Microbial Communities of Meat and Meat Products: An Exploratory Analysis of the Product Quality and Safety at Selected Enterprises in South Africa

Annotated genome sequences of Salmonella Haifa, Salmonella Bangkok, and Salmonella Reading, isolated from chicken meat in South Africa

This paper presents the annotated genomes of Salmonella Haifa, Salmonella Bangkok, and Salmonella Reading, which are uncommonly isolated from meat in South Africa. Despite their rarity in South Africa, these serotypes have been linked to several high-profile outbreaks in other parts of the world.

"One Health" Perspective on Prevalence of ESKAPE Pathogens in Africa: A Systematic Review and Meta-Analysis

The leading cause of hospital-acquired infections worldwide includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) infections. These bacteria are commonly isolated from clinical settings and linked to a number of potentially fatal diseases associated with hospitals. The objective of this study was to review the prevalence of ESKAPE pathogens in Africa. We gathered and systematically reviewed the literature concerning the prevalence of ESKAPE pathogens, published in the English language from January 2014 to February 2024, from three databases (PubMed, Web of Science and ScienceDirect). Our overall results revealed that S. aureus was the most prevalent species (79.5%), followed by A. baumannii (27.6%), K. pneumoniae (24.2%), Enterobacter spp. (20%), P. aeruginosa (9.0%), and E. faecium (5.1%). Moreover, stool samples had the highest Pooled Prevalence Estimates (PPEs) of 44.0%, followed by urine, nasal, and blood samples with 37.3%, 26.9%, and 22.9%, respectively. For the diagnostic method used to identify these ESKAPE pathogens, VITEK-MS had the highest PPE of 55.2%, followed by whole genome sequencing and PCR with 37.1% and 33.2%, respectively. The highest PPE of ESKAPE pathogens was recorded in West Africa with 77.3%, followed by Central/Middle Africa and East Africa with 43.5% and 25.1%, respectively. The overall PPE of ESKAPE pathogens from humans, animals, the environment (water, soil, and surfaces) and food sources was 35.8%, 37.3%, 47.7%, and 34.2%, respectively. Despite their prevalence in nosocomial settings, studies have shown that the ESKAPE pathogens may be isolated from a range of environmental reservoirs, including soil, dumping sites, beach sand, wastewater, food, and fish farms, among others. This wide source of ESKAPE pathogens substrates indicates the need for a multidisciplinary collaborative partnership for epidemiological studies and intervention efforts by the human, veterinary, and environmental health sectors in Africa.

Foodborne Microbiological Hazards in Ghana: A Scoping Review

Background

Foodborne diseases pose a significant public health threat, particularly in regions with poor sanitation and food handling practices. These diseases, mainly caused by microbiological hazards like bacteria, fungi, and parasites, affect millions globally. Despite the global burden, the true extent of these hazards remains underestimated, especially in low- and middle-income countries like Ghana. This study aimed to map the available literature on foodborne microbiological hazards in Ghana, providing an overview of the evidence and identifying areas where further research is needed.

Method

This review followed the Preferred Reporting Items for Systematic Reviews and Meta-analysis Extension for Scoping Reviews. A detailed search was done in PubMed, Scopus, Web of Science, and Google Scholar, and articles were exported to Rayyan for screening. A three-phase screening process was used to identify relevant articles. Data from the included articles were extracted and analysed, with specific information related to food type, specific hazards, sample population, and hazard groups summarised using proportions and tables.

Results

This review included 72 studies which were published between 2001 and 2023. Eighty-five percent of these studies (85%) reported on bacterial hazards, while 19%, 11%, and 6% reported on fungi, parasites, and mycotoxins, respectively. The most reported bacterial, fungal, and parasitic hazards were Escherichia coli, Aspergillus spp. and Trichuris trichiura, respectively. Aflatoxins were reported in maize, groundnut, and spices, with prevalence ranging from 61% to 100% and at levels exceeding standards set by Ghana Standards Authority and European Food Safety Authority.

