Antimicrobial Resistance Patterns and Risk Factors Associated with Salmonella spp. Isolates from Poultry Farms in the East Coast of Peninsular Malaysia: A Cross-Sectional Study
Abstract
:1. Introduction
2. Results
3. Discussion
4. Materials and Methods
4.1. Ethics Approval
4.2. Study Design and Data Sources
4.3. Data and Sample Collection
4.4. Samples Collection and Laboratory Methods
4.5. Microbiological Testing
4.6. Antimicrobial Susceptibility Testing
4.7. DNA Extraction of Salmonella spp. Isolates
4.8. PCR Confirmation of Salmonella spp.
4.9. PCR Assay for Detection of Resistance Genes
4.10. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Risk Factors | Samples Tested | Affected (%) | p-Value |
---|---|---|---|
Age | 0.504 | ||
Young | 187 | 86 (46%) | |
Adult | 184 | 91 (49.5%) | |
Management system | 0.478 | ||
Intensive | 187 | 95 (50.8%) | |
Semi-intensive | 158 | 70 (44.3%) | |
Mixed | 26 | 12 (46.2%) | |
Production system | 0.188 | ||
Broiler | 212 | 109 (51.4%) | |
Layer | 53 | 25 (47.2%) | |
Mixed | 106 | 43 (40.6%) | |
State | 0.065 | ||
Kelantan | 158 | 79 (50%) | |
Terengganu | 80 | 29 (36.3%) | |
Pahang | 133 | 69 (51.9%) | |
Districts | 0.010 | ||
Kelantan | |||
Bachok | 52 | 29 (55.8%) | |
Kota Bharu | 26 | 12 (46.2%) | |
Machang | 28 | 16 (57.1%) | |
Pasir Mas | 26 | 13 (50%) | |
Jeli | 26 | 9 (34.6%) | |
Pahang | |||
Kuantan | 79 | 50 (63.3%) | |
Pekan | 54 | 19 (35.2%) | |
Terengganu | |||
Kuala Terengganu | 26 | 8 (30.8%) | |
Marang | 54 | 21 (38.9%) | |
Sample source | 0.007 | ||
Cloaca swab | 259 | 120 (46.3%) | |
Fecal Sample | 84 | 50 (59.5%) | |
Sewage | 14 | 5 (35.7%) | |
Tap Water | 14 | 2 (14.3%) | |
Farm size | 0.098 | ||
Small | 104 | 50 (48.1%) | |
Medium | 187 | 97 (51.9%) | |
Large | 80 | 30 (37.5%) | |
Origin of the poultry | 0.113 | ||
Local | 26 | 12 (46.2%) | |
Imported | 133 | 73 (54.9%) | |
Both | 212 | 92 (43.4%) | |
Sewage system | 0.021 | ||
Excellent | 109 | 64 (58.7%) | |
Good | 210 | 92 (43.8%) | |
Poor | 52 | 21 (40.4%) | |
Water Source | 0.013 | ||
Surface water | 106 | 38 (35.8%) | |
Bond water | 133 | 72 (54.1%) | |
Pump water | 132 | 67 (50.8%) |
Antimicrobial Resistance | Percentage (%) |
---|---|
Resistance | |
No resistance | 24 (13.6%) |
Resistance | 153 (86.4%) |
Number of classes | |
No resistance | 24 (13.6%) |
Resistant to 1 class | 46 (26%) |
Resistant to 2 classes | 34 (19.2%) |
Resistant to 3–4 classes | 56 (31.6%) |
Resistant to 5 or more classes | 17 (9.6%) |
Tetracyclines | |
Resistant | 70 (39.5%) |
Penicillins | |
