ± 0.19 µg/mL, respectively., Conclusion: MBL protein was detected and quantified with distinct differences in concentration and expression levels  at the presence of mycoplasma gallisepticum among the sampled South African chicken breeds. This highlights the genetic diversity of MBL as a tool for disease prevention in South African chicken breeds., (© 2024 The Author(s). Veterinary Medicine and Science published by John Wiley & Sons Ltd.)

Background: Prostate cancer is the second leading cause of cancer deaths in men, second only to lung cancer. Despite this, diagnosis and prognosis methods remain limited, with effective treatments being few and far between. Traditionally, prostate cancer is initially tested for through a prostate serum antigen (PSA) test and a digital rectum examination (DRE), followed by confirmation through an invasive prostate biopsy. The DRE and biopsy are uncomfortable for the patient, so less invasive, accurate diagnostic tools are needed. Current diagnostic tools, along with genes that hold possible biomarker uses in diagnosis, prognosis and indications for personalised treatment plans, were reviewed in this article., Recent Findings: Several genes from multiple families have been identified as possible biomarkers for disease, including those from the MYC and ETS families, as well as several tumour suppressor genes, Androgen Receptor signalling genes and DNA repair genes. There have also been advances in diagnostic tools, including MRI-targeted and liquid biopsies. Several personalised treatments have been developed over the years, including those that target metabolism-driven prostate cancer or those that target inflammation-driven cancer., Conclusion: Several advances have been made in prostate cancer diagnosis and treatment, but the disease still grows year by year, leading to more and more deaths annually. This calls for even more research into this disease, allowing for better diagnosis and treatment methods and a better chance of patient survival., (© 2024 The Author(s). Cancer Reports published by Wiley Periodicals LLC.)

Background: The impact of chickens on maintaining the economy and livelihood of rural communities cannot be overemphasized. In recent years, mycoplasmosis has become one of the diseases that affect the success of South African chicken production. Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) are the most prevalent strains of Mycoplasma in South Africa. MG and MS are significant respiratory pathogens affecting the productivity of chickens. The present study aimed to molecularly detect using qPCR and characterize the presence of MG and MS using phylogenetic analysis. The phylogenetic analysis was utilized to clarify general evolutionary relationships between related taxa of different MG and MS observed in tracheal swabs from South African chicken breeds., Methods: Forty-five tracheal swabs of the Lohmann Brown (n = 9), Rhode Island Red (n = 9), Ovambo (n = 9), Venda (n = 9), and Potchefstroom Koekoek (n = 9) breeds were collected from symptomatic chickens present in the commercial farm. To detect MG and MS, DNA was extracted from tracheal swabs and faecal samples, and qPCR was performed with a 16 s rRNA (310 bp) and vlhA (400 bp) gene fragment. Following the sequencing of all the amplicons, MG, and MS dendrograms showing the evolutionary relationships among the five South African chicken breeds and the GeneBank reference population were constructed., Results: The qPCR revealed the presence of MG and MS in 22% (2/9) of the tracheal swab samples tested for MS only in Rhode Island Red breeds; 66.6% (6/9) and 33% (3/9) of the tested samples in Ovambo breeds; and 11.1% (1/9) and 44.4% (4/9) of the tested samples in Venda breeds. No MG or MS were detected in the Lohmann Brown or Potchefstroom Koekoek breed. Furthermore, qPCR revealed the presence of MG in pooled faecal samples from Lohmann Brown and Ovambo breeds. Eight different bacterial isolates were recognized from both samples. Four isolates were of the 16 s ribosomal ribonucleic acid (rRNA) gene (named PT/MG51/ck/00, PT/MG48/ck/00, PT/MG41/ck/00 and PT/MG71/ck/00) gene of Mycoplasma gallisepticum, and the other was Mycoplasma Synoviae variable lipoprotein hemagglutinin A (vlhA) gene (named PT/MSA22/ck/01, PT/MS41/ck/01, PT/MS74/ck/01 and PT/MS46/ck/01) which were available in GenBank. These isolates were successfully sequenced with 95-100% similarity to the isolates from the gene bank., Conclusion: The study revealed the presence of both MG and MS in the chicken breeds sampled. Furthermore, the different breeds of chicken were found to be susceptible to infection under the intensive or commercial management system. Therefore, continuous surveillance is encouraged to prevent the spread and outbreak of MG and MS in the poultry industry in South Africa., (© 2024. The Author(s).)

Here, we report the draft genome sequences of two Bacillus licheniformis strains harboring the lichenysin operon that were isolated from healthy goat and horse in South Africa. The genomes were sequenced using Illumina MiSeq and had a length of 4,152,826 and 4,110,075 bp, respectively, with a G + C content of 46%., Competing Interests: The authors declare no conflict of interest.

