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Scientific Reports
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10.1038/s41598-024-72317-y
Article
Low-cost biosecurity measures are associated with reduced detection of non-Typhoidal Salmonella in Nigerian poultry while inappropriate antibiotic use is widespread
Hambolu Dupe Arinola 1
Olatoye Olufemi Isaac 23
Besong Mathias Ayuk 1
Call Douglas Ruben drcall@wsu.edu

3
1 Department of Veterinary and Pest Control Services, Federal Ministry of Agriculture and Food Security, Abuja, Nigeria
2 https://ror.org/03wx2rr30 grid.9582.6 0000 0004 1794 5983 Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, Ibadan, Nigeria
3 https://ror.org/05dk0ce17 grid.30064.31 0000 0001 2157 6568 Paul G. Allen School for Global Health, Washington State University, 240 SE Ott Road, Pullman, WA 99164-7090 USA
9 9 2024
9 9 2024
2024
14 2097422 11 2023
5 9 2024
© The Author(s) 2024
2024
https://creativecommons.org/licenses/by-nc-nd/4.0/ Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
Large-scale poultry production in low- and middle-income countries may be a source of adulterated products (e.g., Salmonella contamination, antibiotic residues) that can be disseminated over wide areas. We employed a cross-sectional survey of 199 randomly selected poultry farms in Lagos State, Nigeria, to estimate the prevalence of non-typhoidal Salmonella (NTS), and biosecurity and antibiotic use practices. Pooled fecal samples were collected from laying chickens and from poultry handlers. Selective culture, biochemical assays, and PCR (invA) were used to isolate and confirm NTS isolates. NTS was detected at 14% of farms (28/199) and from 10% of farm workers (6/60). Multivariate logistic regression analysis indicated that antiseptic foot dips reduced the odds ratio (OR) for detecting NTS in chicken feces [OR: 0.55; 95% confidence interval (CI) 0.07–0.58]. Most farms (94.5%, 188/199) used antibiotics for treatment and prophylaxis, but no farms (0/199) exercised withdrawal before sale of products. Most farms (86.4%, 172/199) reported using antibiotic cocktails that included medically important colistin, ciprofloxacin, chloramphenicol, and gentamicin. Egg production in Lagos State relies heavily on antibiotics and antibiotic residues are likely passed to consumers through poultry products, but there is evidence that low-cost biosecurity controls are effective for limiting the presence of NTS on farms.

Subject terms

Risk factors
Antimicrobials
Bacteria
Pathogens
Policy and public health in microbiology
Ministry of Agriculture, Lagos State, the Lagos State Agriculture Empowerment SchemePoultry Farmers Association of Nigeria, Lagos State Branchissue-copyright-statement© Springer Nature Limited 2024
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pmcIntroduction

Non-typhoidal Salmonella enterica (NTS) is an important cause of invasive infections in people with significant public health and economic impacts in Africa1,2. NTS bacteremia is particularly problematic for people living with HIV and is associated with malaria, particularly in children and elderly individuals2,3. Annually, NTS causes an estimated 31.8–211.2 million illnesses and 36.3–89.1 million deaths worldwide4. Poultry is an important reservoir for NTS with zoonotic transmission occurring through food products, water, and direct contact5.

NTS infections usually resolve without treatment, but the disease can progress to severe bacteremia or invasive infection6 with cephalosporins being the treatment of choice in countries such as Nigeria7. Frequent use of antibiotics likely ensures that NTS from poultry farms will harbor resistant strains that become more numerous in the presence of antibiotic selection pressure8. Such practices may include in ovo administration to limit chick bacteremia, and oral metaphylactic administration intended to insure against widescale bacterial infections9. And while the cost of cephalosporins probably limits their use for poultry production within low- and middle-income countries, use of antibiotics such as ampicillin will selectively favor extended-spectrum cephalosporin-resistant Enterobacteriaceae10 that are resistant to multiple antibiotics11,12. Consequently, widescale antibiotic use on poultry farms will likely increase the prevalence of antimicrobial resistant NTS on farms, with a commensurate increase in the likelihood that NTS strains will be transmitted to farm workers and poultry products. Like other enteric bacteria, Salmonella enterica acquires of resistance genes by plasmid conjugation, usually with other Enterobacteriaceae. Bacteria that develop resistance via extended-spectrum β-lactamase genes could become a reservoir of resistance genes, that further proliferate these genes in food animal microbiomes.

Like many low- and middle-income countries, Nigeria does not have a surveillance network to track the prevalence of antimicrobial resistance in human or animal settings. Further, Nigeria has no regulatory control of antibiotic use in food-animal production13,14, which leaves opportunities to employ low-cost antibiotics as a primary disease prevention measure. To better understand the prevalence of NTS and antibiotic use practices in the Nigerian poultry industry, we assessed fecal samples from birds and farm workers and assessed the relationship between the probability of detecting NTS on farms relative to basic biosecurity controls. The farms from this study are in Lagos State, which has one of the highest concentrations of poultry operations in Nigeria and is a significant source of egg production for the country15.

