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Omulo S, Mugoh M, Obiya J, Alando M, Call DR. Estimating the population-level prevalence of antimicrobial-resistant enteric bacteria from latrine samples. Antimicrob Resist Infect Control 2022; 11:106. [PMID: 35987780 PMCID: PMC9392229 DOI: 10.1186/s13756-022-01145-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 08/13/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Logistical and economic barriers hamper community-level surveillance for antimicrobial-resistant bacteria in low-income countries. Latrines are commonly used in these settings and offer a low-cost source of surveillance samples. It is unclear, however, whether antimicrobial resistance prevalence estimates from latrine samples reflect estimates generated from randomly sampled people.
Methods
We compared the prevalence of antimicrobial-resistant enteric bacteria from stool samples of people residing in randomly selected households within Kibera—an informal urban settlement in Kenya—to estimates from latrine samples within the same community. Fecal samples were collected between November 2015 and Jan 2016. Presumptive Escherichia coli isolates were collected from each household stool sample (n = 24) and each latrine sample (n = 48), resulting in 8935 and 8210 isolates, respectively. Isolates were tested for resistance to nine antibiotics using the replica-plating technique. Correlation- and Kolmogorov–Smirnov (K–S) tests were used to compare results.
Results
Overall, the prevalence values obtained from latrine samples closely reflected those from stool samples, particularly for low-prevalence (< 15%) resistance phenotypes. Similarly, the distribution of resistance phenotypes was similar between latrine and household samples (r > 0.6; K–S p-values > 0.05).
Conclusions
Although latrine samples did not perfectly estimate household antimicrobial resistance prevalence, they were highly correlated and thus could be employed as low-cost samples to monitor trends in antimicrobial resistance, detect the emergence of new resistance phenotypes and assess the impact of community interventions.
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Omulo S, Lofgren ET, Lockwood S, Thumbi SM, Bigogo G, Ouma A, Verani JR, Juma B, Njenga MK, Kariuki S, McElwain TF, Palmer GH, Call DR. Carriage of antimicrobial-resistant bacteria in a high-density informal settlement in Kenya is associated with environmental risk-factors. Antimicrob Resist Infect Control 2021; 10:18. [PMID: 33482919 PMCID: PMC7821723 DOI: 10.1186/s13756-021-00886-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The relationship between antibiotic use and antimicrobial resistance varies with cultural, socio-economic, and environmental factors. We examined these relationships in Kibera, an informal settlement in Nairobi-Kenya, characterized by high population density, high burden of respiratory disease and diarrhea. METHODS Two-hundred households were enrolled in a 5-month longitudinal study. One adult (≥ 18 years) and one child (≤ 5 years) participated per household. Biweekly interviews (n = 1516) that included questions on water, sanitation, hygiene, and antibiotic use in the previous two weeks were conducted, and 2341 stool, 2843 hand swabs and 1490 drinking water samples collected. Presumptive E. coli (n = 34,042) were isolated and tested for susceptibility to nine antibiotics. RESULTS Eighty percent of presumptive E. coli were resistant to ≥ 3 antibiotic classes. Stool isolates were resistant to trimethoprim (mean: 81%), sulfamethoxazole (80%), ampicillin (68%), streptomycin (60%) and tetracycline (55%). Ninety-seven households reported using an antibiotic in at least one visit over the study period for a total of 144 episodes and 190 antibiotic doses. Enrolled children had five times the number of episodes reported by enrolled adults (96 vs. 19). Multivariable linear mixed-effects models indicated that children eating soil from the household yard and the presence of informal hand-washing stations were associated with increased numbers of antimicrobial-resistant bacteria (counts increasing by 0·27-0·80 log10 and 0·22-0·51 log10 respectively, depending on the antibiotic tested). Rainy conditions were associated with reduced carriage of antimicrobial-resistant bacteria (1·19 to 3·26 log10 depending on the antibiotic tested). CONCLUSIONS Antibiotic use provided little explanatory power for the prevalence of antimicrobial resistance. Transmission of resistant bacteria in this setting through unsanitary living conditions likely overwhelms incremental changes in antibiotic use. Under such circumstances, sanitation, hygiene, and disease transmission are the limiting factors for reducing the prevalence of resistant bacteria.
