Pigs as a potential source of emerging livestock-associated Staphylococcus aureus in Africa: a systematic review

Epidemiology and antibiotic resistance of staphylococci on commercial pig farms in Cape Town, South Africa

Staphylococci are responsible for a wide range of infections in animals. The most common species infecting animals include Staphylococcus aureus, Staphylococcus epidermidis and Staphylococcus intermedius. Recent increases in antibiotic use and antibiotic resistance in animals highlight the need to understand the potential role of commercial livestock as a reservoir of staphylococci and antibiotic resistance genes. Nasal swabs were collected from 143 apparently healthy pigs and 21 pig farm workers, and 45 environmental swabs of feed and water troughs, from two commercial pig farms in the Western Cape, South Africa. Staphylococci were isolated, identified using mass-spectrometry, and antimicrobial susceptibility testing and Illumina whole genome sequencing were performed. One hundred and eighty-five (185) Staphylococcus spp. isolates were obtained, with Mammalicoccus sciuri (n = 57; 31%) being the most common, followed by S. hyicus (n = 40; 22%) and S. aureus (n = 29; 16%). S. epidermidis was predominantly identified in the farm workers (n = 18; 86%). Tetracycline resistance was observed across all species, with rates ranging from 67 to 100%. Majority of M. sciuri isolates (n = 40; 70%) were methicillin resistant, with 78% (n = 31) harbouring mecA. M. sciuri isolates had genes/elements which were associated with SCCmec_type_III (3A) and SCCmec_type_VIII(4A) and were mostly observed in ST61 strains. ST239 strains were associated with SCCmec_type_III(3A). High rates of tetracycline resistance were identified among staphylococci in the pig farms in Western Cape, South Africa. This highlights the need for policy makers to regulate the use of this antibiotic in pig farming.

Development of triplex assay for simultaneous detection of Escherichia coli, methicillin resistant and sensitive Staphylococcus aureus in raw pork samples of retail markets

Escherichia coli and Staphylococcus aureus are the most important food borne pathogen transmitting from animal meat and meat products. Therefore, it is vital to design an accurate and specific diagnostic tool for identifying those food-borne pathogens in animal meat and meat products. In the current study, E. coli, methicillin-resistant and sensitive S. aureus (MRSA and MSSA) were simultaneously detected using a developed triplex PCR-based technique. To obtain an optimal reaction parameter, the multiplex assay was optimised by changing just one parameter while holding the others constant. Specificity of the assay was assessed using several porcine bacterial template DNA. The plasmid DNA was used to test the multiplex PCR assay's sensitivity and interference in spiked pork samples. E. coli, MRSA, and MSSA each have PCR amplified products with sizes of 335, 533, and 209 bp, respectively. The assay detects a minimum microbial load of 102 CFU/μl for all the three pathogens and can identify bacterial DNA as low as 10-2 ng/µl. The assay was validated employing 210 pork samples obtained from retail meat shops and slaughter houses, with MRSA, E. coli, and MSSA with the occurrence rate of 1.9%, 42.38%, and 18.1%, respectively. The rate of mixed bacterial contamination in pork meat samples examined with the developed method was 6.19%, 1.43%, 1.90%, and 1.43% for MSSA & E. coli, MRSA & E. coli, MSSA & MRSA, and E. coli, MSSA & MRSA, respectively. The developed multiplex PCR assay is quick and efficient, and it can distinguish between different bacterial pathogens in a single reaction tube.

Heterogeneity and transmission of food safety-related enterotoxigenic Staphylococcus aureus in pig abattoirs in Hubei, China