Conclusion

This review highlighted the spectrum of microbiological hazards in foods in Ghana. The hazards identified pose significant public health risks, particularly among vulnerable populations. It is crucial that stricter enforcement of food safety laws and improved food handling practices are implemented in the country, particularly in the informal food sector, to protect consumers.

Contamination of Plant Foods with Bacillus cereus in a Province and Analysis of Its Traceability

Bacillus cereus is an important zoonotic foodborne conditional pathogen. It is found in vegetables, dairy products, rice, and other foods, thereby greatly endangering human health. Investigations on B. cereus contamination in China primarily focus on raw milk, dairy products, meat, and others, and limited research has been conducted on plant-based foodstuffs. The rapid development of sequencing technology and the application of bioinformatics-related techniques means that analysis based on whole-genome sequencing has become an important tool for the molecular-epidemiology investigation of B. cereus. In this study, we investigated the contamination of B. cereus in six types of commercially available plant foods from eight regions of a province. The molecular epidemiology of the isolated B. cereus was analyzed by whole-genome sequencing. We aimed to provide fundamental data for the surveillance and epidemiology analysis of B. cereus in food products in China. The rapid traceability system of B. cereus established in this study can provide a basis for rapid molecular epidemiology analysis of B. cereus, as well as for the prevention and surveillance of B. cereus. Moreover, it can also be expanded to monitoring and rapid tracing of more foodborne pathogens.

A South African Perspective on the Microbiological and Chemical Quality of Meat: Plausible Public Health Implications

Meat comprises proteins, fats, vitamins, and trace elements, essential nutrients for the growth and development of the body. The increased demand for meat necessitates the use of antibiotics in intensive farming to sustain and raise productivity. However, the high water activity, the neutral pH, and the high protein content of meat create a favourable milieu for the growth and the persistence of bacteria. Meat serves as a portal for the spread of foodborne diseases. This occurs because of contamination. This review presents information on animal farming in South Africa, the microbial and chemical contamination of meat, and the consequential effects on public health. In South Africa, the sales of meat can be operated both formally and informally. Meat becomes exposed to contamination with different categories of microbes, originating from varying sources during preparation, processing, packaging, storage, and serving to consumers. Apparently, meat harbours diverse pathogenic microorganisms and antibiotic residues alongside the occurrence of drug resistance in zoonotic pathogens, due to the improper use of antibiotics during farming. Different findings obtained across the country showed variations in prevalence of bacteria and multidrug-resistant bacteria studied, which could be explained by the differences in the manufacturer practices, handling processes from producers to consumers, and the success of the hygienic measures employed during production. Furthermore, variation in the socioeconomic and political factors and differences in bacterial strains, geographical area, time, climatic factors, etc. could be responsible for the discrepancy in the level of antibiotic resistance between the provinces. Bacteria identified in meat including Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, Campylobacter spp., Salmonella spp., etc. are incriminated as pathogenic agents causing serious infections in human and their drug-resistant counterparts can cause prolonged infection plus long hospital stays, increased mortality and morbidity as well as huge socioeconomic burden and even death. Therefore, uncooked meat or improperly cooked meat consumed by the population serves as a risk to human health.

Meat Irradiation: A Comprehensive Review of Its Impact on Food Quality and Safety

