Background and Aim: Previous studies recorded the prevalence of gastrointestinal nematodes (GIN) in Limpopo Province. However, the studies did not address the seasonal patterns of infection and did not cover all districts of Limpopo Province, namely; Capricorn, Sekhukhune, Waterberg, Mopani, and Vhembe. It is, therefore, important to provide up to date information on the prevalence and seasonal occurrence data of GIN in all districts of Limpopo province. The present study was conducted to determine the occurrence of anthelmintic resistance (AR) and document the prevalence of GIN infecting sheep in five districts of Limpopo Province, South Africa. Materials and Methods: Forty animals in each district were used for fecal egg count reduction test (FECRT) to determine AR against ivermectin (0.2 mg/kg), levamisole (LEV) (5 mg/kg), and albendazole (7.5 mg/kg). Egg hatch test (EHT) was used to determine AR against thiabendazole (TBZ) and micro-agar larval development test (MALDT) was used for both TBZ and LEV. Naturally, infected sheep (n=780) were sampled for prevalence across five districts of Limpopo. FAMACHA© eye-color score estimations were also performed for each study animal. Results: FECRT showed occurrence of AR in most of the districts and a few with suspected resistance. EHT results showed AR development against TBZ for all districts, while the MALDT showed no AR against LEV in all districts, but detected AR against TBZ in Sekhukhune, Capricorn, and Waterberg. Haemonchus contortus was the most resistant species. A high nematode prevalence (88-100%) and 1210-1861 eggs per gram (EPG) was observed in all districts during the hot wet season, decreasing to 75-80% (453-1202 EPG) during the cold dry season. The sheep revealed a FAMACHA© mean score of 3, indicating mild anemia during the hot wet season except for Vhembe district that revealed a FAMACHA© mean score of 4 during the hot wet season, indicating anemia. Conclusion: AR recorded in Limpopo Province may be due to under-dosing caused by lack of weighing equipment and high treatment frequencies due to lack of proper training on anthelmintic use. The detection of AR in Limpopo is an important finding because it will help in outlining effective management systems against GIN.

Listeria monocytogenes is a ubiquitous bacterial pathogen that threatens the food chain and human health. In this study, whole-genome sequencing (WGS) was used for the genomic characterization of L. monocytogenes (n = 24) from beef and beef-based products. Multilocus Sequence Type (MLST) analysis revealed that ST204 of CC204 was the most common sequence type (ST). Other sequence types detected included ST1 and ST876 of CC1, ST5 of CC5, ST9 of CC9, ST88 of CC88, ST2 and ST1430 of CC2, and ST321 of CC321. Genes encoding for virulence factors included complete LIPI-1 (pfrA-hly-plcA-plcB-mpl-actA) from 54% (13/24) of the isolates of ST204, ST321, ST1430, and ST9 and internalin genes inlABC that were present in all the STs. All the L. monocytogenes STs carried four intrinsic/natural resistance genes, fosX, lin, norB, and mprF, conferring resistance to fosfomycin, lincosamide, quinolones, and cationic peptides, respectively. Plasmids pLGUG1 and J1776 were the most detected (54% each), followed by pLI100 (13%) and pLM5578 (7%). The prophage profile, vB_LmoS_188, was overrepresented amongst the isolates, followed by LP_101, LmoS_293_028989, LP_030_2_021539, A006, and LP_HM00113468. Listeria genomic island 2 (LGI-2) was found to be present in all the isolates, while Listeria genomic island 3 (LGI-3) was present in a subset of isolates (25%). The type VII secretion system was found in 42% of the isolates, and sortase A was present in all L. monocytogenes genomes. Mobile genetic elements and genomic islands did not harbor any virulence, resistance, or environmental adaptation genes that may benefit L. monocytogenes. All the STs did not carry genes that confer resistance to first-line antibiotics used for the treatment of listeriosis. The characterization of L. monocytogenes in our study highlighted the environmental resistance and virulence potential of L. monocytogenes and the risk posed to the public, as this bacterium is frequently found in food and food processing environments.

Whole-genome sequencing (WGS) was used for the genomic characterization of one hundred and ten strains of Listeria innocua (L. innocua) isolated from twenty-three cattle farms, eight beef abattoirs, and forty-eight retail outlets in Gauteng province, South Africa. In silico multilocus sequence typing (MLST) was used to identify the isolates’ sequence types (STs). BLAST-based analyses were used to identify antimicrobial and virulence genes. The study also linked the detection of the genes to the origin (industries and types of samples) of the L. innocua isolates. The study detected 14 STs, 13 resistance genes, and 23 virulence genes. Of the 14 STs detected, ST637 (26.4%), ST448 (20%), 537 (13.6%), and 1085 (12.7%) were predominant, and the frequency varied significantly (p < 0.05). All 110 isolates of L. innocua were carriers of one or more antimicrobial resistance genes, with resistance genes lin (100%), fosX (100%), and tet(M) (30%) being the most frequently detected (p < 0.05). Of the 23 virulence genes recognized, 13 (clpC, clpE, clpP, hbp1, svpA, hbp2, iap/cwhA, lap, lpeA, lplA1, lspA, oatA, pdgA, and prsA2) were found in all 110 isolates of L. innocua. Overall, diversity and significant differences were detected in the frequencies of STs, resistance, and virulence genes according to the origins (source and sample type) of the L. innocua isolates. This, being the first genomic characterization of L. innocua recovered from the three levels/industries (farm, abattoir, and retail) of the beef production system in South Africa, provides data on the organism’s distribution and potential food safety implications.