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Affiliation(s)
- Sylvia Omulo
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA. .,Washington State University Global Health-Kenya, Nairobi, Kenya. .,Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya.
| | - Eric T Lofgren
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Svetlana Lockwood
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Samuel M Thumbi
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,Washington State University Global Health-Kenya, Nairobi, Kenya.,Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Godfrey Bigogo
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Alice Ouma
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | | | - M Kariuki Njenga
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,Washington State University Global Health-Kenya, Nairobi, Kenya
| | - Samuel Kariuki
- Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Terry F McElwain
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
| | - Guy H Palmer
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,Washington State University Global Health-Kenya, Nairobi, Kenya.,Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
| | - Douglas R Call
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA.,Washington State University Global Health-Kenya, Nairobi, Kenya.,Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
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Ramay BM, Caudell MA, Cordón-Rosales C, Archila LD, Palmer GH, Jarquin C, Moreno P, McCracken JP, Rosenkrantz L, Amram O, Omulo S, Call DR. Antibiotic use and hygiene interact to influence the distribution of antimicrobial-resistant bacteria in low-income communities in Guatemala. Sci Rep 2020; 10:13767. [PMID: 32792543 PMCID: PMC7426860 DOI: 10.1038/s41598-020-70741-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/30/2020] [Indexed: 11/09/2022] Open
Abstract
To examine the effects of poor sanitation and hygiene on the prevalence of antimicrobial-resistant bacteria, we surveyed households in two rural and two urban communities in Guatemala (N = 196 randomly selected households). One adult (≥ 18-years old) and, when available, one child (≤ 5 years-old) provided a stool sample. Up to 48 presumptive Escherichia coli isolates were collected from each stool sample (n = 21,256 total) and were subjected to breakpoint assays for ten antibiotics. Mixed-effects logistic models were used to identify potential factors influencing the likelihood of harboring antibiotic-resistant bacteria. For nine out of ten antibiotics, the odds of detecting resistant bacteria decreased by ~ 32% (odds ratios, OR 0.53-0.8, P < 0.001) for every unit of improvement of a hygiene scale. Hygiene differences between households had a greater impact on prevalence compared to antibiotic use differences. The likelihood of detecting resistant isolates was lower for five antibiotics among households that boiled raw milk before consumption (OR 0.31-0.69), and higher for nine antibiotics in urban households (OR > 1.89-9.6). Poor hygiene conditions likely obscure effects of individual antibiotic use, presumably due to enhanced microbial transmission. Consequently, efforts to improve antibiotic stewardship should be coupled with improving hygiene conditions.
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Affiliation(s)
- Brooke M Ramay
- Center for Health Studies, Universidad del Valle de Guatemala, 181 Avenida 11-95, Guatemala City, 01015, Guatemala
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164, USA
| | - Mark A Caudell
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164, USA
- Food and Agriculture Organization of the United Nations, United Nations Complex, UN Avenue, Gigiri, PO Box: 30470, Nairobi, 00100, Kenya
| | - Celia Cordón-Rosales
- Center for Health Studies, Universidad del Valle de Guatemala, 181 Avenida 11-95, Guatemala City, 01015, Guatemala.
| | - L Diego Archila
- Center for Health Studies, Universidad del Valle de Guatemala, 181 Avenida 11-95, Guatemala City, 01015, Guatemala
| | - Guy H Palmer
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164, USA
- Nelson Mandela African Institution of Science and Technology, P.O.BOX 447, Arusha, Tanzania
| | - Claudia Jarquin
- Center for Health Studies, Universidad del Valle de Guatemala, 181 Avenida 11-95, Guatemala City, 01015, Guatemala
| | - Purificación Moreno
- Center for Health Studies, Universidad del Valle de Guatemala, 181 Avenida 11-95, Guatemala City, 01015, Guatemala
| | - John P McCracken
- Center for Health Studies, Universidad del Valle de Guatemala, 181 Avenida 11-95, Guatemala City, 01015, Guatemala
| | - Leah Rosenkrantz
- Department of Geography, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Ofer Amram
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164, USA
- Elson S. Floyd College of Medicine, Washington State University, PO Box 1495, Spokane, WA, USA
| | - Sylvia Omulo
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164, USA
| | - Douglas R Call
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164, USA
- Nelson Mandela African Institution of Science and Technology, P.O.BOX 447, Arusha, Tanzania
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Screening methods for intestinal carriage of multidrug-resistant Enterobacterales: interest of enrichment broth. Diagn Microbiol Infect Dis 2020; 97:115079. [DOI: 10.1016/j.diagmicrobio.2020.115079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 11/19/2022]
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Brown K, Mugoh M, Call DR, Omulo S. Antibiotic residues and antibiotic-resistant bacteria detected in milk marketed for human consumption in Kibera, Nairobi. PLoS One 2020; 15:e0233413. [PMID: 32463823 PMCID: PMC7255607 DOI: 10.1371/journal.pone.0233413] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
The use of veterinary antibiotics is largely unregulated in low-income countries. Consequently, food producers rarely observe drug withdrawal periods, contributing to drug residues in food products. Drug residues in milk can cause immunogenic reactions in people, and selectively favor antibiotic-resistant bacteria in unpasteurized products. We quantified the prevalence of antibiotic residues in pasteurized and unpasteurized milk, and antibiotic-resistant bacteria from unpasteurized milk sold within Kibera, an informal settlement in Nairobi, Kenya. Ninety-five milk samples (74 pasteurized and 21 unpasteurized) were collected from shops, street vendors or vending machines, and tested for the presence of β-lactam and tetracycline residues using IDEXX SNAP kits. MacConkey agar without- and with antibiotics (ampicillin, 32 μg/ml; tetracycline, 16 μg/ml) was used to enumerate presumptive E. coli based on colony morphology (colony forming units per ml, CFU/ml). β-lactam and tetracycline residues were found in 7.4% and 3.2% of all milk samples, respectively. Residues were more likely to be present in unpasteurized milk samples (5/21, 23.8%) compared to pasteurized samples (5/75, 6.8%); P = 0.039. Two thirds of unpasteurized samples (14/21, 66.7%) contained detectable numbers of presumptive E. coli (mean 3.5 Log10 CFU/ml) and of these, 92.8% (13/14) were positive for ampicillin- (mean 3.2 Log10 CFU/ml) and 50% (7/14) for tetracycline-resistant E. coli (mean 3.1 Log10 CFU/ml). We found no relationship between the presence of antibiotic residues and the presence of antibiotic-resistant E. coli in unpasteurized milk sold within Kibera (P > 0.2).