Food irradiation is a proven method commonly used for enhancing the safety and quality of meat. This technology effectively reduces the growth of microorganisms such as viruses, bacteria, and parasites. It also increases the lifespan and quality of products by delaying spoilage and reducing the growth of microorganisms. Irradiation does not affect the sensory characteristics of meats, including color, taste, and texture, as long as the appropriate dose is used. However, its influence on the chemical and nutritional aspects of meat is complex as it can alter amino acids, fatty acids, and vitamins as well as generate free radicals that cause lipid oxidation. Various factors, including irradiation dose, meat type, and storage conditions, influence the impact of these changes. Irradiation can also affect the physical properties of meat, such as tenderness, texture, and water-holding capacity, which is dose-dependent. While low irradiation doses potentially improve tenderness and texture, high doses negatively affect these properties by causing protein denaturation. This research also explores the regulatory and public perception aspects of food irradiation. Although irradiation is authorized and controlled in many countries, its application is controversial and raises concerns among consumers. Food irradiation is reliable for improving meat quality and safety but its implication on the chemical, physical, and nutritional properties of products must be considered when determining the appropriate dosage and usage. Therefore, more research is needed to better comprehend the long-term implications of irradiation on meat and address consumer concerns.

Virulence and Antimicrobial Resistance Profiling of Salmonella Serovars Recovered from Retail Poultry Offal in KwaZulu-Natal Province, South Africa

As poultry organ meat is widely consumed, especially in low- and middle-income countries, there is reason to investigate it as a source of Salmonella infections in humans. Consequently, the aim of this study was to determine the prevalence, serotypes, virulence factors and antimicrobial resistance of Salmonella isolated from chicken offal from retail outlets in KwaZulu-Natal, South Africa. Samples (n = 446) were cultured for the detection of Salmonella using ISO 6579-1:2017. Presumptive Salmonella were confirmed using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry. Salmonella isolates were serotyped using the Kauffmann-White-Le Minor scheme and antimicrobial susceptibility was determined by the Kirby-Bauer disk diffusion technique. A conventional PCR was used for the detection of Salmonella invA, agfA, lpfA and sivH virulence genes. Of the 446 offal samples, 13 tested positive for Salmonella (2.91%; CI = 1.6-5). The serovars included S. Enteritidis (n = 3/13), S. Mbandaka (n = 1/13), S. Infantis (n = 3/13), S. Heidelberg (n = 5/13) and S. Typhimurium (n = 1/13). Antimicrobial resistance against amoxicillin, kanamycin, chloramphenicol and oxytetracycline was found only in S. Typhimurium and S. Mbandaka. All 13 Salmonella isolates harboured invA, agfA, lpfA and sivH virulence genes. The results show low Salmonella prevalence from chicken offal. However, most serovars are known zoonotic pathogens, and multi-drug resistance was observed in some isolates. Consequently, chicken offal products need to be treated with caution to avoid zoonotic Salmonella infections.

Characterisation and antibiotic resistance of Yersinia enterocolitica from various meat categories, South Africa

Yersinia enterocolitica infections impose a significant public health and socioeconomic burden on human population in many countries. The current study investigated the prevalence, antimicrobial resistance profile and molecular diversity of Y. enterocolitica in meat and meat products across various retail outlets in selected provinces of South Africa (SA). In a cross-sectional study, a total of 581 retail meat and meat products were collected from four cities across three provinces of SA. Samples were from beef and pork products, which included 292 raw intact, 167 raw processed, and 122 ready-to-eat (RTE) meats. Samples were analysed using classical microbiological methods for isolation, identification and biotyping of Y. enterocolitica. Conventional polymerase chain reaction (PCR) was performed for confirmation, serotyping, screening of virulence (n = 11) and antimicrobial resistance (n = 18) genes. Phenotypic antimicrobial resistance profiles were determined against 12 antibiotics discs, using disc diffusion method. The overall prevalence of 12% (70/581) was reported across all cities with contamination proportion reported in samples collected from raw intact 15% (43/292), followed by raw processed 11% (18/167) and RTE meats 7% (9/122). All positive isolates were of biotype 1A with 7% (5/70) belonging to bioserotype 1A/O:8. Most of the isolates harboured ymoA, ystB, fepD, ail, fepA, invA and myfA virulence genes. High antimicrobial resistance frequency was observed for ampicillin (94%), cephalothin (83%) and amoxicillin (41%), respectively. Of the 18 tested antimicrobial resistance genes, blaTEM was the most predominant (40%) followed by cmlA (21%). This study reveals the presence of antimicrobial resistant Y. enterocolitica possessing virulent genes of public health importance in products of animal origin, therefore, health monitoring and surveillance of this pathogen is required.