Resistant | 57 (32.2%) |
Aminoglycosides | |
Resistant | 63 (35.6%) |
Sulfonamides | |
Resistant | 92 (52%) |
Cephalosporins | |
Resistant | 21 (11.9%) |
Chloramphenicol | |
Resistant | 14 (7.9%) |
Macrolides | |
Resistant | 33 (18.6%) |
Quinolones | |
Resistant | 45 (25.4%) |
Risk Factors | Antimicrobials | |||||||
---|---|---|---|---|---|---|---|---|
No Identified Resistance | Antimicrobial Class Resistance | |||||||
No Antimicrobial Resistance | Resistance to at Least One Antimicrobial | No Antimicrobial Resistance | Resistant to 1 Class | Resistant to 2 Classes | Resistant to 3–4 Classes | Resistant to 5 or More Classes | ||
Sample type | Cloacal (n = 259) | 20 (7.7%) | 100 (38.6%) | 22 (8.5%) | 36 (13.9%) | 24 (9.3%) | 35 (13.5%) | 3 (1.2%) |
Faecal (n = 84) | 0 | 50 (59.5%) | 0 | 7 (8.3%) | 9 (10.7%) | 21 (34.2%) | 13 (15.5%) | |
Sewage (n = 14) | 2 (14.3%) | 3 (21.4%) | 2 (14.3%) | 2 (14.3%) | 0 | 0 | 1 (7.1%) | |
Tap water (n = 14) | 2 (14.3%) | 0 | 2 (14.3%) | 0 | 0 | 0 | 0 | |
Age | Young (n = 187) | 12 (6.4%) | 74 (39.6%) | 13 (7%) | 20 (10.7%) | 13 (7%) | 30 (16%) | 10 (5.3%) |
Adult (n = 184) | 12 (6.5%) | 79 (43%) | 13 (7.1%) | 24 (13%) | 21 (11.4%) | 26 (14.1%) | 7 (3.8%) | |
Poultry origin | Local (n = 26) | 3 (11.5%) | 9 (34.6%) | 3 (11.5%) | 5 (19.2%) | 0 | 4 (15.4%) | 0 |
Imported (n = 133) | 5 (3.8%) | 68 (51.1%) | 6 (4.5%) | 21 (15.8%) | 20 (15%) | 20 (15%) | 6 (4.5%) | |
Both (n = 212) | 16 (7.5%) | 76 (35.8%) | 17 (8%) | 19 (9%) | 13 (6.1%) | 32 (15.9%) | 11 (5.2%) | |
Management system | Intensive (n = 187) | 7 (3.7%) | 88 (47.1%) | 9 (4.8%) | 21 (11.2%) | 18 (9.6%) | 34 (18.2%) | 13 (7%) |
Semi-intensive (n = 158) | 14 (8.9%) | 56 (35.4%) | 14 (8.9%) | 19 (12%) | 15 (9.5%) | 18 (11.4%) | 4 (2.5%) | |
Mixed (n = 26) | 3 (11.5%) | 9 (34.6%) | 3 (11.5%) | 5 (19.2%) | 0 | 4 (15.4%) | 0 | |
Production system | Broiler (n = 212) | 13 (6.1%) | 96 (45.3%) | 15 (7.1%) | 26 (12.3%) | 20 (9.4%) | 36 (17%) | 12 (5.7%) |
Layer (n = 53) | 1 (1.9%) | 24 (45.3%) | 1 (1.9%) | 9 (17%) | 6 (11.3%) | 8 (15.1%) | 1 (1.9%) | |
Mixed (n = 106) | 10 (9.4%) | 33 (31.1%) | 10 (9.4%) | 10 (9.4%) | 7 (6.6%) | 12 (11.3%) | 4 (3.8%) | |
Farm size | Small (n = 104) | 9 (8.7%) | 41 (39.4%) | 9 (8.7%) | 18 (17.3%) | 8 (7.7%) | 13 (12.5%) | 2 (1.9%) |
Medium (n = 187) | 14 (7.5%) | 83 (44.4%) | 15 (8%) | 21 (11.2%) | 19 (10.2%) | 33 (17.6%) | 9 (4.8%) | |
Large (n = 80) | 1 (1.3%) | 29 (23.8%) | 2 (2.5%) | 6 (7.5%) | 6 (7.5%) | 10 (12.5%) | 6 (7.5%) | |