Staphylococcus aureus is an important human and veterinary pathogen. The present study aimed to determine the prevalence of antibiotic resistance among S. aureus isolated from samples obtained from free-flying wild pigeons and houseflies from different locations surrounding a local hospital in the Greater Durban area in KwaZulu-Natal Province, South Africa. Environmental fecal samples were obtained from wild pigeons that inhabits the grounds of a local public hospital located on the South Beach area, Durban, South Africa. Housefly samples were collected from three different locations (Kenneth Stainbank Nature Reserve, Montclair/Clairwood, and Glenwood/Berea) in the greater Durban area, all within a close proximity to the hospital. Following enrichment, identification, and antimicrobial resistance profiling, S. aureus isolates were subjected to DNA extraction using the boiling method. It was found that 57 out of 252 samples (22.62%) were positive for S. aureus . The Kirby-Bauer disk diffusion method of antibiotic susceptibility testing was performed and revealed that antibiotic resistance rates to penicillin and rifampicin were the most common, with both returning 48 (84.2%) out of the 57  S. aureus isolates being resistant to penicillin and rifampicin. Antibiotic resistance rates to clindamycin, linezolid, erythromycin, tetracycline, cefoxitin, and ciprofloxacin were 82.5%, 78.9%, 73.7%, 63.2%, 33.3%, and 15.8% respectively. Antibiotic resistance genes were detected using primer-specific PCR and it was found that the prevalence rates of tetM, aac(6')-aph(2″), mecA, tetK, ermc , and blaZ genes were 66.7%, 40.4%, 40.4%, 38.6%, 24.6%, and 3.51% respectively. Statistical analysis revealed significant ( p  < 0.05) relationships between the tetM, aac(6')-aph(2″), and ermC genes and all parameters tested. A significant correlation between the aac(6')-aph(2″) gene and the tetM (0.506) and ermC (-0.386) genes was identified. It was found that 23 (40.3%) S. aureus isolates were mecA  positive, of which 10 (52.6%) out of 19 cefoxitin-resistant isolates were mecA  positive and 13 (35.1%) out of 37 cefoxitin-sensitive isolates were  mecA  positive. The results of the present study demonstrated the detection of methicillin and multidrug resistant S. aureus isolated from samples obtained from wild pigeons and houseflies in the surroundings of a local public hospital in the Greater Durban area in South Africa. The findings of the study may account for the emergence of multidrug-resistant staphylococcal infections. The findings highlight the significant role of wild pigeons and houseflies in the spread of drug-resistant pathogenic S. aureus including MRSA. The conclusions of the present study highlight the improtant role of wildlife and the environment as interconnected contributors of  One Health ., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this manuscript., (© 2024 The Authors.)

Escherichia coli O157:H7 is a foodborne pathogen that has been linked to global disease outbreaks. These diseases include hemorrhagic colitis and hemolytic uremic syndrome. It is vital to know the features that make this strain pathogenic to understand the development of disease outbreaks. In the current study, a comparative genomic analysis was carried out to determine the presence of structural and functional features of O157:H7 strains obtained from 115 National Center for Biotechnology Information database. These strains of interest were analysed in the following programs: BLAST Ring Image Generator, PlasmidFinder, ResFinder, VirulenceFinder, IslandViewer 4 and PHASTER. Five strains (ECP19-198, ECP19-798, F7508, F8952, H2495) demonstrated a great homology with Sakai because of a few regions missing. Five resistant genes were identified, however, Macrolide-associated resistance gene mdf(A) was commonly found in all genomes. Majority of the strains (97%) were positive for 15 of the virulent genes (espA, espB, espF, espJ, gad, chuA, eae, iss, nleA, nleB, nleC, ompT, tccP, terC and tir). The plasmid analysis demonstrated that the IncF group was the most prevalent in the strains analysed. The prophage and genomic island analysis showed a distribution of bacteriophages and genomic islands respectively. The results indicated that structural and functional features of the many O157:H7 strains differ and may be a result of obtaining mobile genetic elements via horizontal gene transfer. Understanding the evolution of O157:H7 strains pathogenicity in terms of their structural and functional features will enable the development of detection and control of transmission strategies., (© 2023. The Author(s).)

The current study aimed to determine virulence determinants among S. aureus isolated from wild pigeons and houseflies around hospital areas in the Greater Durban area, South Africa. Following enrichment and bacterial growth, DNA extraction using the boiling method was performed. Overall, 57 out of 252 samples (22.6%) were positive for S. aureus . Six known virulence genes were tested, where five known virulence determinants were positive and none of the S. aureus isolates were positive to coagulase ( coa ) gene. The highest prevalence rates were found in the genes encoding haemolysins, with the hla and hld genes having 8 (14%) and 9 (15.8%) positive isolates respectively. The sea , LukS/F-PV , and spa genes had 5 (8.8%), 4 (7%), and 2 (3.5%) positive isolates respectively. These results demonstrated the detection of pathogenic S. aureus from hospital environment in Durban, South Africa which may account for the emergence staphylococcal infections. The findings of the present study highlights the significant role of wild pigeons and houseflies as potenital infectious disease vectors in a One Health context., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this manuscript., (© 2023 The Authors.)