Results

A total of 199 randomly selected farms were included in this survey (Table 1). One farm worker completed a questionnaire from each farm, most of whom were male (78.4%), most had a tertiary education (70.9%), and poultry farming was the only source of income for most workers (70.9%) (Table S3). Farms included small-holder semi-commercial operations (25.1%), small-scale commercial operations (23.1%), medium-scale operations (41.2%), and large-scale operations (10.6%). All farms (100%) employed battery cages for animal housing. Presumptive NTS Salmonella was detected by agar plating and PCR confirmation (invA detected) for 28 out of 199 farms (14%) and for 6 out of 60 of human stool samples (10%) (Table 1).Table 1 Prevalence of non-typhoidal Salmonella (NTS) from pooled fecal samples collected from layer chickens, and individual fecal samples collected from farm workers (one worker per farm).

Division	No of sampled farmsa	No of NTS positive farms	No of pooled samples	No of NTS positive samples (%)	No of human samples	No of NTS positive human samples	
Ikeja	30	4 (13.3)	54	5 (9.2)	10	0 (0.0)	
Ikorodu	51	5 (9.8)	89	8 (8.9)	10	1 (10.0)	
Badagry	63	6 (9.5)	162	6 (3.7)	11	0 (0.0)	
Epe	40	5 (12.5)	65	5 (7.6)	22	3 (13.6)	
Lagos (Eko)	15	8 (53.3)	19	11 (57.8)	7	2 (28.5)	
Total	199	28 (14.0)	389	35 (8.9.)	60	6 (10.0)	
Collections from 199 poultry farms located in southwestern Nigeria (Badagry, Epe, Ikeja, Ikorodu, and Lagos divisions). The study was conducted from June 2018 to December 2019.

aOnly one flock was sampled per farm, but the number of pooled samples depended on flock size (n = 1 for flocks with 200–999 birds; n = 2 for flocks with 1000–4999 birds; n = 3 for flocks with 5000–9999 birds; n = 4 pooled samples for flocks with > 10,000 birds).

Most poultry farms (84.4%, 168/199) were fenced with most farms (58.8%, 117/199) using foot dips, and most used disinfectants in the dips (Table 2). Only 24.6% (49/199) of respondents washed hands with soap after handling poultry, while the majority (71.9%, 143/199) had farm-dedicated work clothing. Biosecurity measures (foot dips, fencing, dedicated clothing, hand washing) were disproportionately represented by farms that were NTS negative (p < 0.03, Table 2). Use of tire dips and awareness of Salmonella as a hazard were not related to NTS status. Manure sales represent another potential route of transmitting NTS to the public, and selling such products appeared to be equally likely for NTS positive and negative farms. A logistic regression model emphasized the importance of using foot dips (odds ratio = 0.23, 95% confidence interval 0.07–0.58), p = 0.0036) (Table 3).Table 2 Cross tabulation of biosecurity measures and presence of non-typhoidal Salmonella (NTS) on 199 chicken layer farms in located in southwestern Nigeria (Badagry, Epe, Ikeja, Ikorodu, and Lagos divisions).

Variable	Response	Percent of farms	No. of farms responding ‘no’ by NTS status	Odds ratio	95% CI4 (α = 0.05)	P	
Positive	Negative	
Did farm use foot dips?1	No	39.7% (79/199)	17	62	2.7	1.2–6.2	0.021	
Yes	60.3% (120/199)	11	109	
Was disinfectant added to foot dip?2	No	41.2% (82/199)	20	62	4.4	1.8–10.6	 < 0.001	
Yes	58.8% (117/199)	8	109	
Was the farm fenced?	No	15.6% (31/199)	9	22	3.2	1.3–8.0	0.02	
Yes	84.4% (168/199)	19	149	
Did workers use farm-dedicated clothes?	No	28.1% (56/199)	13	43	2.6	1.1–5.9	0.025	
Yes	71.9% (143/199)	15	128	
Was soap used for hand washing?	No	75.4% (150/199)	23	127	1.6	0.6–4.4	0.48	
Yes	24.6% (49/199)	5	44	
Did farms employ a tire dip?3	No	83.4% (166/199)	22	144	0.69	0.5–3.9	0.42	
Yes	16.6% (33/199)	6	27	
Was the business ≤ 5 years old?	No	33.2% (66/199)	8	58	0.8	0.3–1.9	0.67	
Yes	66.8% (133/199)	20	113	
Was the farm representative aware that Salmonella is a hazard	No	17.1% (34/199)	5	29	1.1	0.4–3.0	1.0	
Yes	82.9% (165/199)	23	142	
Did the farm sell manure for fertilizer	No	57.3% (114/199)	16	98	1.0	0.4–2.2	1.0	
Yes	42.7% (85/199)	12	73	
Significant values are given in bold.

1Foot baths are usually filled with disinfectant containing water daily and are usually located at the entrance of a poultry pens. Workers dip footwear into bath water to reduce potential pathogen transmission between facilities.