The dissemination of Staphylococcus aureus in the pork production chain is a major food safety concern. Abattoirs can serve both as disruptor and transmitter for S. aureus. In this study, we conducted a systematic genomic epidemiology research on the prevalence, heterogeneity, and transmission of S. aureus in 3,638 samples collected from four pig abattoirs in Hubei province, China. Our findings revealed substantial heterogeneity between S. aureus recovered from samples collected at upstream (from stunning step to head-removal step) and downstream (from splitting step to chilling step) locations within the slaughter process. Overall, 966 (26.6%) samples were positive for S. aureus, with significantly higher overall prevalence for upstream samples (29.0%, 488/1,681) compared to downstream samples (24.4%, 478/1,957). Antimicrobial susceptibility testing demonstrated that the isolates from the upstream exhibited significantly higher resistance proportions to different antimicrobials than those from the downstream. Whole-genome sequencing of 126 isolates revealed that ST398 (32.9%, 23/70) and ST9 (22.9%, 16/70) were more common among upstream isolates, while ST7 (35.7%, 20/56) and ST97 (28.6%, 16/56) were most frequently observed among downstream isolates. Additionally, molecular characterization analysis demonstrated that upstream isolates possessed significantly higher enterotoxigenic potential, more antimicrobial resistance genes, and S. aureus pathogenicity islands than downstream isolates. Notably, we discovered that enterotoxigenic S. aureus could be transmitted across different slaughter stages, with knives, water, and air serving as vectors. Although slaughtering processes had a substantial effect on reducing the food safety risk posed by enterotoxigenic S. aureus, the possibility of its widespread transmission should not be disregarded. IMPORTANCE Staphylococcus aureus (S. aureus) is one of the most important foodborne pathogens, and can cause foodborne poisoning by producing enterotoxins. Pork is a preferable reservoir and its contamination often occurs during the slaughter process. Our findings revealed significant differences in the prevalence, antimicrobial resistance, and enterotoxigenic potential between the upstream and downstream isolates within the slaughter process. Also, it is imperative not to overlook enterotoxigenic S. aureus transmitted across all stages of the slaughter process, with notable vectors being knives, water, and air. These findings hold significant implications for policy-makers to reassess their surveillance projects, and underscore the importance of implementing effective control measures to minimize the risk of S. aureus contamination in pork production. Moreover, we provide a more compelling method of characterizing pathogen transmission based on core-SNPs of bacterial genomes.

Clonal diversity of Staphylococcus aureus isolates in clinical specimens from selected health facilities in Ethiopia

Staphylococcus aureus is among the top three causative agents of nosocomial infection in Ethiopia. The majority of studies in Ethiopia have focused on the epidemiology of S. aureus in hospital settings, with limited molecular genotyping results. Molecular characterization of S. aureus is essential for identification of strains, and contributes to the control and prevention of S. aureus infection. The aim of the current study was to determine the molecular epidemiology of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) isolates recovered from clinical specimens in Ethiopia. A total of 161 MSSA and 9 MRSA isolates were characterized using pulsed-field gel electrophoresis (PFGE) and staphylococcal protein A (spa) typing. Based on the PFGE analysis, MSSA isolates were grouped into eight pulso-types groups (from A to I), while MRSA isolates clustered into three (A, B and C) pulso-types with more than 80% similarity. The spa typing analysis showed diversity of S. aureus with 56 distinct spa types. Spa type t355 was most prevalent (56/170, 32.9%), while eleven new spa types were detected including t20038, t20039, and t20042. The identified spa types were clustered into 15 spa-clonal complexes (spa-CCs) using BURP analysis; novel/unknown spa types were further subjected to MLST analysis. The majority of isolates belonged to spa-CC 152 (62/170, 36.4%), followed by spa-CC 121 (19/170, 11.2%), and spa-CC 005 (18 /170, 10.6%). Of the nine MRSA isolates, 2 (22.2%) were spa-CC 239 with staphylococcal cassette chromosome (SCC)mec III. These findings highlight the diversity of S. aureus strains in Ethiopia, as well as the presence of potentially epidemic strains circulating in the country necessitating further characterization of S. aureus for antimicrobial resistance detection and infection prevention purposes.