The emergence of antimicrobial-resistant, livestock-associated Enterococcus faecalis represents a public health concern. Here, we report the isolation, molecular detection of virulence and antimicrobial resistance determinants, in addition to the phylogenetic analyses of 20 Enterococcus species using whole genome sequencing analysis of 15 Enterococcus faecalis strains including six strains of three novel sequence types, three Enterococcus faecium and two Enterococcus durans. All strains were isolated from food chain animals in South Africa. Enterococcus strains were isolated on bile aesculin azide agar, followed by identification using MALDI-TOF MS analysis. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk diffusion method. The genomic DNA of the isolates was extracted and sequencing was performed using the Illumina MiSeq platform. Sequence reads were trimmed and de novo assembled. The assembled contigs were analyzed for antimicrobial resistance genes and chromosomal mutations, extra-chromosomal plasmids, and multi-locus sequence type (MLST). Multidrug antimicrobial resistance genes conferring resistance to aminoglycosides (ant(6)-Ia, aph(3')-IIIa, sat4, and spw), lincosamides (lnu(B), lsa(A), and lsa(E)), macrolides (erm(B)), trimethoprim (dfrG) and tetracyclines (tet(L) and tet(M)) were identified. Plasmid replicons were detected in seven E. faecalis and three E. faecium isolates. The sequence type (ST) of each isolate was determined using the Enterococcus PubMLST database. Ten STs were identified in the collection, three of which (ST1240, ST1241, and ST1242) have not been previously reported and are described in the present study for the first time. To compare the sequenced strains to other previously sequenced E. faecalis strains, assembled sequences of E. faecalis from livestock were downloaded from the PubMLST database. Core genome-based phylogenetic analysis was performed using ParSNP. The detection of multiple drug-resistance in Enterococcus including E. faecalis and E. faecium highlights the significance of genomic surveillance to monitor the spread of antimicrobial resistance in food chain animals. In addition, the genome sequences of Enterococcus strains reported in the present study will serve as a reference point for future molecular epidemiological studies of livestock-associated and antibiotic-resistant E. faecalis in Africa. In addition, this study enables the in-depth analysis of E. faecalis genomic structure, as well as provides valuable information on the phenotypic and genotypic antimicrobial resistance, and the pathogenesis of livestock-associated E. faecalis and E. faecium., (© 2023. The Author(s).)

Here, we report the draft genome sequence of Listeria innocua strain MEZLIS29, which was isolated from a healthy cow in Flagstaff, Eastern Cape Province, South Africa. The genome was sequenced using the Illumina MiSeq platform and had a length of 2,805,865 bp, with a G+C content of 37.5% and 2,783 coding DNA sequences, 58 tRNAs, 4 noncoding RNAs, and 8 rRNA genes.

The hospital environment acts as a reservoir in the transmission of pathogens, such as MRSA, which may cause hospital-acquired infections. This study aimed to ascertain the prevalence, genetic relatedness, antibiotic resistance, and virulence profile of MRSA on some frequently touched hospital sites in South Africa. A total of 777 swabs were randomly collected from 11 frequently touched sites in the hospital environment of three wards of four public hospitals in the KwaZulu-Natal province of South Africa. Isolation of S. aureus and confirmation were done using genotypic and phenotypic methods. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk-diffusion method. MRSA isolates were determined by the presence of the mecA gene. Virulence and resistance genes were detected using a standard monoplex PCR assay. ERIC-PCR was conducted to evaluate the genetic relatedness. An overall prevalence of 12.7% for S. aureus isolates was obtained. Out of these, 89.9% (89/99) were confirmed to be MRSA. The sites with the highest prevalence were the occupied beds (16.2% (16/99)), unoccupied beds (16.2% (16/99)), patient files (14.1% (14/99)), ward phones (13.1% (13/99)), and nurses' tables (14.1% (14/99)). The virulence genes with the highest observed frequency were hld (87 (87.9%)) and LukS/F-PV (53 (53.5%)). The resistance genes with the highest frequency were the tetM and tetK genes detected in 60 (60.6%) and 57 (57.6%) isolates, respectively. The ERIC-PCR results obtained indicated a high level of genetic diversity; however, intraclonal (within a hospital) and interclonal (between hospitals) clusters of MRSA were observed. The study showed that MRSA can contaminate various surfaces, and this persistence allows for the dissemination of bacteria within the hospital environment. This highlights the need for improved infection prevention and control (IPC) strategies in public hospitals in the country to curb their potential transmission risks., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2021 Siyethaba Mkhize et al.)