2Disinfectants with broad spectrum efficacy against viral, bacterial and fungal pathogens include aldehydes, phenolic compounds, iodine or iodophors, chlorine compounds, quaternary ammonium compound and oxidizing compounds.

3Tire dips are wheel washes that are filled daily with disinfectant for vehicle tires to be disinfected when entering poultry farms.

Table 3 Multivariate logistic regression analysis of factors associated with non-Typhoidal Salmonella occurrence in 29 of 199 poultry farms located in southwestern Nigeria (Badagry, Epe, Ikeja, Ikorodu, and Lagos divisions).

Variable	Coefficient	Odds ratio	95% Confidence limit	P	
Awareness of Salmonellosis	− 0.001	0.55	0.14–1.92	0.99	
Use disinfectant in foot dip	− 1.53	0.23	0.07–0.58	0.0036	
Use dedicated farm cloths	− 0.6618	0.52	0.19–1.48	0.21	
Perimeter fence present	− 0.3011	0.74	0.24–2.4	0.6	
Sell manure	− 0.2976	0.74	0.30–1.79	0.51	
Presence of tire dip	1.188	3.28	0.98–10.81	0.05	
Significant values are given in bold.

Most farms (94.5%, 188/199) reported using antibiotics with a combination of prophylactic and therapeutic applications, and the frequency of use varied from weekly to once every one to two months (Table 4). A minority of participants were aware of recommended withdrawal periods (22.6%, 45/199) or were aware that residuals can be found in food products (< 20%). None of the sampled farms complied with antibiotic withdrawal recommendations. Most farms reported using commercially available antibiotics including cocktails with more than one antibiotic (Table 4). In several cases the products contained medically important antibiotics (e.g., colistin), antibiotics that should not be used in food animals (e.g., chloramphenicol), and human rather than the veterinary analogues (e.g., ciprofloxacin instead of enrofloxacin) (Table 5). Products containing sulfa and tetracycline class antibiotics were used most frequently.Table 4 Antibiotic use practices at 199 poultry farms located in southwestern Nigeria (Badagry, Epe, Ikeja, Ikorodu, and Lagos divisions).

Variable	Response	n (%)	
Does the farm use antibiotics?	Yes	188 (94.5)	
No	11 (5.5)	
Purpose of antibiotics use	Prevention only	84 (42.2)	
Treatment only	38 (19.1)	
Prevention and treatment	71 (35.7)	
All the above	6 (3.0)	
Awareness of antibiotic withdrawal period	Yes	45 (22.6)	
No	154 (77.4)	
Withdrawal period compliance	Yes	0.0 (0)	
No	199 (100)	
Antibiotic resistance awareness	Yes	99 (49.7)	
No	100 (50.3)	
Frequency of antibiotic use	Weekly	12 (6.0)	
Monthly	43 (21.6)	
Every other month	68 (34.2)	
When sick only	51 (25.6)	
Others	25 (12.6)	
Understands that antibiotic can be passed to people via consumption of eggs from poultry	Yes	34 (17.1)	
No	165 (82.9)	
Understands that antibiotic administered to hens can be passed to people via consumption from poultry meat	Yes	36 (18.1)	
No	163 (81.9)	
Farm uses a cocktail of antibiotics or antibiotics with more than one active ingredient	Yes	172 (86.4)	
No	27 (13.6)	

Table 5 Antibiotic use practices at 199 poultry farms located in southwest Nigeria (Badagry, Epe, Ikeja, Ikorodu, and Lagos divisions).

Product name	Route of administration	Ingredient(s)	Antibiotics used for	Number of farms reporting use in layer chickens (%)	Approved for use in layer hens	
Tetracycline	Water/feed/i.m.a	Oxytetracycline hydrochloride	Broad-spectrum activity against chlamydia, Mycoplasma, some protozoa, and several rickettsia. Genera normally susceptible to tetracycline include Escherichia, Klebsiella, Pasteurella, Salmonella, Staphylococcus, and Streptococcus	25 (12.6)	Yes	
Triple sulpha trim(R)	Water	Sulfphadiazine sodium, sulfamerazine sodium, and sulphadirine sodium	Broad-spectrum activity against Escherichia, Salmonella, Staphylococcus, Streptococcus, Pasteurella, Proteus, Chlamydia. Also effective against Eimeria (coccidia)	51 (25.6)	No	
Tylodlox(R)	Water	Tylosin tartarate and doxycycline hyclate	Broad-spectrum activity against bacterial infections causing respiratory and enteritis infections	24 (12.2)	No	
Furatadone	Water	Furaltadone hydrochloride	Effective against bacterial infections from E. coli and Salmonella causing colibacillosis and salmonellosis	19 (9.6)	No	
Keproceryl(R)	Water	Colistin sulphate, oxytetracycline hydrochloride, erythromycin thiocyanate, streptomycin sulphate, vitamins, and minerals	Prevention and treatment of bacterial infections including chronic respiratory disease, coryza, pullorosis, fowl cholera, streptococcal and staphylococcal infections

