Risk Factors of Extended-Spectrum β-Lactamase Producing Enterobacteriaceae Occurrence in Farms in Reunion, Madagascar and Mayotte Islands, 2016–2017
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Population
2.2. Sampling
2.3. Laboratory Investigations
2.3.1. ESBL-E Phenotype
2.3.2. Characterization of ESBL Genes
2.4. Questionnaire
2.5. Risk Factors Analyses
3. Results
3.1. Prevalence Observed, Bacterial Diversity and Antibiogram Results
3.2. ESBL Identification
3.3. Explanatory Factors of ESBL-E Occurrence in Livestock Sectors Production in Reunion, Madagascar and Mayotte, 2016–2017
4. Discussion
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Territory | N (Positive Farm) | ESBL-E Positive Farms | p-Value (1) | p-Value (2) |
---|---|---|---|---|
Reunion | <0.001 | |||
Poultry | 30 (21) | 70.0% [53.3–86.7] | − | 0.94 |
Pigs | 30 (16) | 53.3% [35.1–71.5] | − | <0.005 |
Beef cattle | 54 (2) | 03.7% [00.0–08.8] | − | <0.001 |
Mayotte | 0.70 | |||
Poultry | 23 (17) | 73.9% [55.6–92.2] | − | − |
Beef cattle | 19 (13) | 68.4% [47.1–89.7] | − | − |
Madagascar | 0.16 | |||
Poultry | 30 (21) | 70.0% [53.6–86.7] | − | − |
Pigs | 30 (26) | 86.7% [74.3–99.1] | − | − |
Beef cattle | 30 (20) | 66.7% [49.5–83.9] | − | − |
Bacterial Species | Reunion | Mayotte | Madagascar | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Poultry | Pig | Cattle | Poultry | Cattle | Poultry | Pig | Cattle | ||||||||||
N (% ESBL-E) | n | ESBL-E (%) | n | ESBL-E (%) | n | ESBL-E (%) | n | ESBL-E (%) | n | ESBL-E (%) | n | ESBL-E (%) | n | ESBL-E (%) | n | ESBL-E (%) | |
Citrobacter freundii | 6 (100.0%) | - | - | 2 | 2 (100.0%) | - | - | - | - | - | - | - | - | 4 | 4 (100.0%) | - | - |
Escherichia coli | 307 (95.1%) | 145 | 136 (93.8%) (93.8%) | 45 | 40 (88.9%) | 2 | 2 (100.0) | 19 | 19 (100.0%) | 17 | 17 (100.0%) | 28 | 28 (100.0%) (100.0%) | 29 | 28 (96.6%) | 22 | 22 (100.0%) |
Escherichia hermannii | 2 (100.0%) | - | - | - | - | - | - | - | - | - | - | - | - | - | 2 | 2 (100.0%) | |
Enterobacter cloacae complex | 13 (92.3%) | 1 | 1 (100.0%) | - | - | 1 | 0 (00.0%) | 1 | 1 (100.0%) | 1 | 1 (100.0%) | 1 | 1 (100.0%) | 6 | 6 (100.0%) | 2 | 2 (100.0%) |
Klebsiella pneumoniae | 11 (100.0%) | - | - | 2 | 2 (100.0%) | - | - | - | - | - | - | 2 | 2 (100.0%) | 7 | 7 (100.0%) | - | - |
Morganella morganii | 2 (100.0%) | - | - | - | - | - | - | - | - | - | - | - | - | 2 | 2 (100.0%) | - | - |
ETP | NA | OFL | GEN | AMK | SXT | TCN | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
S | I | R | S | I | R | S | I | R | S | I | R | S | I | R | S | I | R | S | I | R | ND | |
Reunion | ||||||||||||||||||||||
Broiler | ||||||||||||||||||||||
E. coli (N = 136) | 136 (100.0%) | 0 (00.0%) | 0 (00.0%) | 102 (75.0%) | 5 (03.7%) | 29 (21.3%) | 131 (96.3%) | 2 (01.5%) | 3 (02.2%) | 128 (94.1%) | 0 (00.0%) | 8 (05.9%) | 134 (100.0%) | 0 (00.0%) | 0 (00.0%) | 34 (25.0%) | 0 (00.0%) | 102 75.0%) | 33 (24.3%) | 0 (00.0%) | 65 (47.8%) | 38 (27.9%) |
