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Vougat Ngom R, Jajere SM, Ayissi GJ, Tanyienow A, Moffo F, Watsop HM, Mimboe LM, Mouiche MM, Schüpbach-Regula G, Carmo LP. Unveiling the landscape of resistance against high priority critically important antimicrobials in food-producing animals across Africa: A scoping review. Prev Vet Med 2024; 226:106173. [PMID: 38503073 DOI: 10.1016/j.prevetmed.2024.106173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/10/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
The rapid population growth in Africa is associated with an increasing demand for livestock products which in turn can lead to antimicrobial use. Antimicrobial usage in animals contributes to the emergence and selection of resistant bacteria which constitutes a serious public health threat. This study aims to review and summarize the available information on highest priority critically important antimicrobials (HPCIAs) resistance in livestock production in Africa. This work will help to inform future policies for controlling antimicrobial resistance (AMR) in the food production chain. A scoping review was conducted according to the Cochrane handbook and following PRISMA 2020 guidelines for reporting. Primary research studies published after 1999 and reporting resistance of Escherichia coli, Enterococcus spp, Staphylococcus aureus, Salmonella spp, and Campylobacter spp to HPCIAs in poultry, cattle, pigs, goats, and sheep in Africa were searched in four databases. A total of 312 articles were included in the review. The majority of the studies (40.7) were conducted in North African countries. More than 49.0% of included studies involved poultry and 26.2% cattle. Cephalosporins and quinolones were the most studied antimicrobial classes. Of the bacteria investigated in the current review, E. coli (41.7%) and Salmonella spp (24.9%) represented the most commonly studied. High levels of resistance against erythromycin in E. coli were found in poultry (MR 96.1%, IQR 83.3-100.0%), cattle (MR 85.7%, IQR 69.2-100.0%), and pigs (MR 94.0%, IQR 86.2-94.0%). In sheep, a high level of resistance was observed in E. coli against nalidixic acid (MR 87.5%, IQR 81.3-93.8%). In goats, the low level of sensibility was noted in S. aureus against streptomycin (MR 86.8%, IQR 19.4-99.0%). The study provides valuable information on HPCIAs resistance in livestock production in Africa and highlights the need for further research and policies to address the public health risk of AMR. This will likely require an investment in diagnostic infrastructure across the continent. Awareness on the harmful impact of AMR in African countries is a requirement to produce more effective and sustainable measures to curb AMR.
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Affiliation(s)
- Ronald Vougat Ngom
- School of Veterinary Medicine and Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Saleh M Jajere
- Faculty of Veterinary Medicine, University of Maiduguri, Borno State, Nigeria
| | - Gaspard Ja Ayissi
- School of Veterinary Medicine and Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Akenghe Tanyienow
- School of Veterinary Medicine and Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Frédéric Moffo
- School of Veterinary Medicine and Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Hippolyte M Watsop
- School of Veterinary Medicine and Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Leina M Mimboe
- School of Veterinary Medicine and Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | - Mohamed Mm Mouiche
- School of Veterinary Medicine and Sciences, University of Ngaoundéré, Ngaoundéré, Cameroon
| | | | - Luís Pedro Carmo
- Veterinary Public Health Institute, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Norwegian Veterinary Institute, Elizabeth Stephansens vei 1, Ås 1433, Norway
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Omar KM, Kitundu GL, Jimoh AO, Namikelwa DN, Lisso FM, Babajide AA, Olufemi SE, Awe OI. Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics. PeerJ 2024; 12:e17181. [PMID: 38666081 PMCID: PMC11044882 DOI: 10.7717/peerj.17181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.