Tick-borne diseases (TBDs) hamper the growth of the livestock sector and impose major constraints for the health and management of domestic animals in the tropic and subtropical regions globally. Currently, there is no scientific report on the presence of zoonotic pathogens transmitted by tick species in Lesotho. This study aimed to identify zoonotic tick-borne pathogens of economic importance from ticks infesting domestic animals in Lesotho using molecular techniques. A total of 322 tick DNA pools were subjected to PCR screening for the presence of zoonotic pathogens and sequenced. The overall prevalence of Anaplasma spp. was 35% (113/322), with a 100% infection rate in Rhipicephalus microplus , followed by R . evertsi evertsi (92%), Hyalomma rufipes and Otobius megnini sharing 50% and the lowest infection rate was observed in R . decoloratus with 40%. The prevalence of Coxiella burnetii , a gram-negative pleomorphic etiological agent of Query fever (Q fever), was 1% (2/322) for all screened samples, with 20% of R . decoloratus and 1% of R . e . evertsi infected. Rickettsia africae was detected from Hyalomma rufipes with a 70% prevalence. This study provides a baseline knowledge of tick-borne pathogens of medical and veterinary importance in Lesotho and raises awareness of the prevalence of such diseases within the tourism sector as they are mostly affected.

The bovine lymphocyte antigen ( BoLA-DRB3 ) gene is an important region that codes for glycoproteins responsible for the initiation of an immune response. BoLA-DRB3 alleles have been demonstrated to be associated with disease resistance/tolerance. Therefore, great genetic diversity is correlated with better adaptation, fitness, and robustness. The current study was conducted to assess the population genetic structure of the BoLA-DRB3 gene in Nguni crossbred cattle using polymerase chain reaction-sequence based typing (PCR-SBT). High genetic diversity was detected, with 30 alleles, 11 of which are novel to the study. Alleles DRB3*0201, DRB3*0701, DRB*0901 , and DRB*1601 were present in all populations and accounted for nearly around 50% of all observed alleles. A mean genetic diversity (H E ) of 0.93 was detected. The high overall genetic diversity is possibly associated with pathogen-assisted selection and heterozygote advantage. Such high diversity might explain the hardiness of the Nguni crossbred cattle to the Southern African region. Low population genetic structure was identified (F ST = 0.01), suggesting possible gene flow between populations and retention of similar alleles. The study was undertaken to bridge the dearth of such studies in South African breeds and it is imperative for effective sustainability of indigenous breeds and the implementation of effective breeding strategies.

The rising trend of antimicrobial resistance (AMR) by foodborne bacteria is a public health concern as these pathogens are easily transmitted to humans through the food chain. Non-typhoid Salmonella spp. is one of the leading foodborne pathogens which infect humans worldwide and is associated with food and livestock. Due to the lack of discovery of new antibiotics and the pressure exerted by antimicrobial resistance in the pharmaceutical industry, this review aimed to address the issue of antibiotic use in livestock which leads to AMR in Salmonella . Much attention was given to resistance to carbapenems and colistin which are the last-line antibiotics used in cases of multi drug resistant bacterial infections. In the present review, we highlighted data published on antimicrobial resistant Salmonella species and serovars associated with livestock and food chain animals. The importance of genomic characterization of carbapenem and colistin resistant Salmonella in determining the relationship between human clinical isolates and food animal isolates was also discussed in this review. Plasmids, transposons, and insertion sequence elements mediate dissemination of not only AMR genes but also genes for resistance to heavy metals and disinfectants, thus limiting the therapeutic options for treatment and control of Salmonella . Genes for resistance to colistin ( mcr-1 to mcr-9 ) and carbapenem ( blaVIM-1 , blaDNM-1 , and blaNDM-5 ) have been detected from poultry, pig, and human Salmonella isolates, indicating food animal-associated AMR which is a threat to human public health. Genotyping, plasmid characterization, and phylogenetic analysis is important in understanding the epidemiology of livestock-related Salmonella so that measures of preventing foodborne threats to humans can be improved.

In recent years, diseases caused by pathogenic bacteria have profoundly impacted chicken production by causing economic loss in chicken products and by-product revenues. MBL (mannose-binding lectin) is part of the innate immune system (IIS), which is the host's first line defense against pathogens. The IIS functions centrally by identifying pathogen-specific microorganism-associated molecular patterns (MAMPs) with the help of pattern recognition receptors (PRRs). Studies have classified mannose-binding lectin (MBL) as one of the PRR molecules which belong to the C-type lectin family. The protective role of MBL lies in its ability to activate the complement system via the lectin pathway and there seems to be a direct link between the chicken's health status and the MBL concentration in the serum. Several methods have been used to detect the presence, the level and the structure of MBL in chickens such as Enzyme-linked immunosorbent assay (ELISA), Polymerase Chain Reaction (PCR) among others. The concentration of MBL in the chicken ranges from 0.4 to 35 µg/mL and can be at peak levels at three to nine days at entry of pathogens. The variations observed are known to depend on the bacterial strains, breed and age of the chicken and possibly the feed manipulation strategies. However, when chicken MBL (cMBL) becomes deficient, it can result in malfunctioning of the innate immune system, which can predispose chickens to diseases. This article aimed to discuss the importance and components of mannose-binding lectin (MBL) in chickens, its mode of actions, and the different methods used to detect MBL. Therefore, more studies are recommended to explore the causes for low and high cMBL production in chicken breeds and the possible effect of feed manipulation strategies in enhancing cMBL production.