E. cloacae (N = 1) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | |
Pig | ||||||||||||||||||||||
E. coli (N = 40) | 39 (97.5%) | 1 (02.5%) | 0 (00.0%) | 29 (72.5%) | 1 (02.5%) | 10 (25.0%) | 30 (75.0%) | 0 (00.0%) | 10 (25.0%) | 35 (87.5%) | 0 (00.0%) | 5 (12.5%) | 40 (100.0%) | 0 (00.0%) | 0 (00.0%) | 5 (12.5%) | 0 (00.0%) | 35 (87.5%) | 5 (12.5%) | 1 (02.5%) | 23 (57.5%) | 11 (27.5%) |
C. freundii (N = 2) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | |
K. pneumoniae (N = 2) | 1 (50.0%) | 1 (50.0%) | 0 (00.0%) | 1 (50.0%) | 0 (00.0%) | 1 (50.0%) | 1 (50.0%) | 0 (00.0%) | 1 (50.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (50.0%) | 2 (100.0%) | 1 (50.0%) | 1 (50.0%) | 0 (00.0%) | 1 (50.0%) | |
Beef cattle | ||||||||||||||||||||||
E. coli (N = 2) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (50.0%) | 0 (00.0%) | 1 (50.0%) | 1 (50.0%) | 1 (50.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | |
Mayotte | ||||||||||||||||||||||
Broiler | ||||||||||||||||||||||
E. coli (N = 19) | 19 (100.0%) | 0 (00.0%) | 0 (00.0%) | 14 (73.7%) | 4 (21.1%) | 1 (05.3%) | 19 (100.0%) | 0 (00.0%) | 0 (00.0%) | 18 (94.7%) | 0 (00.0%) | 1 (05.3%) | 19 (100.0%) | 0 (00.0%) | 0 (00.0%) | 14 (73.7%) | 0 (00.0%) | 5 (26.3%) | 3 (15.8%) | 0 (00.0%) | 16 (84.2%) | |
E. cloacae (N = 1) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | |
Beef cattle | ||||||||||||||||||||||
E. coli (N = 16) * | 16 (100.0%) | 0 (00.0%) | 0 (00.0%) | 7 (43.8%) | 5 (31.3%) | 4 (25.0%) | 14 (87.5%) | 2 (12.5%) | 0 (00.0%) | 12 (75.0%) | 0 (00.0%) | 4 (25.0%) | 16 (100.0%) | 0 (00.0%) | 0 (00.0%) | 15 (93.8%) | 0 (00.0%) | 1 (06.3%) | 12 (75.0%) | 0 (00.0%) | 4 (25.0%) | |
E. cloacae (N = 1) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | |
Madagascar | ||||||||||||||||||||||
Broiler | ||||||||||||||||||||||
E. coli (N = 28) | 28 (100.0%) | 0 (00.0%) | 0 (00.0%) | 13 (46.4%) | 7 (25.0%) | 8 (28.6%) | 22 (78.6%) | 3 (10.7%) | 3 (10.7%) | 27 (96.4%) | 0 (00.0%) | 1 (03.6%) | 28 (100.0%) | 0 (00.0%) | 0 (00.0%) | 27 (96.4%) | 0 (00.0%) | 1 (03.6%) | 1 (03.6%) | 1 (03.6%) | 26 (92.9%) | |
E. cloacae (N = 1) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | |
K. pneumoniae (N = 2) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | 1 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (100.0%) | |
Pig | ||||||||||||||||||||||
E. coli (N = 28) | 28 (100.0%) | 0 (00.0%) | 0 (00.0%) | 13 (46.4%) | 8 (28.6%) | 7 (25.0%) | 20 (71.4%) | 2 (07.1%) | 6 (21.4%) | 28 (100.0%) | 0 (00.0%) | 0 (00.0%) | 28 (100.0%) | 0 (00.0%) | 0 (00.0%) | 28 (100.0%) | 0 (00.0%) | 0 (00.0%) | 7 (25.0%) | 0 (00.0%) | 21 (75.0%) | |
E. cloacae (N = 6) | 6 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (33.3%) | 2 (33.3%) | 2 (33.3%) | 6 (100.0%) | 0 (00.0%) | 0 (00.0%) | 4 (66.7%) | 0 (00.0%) | 2 (33.3%) | 6 (100.0%) | 0 (00.0%) | 0 (00.0%) | 4 (66.7%) | 0 (00.0%) | 2 (33.3%) | 0 (00.0%) | 0 (00.0%) | 6 (100.0%) | |