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Affiliation(s)
- Kelsey Brown
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States of America
| | - Maina Mugoh
- Washington State University Global Health Kenya, Nairobi, Kenya
| | - Douglas R. Call
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States of America
| | - Sylvia Omulo
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States of America
- Washington State University Global Health Kenya, Nairobi, Kenya
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Caudell MA, Mair C, Subbiah M, Matthews L, Quinlan RJ, Quinlan MB, Zadoks R, Keyyu J, Call DR. Identification of risk factors associated with carriage of resistant Escherichia coli in three culturally diverse ethnic groups in Tanzania: a biological and socioeconomic analysis. Lancet Planet Health 2018; 2:e489-e497. [PMID: 30396440 PMCID: PMC6215761 DOI: 10.1016/s2542-5196(18)30225-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/10/2018] [Indexed: 05/07/2023]
Abstract
BACKGOUND Improved antimicrobial stewardship, sanitation, and hygiene are WHO-inspired priorities for restriction of the spread of antimicrobial resistance. Prioritisation among these objectives is essential, particularly in low-income and middle-income countries, but the factors contributing most to antimicrobial resistance are typically unknown and could vary substantially between and within countries. We aimed to identify the biological and socioeconomic risk factors associated with carriage of resistant Escherichia coli in three culturally diverse ethnic groups in northern Tanzania. METHODS We developed a survey containing more than 200 items and administered it in randomly selected households in 13 Chagga, Arusha, or Maasai villages chosen on the basis of ethnic composition and distance to urban centres. Human stool samples were collected from a subset of households, as were liquid milk samples and swabs of milk containers. Samples were processed and plated onto MacConkey agar plates, then presumptive E coli isolates were identified on the basis of colony morphology. Susceptibility of isolates was then tested against a panel of nine antimicrobials (ampicillin, ceftazidime, chloramphenicol, ciprofloxacin, kanamycin, streptomycin, sulfamethoxazole, tetracycline, and trimethoprim) via a breakpoint assay. Susceptibility findings were matched with data across a wide range of household characteristics, including education, hygiene practices, wealth, livestock husbandry, and antibiotic use. FINDINGS Between March 23, 2012, and July 30, 2015, we interviewed 391 households (118 Arusha, 100 Chagga, and 173 Maasai). Human stool samples were collected at 226 (58%) households across the 13 villages. 181 milk samples and 191 milk-container swabs were collected from 117 households across seven villages. 11 470 putative E coli samples were isolated from stool samples. Antimicrobial use in people and livestock was not associated with prevalence of resistance at the household level. Instead, the factors with the greatest predictive value involved exposure to bacteria, and were intimately connected with fundamental cultural differences across study groups. These factors included how different subsistence types (pastoralists vs farmers) access water sources and consumption of unboiled milk, reflecting increased exposure to resistant bacteria in milk. INTERPRETATION When cultural and ecological conditions favour bacterial transmission, there is a high likelihood that people will harbour antimicrobial-resistant bacteria irrespective of antimicrobial use practices. Public health interventions to limit antimicrobial resistance need to be tailored to local practices that affect bacterial transmission. FUNDING US National Science Foundation; Biotechnology and Biological Sciences Research Council, UK Medical Research Council; and the Allen School.
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Affiliation(s)
- Mark A Caudell
- Paul G Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Department of Anthropology, Washington State University, Pullman, WA, USA
| | - Colette Mair
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Murugan Subbiah
- Paul G Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
| | - Louise Matthews
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Robert J Quinlan
- Paul G Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Department of Anthropology, Washington State University, Pullman, WA, USA
| | - Marsha B Quinlan
- Paul G Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Department of Anthropology, Washington State University, Pullman, WA, USA
| | - Ruth Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Julius Keyyu
- Tanzania Wildlife Research Institute, Arusha, Tanzania
| | - Douglas R Call
- Paul G Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
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