Used as growth promoter and for vitamin deficiency during and after stressful conditions

	15 (7.5)	No	
NCO(R)	Water	Neomycin sulphate, chloramphenicol and oxytetracycline hydrochloride	Broad-spectrum activity against bacterial infections causing chronic respiratory infections and intestinal infections including Salmonella, Campylobacter, Escherichia, Klebsiella, and Pasteurella	14 (7.0)	No	
Neoceryl plus(R)	Water	Oxytetracycline, neomycin sulphate, and vitamins A, D	Effective against bacterial causing enteritis and chronic respiratory diseases including Salmonella, Escherichia, Klebsiella, and Pasteurella	14 (7.0)	No	
Enrofloxacin	i.m	Enrofloxacin	Broad-spectrum activity against a wide range of bacteria including Mycoplasma and Chlamydia	11 (5.5)	No	
Ampicillin	Water	Ampicillin trihydrate and aluminum magnesium silicate	Effective against Gram-positive bacteria and genera from the family Enterobacteriaceae	10 (5.0)	No	
Ciprofloxacin	Water	Ciprofloxacin hydrochloride	Effective against most Gram-negative bacteria, including Enterobacter, Escherichia, Klebsiella, Pasteurella, Proteus, Salmonella, and some Pseudomonas	10 (5.0)	No	
Gentamicin	Water/i.m	Gentamicin sulphate	Effective against a range of bacteria including as Escherichia, Klebsiella, Pseudomonas, Salmonella, and Staphylococcus	6 (3.0)	No	
ai.m. intramuscular.

Discussion

Poultry is a reservoir for NTS, and regions that produce large quantities of birds and eggs are potential foci for disseminating contaminated products over large geographic areas. Our study region is important because it is the hub of poultry farming and open market trading of veterinary drugs (including antibiotics) in Nigeria. To better understand the magnitude of antibiotic use and prevalence of NTS on farms, it is important to generate unbiased prevalence estimates from a representative sample of farms in our study region. In our case, we approached 217 randomly selected farms of which 199 agreed to provide information and fecal samples for which we found the prevalence of NTS to be 14% (28/199) in poultry farms and 10% (10/60) for otherwise presumptively healthy farm workers. This is likely to be an underestimate given a relatively low-intensity sampling effort, although the prevalence obtained in the our study is similar to the overall prevalence of NTS reported by Fagbamila et al., for laying chickens in Nigeria (14.3%), but lower than what Fagbamila et al. reported for Lagos State (20%)18. Jibril et al.23, however, detected a higher prevalence (47.9%) in northwestern Nigeria. This difference could be due to different sampling methods, collection seasons, culture methods, laying period, housing system and frequency of use of antibiotics administered to poultry.

Estimates of colonization with NTS varied across other regions as well. A similar prevalence (13.3%) was detected in Argentina24 while higher NTS prevalences were reported for Vietnam (45.8%)25 and Morocco (73.3%)26 laying hens. Salmonella found in otherwise healthy laying chickens represents a significant risk factor for transmission to people27, which could be reflected by the detection of NTS in 10% of poultry workers, which was higher than NTS-positive workers reported in Ethiopia (2.8%)28 and in the Mekong Delta of Vietnam (4.4%)25.

Salmonella can be a health challenge for flock health, and thus producers should be incentivized to employ biosecurity measures to reduce the spread of this pathogen and others within and between farms. Bivariate analysis showed that employing low-cost biosecurity measures (Tables 2 and 3) reduced the odds of detecting Salmonella on farms, and a multivariate logistic regression analysis suggested that having foot baths with disinfectant is a particularly effective tool, which benefits both producers and consumers. This finding is consistent with other work showing that relatively simple biosecurity measures on a farm (e.g., foot baths, fenced farms, using farm-dedicated clothing) will limit the risk of entry of a pathogen on a farm18,29.

Antibiotics are widely used around the world to manage food-animal production (growth promotion, disease treatment and prevention), but the current laissez faire market model in southwest Nigeria appears to encourage particularly egregious antibiotic use practices. For example, only one out of eleven antibiotic products (oxytetracycline hydrochloride) observed on farms appeared to be used appropriately, and most farms (86.4%, 172/199) reported using antibiotic cocktails that included medically important antibiotics such as colistin and ciprofloxacin, and antibiotics that are prohibited in food animals raised in the European Union and in the United States. For example, chloramphenicol was banned from food-animal production in the US (1984) because residues can cause dose-independent hemolytic anemia in people30,31. This study corroborates similar findings about use of prohibited drugs in poultry in Oyo, Ogun and Borno states, Nigeria14,32,33.

More generally, no farms followed recommended withdrawal times as corroborated by studies conducted in Oyo, Ogun and Borno States, Nigeria14,32,33. Withdrawal times are intended to protect consumers by allowing time for residues to clear meat products before they are sold to consumers. When withdrawal periods are not followed, consumers are exposed to residues from antibiotics that are can be dangerous, such as chloramphenicol and beta-lactam antibiotics with the latter potentially causing dangerous hypersensitive anaphylaxis in people34.