C. freundii (N = 4) | 4 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 4 (100.0%) | 0 (00.0%) | 0 (00.0%) | 4 (100.0%) | 1 (25.0%) | 0 (00.0%) | 3 (75.0%) | 4 (100.0%) | 0 (00.0%) | 0 (00.0%) | 1 (25.0%) | 0 (00.0%) | 3 (75.0%) | 0 (00.0%) | 0 (00.0%) | 4 (100.0%) | |
M. morganii (N = 6) | 6 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 6 (100.0%) | 0 (00.0%) | 0 (00.0%) | 6 (100.0%) | 0 (00.0%) | 0 (00.0%) | 6 (100.0%) | 6 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 6 (100.0%) | 0 (00.0%) | 0 (00.0%) | 6 (100.0%) | |
K. pneumoniae (N = 7) | 7 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 3 (42.9%) | 4 (57.1%) | 5 (71.4%) | 0 (00.0%) | 2 (28.6%) | 0 (00.0%) | 0 (00.0%) | 7 (100.0%) | 7 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 7 (100.0%) | 0 (00.0%) | 0 (00.0%) | 7 (100.0%) | |
Beef cattle | ||||||||||||||||||||||
E. coli (N = 22) | 22 (100.0%) | 0 (00.0%) | 0 (00.0%) | 15 (68.2%) | 3 (13.6%) | 4 (18.2%) | 18 (81.8%) | 3 (13.6%) | 1 (04.5%) | 21 (95.5%) | 0 (00.0%) | 1 (04.5%) | 22 (100.0%) | 0 (00.0%) | 0 (00.0%) | 21 (95.5%) | 0 (00.0%) | 1 (04.5%) | 11 (50.0%) | 0 (00.0%) | 11 (50.0%) | |
E. cloacae (N = 2) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | |
E. hermannii (N = 2) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 0 (00.0%) | 2 (100.0%) |
Territory/ | E. coli Tested | ESBL Genes Identified (%) | |||||||
---|---|---|---|---|---|---|---|---|---|
Production Type | ND | CTX-M-1 Group | CTX-M-9 Group | SHV | TEM | ||||
Enzymes | CTX-M-1 | CTX-M-3 | CTX-M-15 | CTX-M-32 | |||||
Reunion | |||||||||
Poultry | 35 | 3 | 29 (90.6%) | - | - | - | - | 1 (3.1%) | 2 (6.3%) |
Pigs | 10 | - | 7 (70.0%) | 1 (10.0%) | 2 (20.0%) | - | - | - | - |
Beef cattle | 2 | - | 2 (100.0%) | - | - | - | - | - | - |
Mayotte | |||||||||
Poultry | 10 | 1 | 7 (77.8%) | 1 (11.1%) | 1 (11.1%) | - | - | - | - |
Beef cattle | 10 | 3 | 1 (14.3%) | - | 5 (71.4%) | 1 (14.3%) | - | - | - |
Madagascar | |||||||||
Poultry | 10 | - | 5 (50.0%) | - | 2 (20.0%) | - | 3 (30.0%) | - | - |
Pigs | 9 * | - | - | - | 9 (100.0%) | - | - | - | - |
Beef cattle | 9 * | - | - | - | 9 (100.0%) | - | - | - | - |
TOTAL | 95 (100.0%) | 7 (7.4%) | 51 (53.7%) | 2 (2.1%) | 28 (29.5%) | 1 (1.1%) | 3 (3.2%) | 1 (1.1%) | 2 (2.1%) |
Country | Livestock | Variable | OR, IC95% | p-Value |
---|---|---|---|---|
Reunion | Broiler | Premises building constructed > 1999 | 12.72 [1.25–671.77] | 0.01 |
Pigs | Change clothes before entering house/pen | 6.52 [0.92–80.50] | 0.05 | |
Change shoes/boots before entering house/pen | 13.62 [1.35–716.37] | 0.01 | ||
Rodent control by a company | 0.11 [0.01–0.75] | 0.01 | ||
Lightning in the building | 0.18 [0.01–2.13] | 0.04 | ||
Two disinfections between two consecutive batches | 0 [0–0.92] | 0.04 | ||
Beef cattle cows | − | − | − | |