A participatory research model was used in six village communities in the Central Region of the North West Province of South Africa in order to achieve the following broad objectives : to obtain information on the challenges owners face in raising livestock in these areas and to evaluate the livestock owners' level of knowledge of internal parasites in their animals. Information obtained at participatory workshops clearly indicated a need for improvements in water supply, schools, job creation, and health services. Lack of pasture for grazing livestock was also cited as being important. Other most frequently mentioned livestock problems included 'gall sickness' (a vaguely defined condition not necessarily referring to anaplasmosis), parasites (both external and internal), chicken diseases and ingestion of plastic bags discarded in the environment. When livestock owners were questioned during individual interviews, most were able to identify the presence of parasites in either the live or dead animal. However, it seems likely that this is limited to the identification of tapeworms. It was found that most livestock owners use a combination of treatments, ranging from traditional to folklore to commercial. There were some difficulties in using the participatory methods since it was the first time that the facilitators and the communities had been exposed to them. Many communities had difficulty in dealing with the concept of finding solutions within the community, which is such an integral part of participatory methods.

In this study, Listeria isolates (214) were characterized as follows: L. innocua (77.10%), L. monocytogenes (11.21%), L. welshimeri (5.61%), L. grayi (1.40%), L. seeligeri (0.93%), and L. species (3.73%) that were not identified at the species level, from beef and beef based products from retail and farms in Mpumalanga and North West provinces of South Africa. MLVA was further used to type Listeria innocua isolates (165) and Listeria monocytogenes isolates (24). The L. monocytogenes isolates were also serogrouped using PCR. The MLVA protocol for L. monocytogenes typing included six tandem repeat primer sets, and the MLVA protocol for L. innocua included the use of three tandem repeats primer sets. The L. monocytogenes serogroups were determined as follows: 4b-4d-4e (IVb) (37.50%), 1/2a-3a (IIa) (29.16%), 1/2b-3b (IIb) (12.50%), 1/2c-3c (IIc) (8.33%), and IVb-1 (4.16%). MLVA could cluster isolates belonging to each specie, L. monocytogenes, and L. innocua isolates, into MLVA-related strains. There were 34 and 10 MLVA types obtained from the MLVA typing of L. innocua and L. monocytogenes, respectively. MLVA clustered the L. monocytogenes isolates irrespective of sample category, serogroups, and geographical origin. Similarly, the L. innocua isolates clustered irrespective of meat category and geographical origin. MLVA was able to cluster isolates based on MLVA relatedness. The clustering of isolates from farms and retailers indicates transmission of Listeria spp. MLVA is an affordable, simple, and discriminatory method that can be used routinely to type L. monocytogenes and L. innocua isolates.

The study used whole-genome sequencing (WGS) and bioinformatics analysis for the genomic characterization of 60 isolates of Listeria monocytogenes obtained from the beef production chain (cattle farms, abattoirs, and retail outlets) in Gauteng province, South Africa. The sequence types (STs), clonal complexes (CCs), and the lineages of the isolates were determined using in silico multilocus sequence typing (MLST). We used BLAST-based analyses to identify virulence and antimicrobial genes, plasmids, proviruses/prophages, and the CRISPR-Cas system. The study investigated any association of the detected genes to the origin in the beef production chain of the L. monocytogenes isolates. Overall, in 60 isolates of Listeria monocytogenes, there were seven STs, six CCs, forty-four putative virulence factors, two resistance genes, one plasmid with AMR genes, and three with conjugative genes, one CRISPR gene, and all 60 isolates were positive for proviruses/prophages. Among the seven STs detected, ST204 (46.7%) and ST2 (21.7%) were the most prominent, with ST frequency varying significantly (p < 0.001). The predominant CC detected were CC2 (21.7%) and CC204 (46.7%) in lineages I and II, respectively. Of the 44 virulence factors detected, 26 (across Listeria Pathogenicity Islands, LIPIs) were present in all the isolates. The difference in the detection frequency varied significantly (p < 0.001). The two AMR genes (fosX and vga(G)) detected were present in all 60 (100%) isolates of L. monocytogenes. The only plasmid, NF033156, was present in three (5%) isolates. A CRISPR-Cas system was detected in six (10%), and all the isolates carried proviruses/prophages. The source and sample type significantly affected the frequencies of STs and virulence factors in the isolates of L. monocytogenes. The presence of fosX and vga(G) genes in all L. monocytogenes isolates obtained from the three industries of the beef production chain can potentially cause therapeutic implications. Our study, which characterized L. monocytogenes recovered from the three levels in the beef production chain, is the first time genomics was performed on this type of data set in the country, and this provides insights into the health implications of Listeria.