Objectives: The emergence of antimicrobial-resistant livestock-associated Escherichia coli represents a great public health concern. Here we report the draft genome sequences of two multidrug-resistant livestock-associated E. coli strains MEZEC8 and MEZEC10 isolated from sheep in South Africa., Methods: Genomic DNA of E. coli strains MEZEC8 and MEZEC10 was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids, and the sequence type (ST) was determined by multilocus sequence typing (MLST). To compare strains MEZEC8 and MEZEC10 with other previously published sequences of E. coli strains, raw read sequences of E. coli from livestock were downloaded from the NCBI's Sequence Read Archive and all sequence files were treated identically to generate a core genome bootstrapped maximum likelihood phylogenetic tree., Results: Antimicrobial resistance genes were detected in MEZEC8 and MEZEC10 conferring resistance to tetracycline and macrolides. MEZEC10 harboured two extrachromosomal plasmids (pO111 and Incl2), while MEZEC8 did not contain any extrachromosomal plasmids. Strain MEZEC8 belonged to serotype H25:O9 and ST58, whereas strain MEZEC10 belonged to serotype H49:O8 and ST1844., Conclusion: The genome sequences of E. coli strains MEZEC8 and MEZEC10 will serve as a reference point for molecular epidemiological studies of antimicrobial-resistant livestock-associated E. coli in Africa. In addition, this study allows in-depth analysis of genomic structure and will provide valuable information enabling us understand the antimicrobial resistance of livestock-associated E. coli., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

This study was conducted from January to October 2018 with the objective to determine the prevalence and genetic diversity of Eimeria species in broiler and free-range chickens in KwaZulu-Natal province, South Africa. A total of 342 faecal samples were collected from 12 randomly selected healthy broiler chicken farms and 40 free-range chickens from 10 different locations. Faecal samples were screened for the presence of Eimeria oocysts using a standard flotation method. The species of Eimeria isolates were confirmed by amplification of the internal transcribed spacer 1 (ITS-1) partial region and sequences analysis. Among broiler and free-ranging chickens, 19 out of 41 pens (46.3%) and 25 out of 42 faecal samples (59.5%) were positive for Eimeria infection. Molecular detection revealed the following species: Eimeria maxima, Eimeria tenella, Eimeria acervulina, Eimeria brunetti and Eimeria mitis in all the samples screened. Similarly, polymerase chain reaction assays specific for three cryptic Eimeria operational taxonomic units were negative for all the samples. Phylogenetic analysis of the ITS-1 sequences supported species identity with the greatest variation detected for E. mitis. This study provides information on the range and identity of Eimeria species, and their genetic relatedness, circulating in commercially reared broilers and free-ranging chickens from different locations in KwaZulu-Natal province.

Objectives: Antimicrobial-resistant livestock-associated Salmonella enterica infections pose a significant public-health threat worldwide. Here we report for the first time the draft genome sequences of two multidrug-resistant livestock-associated S. enterica strains isolated from a chicken and a cow in South Africa., Methods: Genomic DNA of S. enterica strains MEZSAL74 and MEZSAL81 was sequenced using an Illumina MiSeq platform. The generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids. Multilocus sequence typing (MLST) was also performed. In order to compare isolates MEZSAL74 and MEZSAL81 with other previously sequenced S. enterica isolates, raw read sequences were downloaded and all sequence files were treated identically to generate a bootstrapped maximum likelihood phylogenetic tree., Results: Extrachromosomal plasmids and genetic determinants of antimicrobial resistance were detected in both sequenced bacterial isolates to aminoglycosides and fluoroquinolones. By MLST, strain MEZSAL74 belonged to an unknown sequence type (ST) and strain MEZSAL81 belonged to ST33., Conclusion: The genome sequences of strains MEZSAL74 and MEZSAL81 reported here will serve as a reference for molecular epidemiological studies of antimicrobial-resistant livestock-associated S. enterica in Africa., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Here, we report the draft genome sequence of Listeria innocua strain MEZLIS26, isolated from a healthy goat in Flagstaff, Eastern Cape Province, South Africa. The genome was sequenced using the Illumina MiSeq platform and had a length of 2,800,777 bp, with a G+C content of 37.4%, 2,755 coding DNA sequences (CDSs), 49 transfer RNAs (tRNAs), and 4 noncoding RNAs (ncRNAs)., (Copyright © 2019 El Zowalaty et al.)