Conclusions

This study likely underestimated the prevalence of NTS on farms because of limited on-farm sampling, but the large number of farms included in the random sampling frame provided sufficient power to detect the benefits of improved biosecurity, and we assume that the prevalence estimates for antibiotic use are unbiased. Given these findings, we recommend that public health and agricultural measures include increased efforts to educate producers about effective and low-cost biosecurity measures to limit NTS on farms, about use of appropriate antibiotics for poultry, and most importantly, about the importance of adhering to recommended drug withdrawal periods to limit harm to consumers. It is also advisable for the Federal Ministry of Agriculture to develop intervention strategies and relevant policies for microbial food safety monitoring programs, and control of antibiotic use in poultry farms in Nigeria.

Methods

Sampling frame

A cross-sectional study was conducted across the five government divisions of Lagos State (Table 1) between June 2018 and December 2019. A stratified random sampling method was used to select commercial chicken layer farms from a list 785 registered commercial poultry farms obtained from the Lagos State Agricultural Development Authority. Selection was proportional to the number of registered commercial chicken layer farms in each district. If a selected farm refused to participate, it was replaced with a randomly selected farm for a total of 199 participating farms.

Questionnaires

Five research assistants from the University of Ibadan received training and to ensure that there was a common understanding of the questions among the team and to ensure that questions were administered in a consistent manner (each assistant worked in a different district). Questionnaires were administered to consenting farm workers (one per farm) to collect information about the demographic characteristics of farmers, farm characteristics, and antibiotic use practices (Table S3). A subset of these same individuals provided stool samples for bacteriological testing (see below). Study protocols were approved by the University of Ibadan, and University College Hospital Ethics committee (#UI/EC/18/0104), and by the Animal Care and Use Ethics Committee (#UI-ACUREC/17/0108). As such, all research was performed in accordance with relevant guidelines/regulations, and verbal informed consent was obtained from all participants (Table S2).

Sample collection

Only one flock per farm was sampled to estimate the prevalence of Salmonella at the level of farm. Low-intensity sampling of this nature could lead to false negative findings, but this was compensated to some extent by sampling from the longest continuously occupied layer pens that are more likely to be contaminated with Salmonella16. Within flocks, pooled samples were collected to increase the likelihood of detecting Salmonella [shedding is generally intermittent17] and the number of pooled samples depended on flock size (Table 1). Each pool consisted of five freshly voided fecal samples (200–300 g each)18. Poultry handlers were given swabs with Cary-Blair transport medium for stool sample collection, and an appointment was fixed for sample collection. NTS remains viable for at least 48 h in Cary-Blair medium16,18. Human and poultry samples were stored with ice in separate well-labelled containers and transported to the Food and Meat Hygiene Laboratory, Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, within 24 h of collection for processing.

Sample processing and assays

Fecal samples were suspended in buffered peptone water (BPW; 1:10 w/v) and incubated at 37 °C for 24 h. Following ISO 6579 (ISO, 2002), aliquots of cultured BPW were transferred to Rappaport Vassiliadis Soya broth (Oxoid) and Muller-Kauffman tetrathionate novobiocin (Oxoid) broth and incubated for 24 h at 42 °C and 37 °C, respectively. Afterwards, cultures were streaked onto xylose lysine deoxycholate agar (Oxoid) and MacConkey agar (Oxoid) and were incubated at 37 °C for 24 h. Up to three colonies that appeared typical of NTS were chosen and sub-cultured on nutrient agar plates for 24 h at 37 °C19. Putative NTS were isolated and identified according to WHO Global Foodborne Infections Network (2010)20, including a triple sugar iron test (TSI), methylene red (MR) test, Voges-Proskauer test, and indole test (Kovac's reagent)19. Isolates were further confirmed by PCR detection of the invA locus following the methods of Kadry et al.21. S. enterica ATCC S26501 was used as a positive control. Primer sequences, PCR conditions and interpretation are described in Table S1.

DNA for PCR was prepared as boiled extracts following Dias et al.22. Each PCR reaction (25 µl total volume) included 12.5 µl Taq master mix, forward and reverse primers (1.5 μl. conc. 15 pmol. stock solutions), 6.5 µl sterile distilled water, and 5 µl boiled extract. Thermalcycler conditions included 5 min initial denaturation (95 °C), followed by 40 cycles of 45 s at 95 °C, and 45 s at 52 °C. After cycling, reactions were held at 72 °C for 10 min. Each assay run included a no-template negative control, and S. enterica ATCC S26501 was used as a positive control. PCR products were separated by electrophoresis on 1.5% agarose gels, stained with GelRed (Biotium Inc., Hayward, CA, USA) and visualized with a UV transilluminator.

Data from questionnaire and laboratory results were entered and managed using spread sheet software, and data analysis was completed using Epiinfo 7® software (version 7.2.2) and STATA (verion 14.0, STATA Corp). A farm was considered NTS positive if at least one of the pooled poultry samples from that farm tested positive for PCR-confirmed Salmonella. The data was summarized using mean, frequencies, and proportions using bivariate analyses. Variables that were statistically significant at 95% confidence interval (α = 0.05) were subjected to backwards stepwise multivariate logistic regression model using STATA® to estimate the magnitude of association between biosecurity measures and the presence or absence of NTS on the participating farms.