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Affiliation(s)
- Kauthar M. Omar
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - George L. Kitundu
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - Adijat O. Jimoh
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Genetics, Genomics and Bioinformatics Department, National Biotechnology Development Agency, Abuja, Nigeria
| | - Dorcus N. Namikelwa
- Department of Data Management, Modelling and Geo-Information Unit, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Felix M. Lisso
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - Abiola A. Babajide
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Seun E. Olufemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Olaitan I. Awe
- African Society for Bioinformatics and Computational Biology, Cape Town, South Africa
- Department of Computer Science, University of Ibadan, Ibadan, Oyo State, Nigeria
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Tuhamize B, Asiimwe BB, Kasaza K, Sabiiti W, Holden M, Bazira J. Klebsiella pneumoniae carbapenamases in Escherichia coli isolated from humans and livestock in rural south-western Uganda. PLoS One 2023; 18:e0288243. [PMID: 37440483 PMCID: PMC10343067 DOI: 10.1371/journal.pone.0288243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The accumulation of resistance genes in Escherichia coli (E. coli) strains imposes limitations in the therapeutic options available for the treatment of infections caused by E.coli. Production of Klebsiella pneumoniae carbapenemase (KPC) by E. coli renders it resistant to broad-spectrum β-lactam antibiotics. Globally there is existing evidence of spread of carbapenem-resistant E. coli in both humans and livestock driven by acquisition of the several other carbapenemase genes. Overall, there is little information regarding the extent of KPC gene distribution in E. coli. We set out to determine the prevalence, and evaluate the phenotypic and genotypic patterns of KPC in E. coli isolated from humans and their livestock in rural south western Uganda. METHODS A laboratory-based, descriptive cross-sectional study was conducted involving 96 human and 96 livestock isolates collected from agro-pastoralist communities in Mbarara district in south western Uganda. Phenotypic and molecular methods (PCR) were used for presence and identification of KPC genes in the E. coli isolates. A chi-square test of independence was used to evaluate the differences in resistant patterns between carbapenems and isolates. RESULTS The overall prevalence of carbapenem resistance by disk diffusion susceptibility testing (DST) for both humans and livestock isolates were 41.7% (80/192). DST-based resistance was identical in both human and livestock isolates (41.7%). The prevalence of carbapenem resistance based on Modified Hodge Test (MHT) was 5% (2/40) and 10% (4/40) for humans and livestock isolates respectively. Both human and livestock isolates, 48.7% (95/192) had the KPC gene, higher than phenotypic expression; 41.7% (80/192). blaKPC gene prevalence was overall similar in human isolates (51%; 49/96) vs livestock isolates (47.9%; 46/96). Approximately, 19% (15/80) of the isolates were phenotypically resistant to carbapenems and over 70% (79/112) of the phenotypically sensitive strains harbored the blaKPC gene. CONCLUSION Our results suggest that both human and livestock isolates of E. coli in our setting carry the blaKPC gene with a high percentage of strains not actively expressing the blaKPC gene. The finding of fewer isolates carrying the KPC gene than those phenotypically resistant to carbapenems suggests that other mechanisms are playing a role in this phenomenon, calling for further researcher into this phenomenon.
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Affiliation(s)
- Barbra Tuhamize
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Benon B. Asiimwe
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Kennedy Kasaza
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Wilber Sabiiti
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Mathew Holden
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Joel Bazira
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
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Foyle L, Burnett M, Creaser A, Hens R, Keough J, Madin L, Price R, Smith H, Stone S, Kinobe RT. Prevalence and distribution of antimicrobial resistance in effluent wastewater from animal slaughter facilities: A systematic review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120848. [PMID: 36563990 DOI: 10.1016/j.envpol.2022.120848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/18/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The extensive use of antibiotics in food animal production and disposal of untreated wastewater from food animal slaughter facilities may create a shift in microbiomes of different ecosystems by generating reservoirs of antimicrobial resistance along the human-animal-environmental interface. This epidemiological problem has been studied, but its magnitude and impact on a global scale is poorly characterised. A systematic review was done to determine global prevalence and distribution patterns of antimicrobial resistance in effluent wastewater from animal slaughter facilities. Extracted data were stratified into rational groups for secondary analyses and presented as percentages. Culture and sensitivity testing was the predominant method; Escherichia spp., Enterococcus spp., and Staphylococcus aureus were the most targeted isolates. Variable incidences of resistance were detected against all major antimicrobial classes including reserved drugs such as ceftazidime, piperacillin, gentamicin, ciprofloxacin, and chloramphenicol; the median frequency and range in resistant Gram-negative isolates were: 11 (0-100), 62 (0-100), 8 (0-100), 14 (0-93) and 12 (0-62) respectively. Ciprofloxacin was the most tested drug with the highest incidences of resistance in livestock slaughterhouses in Iran (93%), Nigeria (50%) and China (20%), and poultry slaughterhouses in Germany (21-81%) and Spain (56%). Spatial global distribution patterns for antimicrobial resistance were associated with previously reported magnitude of antibiotic use in livestock or poultry farming and, the implicit existence of jurisdictional policies to regulate antibiotic use. These data indicate that anthropogenic activities in farming systems are a major contributor to the cause and dissemination of antimicrobial resistance into the environment via slaughterhouse effluents.
