Characterization, prevalence and antibiogram study of Staphylococcus aureus in poultry

Epidemiology of Antimicrobial Resistance Genes in Staphylococcus aureus Isolates from a Public Database from a One Health Perspective-Sample Origin and Geographical Distribution of Isolates

Staphylococcus aureus are commensal bacteria that are found in food, water, and a variety of settings in addition to being present on the skin and mucosae of both humans and animals. They are regarded as a significant pathogen as well, with a high morbidity that can cause a variety of illnesses. The Centers for Disease Control and Prevention (CDC) has listed them among the most virulent and resistant to antibiotics bacterial pathogens, along with Escherichia coli, Staphylococcus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterococcus faecalis, and Enterococcus faecium. Additionally, S. aureus is a part of the global threat posed by the existence of antimicrobial resistance (AMR). Using 26,430 S. aureus isolates from a global public database (NPDIB; NCBI Pathogen Detection Isolate Browser), epidemiological research was conducted. The results corroborate the evidence of notable variations in isolate distribution and ARG (Antimicrobial Resistance Gene) clusters between isolate sources and geographic origins. Furthermore, a link between the isolates from human and animal populations is suggested by the ARG cluster patterns. This result and the widespread dissemination of the pathogens among animal and human populations highlight how crucial it is to learn more about the epidemiology of these antibiotic-resistance-related infections using a One Health approach.

Antibiotic resistance genes of public health importance in livestock and humans in an informal urban community in Nepal

Efforts to mitigate the increasing emergence of antimicrobial resistance (AMR) will benefit from a One Health perspective, as over half of animal antimicrobials are also considered medically important in humans, and AMR can be maintained in the environment. This is especially pertinent to low- and middle-income countries and in community settings, where an estimated 80% of all antibiotics are used. This study features AMR genes found among humans, animals, and water at an urban informal settlement in Nepal with intensifying livestock production. We sampled humans, chickens, ducks, swine, and water clustered by household, as well as rodents and shrews near dwellings, concurrently in time in July 2017 in southeastern Kathmandu along the Manohara river. Real-time qualitative PCR was performed to screen for 88 genes. Our results characterize the animal-human-environmental interfaces related to the occurrence of specific resistance genes (bla_SHV-1 (SHV(238G240E) strain), QnrS, ermC, tetA, tetB, aacC2, aadA1) associated with antibiotics of global health importance that comprise several drug classes, including aminoglycosides, beta-lactams, tetracyclines, macrolides, and fluoroquinolones. By characterizing risk factors across AMR genes of public health importance, this research highlights potential transmission pathways for further investigation and provides prioritization of community-based prevention and intervention efforts for disrupting AMR transmission of critically important antibiotics used in both humans and animals in Nepal.

Sink survey to investigate multidrug resistance pattern of common foodborne bacteria from wholesale chicken markets in Dhaka city of Bangladesh

Antimicrobial resistance (AMR) among foodborne bacteria is a well-known public health problem. A sink survey was conducted to determine the AMR pattern of common foodborne bacteria in cloacal swab of broiler chickens and sewage samples from five wholesale chicken markets of Dhaka city in Bangladesh. Bacteria were identified by culture-based and molecular methods, and subjected to antimicrobial susceptibility testing. Resistance genes were identified by multiplex PCR and sequencing. Multidrug resistance (MDR) was observed in 93.2% of E. coli, 100% of Salmonella spp., and 97.2% of S. aureus from cloacal swab samples. For sewage samples, 80% of E. coli, and 100% of Salmonella and S. aureus showed MDR. Noteworthy, 8.3% of S. aureus from cloacal swab samples showed possible extensively drug resistance. Antimicrobial resistance genes (beta-lactamase—blaTEM, blaSHV; quinolone resistance gene—qnrS) were detected in a number of E. coli and Salmonella isolates from cloacal swab and sewage samples. The methicillin resistance gene (mecA) was detected in 47.2% and 25% S. aureus from cloacal swab and sewage samples, respectively. The findings envisage the potential public health risk and environmental health hazard through spillover of common foodborne MDR bacteria.