The Genetic Diversity and Antimicrobial Resistance of Pyogenic Pathogens Isolated from Porcine Lymph Nodes

According to the Food and Agriculture Organization of the United Nations, pork remains the most consumed meat in the world. Consequently, it is very important to ensure that it is of the highest microbiological quality. Many of the pathogens that cause lymph node lesions in pigs are zoonotic agents, and the most commonly isolated bacteria are Mycobacterium spp., Streptococcus spp., Staphylococcus aureus and Rhodococcus equi (synonymous with Prescottella equi). The prevention and treatment of zoonotic infections caused by these bacteria are mainly based on antimicrobials. However, an overuse of antimicrobials contributes to the emergence and high prevalence of antimicrobial-resistant strains, which are becoming a serious challenge in many countries. The aim of this study was to evaluate the genetic diversity and antimicrobial resistance of the Streptococcus spp. (n = 48), S. aureus (n = 5) and R. equi (n = 17) strains isolated from swine lymph nodes with and without lesions. All isolates of S. dysgalactiae, S. aureus and R. equi were subjected to PFGE analysis, which showed the genetic relatedness of the tested bacteria in the studied pig populations. Additionally, selected tetracycline and macrolide resistance genes in the streptococcal strains were also studied. The results obtained in the present study provide valuable data on the prevalence, diversity, and antimicrobial resistance of the studied bacteria. Numerous isolated bacterial Streptococcus spp. strains presented resistance to doxycycline, and almost half of them carried tetracycline resistance genes. In addition, R. equi and S. aureus bacteria presented a high level of resistance to beta-lactam antibiotics and to cefotaxime, respectively.

Physicochemical, microbiological, and sensory characteristics of "Sui Wu'u" traditional pork products from Bajawa, West Flores, Indonesia

Background and Aim

Sui Wu'u is a traditional meat preservation product from Bajawa, a region in East Nusa Tenggara. It is made by mixing pork with salt and corn flour, which is then stored in a bamboo container (tuku) for months. After 6 months of storage, this study examined the physicochemical, microbiological, and sensory properties of Sui Wu'u.

Materials and Methods

Sui Wu'u products were prepared using the traditional recipe from the Bajawa community. Fresh pork (pork belly and backfat), corn flour, and salt were purchased from local/traditional markets at proportions of 65%, 30%, and 5%, respectively. The physicochemical, amino acid, fatty acid profile, microbiological, and sensory properties of Sui Wu'u were evaluated after being stored for 6 months in a bamboo container (tuku).

Results

The results indicated that these Sui Wu'u were mainly characterized by high-fat levels, followed by protein. The pH value, salt content, moisture content, and water activity were 4.72%, 1.72%, 6.11%, and 0.62%, respectively. Minerals (K, P, Se, and Zn) and vitamin B6, as well as amino acids, such as leucine, phenylalanine, lysine (essential amino acids), glycine, proline, glutamic acid, and alanine (non-essential amino acids), are present in Sui Wu'u. The fatty acid profile was dominated by monounsaturated fatty acids (MUFA) (21.69%), saturated fatty acids (SFA) (17.78%), and polyunsaturated fatty acids (PUFA) (5.36%). Monounsaturated fatty acids, oleic acid (C18:1n9) was the most abundant fatty acid in Sui Wu'u, followed by palmitic acid SFA (C16:0); MUFA stearic acid (C18:0); and PUFA linoleic (C18:2n-6). The microbiological characteristics of Sui Wu'u showed no detectable microorganisms (<10 CFU/g) for Salmonella, total E. coli and total Staphylococcus, and average values of 4.4 × 105 CFU/g for total microbes, which were still below the maximum limit of microbial contamination according to the regulations of the Food and Drug Supervisory Agency of the Republic of Indonesia. The sensory assessment indicated that panelists highly preferred (rated as very like) Sui Wu'u for all sensory attributes.

Conclusion

The physicochemical, microbiological, and sensory characteristics of Sui Wu'u after 6 months of storage indicated that it still provides essential nutrients for the body and is quite safe for consumption. The stability of Sui Wu'u's shelf life can be attributed to the appropriate combination of pork, salt, corn flour, bamboo packaging (tuku), and storage temperature. The high-fat content in Sui Wu'u can be reduced by increasing the proportion of lean meat. Ensuring strict sanitation during the manufacturing process, using high-quality pork, salt, corn flour, and proper packaging with bamboo can further improve the safety of Sui Wu'u for consumption.

