Genomic diversity and antibiotic resistance of Escherichia coli and Salmonella from poultry farms in Oyo State, Nigeria
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PROVIDER: PRJNA1246560 | ENA |
REPOSITORIES: ENA
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Project description:Salmonella remains the leading cause of foodborne illness in the United States, and the dissemination of drug-resistant Salmonellae through the food chain has important implications for treatment failure of salmonellosis. We investigated the ecology of Salmonella in integrated broiler production in order to understand the flow of antibiotic susceptible and resistant strains within this system. Data were analyzed from a retrospective study focused on antimicrobial resistant Salmonella recovered from commercial broiler chicken farms conducted during the initial years of the US FDA's foray into retail meat surveillance by the National Antimicrobial Resistance Monitoring System (NARMS). Sixty-three percentage of Salmonella were pan-susceptible to a panel of 19 antimicrobials used by the NARMS program. Twenty-five antimicrobial resistance phenotypes were observed in Salmonella isolated from two broiler chicken farms. However, Salmonella displaying resistance to streptomycin, alone, and in combination with other antibiotics was the most prevalent (36.3%) antimicrobial resistance phenotype observed. Resistance to streptomycin and sulfadimethoxine appeared to be linked to the transposon, Tn21. Combinations of resistance against streptomycin, gentamicin, sulfadimethoxine, trimethoprim, and tetracycline were observed for a variety of Salmonella enterica serovars and genetic types as defined by pulsed-field gel electrophoresis. There were within and between farm differences in the antibiotic susceptibilities of Salmonella and some of these differences were linked to specific serovars. However, farm differences were not linked to antibiotic usage. Analysis of the temporal and spatial distribution of the endemic Salmonella serovars on these farms suggests that preventing vertical transmission of antibiotic-resistant Salmonella would reduce carcass contamination with antibiotic-resistant Salmonella and subsequently human risk exposure.
| S-EPMC5482141 | biostudies-other
Project description:Salmonella is an important human pathogen and poultry products constitute an important source of human infections. This study investigated prevalence; identified serotypes based on whole genome sequence, described spatial distribution of Salmonella serotypes and predicted risk factors that could influence the prevalence of Salmonella infection in commercial poultry farms in Nigeria. A cross sectional approach was employed to collect 558 pooled shoe socks and dust samples from 165 commercial poultry farms in North West Nigeria. On-farm visitation questionnaires were administered to obtain information on farm management practices in order to assess risk factors for Salmonella prevalence. Salmonella was identified by culture, biotyping, serology and polymerase chain reaction (PCR). PCR confirmed isolates were paired-end Illumina- sequenced. Following de novo genome assembly, draft genomes were used to obtain serotypes by SeqSero2 and SISTR pipeline and sequence types by SISTR and Enterobase. Risk factor analysis was performed using the logit model. A farm prevalence of 47.9% (CI95 [40.3-55.5]) for Salmonella was observed, with a sample level prevalence of 15.9% (CI95 [12.9-18.9]). Twenty-three different serotypes were identified, with S. Kentucky and S. Isangi as the most prevalent (32.9% and 11%). Serotypes showed some geographic variation. Salmonella detection was strongly associated with disposal of poultry waste and with presence of other livestock on the farm. Salmonella was commonly detected on commercial poultry farms in North West Nigeria and S. Kentucky was found to be ubiquitous in the farms.
| S-EPMC7510976 | biostudies-literature
Project description:BackgroundAntimicrobial resistance (AMR) is a global health threat affecting treatment outcome in animals and humans. A pre-requisite for development of AMR reduction strategies is knowledge of antimicrobial use patterns, and how these affect resistance development. The aim of this study was to determine antimicrobial usage (AMU) and whether such usage was associated with AMR in Salmonella from poultry farms in Northwest Nigeria.ResultsFifteen (37%) of antimicrobial products observed contained compounds that are of highest priority and critically important for human medicine. Broilers chicken consumed higher (28 ± 14 mg/kg active ingredients) amounts of antimicrobials compared to layers (13 ± 8 mg/kg) per week (p = 0.0009). Surprisingly, chickens raised under backyard system consumed higher amounts of antimicrobials (34 ± 7 mg/kg) than poultry in other systems (p = 0.02). High levels of resistance to tetracycline (58%), sulphonamides (65%), ciprofloxacin (46%) and gentamicin (42%) correlated with high farm level usage of these antimicrobials, and there was a strong correlation (r = 0.9) between farm usage and resistance of isolates to the same antimicrobials (p = 0.03).ConclusionHigh AMU, including use of highest priority critically important antimicrobials was observed at poultry farms in Northwest Nigeria. AMU correlated with high levels of resistance. Communication of prudent use of antimicrobials to farmers and regulation to obtain reduction in AMU should be a priority.