Supplementary Information

Supplementary Tables.

Supplementary Information 2.

Supplementary Information

The online version contains supplementary material available at 10.1038/s41598-024-72317-y.

Acknowledgements

We acknowledge the laboratory contributions from L. Jones and J. Horton. This work was supported by the Ministry of Agriculture, Lagos State, the Lagos State Agriculture Empowerment Scheme, the Poultry Farmers Association of Nigeria, Lagos State Branch, and the Paul G. Allen School for Global Health, Washington State University, USA. No external funding sources contributed to this work.

Author contributions

This project was conceived and designed by D.H., M.B., and O.O. O.O., M.B., and D.C. contributed to field or laboratory training. O.O. supervised field data collection. D.H., O.O., and D.C. conducted laboratory and statistical analyses. All authors contributed to manuscript preparation.

Data availability

Raw data used to construct Tables S1, S2 and S3 is provided as a supplemental file.

Competing interests

The authors declare no competing interests.

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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References

1. Scallan E Foodborne illness acquired in the United States—major pathogens Emerg. Infect. Dis. 2011 17 7 15 10.3201/eid1701.P11101 21192848
Scallan, E. et al. Foodborne illness acquired in the United States—major pathogens. Emerg. Infect. Dis. 17, 7–15 (2011).21192848 10.3201/eid1701.P11101
2. Haeusler, G. M. & Curtis N. Non-typhoidal Salmonella in children: Microbiology, epidemiology and treatment. Adv. Exp. Med. Biol. 764, 13–26.
3. Kariuki S Gordon MA Feasey N Parry CM Antimicrobial resistance and management of invasive Salmonella disease Vaccine 2015 33 S21 S29 10.1016/j.vaccine.2015.03.102
Kariuki, S., Gordon, M. A., Feasey, N. & Parry, C. M. Antimicrobial resistance and management of invasive Salmonella disease. Vaccine 33, S21–S29 (2015).10.1016/j.vaccine.2015.03.102
4. WHO. Global action plan on antimicrobial resistance. Geneva, Switzerland. Available from: https://www.who.int/publications/i/item/9789241509763 (2016).
5. Wibisono FM A review of salmonellosis on poultry farms: Public health importance Syst. Rev. Pharm. 2020 11 481 486
Wibisono, F. M. et al. A review of salmonellosis on poultry farms: Public health importance. Syst. Rev. Pharm. 11, 481–486 (2020).
6. Katiyo S Epidemiology and outcomes of nontyphoidal Salmonella bacteremias from England, 2004 to 2015 J. Clin. Microbiol. 2019 57 e01189 e1218 10.1128/JCM.01189-18 30381422
Katiyo, S. et al. Epidemiology and outcomes of nontyphoidal Salmonella bacteremias from England, 2004 to 2015. J. Clin. Microbiol. 57, e01189-e1218 (2019).30381422 10.1128/JCM.01189-18
7. Federal Ministries of Agriculture, Environment and Health. Anitimicrobial use and resistance in Nigeria. In Situation Analysis and Recommendations. Nigeria Centre for Disease Control (NCDC), Jabi Abuja, Nigeria (2017).
8. Sanni, A. O. et al. Risk factors for persistent infection of non-typhoidal Salmonella in poultry farms, North Central Nigeria. Antibiotics (Basel) 11, 1121 (2022).
9. Gharieb RM Tartor YH Khedr MHE Non-typhoidal Salmonella in poultry meat and diarrhoeic patients: Prevalence, antibiogram, virulotyping, molecular detection and sequencing of class I integrons in multidrug resistant strains Gut. Pathog. 2015 7 34 10.1186/s13099-015-0081-1 26705426
Gharieb, R. M., Tartor, Y. H. & Khedr, M. H. E. Non-typhoidal Salmonella in poultry meat and diarrhoeic patients: Prevalence, antibiogram, virulotyping, molecular detection and sequencing of class I integrons in multidrug resistant strains. Gut. Pathog. 7, 34 (2015).26705426 10.1186/s13099-015-0081-1
10. Avillan JJ Excreted antibiotics may be key to emergence of increasingly efficient antibiotic resistance in food animal production Appl. Environ. Microbiol. 2022 88 e0079122 10.1128/aem.00791-22 35867586
Avillan, J. J. et al. Excreted antibiotics may be key to emergence of increasingly efficient antibiotic resistance in food animal production. Appl. Environ. Microbiol. 88, e0079122 (2022).35867586 10.1128/aem.00791-22
11. Laxminarayan R Access to effective antimicrobials: A worldwide challenge Lancet 2016 387 168 175 10.1016/S0140-6736(15)00474-2 26603918