Madagascar | Broiler | Chicks produced in the farm | 0 [0.00–0.91] | 0.02 |
Pigs | Use of antibiotic for prophylaxis | 0.09 [0.00–1.36] | 0.05 | |
Beef cattle | Clearing space around the building | 0 [0.00–0.94] | 0.03 | |
Clean condition around the farm | 0 [0–1.94] | 0.003 | ||
Mayotte | Broiler | Distance from another poultry farm (>500 m) | 13.39 [0.79–883.37] | 0.04 |
Beef cattle | − | − | − |
Dependent Variables | Independent Variables | Adj. OR (CI95%) | p-Value | AIC |
---|---|---|---|---|
Broiler occurrence (a) | Distance elev oth species >500 m | 3.18 (0.65–15.56) | 0.15 | 93.68 |
Distance elev oth species <500 m | 0.99 (0.26–4.39) | 0.99 | ||
Foot bath at room entrance | 5.89 (0.61–57.17) | 0.13 | ||
Water quality control | 0.12 (0.02–0.82) | 0.03 | ||
Water storage tank | 2.58 (0.85–7.79) | 0.09 | ||
Pig occurrence * (b) | Farmers visits | 14.15 (1.17–171.35) | 0.04 | 65.09 |
Soak the floor | 22.34 (1.51–330.98) | 0.02 | ||
Detergent use for cleaning | 0.12 (0.02–0.75) | 0.02 | ||
Antibiotic use recently (<1 year) | 8.82 (1.09–71.4) | 0.04 | ||
Beef cattle occurrence (c) | Livestock size > 25 | 0.07 (0.02–0.28) | <0.001 | 83.53 |
Antibiotic drug use recently (<1 year) | 3.94 (1.04–14.98) | 0.04 | ||
Disinfestation | 0.19 (0.04–0.91) | 0.04 | ||
Clearing space around the building | 0.22 (0.04–1.29) | 0.09 | ||
Water storage tank | 0.38 (0.11–1.35) | 0.14 | ||
Pet presence | 6.87 (1.13–41.67) | 0.04 |
© 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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Gay, N.; Leclaire, A.; Laval, M.; Miltgen, G.; Jégo, M.; Stéphane, R.; Jaubert, J.; Belmonte, O.; Cardinale, E. Risk Factors of Extended-Spectrum β-Lactamase Producing Enterobacteriaceae Occurrence in Farms in Reunion, Madagascar and Mayotte Islands, 2016–2017. Vet. Sci. 2018, 5, 22. https://doi.org/10.3390/vetsci5010022
Gay N, Leclaire A, Laval M, Miltgen G, Jégo M, Stéphane R, Jaubert J, Belmonte O, Cardinale E. Risk Factors of Extended-Spectrum β-Lactamase Producing Enterobacteriaceae Occurrence in Farms in Reunion, Madagascar and Mayotte Islands, 2016–2017. Veterinary Sciences. 2018; 5(1):22. https://doi.org/10.3390/vetsci5010022
Chicago/Turabian StyleGay, Noellie, Alexandre Leclaire, Morgane Laval, Guillaume Miltgen, Maël Jégo, Ramin Stéphane, Julien Jaubert, Olivier Belmonte, and Eric Cardinale. 2018. "Risk Factors of Extended-Spectrum β-Lactamase Producing Enterobacteriaceae Occurrence in Farms in Reunion, Madagascar and Mayotte Islands, 2016–2017" Veterinary Sciences 5, no. 1: 22. https://doi.org/10.3390/vetsci5010022
APA StyleGay, N., Leclaire, A., Laval, M., Miltgen, G., Jégo, M., Stéphane, R., Jaubert, J., Belmonte, O., & Cardinale, E. (2018). Risk Factors of Extended-Spectrum β-Lactamase Producing Enterobacteriaceae Occurrence in Farms in Reunion, Madagascar and Mayotte Islands, 2016–2017. Veterinary Sciences, 5(1), 22. https://doi.org/10.3390/vetsci5010022