Livestock are an important source of protein and food for humans, however opportunistic pathogens such as Salmonella spp. turn livestock into vehicles of foodborne diseases. This study investigated the prevalence of virulence genes in Salmonella spp. isolated from livestock production systems in two provinces of South Africa. During the period from May to August, 2018, a total of 361 faecal (189), oral (100), environmental (soil (36) and water (27)) and feed (9) samples were randomly collected from different animals (cattle, sheep, goats, pigs, ducks and chickens) that were housed in small-scale livestock production systems from Eastern Cape and KwaZulu-Natal Provinces in South Africa. Salmonella spp. were isolated and identified using microbiological and DNA molecular methods. Salmonella spp. were present in 29.0% of the samples of which 30.2% belonged to the Salmonella enterica species as confirmed by the positive amplification of the species specific iroB gene. Virulence genes that were screened from livestock-associated Salmonella were invA , iroB , s piC , pipD and int1 . Statistically significant associations ( p < 0.05) were established between the virulence genes, sampling location, animal host as well as the season when samples were collected. Furthermore, statistically significant ( p < 0.05) positive correlations were observed between most of the virulence genes investigated. This is one of the recent studies to detect and investigate livestock-associated Salmonella spp. in South Africa. This study highlights the importance of continuous monitoring and surveillance for pathogenic salmonellae. It also demonstrated the detection and prevalence of virulent Salmonella spp. harbored by livestock in South Africa. This study demonstrated the potential risks of pathogenic Salmonella enterica to cause foodborne diseases and zoonotic infections from farm-to-fork continuum using the global one-health approach., Competing Interests: The authors declare that they have no financial or personal relationships that may have inappropriately influenced them in writing this article.

Fasciola spp. are the causative agents of fascioliasis in humans and livestock. Before the development of control and management measures, the geographical distribution of the species and patterns of infection must be considered. Because of difficulties in the phenotypic differentiation and morphometric classification of Fasciola spp., DNA molecular markers have become more useful for fluke differentiation and description of phylogenetic patterns. This study aimed to differentiate and describe the phylogenetic background of Fasciola spp. isolated from cattle slaughtered at three abattoirs in the Mpumalanga and KwaZulu-Natal provinces of South Africa. The cytochrome c oxidase I (COI) - FHCO1 (forward: 5'-TTGGTTTTTTGGGCATCCT-3') and FHCO1 (reverse: 5' -AGGCCACCACCAAATAAAAGA3') - marker was sequenced from 55 Fasciola flukes that were collected from abattoirs in catchment areas of the KwaZulu-Natal and Mpumalanga provinces. Fasciola hepatica was demonstrated to have 100% prevalence in KwaZulu-Natal and Mpumalanga (highveld), respectively, and 76% prevalence in the lowveld (Belfast area) of Mpumalanga. Two animals from the Belfast metapopulation were co-infected with both Fasciola gigantica and F. hepatica. DNA sequence analysis of all the isolates demonstrated a sequence conservation of 0.472, nucleotide diversity of 0.082 and Tajima's D of -1.100; however, it was not statistically significant (p > 0.05). Twenty-two haplotypes were identified, with 18 novel haplotypes being unique to the isolates from South Africa. Within the study samples, 12 haplotypes were isolated to a few individuals, with a haplotype diversity of 0.8957 indicating high genetic diversity. Principal coordinate analysis supported the clustering and distribution of the haplotypes, with 11.38% of the variation being attributed to coordinate 2 and 55.52% to coordinate 1. The distribution of Fasciola spp. has been demonstrated to be related to the distribution of the freshwater intermediate host snails, Lymnaea spp., as well as the relative altitude of the localities in South Africa. Information provided by this study serves as preliminary evidence for further studies on the mapping of the distribution of F. gigantica and F. hepatica in South Africa, which is key in designing control programmes for fascioliasis in humans and livestock.

Staphylococcus aureus is one of the most important pathogens of humans and animals. Livestock production contributes a significant proportion to the South African Gross Domestic Product. Consequently, the aim of this study was to determine for the first time the prevalence, virulence, antibiotic and heavy metal resistance in livestock-associated S. aureus isolated from South African livestock production systems. Microbial phenotypic methods were used to detect the presence of antibiotic and heavy metal resistance. Furthermore, molecular DNA based methods were used to genetically determine virulence as well as antibiotic and heavy metal resistance determinants. Polymerase chain reaction (PCR) confirmed 217 out of 403 (53.8%) isolates to be S. aureus . Kirby-Bauer disc diffusion method was conducted to evaluate antibiotic resistance and 90.8% of S. aureus isolates were found to be resistant to at least three antibiotics, and therefore, classified as multidrug resistant. Of the antibiotics tested, 98% of the isolates demonstrated resistance towards penicillin G. High resistance was shown against different heavy metals, with 90% (196/217), 88% (192/217), 86% (188/217) and 84% (183/217) of the isolates resistant to 1500 µg/mL concentration of Cadmium (Cd), Zinc (Zn), Lead (Pb) and Copper (Cu) respectively. A total of 10 antimicrobial resistance and virulence genetic determinants were screened for all livestock associated S. aureus isolates. Methicillin-resistant S. aureus (MRSA) isolates were identified, by the presence of mecC , in 27% of the isolates with a significant relationship ( p < 0.001)) with the host animal. This is the first report of mecC positive LA-MRSA in South Africa and the African continent. The gene for tetracycline resistance ( tetK) was the most frequently detected of the screened genes with an overall prevalence of 35% and the highest prevalence percentage was observed for goats (56.76%) followed by avian species (chicken, duck and wild birds) (42.5%). Virulence-associated genes were observed across all animal host species. The study reports the presence of luks/pv , a gene encoding the PVL toxin previously described to be a marker for community acquired-MRSA, suggesting the crossing of species between human and livestock. The high prevalence of S. aureus from the livestock indicates a major food security and healthcare threat. This threat is further compounded by the virulence of the pathogen, which causes numerous clinical manifestations. The phenomenon of co-selection is observed in this study as isolates exhibited resistance to both antibiotics and heavy metals. Further, all the screened antibiotic and heavy metal resistance genes did not correspond with the phenotypic resistance.