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Affiliation(s)
- Leo Foyle
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Solander Drive, Townsville, Queensland, 4811, Australia
| | - Matthew Burnett
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Abbey Creaser
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Rachel Hens
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Julia Keough
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Lauren Madin
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Ruby Price
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Hayley Smith
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Samuel Stone
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia
| | - Robert T Kinobe
- College of Public Health, Medical and Veterinary Sciences, 1 Solander Drive, James Cook University, Townsville, Queensland, 4811, Australia; Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Solander Drive, Townsville, Queensland, 4811, Australia.
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Azabo R, Dulle F, Mshana SE, Matee M, Kimera S. Antimicrobial use in cattle and poultry production on occurrence of multidrug resistant Escherichia coli. A systematic review with focus on sub-Saharan Africa. Front Vet Sci 2022; 9:1000457. [PMID: 36353252 PMCID: PMC9637661 DOI: 10.3389/fvets.2022.1000457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/30/2022] [Indexed: 11/25/2022] Open
Abstract
Antimicrobial use in livestock production has been linked to antimicrobial resistance (AMR) worldwide; however, optimization of their use has been considered an important strategy in dealing with it. The aims of this study were as follows: (a) to assess the literature on antimicrobial usage (practices, frequency, class, type) in cattle and poultry production with regard to resistance in Escherichia coli (E. coli) including multidrug resistance (MDR) (b) summarize evidence for quantitative (volumes of active antimicrobial ingredients) and quality (identify and quantify active ingredient) and (c) to identify data gaps. Peer reviewed literature search was conducted by querying two online databases: PubMed and Google scholar from November 15, 2018 to February 2019. The inclusion criteria for eligibility were articles: published in English between 2008 and 2018, including poultry (chicken) or cattle or both, E. coli bacteria of choice, antimicrobial use on farms, quantitative data and quality of antimicrobial used. Microsoft Excel was used for data extraction and Rayyan software for eligibility studies. The search retrieved 1,446 probable articles including those from the reference list of significant papers, of which twenty-four articles remained on full text review with more than a third of the studies being conducted in Nigeria. Farm surveys and antimicrobial sales were identified as the main sources of data and the mean quantities of antimicrobials based on sales data were 23,234, 41,280.87, and 1,538,443 kg of the active ingredient in Nigeria, Zambia and South Africa, respectively. One study from Cameroon determined the quantities of active ingredients based on dose metrics while another study still from Cameroon mentioned the quality of antimicrobials. Tetracyclines, beta-lactams/aminoglycosides and fluoroquinolones were the most common classes of antimicrobials (antibiotics) used. Our review reveals a dearth of information in Sub- Saharan Africa on the quantity and quality of veterinary drugs and yet they play a role in the overall picture of antimicrobial resistance. This finding gives an opportunity in the area of focus for future research as far as resistance and multidrug resistance are concerned in food producing animals.