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.

Laboratory Misidentifications Resulting from Taxonomic Changes to Bacillus cereus Group Species, 2018-2022

Whole-genome sequencing (WGS) is being applied increasingly to Bacillus cereus group species; however, misinterpretation of WGS results may have severe consequences. We report 3 cases, 1 of which was an outbreak, in which misinterpretation of B. cereus group WGS results hindered communication within public health and industrial laboratories.

Research Update on the Impact of Lactic Acid Bacteria on the Substance Metabolism, Flavor, and Quality Characteristics of Fermented Meat Products

This paper reviews the effects of domestic and foreign influences on the substance metabolism pathways and the flavor and flora of LAB in fermented meat products to provide a new theoretical basis for developing new products for the industrial application of lactic acid bacteria (LAB) in fermented meat products. LAB are extensively used among commonly fermented ingredients, such as fermented meat products and yogurt. As fermenting agents, LAB metabolize proteins, lipids, and glycogen in meat products through their enzyme system, which affects the tricarboxylic acid cycle, fatty acid metabolism, amino acid decomposition, and other metabolic processes, and decompose biological macromolecules into small molecules, adding a special flavor with a certain functionality to the final product. Metabolites of LAB in the fermentation process also exert nitrite degradation, as well as antibacterial and antioxidant functions, which improve the physical and chemical qualities of fermented meat products. While fermenting meat products, LAB not only add unique flavor substances to the products, but also improve the safety profile of fermented foods.

Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking

Members of the Bacillus cereus sensu lato species complex, also known as the B. cereus group, vary in their ability to cause illness but are frequently isolated from foods, including meat products; however, food safety surveillance efforts that use whole-genome sequencing (WGS) often neglect these potential pathogens. Here, we evaluate the surveillance and source tracking potential of WGS as applied to B. cereus sensu lato by (i) using WGS to characterize B. cereus sensu lato strains isolated during routine surveillance of meat products across South Africa (n = 25) and (ii) comparing the genomes sequenced here to all publicly available, high-quality B. cereus sensu lato genomes (n = 2,887 total genomes). Strains sequenced here were collected from meat products obtained from (i) retail outlets, processing plants, and butcheries across six South African provinces (n = 23) and (ii) imports held at port of entry (n = 2). The 25 strains sequenced here were partitioned into 15 lineages via in silico seven-gene multilocus sequence typing (MLST). While none of the South African B. cereus sensu lato strains sequenced here were identical to publicly available genomes, six MLST lineages contained multiple strains sequenced in this study, which were identical or nearly identical at the whole-genome scale (≤3 core single nucleotide polymorphisms). Five MLST lineages contained (nearly) identical genomes collected from two or three South African provinces; one MLST lineage contained nearly identical genomes from two countries (South Africa and the Netherlands), indicating that B. cereus sensu lato can spread intra- and internationally via foodstuffs. IMPORTANCE Nationwide foodborne pathogen surveillance programs that use high-resolution genomic methods have been shown to provide vast public health and economic benefits. However, Bacillus cereus sensu lato is often overlooked during large-scale routine WGS efforts. Thus, to our knowledge, no studies to date have evaluated the potential utility of WGS for B. cereus sensu lato surveillance and source tracking in foodstuffs. In this preliminary proof-of-concept study, we applied WGS to B. cereus sensu lato strains collected via South Africa's national surveillance program of domestic and imported meat products, and we provide strong evidence that B. cereus sensu lato can be disseminated intra- and internationally via the agro-food supply chain. Our results showcase that WGS has the potential to be used for source tracking of B. cereus sensu lato in foods, although future WGS and metadata collection efforts are needed to ensure that B. cereus sensu lato surveillance initiatives are on par with those of other foodborne pathogens.