| S-EPMC8254292 | biostudies-literature
Project description:Molecular epidemiology of ESBL-E.coli Poultry Nigeria
| PRJEB58679 | ENA
Project description:Overwhelming empirical evidence has highlighted the contribution of indiscriminate antibiotic usage (ABU) in food animals to the overall burden of antibiotic resistance (ABR) in humans, thus making antibiotic use the main selective pressure driving antibiotic resistance. The social and behavioral perspective on antibiotic use and resistance in poultry is limited. Our study therefore aimed at obtaining information on antibiotic usage, awareness of ABR, and the attitude and perceptions towards prudent antibiotic usage and ABR. A cross-sectional survey using a structured questionnaire was conducted in 125 poultry farms in Kwara state in December 2019. Most farmers (69.6%, n = 87/125) were aware of ABR and had satisfactory knowledge about ABR with a mean knowledge score of 3.2 ± 1.5. Age (older farmers; OR: 1.1, 95% CI: 1.0, 1.2) and gender (male respondents, OR: 8.5, 95% CI: 3.0, 23.9; p < 0.01) were more likely to have satisfactory knowledge of ABR. Tertiary education was significantly associated with ABR awareness (OR: 4.7; 95% CI: 0.1, 0.7; p = 0.007) and the ABR knowledge level (OR: 7.8; 95% CI: 3.3, 18.7; p < 0.01). Higher flock size was significantly associated with a satisfactory knowledge of ABR (OR: 9.5; 95% CI: 3.8, 23.6; p < 0.01). Most of the poultry farmers (68%) had positive attitudes towards prudent antibiotic use with a mean score of 2.7 ± 0.9. On the contrary, only 32.8% of poultry farmers had a desirable perception of ABR with a mean perception score of 4.9 ± 1.1. The ABR knowledge level was significantly associated with the perceptions of farmers (p < 0.05) but not their attitudes toward ABU and ABR (p = 0.083). There was evidence of unprescribed use of antibiotics in poultry and a failure to observe antibiotic withdrawal periods. These constitute a risk of exposure to unacceptable levels of drug residues from poultry products and an increased risk of ABR. Improving education and communication on antibiotic stewardship programs are crucial to prevent the looming antibiotic threat.
| S-EPMC7400114 | biostudies-literature
Project description:BackgroundIndiscriminate use of antimicrobials for the prevention and treatment of bacterial infection in animals is a common practice in Nigeria as in other developing countries. These antimicrobials are purchased over the counter without restrictions and often administered in form of medicated feedstuffs. In Nigeria, like most developing countries, antimicrobial prescription data are not routinely collected or reported at the farm level, instead import data are used in reporting antimicrobial consumption. Farmers can be useful sources of data on the use of antimicrobial agents by class, animal species, production type and age. The objective of the study was to determine the knowledge, attitude and practices of poultry farmers on antimicrobial resistance and to generate data on antimicrobial use (AMU) in poultry farms in Plateau and Oyo states in accordance with the guidelines of the World Organization for Animal Health (WOAH).MethodsA questionnaire used by the Food and Agriculture Organization (FAO) of the United Nations in Ghana was adopted and modified to collect data on the knowledge, attitude and practices of farmers on AMR and AMU and to collect AMU data from selected poultry farms. A focus group discussion (FGD) was conducted in Plateau state with poultry farmers and representatives from the state veterinary services, using a checklist. The aim of the FGD was to have an idea on antimicrobial use among poultry farmers and to generate additional questions that might be added to the questionnaire. Stratified random sampling technique was used to select 50 farms from Plateau and Oyo states, using the list of registered poultry farms in the two states as sampling frame.ResultsNinety eight percent (98%) of farmers gave antibiotics as prophylactic treatment to day old chicks. There were 47 different products used in the two states within the study period. We observed that five classes of antibiotics (Tetracyclines, Penicillins, Aminoglycosides, Polypeptides and Fluoroquinolone) were used in the two states. A total of 351 kg of active ingredients from seven different classes, namely: tetracyclines, penicillins, aminoglycosides, polypeptide, fluoroquinolones, amphenicol and macrolides were recorded from the two states. Some products contained cocktail of antibiotics, having up to six different classes with very high concentration of active ingredients which are not in the list of registered antimicrobials reported to WOAH.ConclusionThe concept used for this survey proved that the approach can be applied for AMU surveillance in the animal health sector. It also provided insight on farmers' knowledge and practices with regards to the use of antimicrobials which is missing in the national import data. The need for "stronger" antibiotics was identified as one of the drivers of antibiotic resistance.