Multidrug-Resistant Methicillin-Resistant Coagulase-Negative Staphylococci in Healthy Poultry Slaughtered for Human Consumption

Coagulase-negative staphylococci are commensals that are known to be prevalent in most environments, and they are also an important reservoir of antimicrobial-resistant genes. Staphylococcal infections in animal husbandry are a high economic burden. Thus, we aimed to determine the prevalence and species diversity of methicillin-resistant coagulase-negative staphylococci (MRCoNS) in poultry slaughtered for human consumption and to study the antimicrobial resistance of the isolates. Swab samples were recovered from 220 commercial chickens, homebred chickens and quails. Species identification was performed using MALDI-TOF. Antimicrobial susceptibility testing was performed by the disc diffusion method against 14 antimicrobials. The presence of antimicrobial-resistant genes was investigated by polymerase chain reaction. Totals of 11 (19.6%), 13 (20.3%), and 51 (51%) MRCoNS were isolated from commercial chickens, homebred chickens and quails, respectively. S. lentus was isolated from all homebred chickens, whereas 11 S. lentus and 2 S. urealyticus were isolated from commercial chickens. As for quails, the most prevalent MRCoNS were S. urealyticus. Almost all isolates had a multidrug-resistant profile and carried the mecA gene. Most isolates showed resistance to erythromycin, clindamycin, penicillin, tetracycline, ciprofloxacin and fusidic acid and harbored the ermA, ermB, ermC, mphC tetK, tetL, tetM and tetO genes. This study showed a frequent occurrence of multidrug resistance in MRCoNS isolated from healthy poultry in Portugal.

Prevalence, antibiotic resistance, and enterotoxin production of Staphylococcus aureus isolated from retail raw beef, sheep, and lamb meat in Turkey

The main objective of this study was to isolate and identify Staphylococcus aureus from retail raw red meat samples and evaluate their enterotoxin gene and antibiotic resistance profiles. A total of 452 retail raw meat samples, including beef (n = 200), sheep (n = 125), and lamb (n = 127) randomly purchased from various supermarkets and butchers in Ankara between July 2019 and November 2020, were tested for the prevalence of S. aureus. The S. aureus strain was identified using morphological and molecular (16S rRNA and nuc gene) methods. Moreover, nine Staphylococcal enterotoxin (SE) genes were screened using polymerase chain reaction. Antibiotic resistance of S. aureus was determined using the phenotypic disc diffusion method. The overall prevalence of S. aureus among screened samples was 21.23%. Additionally, 65.62% of S. aureus strains contained SE gene regions. The predominant SEs in the S. aureus strains were sea (50.79%), followed by sed (25.39%) and seb (23.80%). However, sec, see, seg, seh, sei, and sej genes were never detected. A substantial proportion (40-100%) of the isolates were found resistant to kanamycin, telithromycin, penicillin G, streptomycin, erythromycin, cloxacillin, ampicillin, pristinamycin, nalidixic acid, azithromycin, and ciprofloxacin. Multi-drug resistance (MDR) was observed in 96.87% of the S. aureus strains. These results show a low prevalence of S. aureus in raw red meat samples in Turkey. However, a high rate of SEA raises serious health concerns. Due to the high levels of MDR observed in this study, there is a need to strictly control antibiotic use in animals in Turkey.

Staphylococcus aureus in poultry, with special emphasis on methicillin-resistant strain infection: A comprehensive review from one health perspective