Laxminarayan, R. et al. Access to effective antimicrobials: A worldwide challenge. Lancet 387, 168–175 (2016).26603918 10.1016/S0140-6736(15)00474-2
12. Lupande-Mwenebitu D Current status of resistance to antibiotics in the democratic republic of the Congo: A review J. Glob. Antimicrob. Resist. 2020 22 818 825 10.1016/j.jgar.2020.07.008 32688007
Lupande-Mwenebitu, D. et al. Current status of resistance to antibiotics in the democratic republic of the Congo: A review. J. Glob. Antimicrob. Resist. 22, 818–825 (2020).32688007 10.1016/j.jgar.2020.07.008
13. Agada GOA Prevalence and antibiotic resistance profile of Salmonella isolates from commercial poultry and poultry farm-handlers in Jos, Plateau State Nigeria Br. Microbiol. Res. J. 2014 4 462 479 10.9734/BMRJ/2014/5872
Agada, G. O. A. et al. Prevalence and antibiotic resistance profile of Salmonella isolates from commercial poultry and poultry farm-handlers in Jos, Plateau State Nigeria. Br. Microbiol. Res. J. 4, 462–479 (2014).10.9734/BMRJ/2014/5872
14. Olatoye IO Saraye TK Oxytetracycline residues in retail chicken eggs in Ibadan, Nigeria Food Addit. Contam. Part B Surveill. 2012 5 255 259 10.1080/19393210.2012.702791 24786405
Olatoye, I. O. & Saraye, T. K. Oxytetracycline residues in retail chicken eggs in Ibadan, Nigeria. Food Addit. Contam. Part B Surveill. 5, 255–259 (2012).24786405 10.1080/19393210.2012.702791
15. Poultry Farmers Task Govt to Prioritize Agric Sector. Sub-Sahara Farmers J. (2020). Available from: https://subsaharafarming.com/poultry-farmers-task-govt-to-prioritize-agric-sector.
16. Carrique-Mas JJ Davies RH Sampling and bacteriological detection of Salmonella in poultry and poultry premises: A review Rev. Sci. Tech. 2008 27 665 677 10.20506/rst.27.3.1829 19284036
Carrique-Mas, J. J. & Davies, R. H. Sampling and bacteriological detection of Salmonella in poultry and poultry premises: A review. Rev. Sci. Tech. 27, 665–677 (2008).19284036 10.20506/rst.27.3.1829
17. Desmidt M Ducatelle R Haesebrouck F Pathogenesis of Salmonella enteritidis phage type four after experimental infection of young chickens Vet. Microbiol. 1997 56 99 109 10.1016/S0378-1135(96)01350-8 9228686
Desmidt, M., Ducatelle, R. & Haesebrouck, F. Pathogenesis of Salmonella enteritidis phage type four after experimental infection of young chickens. Vet. Microbiol. 56, 99–109 (1997).9228686 10.1016/S0378-1135(96)01350-8
18. Fagbamila IO Salmonella serovars and their distribution in Nigerian commercial chicken layer farms PLoS ONE 2017 12 e0173097 10.1371/journal.pone.0173097 28278292
Fagbamila, I. O. et al. Salmonella serovars and their distribution in Nigerian commercial chicken layer farms. PLoS ONE 12, e0173097 (2017).28278292 10.1371/journal.pone.0173097
19. Ahmed AO Salmonellosis: Serotypes, prevalence and multi-drug resistant profiles of Salmonella enterica in selected poultry farms, Kwara State, North Central Nigeria Onderstepoort J. Vet. Res. 2019 86 a1667 10.4102/ojvr.v86i1.1667
Ahmed, A. O. et al. Salmonellosis: Serotypes, prevalence and multi-drug resistant profiles of Salmonella enterica in selected poultry farms, Kwara State, North Central Nigeria. Onderstepoort J. Vet. Res. 86, a1667 (2019).10.4102/ojvr.v86i1.1667
20. WHO. WHO Global Foodborne Infections Network: "A WHO network building capacity to detect, control and prevent foodborne and other enteric infections from farm to table”. Pages 1–18 from Laboratory Protocol “Isolation of Salmonella spp. From Food and Animal Faeces ” [Internet]. 5th Ed. Ju. Atlanta GA, USA.: Enteric Diseases Laboratory Branch Centers for Disease Control and Prevention (2010).
21. Kadry M Molecular diversity of the invA gene obtained from human and egg samples Vet. World. 2019 12 1033 1038 10.14202/vetworld.2019.1033-1038 31528029
Kadry, M. et al. Molecular diversity of the invA gene obtained from human and egg samples. Vet. World. 12, 1033–1038 (2019).31528029 10.14202/vetworld.2019.1033-1038
22. Dias RC Dos Santos BC Dos Santos LF Vieira MA Yamatogi RS Mondelli AL Sadatsune T Sforcin JM Gomes TA Hernandes RT Diarrheagenic Escherichia coli pathotypes investigation revealed atypical enteropathogenic E. coli as putative emerging diarrheal agents in children living in Botucatu, São Paulo State Brazil Acta Pathol. Microbiol. Immunol. Scand. 2016 124 299 308 10.1111/apm.12501