| S-EPMC10084607 | biostudies-literature
Project description:Salmonellosis is a bacterial zoonosis causing an array of health conditions. Non-typhoidal salmonellosis (NTS) has a discrete adaptation to certain animals; in poultry, pullorum and fowl typhoid are its primary disease manifestations. The diseases are prevalent in Nigerian poultry and have been well-studied in Nigeria, but less so in North Central Nigeria (NCN). Using field sampling, laboratory methods and a semi-structured questionnaire for 1000 poultry farms in NCN, we explored the incidence and risk factors for the persistence of NTS infection in poultry. Approximately 41.6% of the farms had experienced NTS over the last 18 months. Farm experience of NTS moderately predicted awareness of salmonellosis. Increasing stock in smallholder farms, self-mixing of concentrate on the farm, usage of stream water, pen odour, non-adherence and partial adherence of farms to recommended poultry vaccination against pullorum and fowl typhoid and lack of and non-adherence to biosecurity were identified risk factors that increased the odds of NTS infection in poultry. Antibiotic use practice may have reduced the isolation rate of NTS, yet NTS continues to challenge poultry farms in Nigeria. Identified risk practices must be mitigated intentionally and biosecurity and hygiene must be improved to reduce the burden of NTS.
| S-EPMC9405283 | biostudies-literature
Project description:BackgroundThe irrational use of antibiotics in poultry production has far-reaching consequences and continues to impact the fight against antimicrobial resistance (AMR) in Africa. In Nigeria, antibiotics are available over-the-counter and are widely used in food animal production for various reasons, including prophylaxis and growth promotion. While this practice may support animal production, it also drives the spread of AMR, posing serious health challenges due to close human-livestock interactions and the country's high disease burden. This study examined poultry farmers' knowledge, attitudes, and practices (KAP) regarding antibiotic use and AMR, aiming to highlight the public health risks and challenges in combating AMR in Nigeria.MethodsA cross-sectional survey of 200 poultry farms in Enugu State, Southeast Nigeria, was conducted to evaluate farmers' KAP towards antibiotic usage and AMR. Using a validated, standardized, and self-administered questionnaire, data were collected from farmers responsible for key farm decisions, including input and feed management. The questionnaire comprised three sections: socio-demographic data, knowledge of AMR, and knowledge and practices regarding antibiotic use. Ethical approval was obtained, and participants gave oral consent based on their professional capacity.ResultsThe evaluation of poultry's farmers KAP regarding antibiotic usage and AMR revealed that the majority of farmers (90.5%) reported using antibiotics, primarily for treating infections (80.5%) or for feed enhancement, growth promotion, and prophylaxis (61%). Ampicillin (75%), ciprofloxacin (71.5%), and doxycycline (71%) were the most commonly administered antibiotics. Monthly administration was the most common (48%), and 89% of respondents believed that antibiotics promote poultry growth. Interestingly, a substantial proportion of respondents (65%) were unaware of AMR, highlighting a significant knowledge gap, with only 16% recognizing the risk of AMR infections.ConclusionOur study revealed that the surveyed poultry farmers heavily rely on antibiotics, primarily for treating infections and, to a significant extent, for growth promotion, despite their limited awareness of AMR. Ampicillin was identified as the most commonly used antibiotic, raising concerns due to its potential link to beta-lactamase selection amid the country's carbapenem resistance issues. These findings underscore the urgent need for targeted education to address the AMR knowledge gap and reduce the misuse of antibiotics in poultry farming settings in Nigeria.
| S-EPMC11844400 | biostudies-literature
Project description:Inappropriate antibiotic use in food-producing animals is associated with the emergence and spread of antibiotic resistance. In industrial broiler poultry farms in three districts of Kathmandu valley, Nepal, we assessed antibiotic use prevalence, and their classes, types, and quantities. A cross-sectional questionnaire study involving field visits to large poultry farms (flock size ≥ 3000) of the Kathmandu, Bhaktapur, and Lalitpur districts was conducted. Of 30 farms (total flock size 104,200; range 3000-6000), prevalence of antibiotic use was 90% (95% CI: 73-98%). Six (22%) farms used antibiotics as prophylaxis, while 21 (78%) used it for therapeutics. Seven antibiotics from six classes (including quinolones, macrolides, and polymyxins) were used. The most commonly used antibiotics were tylosin (47%), colistin (47%), and dual therapies with neomycin and doxycycline (33%). A total of 50,000 grams of antibiotics (total weight including active and inactive ingredients) were used (0.5 grams/chicken/45 days of flock life) with eight (26%) farms using more than two antibiotics. No farms had records on clinical indications for prophylaxis or treatment. No post-mortem records of sick birds were available. Prevalence of antibiotic use in broiler farms of Kathmandu valley is high and includes "highest priority critically important antibiotics" for human use, with direct implications on public health.
| S-EPMC8167706 | biostudies-literature
Project description:Molecular characterization of extended-spectrum beta-lactamase genes in Enterobacteriaceae isolates from Nigeria
| PRJEB35517 | ENA