Epidemiology and antimicrobial resistance of staphylococci other than Staphylococcus aureus from domestic animals and livestock in Africa: a systematic review

Introduction

Staphylococci other than Staphylococcus aureus (SOSA) in animals are becoming more pathogenic and antibiotic resistant and can potentially disseminate to humans. However, there is little synthesized information regarding SOSA from animals in Africa. This systematic review provides a comprehensive overview of the epidemiology and antimicrobial resistance of SOSA in companion animals (pets) and livestock in Africa.

Method

This systematic review (PROSPERO-CRD42021252303) was conducted according to the PRISMA guidelines, and 75 eligible studies from 13 countries were identified until August 2022. Three electronic databases (Pubmed, Scopus and Web of Science) were employed.

Results

The frequently isolated SOSA were S. epidermidis, S. intermedius, S. pseudintermedius, S. xylosus, S. chromogenes, S. hyicus, M. sciuri, S. hominis, and S. haemolyticus. Thirty (40%) studies performed antibiotic susceptibility testing (AST). Penicillin (58%) and tetracycline (28%) resistance were most common across all SOSA with high rates of resistance to aminoglycosides, fluoroquinolones, and macrolides in some species. Resistance to last-resort antibiotics such as linezolid and fusidic acid were also reported. Limited data on strain typing and molecular resistance mechanisms precluded analysis of the clonal diversity of SOSA on the continent.

Conclusion

The findings of this review indicate that research on livestock-associated SOSA in Africa is lacking in some regions such as Central and Western Africa, furthermore, research on companion animals and more advanced methods for identification and strain typing of SOSA need to be encouraged.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier: CRD42021252303.

Review of pork and pork products as a source for transmission of methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic bacterium that can cause infection in animals and humans. Recently, MRSA from food-producing or farm animals has been identified as livestock-associated MRSA (LA-MRSA). The spread of LA-MRSA is particularly found in pork and pork products because LA-MRSA has been widely known to infect pigs. The most common type of LA-MRSA identified in pork and pork products is the clonal complex LA-MRSA 398 (LA-MRSA CC398). The MRSA strains on the surface of pork carcasses can be spread during the handling and processing of pork and pork products through human hands, cutting tools, and any surface that comes into direct contact with pork. Food infection is the main risk of MRSA in pork and pork products consumed by humans. Antibiotics to treat food infection cases due to MRSA infection include vancomycin and tigecycline. The spread of MRSA in pork and pork products is preventable by appropriately cooking and cooling the pork and pork products at temperatures above 60°C and below 5°C, respectively. It is also necessary to take other preventive measures, such as having a clean meat processing area and disinfecting the equipment used for processing pork and pork products. This review aimed to explain epidemiology, transmission, risk factors, diagnosis, public health consequences, treatment of food poisoning, and preventing the spread of MRSA in pork and pork products.

Tackling antimicrobial resistance across sub-Saharan Africa: current challenges and implications for the future

INTRODUCTION

Antimicrobial resistance (AMR) is a concern as this increases morbidity, mortality, and costs, with sub-Saharan Africa having the highest rates globally. Concerns with rising AMR have resulted in international, Pan-African, and country activities including the development of national action plans (NAPs). However, there is variable implementation across Africa with key challenges persisting.

AREAS COVERED

Consequently, there is an urgent need to document current NAP activities and challenges across sub-Saharan Africa to provide future guidance. This builds on a narrative review of the literature.

EXPERT OPINION

All surveyed sub-Saharan African countries have developed their NAPs; however, there is variable implementation. Countries including Botswana and Namibia are yet to officially launch their NAPs with Eswatini only recently launching its NAP. Cameroon is further ahead with its NAP than these countries; though there are concerns with implementation. South Africa appears to have made the greatest strides with implementing its NAP including regular monitoring of activities and instigation of antimicrobial stewardship programs. Key challenges remain across Africa. These include available personnel, expertise, capacity, and resources to undertake agreed NAP activities including active surveillance, lack of focal points to drive NAPs, and competing demands and priorities including among donors. These challenges are being addressed, with further co-ordinated efforts needed to reduce AMR.

mecC MRSA in Israel—genomic analysis, prevalence and global perspective

Background

MRSA is a major global healthcare problem. In 2011, a new mec variant designated mecC was described, presenting partial identity at the DNA level, thus undetectable by routine mecA PCR.