Enterococcus species have developed from being commensal bacteria to leading pathogens that cause infections in humans and animals. The gastrointestinal tract of mammals is the normal habitat of these species. Virulence factors are proteins that are produced by the bacterium which are used to enhance their pathogenicity. The objectives of this study were to isolate Enterococcus spp. from livestock and companion animals, differentiate between the different sub-species and detect the presence of important virulence genes. Rectal and saliva swabs were collected from dogs and cats, whereas only rectal swabs were collected from cattle and cloacal swabs from chickens. Presumptive Enterococcus was selected using Bile Esculin Azide (BEA) agar, and Enterococcus species were confirmed using the polymerase chain reaction (PCR) by amplifying the tuf gene. In order to differentiate between E. faecalis and E. faecium, a multiplex PCR was used to detect the SodA gene. The genes responsible for gelatinase production (gelE) and for conjugation (ccf) were also detected using PCR. Out of 211 animal swabs, 182 (86%) were positive for the tuf gene. Overall, there were 55 isolates of E. faecalis (30%) compared to 22 isolates of E. faecium (12%). The virulence genes had a prevalence of 52% and 36% for gelE and ccf, respectively, in all animal hosts. The results demonstrated that chicken cloacal samples had the highest prevalence for E. faecalis, gelE and ccf genes compared to all the other isolates detected from other animal hosts. The results also demonstrated a statistically significant (p < 0.05) association between the prevalence of virulence genes (gelE and ccf) and animal species from which Enterococcus spp. was isolated. We provided evidence that healthy livestock and companion animals can harbour pathogenic Enterococcus that can be transferred via the food chain as well as through close association such as petting and licking of humans. This study partially demonstrated that Enterococci spp. are capable of evolving from being simple commensal bacteria to becoming pathogens that cause infection in humans and animals through the acquisition of virulence factors through mobile genetic elements.

Virulence-associated genes have been recognised and detected in Campylobacter species. The majority of them have been proven to be associated with pathogenicity. This study aimed to detect the presence of virulence genes associated with pathogenicity and responsible for invasion, expression of adherence, colonisation and production of the cytolethal distending toxin (cdt) in Campylobacter jejuni and Campylobacter coli. Commercial chicken faecal samples were randomly sampled from chicken farms within the Durban metropolitan area in South Africa. Furthermore, human clinical Campylobacter spp. isolates were randomly sampled from a private pathology laboratory in South Africa. Out of a total of 100 chicken faecal samples, 78% (n = 78) were positive for Campylobacter growth on modified charcoal cefoperazone deoxycholate and from the random laboratory collection of 100 human clinical isolates, 83% (n = 83) demonstrated positive Campylobacter spp. growth following culturing methods. These samples were screened for the presence of the following virulence genes: cadF, hipO, asp, ciaB, dnaJ, pldA, cdtA, cdtB and cdtC. As expected, the cadF gene was present in 100% of poultry (n = 78) and human clinical isolates (n = 83). Campylobacter jejuni was the main species detected in both poultry and human clinical isolates, whilst C. coli were detected at a significantly lower percentage (p < 0.05). Eight per cent of the C. jejuni from human clinical isolates had all virulence genes that were investigated. Only one C. coli isolate demonstrated the presence of all the virulence genes investigated; however, the pldA virulence gene was detected in 100% of the C. coli isolates in poultry and a high percentage (71%) in human clinical C. coli isolates as well. The detection of cdt genes was found at higher frequency in poultry than human clinical isolates. The high prevalence rates of virulence genes detected in poultry and human clinical isolates demonstrate their significance in the pathogenicity of Campylobacter species.