Antimicrobial Resistance, Enterotoxin and mec Gene Profiles of Staphylococcus aureus Associated with Beef-Based Protein Sources from KwaZulu-Natal Province, South Africa

Annually, approximately 23,000 cases of food poisoning by Staphylococcus aureus enterotoxins are reported worldwide. The aim of this study was to determine the occurrence and characterize S. aureus on beef and beef products in South Africa. Organ meats (n = 169), raw processed meat (n = 110), raw intact (n = 53), and ready-to-eat meats (n = 68) were obtained from 25 retail outlets. S. aureus was isolated and enumerated according to the ISO 6888-1 method. Identification of the strains was performed by MALDI-TOF MS. The antimicrobial resistance was determined using the disc diffusion test. The presence of methicillin-resistance genes and the staphylococcal enterotoxin genes was determined by PCR. Prevalence was low (13/400; CI 1.7–5) and all but one positive sample were from organ meats. Eight isolates were resistant to at least one antibiotic. Two isolates carried the mecC gene. All the isolates tested positive for seg, seh, sei, and sep, whilst 53.8% were positive for sea. None of the isolates was positive for ser, sej, seb, sec, or sed. The prevalence of S. aureus was low, with organ meats being the most contaminated. The presence of mecC-positive MRSA and of enterotoxins warrants further investigation and risk assessment.

Virulence Factors and Antimicrobial Resistance in Salmonella Species Isolated from Retail Beef in Selected KwaZulu-Natal Municipality Areas, South Africa

Salmonellosis and antimicrobial resistance caused by non-typhoidal Salmonella are public health concerns. This study aimed at determining prevalence, serovars, virulence factors and antimicrobial resistance of Salmonella from beef products. Four-hundred beef samples from 25 retail outlets in KwaZulu-Natal, South Africa were analyzed for Salmonella using standard methods, confirmation with matrix-assisted laser desorption ionization–time of flight and serotyping according to the White–Kauffmann–Le Minor scheme. The Kirby Bauer disk diffusion method was used to determine antimicrobial resistance against Cefotaxime, Kanamycin, Ampicillin, Amoxicillin, Trimethoprim Sulfamethoxazole, Ciprofloxacin, Chloramphenicol, Gentamicin Cefoxitin and Tetracycline. A polymerase chain reaction was performed to detect invA, agfA, lpfA, hilA, sivH, sefA, sopE, and spvC virulence genes. Salmonella was observed in 1.25% (5/400) of the samples. Four serovars (Enteritidis, Hadar, Heidelberg, Stanley) were identified. Almost all Salmonella were susceptible to all antimicrobials except S. Enteritidis isolate that was resistant to Tetracycline, Ampicillin and Amoxicillin. All Salmonella isolates carried at least two virulence factors. The findings indicate low Salmonella prevalence in meat from selected KZN retail beef; however, routine surveillance to monitor risk associated with virulence factors is required to mitigate potential outbreaks. The resistant S. Enteritidis highlights a need to routinely monitor antimicrobial resistance in order to enhance human health.

Novel Techniques for Microbiological Safety in Meat and Fish Industries

The consumer tendency towards convenient, minimally processed meat items has placed extreme pressure on processors to certify the safety of meat or meat products without compromising the quality of product and to meet consumer’s demand. This has prompted difficulties in creating and carrying out novel processing advancements, as the utilization of more up-to-date innovations may influence customer decisions and assessments of meat and meat products. Novel advances received by the fish and meat industries for controlling food-borne microbes of huge potential general wellbeing concern, gaps in the advancements, and the requirement for improving technologies that have been demonstrated to be effective in research settings or at the pilot scale shall be discussed. Novel preparing advancements in the meat industries warrant microbiological approval before being named as industrially suitable alternatives and authorizing infra-structural changes. This miniature review presents the novel techniques for the microbiological safety of meat products, including both thermal and non-thermal methods. These technologies are being successfully implemented and rationalized in subsisting processing surroundings.