Objectives

Until now, no reliable information regarding mecC MRSA prevalence was available in Israel. In this study, to the best of our knowledge, we describe the first case of mecC MRSA in Israel, with focus on genomic analysis and global context.

Methods

The mecC MRSA isolate was analysed by WGS with focus on phylogeny, global contextualization, virulence and resistance genes. The strain was characterized by antibiotic susceptibility testing, spa typing and presence of mecA/C and pvl genes.

Results

An MRSA strain (SA10610), isolated from a urine sample of an 83-year old patient, was found negative for the mecA and pvl genes. The MLST and spa type were ST130 and t1736, respectively. SA10610 presented resistance to oxacillin, penicillin and cefoxitin, and susceptibility to all non-β-lactam agents tested. Phylogenetic comparison with a global dataset of 586 mecC MRSA genomes revealed substantial genomic divergence. The nearest genomic relatives were human and animal isolates from Denmark. A screen of 12 761 S. aureus isolates collected during 2011–18 in Israel indicated this is the only mecC-positive strain.

Conclusions

A high degree of genetic variability was found between the SA10610 strain and previously sequenced mecC MRSA isolated worldwide. The genomic and phylogenetic analysis suggest that mecC MRSA isolates have evolved independently rather than from a common ancestor.

Antimicrobial Susceptibility Profiles and Molecular Characterisation of Staphylococcus aureus from Pigs and Workers at Farms and Abattoirs in Zambia

Pigs have been shown to be a reservoir for recently emerging livestock-associated Staphylococcus aureus (LA-SA), including methicillin resistant strains in many countries worldwide. However, there is sparse information about LA-SA strains circulating in Zambia. This study investigated the prevalence, phenotypic and genotypic characteristics of S. aureus from pigs and workers at farms and abattoirs handling pigs in Lusaka Province of Zambia. A total of 492 nasal pig swabs, 53 hand and 53 nasal human swabs were collected from farms and abattoirs in selected districts. Standard microbiological methods were used to isolate and determine antimicrobial susceptibility patterns of S. aureus. Polymerase Chain Reaction was used to confirm the species identity and detect antimicrobial resistance and virulence genes of isolates, whereas genetic diversity was evaluated using spa typing. Overall prevalence of S. aureus was 33.1%, 37.8% for pigs and 11.8% for humans. The isolates were resistant to several antibiotics with resistance ranging from 18% to 98% but were all susceptible to vancomycin. Typical LA-SA spa types were detected. The presence of plasmid mediated resistance genes such as tetM (12.8%), other resistance determinants and immune evasion cluster genes among the isolates is of great public health concern. Thus, continuous surveillance of S. aureus using a “One health” approach is warranted to monitor S.aureus infections and spread of antimicrobial resistance.

Analysis of Environmental and Pathogenic Bacteria Attached to Aerosol Particles Size-Separated with a Metal Mesh Device

Metal mesh devices (MMDs) are novel materials that enable the precise separation of particles by size. Structurally, MMDs consist of a periodic arrangement of square apertures of characteristic shapes and sizes on a thin nickel membrane. The present study describes the separation of aerosol particles using palm-top-size collection devices equipped with three types of MMDs differing in pore size. Aerosols were collected at a farm located in the suburbs of Nairobi, Kenya; aerosol particles were isolated, and pathogenic bacteria were identified in this microflora by next-generation sequencing analysis. The composition of the microflora in aerosol particles was found to depend on particle size. Gene fragments were obtained from the collected aerosols by PCR using primers specific for the genus Mycobacterium. This analysis showed that Mycobacterium obuense, a non-tuberculous species of mycobacteria that causes lung diseases, was present in these aerosols. These findings showed that application of this MMD analytical protocol to aerosol particles can facilitate the investigation of airborne pathogenic bacteria.