Campylobacter spp. are common pathogenic bacteria in both veterinary and human medicine. Infections caused by Campylobacter spp. are usually treated using antibiotics. However, the injudicious use of antibiotics has been proven to spearhead the emergence of antibiotic resistance. The purpose of this study was to detect the prevalence of antibiotic resistance genes in Campylobacter spp. isolated from chickens and human clinical cases in South Africa. One hundred and sixty one isolates of Campylobacter jejuni and Campylobacter coli were collected from chickens and human clinical cases and then screened for the presence of antimicrobial resistance genes. We observed a wide distribution of the tetO gene, which confers resistance to tetracycline. The gyrA genes that are responsible quinolone resistance were also detected. Finally, our study also detected the presence of the blaOXA-61, which is associated with ampicillin resistance. There was a higher (p < 0.05) prevalence of the studied antimicrobial resistance genes in chicken faeces compared with human clinical isolates. The tetO gene was the most prevalent gene detected, which was isolated at 64% and 68% from human and chicken isolates, respectively. The presence of gyrA genes was significantly (p < 0.05) associated with quinolone resistance. In conclusion, this study demonstrated the presence of gyrA (235 bp), gyrA (270 bp), blaOXA-61 and tetO antimicrobial resistance genes in C. jejuni and C. coli isolated from chickens and human clinical cases. This indicates that Campylobacter spp. have the potential of resistance to a number of antibiotic classes.

Antimicrobial resistance of Staphylococcus aureus in human and veterinary medicine is a serious worldwide problem. The aim of this study was to investigate the prevalence of S. aureus in commercial broiler chickens as well as to establish antimicrobial susceptibility and the distribution of genetic determinants conferring resistance and virulence. One hundred and ninety-four samples were aseptically collected from broiler chicken slaughterhouses and retail outlets around the Durban metropolitan area in South Africa. Microbiological and molecular methods were used to detect the presence of S. aureus as well as its resistance- and virulence-associated genes. Polymerase chain reaction (PCR) was used to confirm the presence of S. aureus by amplifying the nuc gene. Approximately 54% of 194 samples were positive for S. aureus. The disc diffusion technique was used to investigate antimicrobial susceptibility profiles of the S. aureus isolates to a battery of 10 antimicrobial agents, namely ampicillin, chloramphenicol, gentamicin, erythromycin, cefoxitin, kanamycin, streptomycin, tetracycline, vancomycin and trimethoprim. The results demonstrated that S. aureus isolates of abattoir origin had a high level (79.4%) of resistance to tetracycline, followed by ampicillin, vancomycin, cefoxitin, trimethoprim, erythromycin and streptomycin with resistance rates of 65.1%, 61.9%, 60.3%, 58.7%, 57.1% and 46.0%, respectively. Staphylococcus aureus isolates of retail origin exhibited higher antimicrobial resistance prevalence rates than those of abattoir origin. Tetracycline had the highest resistance rate (100%), followed by cefoxitin (91.7%), erythromycin (83.3%), streptomycin (83.3%) and kanamycin (66.7%). All isolates were resistant to two or more antimicrobial agents. Out of the four virulence genes that were screened, only two were detected (coagulase and protein A); however, their prevalence rates were very low. All antimicrobial resistance genes screened were detected (mecA, BlaZ and tetK), although their prevalence did not correspond with antimicrobial susceptibility testing.

Salmonellosis is a significant public health concern around the world. The injudicious use of antimicrobial agents in poultry production for treatment, growth promotion and prophylaxis has resulted in the emergence of drug resistant strains of Salmonella. The current study was conducted to investigate the prevalence of virulence and antimicrobial resistance genes from Salmonella isolated from South African and Brazilian broiler chickens as well as human clinical isolates. Out of a total of 200 chicken samples that were collected from South Africa 102 (51%) tested positive for Salmonella using the InvA gene. Of the overall 146 Salmonella positive samples that were screened for the iroB gene most of them were confirmed to be Salmonella enterica with the following prevalence rates: 85% of human clinical samples, 68.6% of South African chicken isolates and 70.8% of Brazilian chicken samples. All Salmonella isolates obtained were subjected to antimicrobial susceptibility testing with 10 antibiotics. Salmonella isolates from South African chickens exhibited resistance to almost all antimicrobial agents used, such as tetracycline (93%), trimethoprim-sulfamthoxazole (84%), trimethoprim (78.4%), kanamycin (74%), gentamicin (48%), ampicillin (47%), amoxicillin (31%), chloramphenicol (31%), erythromycin (18%) and streptomycin (12%). All samples were further subjected to PCR in order to screen some common antimicrobial and virulence genes of interest namely spiC, pipD, misL, orfL, pse-1, tet A, tet B, ant (3")-la, sul 1 and sul. All Salmonella positive isolates exhibited resistance to at least one antimicrobial agent; however, antimicrobial resistance patterns demonstrated that multiple drug resistance was prevalent. The findings provide evidence that broiler chickens are colonised by pathogenic Salmonella harbouring antimicrobial resistance genes. Therefore, it is evident that there is a need for prudent use of antimicrobial agents in poultry production systems in order to mitigate the proliferation of multiple drug resistance across species.