Genotyping and Antimicrobial Susceptibility of Clostridium perfringens and Clostridioides difficile in Camel Minced Meat

The present study aimed to determine the occurrence, genotypes, and antimicrobial resistance of Clostridium perfringens (C. perfringens) and Clostridioides difficile (C. difficile) in camel minced meat samples collected from small butcher shops and supermarkets in Al-Ahsa Governorate, Saudi Arabia. A total of 100 camel minced meat samples were randomly collected from small butcher's shops (n = 50) and supermarkets (n = 50) in Al-Ahsa Governorate, Saudi Arabia. C. perfringens and C. difficile were isolated and identified using the VITEK-2 compact system and 16S rRNA gene amplification. Genotypes, toxin genes, and antimicrobial susceptibility of the isolates were determined. Moreover, ELISA was used to detect C. perfringens and C. difficile toxins. C. perfringens and C. difficile were isolated from 14% and 4% of the tested minced meat samples, respectively. Out of the 14 C. perfringens isolates, type A (64.3%), type B (7.1%), type C (21.5%), and type D (7.1%) were detected. However, out of the four C. difficile isolates, three (75%) were type A+B+ and one (25%) was type A-B+. None of the C. perfringens or C. difficile toxins were identified using ELISA. C. perfringens and C. difficile isolates exhibited a high rate of resistance to tetracycline (56% and 75%, respectively). However, all isolates were susceptible to amoxicillin-clavulanate. Multidrug resistance was observed in three (21.4%) C. perfringens and one (25%) C. difficile isolates. In conclusion, camel minced meat was contaminated with C. perfringens and C. difficile, which present a potential risk of food poisoning. The majority of the isolates were resistant to at least one antimicrobial, and some isolates were multidrug-resistant. Therefore, food safety standards and frequent inspections of abattoirs, small butcher shops, and supermarkets should be enforced.

Prevalence, Enterotoxigenic Potential and Antimicrobial Resistance of Staphylococcus aureus and Methicillin-Resistant Staphylococcus aureus (MRSA) Isolated from Algerian Ready to Eat Foods

Staphylococcus aureus causes a foodborne intoxication due to the production of enterotoxins and shows antimicrobial resistance, as in the case of methicillin-resistant strains (MRSA). Herein, we analyzed 207 ready-to-eat foods collected in Algeria, reporting a S. aureus prevalence of 23.2% (48/207) and respective loads of coagulase positive staphylococci (CPS) ranging from 1.00 ± 0.5 to 5.11 ± 0.24 Log CFU/g. The 48 S. aureus isolates were widely characterized by staphylococcal enterotoxin gene (SEg)-typing and 16S-23S rDNA intergenic spacer region (ISR)-PCR, as well as by detecting tst and mecA genes, genetic determinants of toxic shock syndrome toxin-1 and methicillin resistance, respectively. We found that the S. aureus isolates belonged to seven different SEg-types harboring the following combinations of genes: (1) selW, selX; (2) egc (seG, seI, seM, seN, seO), selW, selX; (3) seA, seH, seK, seQ, selW, selX; (4) seB, selW, selX; (5) seD, selJ, seR, selW, selX; (6) seH, selW, selX, selY; and (7) seA, egc, selW, selX, while among these, 2.1% and 4.2% were tst- and mecA- (staphylococcal chromosomal cassette mec-type IV) positive, respectively. Selected strains belonging to the 12 detected ISR-types were resistant towards antimicrobials including benzylpenicillin, ofloxacin, erythromycin, lincomycin, tetracyclin, kanamycin, oxacillin, and cefoxitin; 8.3% (1/12) were confirmed as MRSA and 16.7% (2/12) were multidrug resistant. The present study shows the heterogeneity of the S. aureus population in Algerian ready-to-eat foods as for their toxigenic potential and antimicrobial resistance, shedding the light on the quality and safety related to the consume of ready-to-eat foods in Algeria.