Water source | Surface water (n = 103) Bond water (n = 133) | 6 (5.8%) 7 (5.3%) | 32 (31.1%) 65 (48.9%) | 7 (6.8%) 8 (6%) | 3 (2.9%) 20 (15.8%) | 5 (4.9%) 16 (12%) | 13 (12.6%) 22 (16.5%) | 10 (9.7%) 6 (4.5%) |
Pump water (n = 132) | 11 (8.3%) | 56 (32.2%) | 11 (8.3%) | 22 (16.7%) | 12 (9.1%) | 21 (16%) | 1 (0.8%) | |
Sewage system | Excellent (n = 109) Good (n = 210) | 4 (3.7%) 16 (7.6%) | 60 (55%) 76 (36.2%) | 5 (4.6%) 17 (8.1%) | 17 (15.6%) 21 (10%) | 12 (11%) 19 (9%) | 25 (23%) 23 (11%) | 5 (4.6%) 12 (5.7%) |
Poor (n = 52) | 4 (7.7%) | 17 (32.7%) | 4 (7.7%) | 7 (13.5%) | 2 (3.8%) | 8 (15.4%) | 0 | |
Feed source | Endogenous (n =132) | 8 (6%) | 53 (40.1%) | 8 (6.1%) | 20 (15.2%) | 14 (10.6%) | 16 (12.1%) | 3 (2.3%) |
Exogenous (n = 213) | 15 (7%) | 88 (41.4%) | 17 (8%) | 19 (9%) | 15 (7%) | 38 (17.8%) | 14 (6.6%) | |
Other (n = 26) | 1 (3.8%) | 12 (46.2%) | 1 (3.8%) | 6 (23.1%) | 4 (15.4%) | 2 (7.7) | 0 |
OR | 2.5% | 97.5% | Pr (>|z|) | |
---|---|---|---|---|
Semi-intensive Mixed | Ref | - | - | - |
Intensive | 1.55 | 1.01 | 2.40 | 0.04 |
Mixed | 0.96 | 0.39 | 2.26 | 0.93 |
Antimicrobial Class/Agent | Resistance Gene | % Isolates |
---|---|---|
Tetracyclines | tet (A) | 7% |
Tetracyclines | tet (B) | 14.2% |
Chloramphenicol | cat1 | 7% |
Chloramphenicol | cat2 | 78% |
Chloramphenicol | floR | 78% |
Sulfonamides | sul1 | 85% |
Sulfonamides | sul2 | 71% |
β-Lactams | blaTEM | 42% |
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Osman, A.Y.; Elmi, S.A.; Simons, D.; Elton, L.; Haider, N.; Khan, M.A.; Othman, I.; Zumla, A.; McCoy, D.; Kock, R. Antimicrobial Resistance Patterns and Risk Factors Associated with Salmonella spp. Isolates from Poultry Farms in the East Coast of Peninsular Malaysia: A Cross-Sectional Study. Pathogens 2021, 10, 1160. https://doi.org/10.3390/pathogens10091160
Osman AY, Elmi SA, Simons D, Elton L, Haider N, Khan MA, Othman I, Zumla A, McCoy D, Kock R. Antimicrobial Resistance Patterns and Risk Factors Associated with Salmonella spp. Isolates from Poultry Farms in the East Coast of Peninsular Malaysia: A Cross-Sectional Study. Pathogens. 2021; 10(9):1160. https://doi.org/10.3390/pathogens10091160
Chicago/Turabian StyleOsman, Abdinasir Yusuf, Sharifo Ali Elmi, David Simons, Linzy Elton, Najmul Haider, Mohd Azam Khan, Iekhsan Othman, Alimuddin Zumla, David McCoy, and Richard Kock. 2021. "Antimicrobial Resistance Patterns and Risk Factors Associated with Salmonella spp. Isolates from Poultry Farms in the East Coast of Peninsular Malaysia: A Cross-Sectional Study" Pathogens 10, no. 9: 1160. https://doi.org/10.3390/pathogens10091160