Staphylococcus aureus is a Gram-positive coccus normally present on the skin and internal organs of animals, birds, and humans. Under certain conditions, S. aureus could produce septicemia and affection of the skin, joints, and heart, as well as sepsis and death. The pathogenicity of S. aureus is associated with the presence of some virulent surface proteins and the production of some virulent toxins and enzymes. This pathogen is considered one of the most important and worldwide foodborne causes as it is incriminated in most cases of food poisoning. The hazardous use of antibiotics in the veterinary field leads to the development of multidrug-resistant S. aureus strains that can be transmitted to humans. The incidence of methicillin-resistant S. aureus (MRSA) strains has increased globally. These resistant strains have been detected in live animals, poultry, and humans. In addition, retail animal products, especially those of avian origin, are considered the main source of MRSA strains that can be easily transmitted to humans. MRSA infection is regarded as nosocomial or occupational. Humans get infected with MRSA strains through improper handling or preparation of contaminated animals or poultry carcasses or improper cooking with contaminated meat. Live birds also can transmit MRSA to close-contact workers in poultry farms. Transmission of MRSA infection in hospitals is from an infected individual to a healthy one. Prevention and control of MRSA are based on the application of hygienic measures in farms as well as proper processing, handling, and cooking of retail poultry products. The cooperation between veterinary and human practitioners is a must to avoid the possibility of zoonotic transmission. Accordingly, this review focused on the sources and transmission of MRSA infection, virulence and resistance factors, incidence and prevalence in poultry and different products, antibiotic resistance, and prevention and control strategies.

Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles

Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6′)-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.

Antimicrobial resistance in the globalized food chain: a One Health perspective applied to the poultry industry

Antimicrobial resistance (AMR) remains a major global public health crisis. The food animal industry will face escalating challenges to increase productivity while minimizing AMR, since the global demand for animal protein has been continuously increasing and food animals play a key role in the global food supply, particularly broiler chickens. As chicken products are sources of low-cost, high-quality protein, poultry production is an important economic driver for livelihood and survival in developed and developing regions. The globalization of the food supply, markedly in the poultry industry, is aligned to the globalization of the whole modern society, with an unprecedented exchange of goods and services, and transit of human populations among regions and countries. Considering the increasing threat posed by AMR, human civilization is faced with a complex, multifaceted problem compromising its future. Actions to mitigate antimicrobial resistance are needed in all sectors of the society at the human, animal, and environmental levels. This review discusses the problems associated with antimicrobial resistance in the globalized food chain, using the poultry sector as a model. We cover critical aspects of the emergence and dissemination of antimicrobial resistance in the poultry industry and their implications to public health in a global perspective. Finally, we provide current insights using the multidisciplinary One Health approach to mitigate AMR at the human-animal-environment interface.

Prevalence and Characteristics of Staphylococcus aureus Associated with Meat and Meat Products in African Countries: A Review

Antimicrobial resistance has been increasing globally, which negatively affects food safety, veterinary, and human medicine. Ineffective antibiotics may cause treatment failure, which results in prolonged hospitalisation, increased mortality, and consequently, increased health care costs. Staphylococcus aureus causes a diverse range of infections including septicaemia and endocarditis. However, in food, it mainly causes food poisoning by the production of enterotoxins. With the discovery of methicillin-resistant S. aureus strains that have a separate reservoir in livestock animals, which were termed as livestock-associated methicillin-resistant S. aureus (LA-MRSA) in 2005, it became clear that animals may pose another health risk. Though LA-MRSA is mainly transferred by direct contact, food transmission cannot be excluded. While the current strains are not very pathogenic, mitigation is advisable, as they may acquire new virulence genes, becoming more pathogenic, and may transfer their resistance genes. Control of LA-MRSA poses significant problems, and only Norway has an active mitigation strategy. There is limited information about LA-MRSA, MRSA in general, and other S. aureus infections from African countries. In this review, we discuss the prevalence and characteristics of antimicrobial susceptible and resistant S. aureus (with a focus on MRSA) from meat and meat products in African countries and compare it to the situation in the rest of the world.

Effect of raw and fermented grape seed on growth performance, antioxidant capacity, and cecal microflora in broiler chickens