Dias, R. C. et al. Diarrheagenic Escherichia coli pathotypes investigation revealed atypical enteropathogenic E. coli as putative emerging diarrheal agents in children living in Botucatu, São Paulo State Brazil. Acta Pathol. Microbiol. Immunol. Scand. 124, 299–308 (2016).10.1111/apm.12501
23. Jibril AH Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria PLoS One 2020 15 e0238190 10.1371/journal.pone.0238190 32966297
Jibril, A. H. et al. Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria. PLoS One 15, e0238190 (2020).32966297 10.1371/journal.pone.0238190
24. Soria, M. C., et al. Salmonella spp. contamination in commercial layer hen farms using different types of samples and detection methods. Poult. Sci. 96, 2820–30 (2017).
25. Nguyen NT Use of colistin and other critical antimicrobials on pig and chicken farms in southern Vietnam and its association with resistance in commensal Escherichia coli bacteria. 2016 82 3727 3735
Nguyen, N. T. et al. Use of colistin and other critical antimicrobials on pig and chicken farms in southern Vietnam and its association with resistance in commensal Escherichia coli bacteria. 82, 3727–3735 (2016).
26. Ziyate N Prevalence and antimicrobial resistance of Salmonella isolates in Moroccan laying hen farms J. Appl. Poult. Res. 2016 25 539 546 10.3382/japr/pfw036
Ziyate, N. et al. Prevalence and antimicrobial resistance of Salmonella isolates in Moroccan laying hen farms. J. Appl. Poult. Res. 25, 539–546 (2016).10.3382/japr/pfw036
27. Eguale T Non-typhoidal Salmonella serovars in poultry farms in central Ethiopia: prevalence and antimicrobial resistance BMC Vet. Res. 2018 14 217 10.1186/s12917-018-1539-4 29980208
Eguale, T. Non-typhoidal Salmonella serovars in poultry farms in central Ethiopia: prevalence and antimicrobial resistance. BMC Vet. Res. 14, 217 (2018).29980208 10.1186/s12917-018-1539-4
28. Dagnew B Prevalence and antimicrobial susceptibility of Salmonella in poultry farms and in-contact humans in Adama and Modjo towns Ethiopia Microbiologyopen 2020 9 e1067 10.1002/mbo3.1067 32510864
Dagnew, B. et al. Prevalence and antimicrobial susceptibility of Salmonella in poultry farms and in-contact humans in Adama and Modjo towns Ethiopia. Microbiologyopen 9, e1067 (2020).32510864 10.1002/mbo3.1067
29. Postma M The biosecurity status and its associations with production and management characteristics in farrow-to-finish pig herds Animal 2016 10 478 489 10.1017/S1751731115002487 26567800
Postma, M. et al. The biosecurity status and its associations with production and management characteristics in farrow-to-finish pig herds. Animal 10, 478–489 (2016).26567800 10.1017/S1751731115002487
30. Payne MA Drugs prohibited from extra label use in food animals J. Am. Vet. Med. Assoc. 1999 215 28 32 10.2460/javma.1999.215.01.28 10490381
Payne, M. A. et al. Drugs prohibited from extra label use in food animals. J. Am. Vet. Med. Assoc. 215, 28–32 (1999).10490381 10.2460/javma.1999.215.01.28
31. Davis JL Update on drugs prohibited from extra label use in food animals J. Am. Vet. Med. Assoc. 2009 235 528 534 10.2460/javma.235.5.528 19719442
Davis, J. L. et al. Update on drugs prohibited from extra label use in food animals. J. Am. Vet. Med. Assoc. 235, 528–534 (2009).19719442 10.2460/javma.235.5.528
32. Adebowale OO Antibiotic use and practices in commercial poultry laying hens in Ogun State Nigeria Rev. Elev. Med. Vet. Pays Trop. 2016 69 41 45 10.19182/remvt.31170
Adebowale, O. O. et al. Antibiotic use and practices in commercial poultry laying hens in Ogun State Nigeria. Rev. Elev. Med. Vet. Pays Trop. 69, 41–45 (2016).10.19182/remvt.31170
33. Galadima HB Survey of antimicrobial residue in table eggs among layer poultry farmers in Maiduguri Metropolis, Borno State Asian J. Anim. Vet. Adv. 2018 13 101 108 10.3923/ajava.2018.101.108
Galadima, H. B. et al. Survey of antimicrobial residue in table eggs among layer poultry farmers in Maiduguri Metropolis, Borno State. Asian J. Anim. Vet. Adv. 13, 101–108 (2018).10.3923/ajava.2018.101.108
34. Baynes RE Health concerns and management of select veterinary drug residues Food Chem. Toxicol. 2016 88 112 122 10.1016/j.fct.2015.12.020 26751035
Baynes, R. E. et al. Health concerns and management of select veterinary drug residues. Food Chem. Toxicol. 88, 112–122 (2016).26751035 10.1016/j.fct.2015.12.020