Grape seed (GS) is a by-product of the fruit juice and wine industry with the potential to be an alternative to synthetic antioxidants due to its antioxidant activity. Agro-industrial residues can be converted to more effective products by solid-state fermentation. The objective of the study was to investigate the effects of GS and fermented grape seed (FGS) on the growth performance, antioxidant capacity, and cecal microflora in broiler chickens. A total of 128 female broilers were randomly allocated into four treatment groups, each consisting of four replicates of eight birds. Throughout the 42-day feeding period, the birds were fed with soybean-corn based diet (CON), 0.15 g/kg synthetic antioxidant (butylated hydroxyanisole) supplemented diet (AO), 5 g/kg GS supplemented diet (GS), and 5 g/kg FGS supplemented diet (FGS). Dietary GS, FGS, and AO supplementation increased the BW (P < 0.05) and average daily weight gain (ADG, P < 0.05) compared with the CON group in the overall period of 42 days. Dietary FGS also increased the ADG (P < 0.05) in the period of 22-42 days compared with the control group. The pH of the breast meat of the chickens fed GS was higher (P < 0.01) than CON and FGS groups. Dietary FGS and AO decreased the b* value (P < 0.01) of breast meat compared with the CON group. Grape seed had the highest serum glutathione peroxidase (P < 0.05) and catalase (CAT, P < 0.01) levels among the treatment groups. The FGS also increased serum CAT level (P < 0.01) compared with the AO group. Moreover, dietary FGS supplementation increased Lactobacillus spp. (P < 0.05) in the cecum compared with the other treatment groups and decreased Staphylococcus aureus (P < 0.05) compared with the CON and AO groups. The present findings indicate that GS and FGS can be used in broiler diets as alternatives to synthetic antioxidants.

Prevalence and antibiotic resistance profiles of Staphylococcus sp. isolated from food, food contact surfaces and food handlers in a Moroccan hospital kitchen

Food poisoning risk related to the consumption of contaminated food with known foodborne pathogens or antibiotic-resistant bacteria is currently a serious threat for public health. Thus, pathogenic methicillin-resistant Staphylococcus strains are considered as one of the major cause of foodborne diseases in hospitals. The present study aims to determine the prevalence and the antibiotic resistance patterns of Staphylococcus in various types of hospital food samples, work surfaces and its carriage by food handlers. A total of 608 collected samples including 300 food samples, 238 food contact surfaces and 70 nasal and hand samples were tested. The identified Staphylococcus and their antibiotic resistance patterns were analysed using the agar disk-diffusion and PCR method was used for mecA resistance gene amplification. The prevalence of S. aureus and the coagulase-negative staphylococci were 17·33 and 23·33%, respectively. The antibiotic resistance reached 100% towards oxacillin and Penicillin G for both S. aureus and CoNs. The mecA gene was detected in 5·71% (4/70) and 7·69% (4/52) of S. aureus and CoNs strains, respectively. The outcome of this study enlightens isolation of MRSA strains and resistant CoNs from food, food contact surfaces and food handlers. The presence of this resistant species in this critical setting, where products were intended to vulnerable and immunocompromised patients, represents a serious threat to this community. It can be a source of nosocomial infection and more precautions must be taken to prevent staphylococci food contamination mainly in hospitals. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study describing the antibiotic resistance patterns of Staphylococcus aureus and coagulase-negative Staphylococcus isolated from hospital food, food contact surfaces and food handlers samples in a Moroccan hospital kitchen. High levels of multi-resistance were reported. The alarming outcome of this study emphasizes the crucial need of implementing an approach to fight multidrug-resistant staphylococci mainly in healthcare settings, where the community have already compromised health issues.

Translating 'big data': better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry

Recent technological advances has led to the generation, storage, and sharing of colossal sets of information ('big data'), and the expansion of 'omics' in science. To date, genomics/metagenomics, transcriptomics, proteomics, and metabolomics are arguably the most ground breaking approaches in food and public safety. Here we review some of the recent studies of foodborne pathogens (Campylobacter spp., Salmonella spp., and Escherichia coli) in poultry using big data. Genomic/metagenomic approaches have reveal the importance of the gut microbiota in health and disease. They have also been used to identify, monitor, and understand the epidemiology of antibiotic-resistance mechanisms and provide concrete evidence about the role of poultry in human infections. Transcriptomics studies have increased our understanding of the pathophysiology and immunopathology of foodborne pathogens in poultry and have led to the identification of host-resistance mechanisms. Proteomic/metabolomic approaches have aided in identifying biomarkers and the rapid detection of low levels of foodborne pathogens. Overall, 'omics' approaches complement each other and may provide, at least in part, a solution to our current food-safety issues by facilitating the development of new rapid diagnostics, therapeutic drugs, and vaccines to control foodborne pathogens in poultry. However, at this time most 'omics' approaches still remain underutilized due to their high cost and the high level of technical skills required.

Antibiotic Resistance in Staphylococcus aureus from Poultry and Poultry Products in uMgungundlovu District, South Africa, Using the "Farm to Fork" Approach

Background: This study determined the prevalence and antibiotic susceptibility profiles of Staphylococcus aureus isolated from selected critical control points (farm, transport, abattoir, and retail product) in an intensive poultry production system in the uMgungundlovu District, South Africa, using the "farm to fork" approach. Materials and Methods: Three hundred eighty-four samples from poultry and poultry products were examined across the "farm to fork" continuum for S. aureus using selective media, biochemical tests, and API Staph kit and confirmed by polymerase chain reaction identification of the nuc gene. Antibiotic susceptibility testing of the isolates was determined by the Kirby-Bauer disc diffusion method to 19 antimicrobials and to vancomycin by the broth microdilution technique. Results: The overall prevalence rate of S. aureus was 31.25% (n = 120/384), distributed across the continuum: farm site (40), transport (15), abattoir (30), and retail point (35). The isolates were resistant to tetracycline (61.67%), penicillin G (55.83%), erythromycin (54.17%), clindamycin (43.33%), doxycycline (36.67%), ampicillin (34.17%), moxifloxacin (30.83%), amikacin (30.83%), trimethoprim-sulfamethoxazole (30.00%), and levofloxacin (23.33%). A 100% susceptibility to tigecycline, teicoplanin, vancomycin, nitrofurantoin, chloramphenicol, and linezolid was observed in all isolates. The rate of multidrug resistance and the multiple antibiotic resistance index of the strains were 39.17% and 0.23%, respectively. The isolates showed similar patterns of resistance to commonly used growth promoters and antibiotics in veterinary and human medicine belonging to the same class. Conclusion: It is evident that the different antibiotics and growth promoters used in poultry production are exerting selection pressure for the emergence and co-selection of antibiotic-resistant bacteria in the production system, necessitating efficient antibiotic stewardship guidelines to streamline their use.

Multidrug-Resistant Bacteria from Raw Meat of Buffalo and Chicken, Nepal

Antimicrobial resistance is a major global issue for human and animals. Increased use of antimicrobials in livestock and poultry has become one of the causes of antimicrobial resistance development in microorganisms. The aim of the study was to characterize antimicrobial resistant bacteria from raw buffalo and chicken meat in standard in vitro condition. A total of 140 raw meat samples were collected from different retail shops of Bhaktapur Metropolitan City, Nepal. Among them, 70 were raw buffalo meat and 70 were raw chicken meat samples. Bacterial growth, identification, and antimicrobial susceptibility test were performed according to Clinical & Laboratory Standards Institute (CLSI) guidelines. Out of 140 samples, bacterial growth was seen in 67 raw buffalo meat and 59 raw chicken meat samples, i.e., bacterial growth was observed in 90.0% of the samples. A total of 161 bacterial isolates were detected. Escherichia coli (35.4%) and Klebsiella spp. (30.4%) were found to be the most prevalent bacteria followed by Citrobacter spp. (11.8%), Staphylococcus aureus (9.3%), Salmonella spp. (7.4%), and Proteus spp. (5.5%). Chicken meat isolates showed higher antimicrobial resistance rates in comparison to buffalo meat isolates, particularly against antimicrobials like Amoxicillin, Tetracycline, Cotrimoxazole and Nalidixic acid, p value<0.05 when compared between buffalo and chicken meat. Overall, 32.7% Multidrug-Resistant (MDR) isolates were found, in which 50.0% MDR isolates were found from chicken raw meat and 21.9% were found from buffalo raw meat. MDR isolates of Escherichia coli, Proteus spp. and Staphylococcus aureus constituted 52.5%, 77.7% and 40.0%, respectively, of both buffalo and chicken raw meat. This study indicates antimicrobials resistant bacteria existing at an alarming rate, higher in chicken meat than in buffalo meat.