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Affiliation(s)
- Rogers Azabo
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
- National Livestock Resources Research Institute, Kampala, Uganda
- Southern African Centre for Infectious Disease Surveillance (SACIDS) Foundation for One Health Sokoine University of Agriculture, Morogoro, Tanzania
| | - Frankwell Dulle
- Department of Knowledge Management, Sokoine National Agricultural Library, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Stephen E. Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Mecky Matee
- Department of Knowledge Management, Sokoine National Agricultural Library, Sokoine University of Agriculture, Morogoro, Tanzania
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Sharadhuli Kimera
- Department of Knowledge Management, Sokoine National Agricultural Library, Sokoine University of Agriculture, Morogoro, Tanzania
- Department of Veterinary Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
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Gil‐Molino M, Gonçalves P, Risco D, Martín‐Cano FE, García A, Rey J, Fernández‐Llario P, Quesada A. Dissemination of antimicrobial-resistant isolates of Salmonella spp. in wild boars and its relationship with management practices. Transbound Emerg Dis 2022; 69:e1488-e1502. [PMID: 35182450 PMCID: PMC9790216 DOI: 10.1111/tbed.14480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 12/30/2022]
Abstract
Antimicrobial resistance (AMR) is a global concern and controlling its spread is critical for the effectiveness of antibiotics. Members of the genus Salmonella are broadly distributed, and wild boar may play an important role in its circulation between peri-urban areas and the environment, due to its frequent interactions both with livestock or human garbage. As the population of these animals is rising due to management on certain hunting estates or the absence of natural predators, the aim of the present work is to identify the mechanisms of AMR present and/or expressed in Salmonella spp. from wild boar populations and to determine the possible role of management-related factors applied to different game estates located in central Spain. The detection of Salmonella spp. was carried out in 121 dead wild boar from 24 game estates, and antimicrobial resistance traits were determined by antibiotic susceptibility testing and screening for their genetic determinants. The effects of feeding supplementation, the proximity of livestock, the existence of a surrounding fence and the density of wild boar on the AMR of the isolates were evaluated. The predominant subspecies and serovar found were S. enterica subsp. enterica (n = 69) and S. choleraesuis (n = 33), respectively. The other subspecies found were S. enterica subsp. diarizonae, S. enterica subsp. salamae and S. enterica subsp. houtenae. AMR was common among isolates (75.2%) and 15.7% showed multi drug resistance (MDR). Resistance to sulphonamides was the most frequent (85.7%), as well as sul1 which was the AMR determinant most commonly found. Plasmids appeared in 38.8% of the isolates, with IncHI1 being the replicon detected with the highest prevalence. The AMR of the isolates increased when the animals were raised with feeding supplementation and enclosed by fences around the estates.
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Affiliation(s)
- María Gil‐Molino
- Facultad de Veterinaria, Unidad de Patología InfecciosaUniversidad de ExtremaduraCáceresSpain
| | - Pilar Gonçalves
- Innovación en Gestión y Conservación de Ingulados S.L. CáceresCáceresSpain
| | - David Risco
- Innovación en Gestión y Conservación de Ingulados S.L. CáceresCáceresSpain,Neobeitar S.L. CáceresCáceresSpain
| | | | | | - Joaquín Rey
- Facultad de Veterinaria, Unidad de Patología InfecciosaUniversidad de ExtremaduraCáceresSpain
| | | | - Alberto Quesada
- Facultad de Veterinaria, Departamento de BioquímicaBiología Molecular y Genética, Universidad de ExtremaduraCáceresSpain,INBIO G+CUniversidad de ExtremaduraCáceresSpain
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Hassen B, Hammami S, Hassen A, Abbassi MS. Molecular mechanisms and clonal lineages of colistin-resistant bacteria across the African continent: A scoping review. Lett Appl Microbiol 2022; 75:1390-1422. [PMID: 36000241 DOI: 10.1111/lam.13818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 07/11/2022] [Accepted: 08/16/2022] [Indexed: 11/28/2022]
Abstract
Colistin (also known as Polymyxin E), a polymyxin antibiotic discovered in the late 1940s, has recently reemerged as a last-line treatment option for multidrug-resistant infections. However, in recent years, colistin-resistant pathogenic bacteria have been increasingly reported worldwide. Accordingly, the presented review was undertaken to identify, integrate and synthesize current information regarding the detection and transmission of colistin-resistant bacteria across the African continent, in addition to elucidating their molecular mechanisms of resistance. PubMed, Google Scholar, and Science Direct were employed for study identification, screening and extraction. Overall, based on the developed literature review protocol and associated inclusion/exclusion criteria, 80 studies published between 2000 and 2021 were included comprising varying bacterial species and hosts. Numerous mechanisms of colistin resistance were reported, including chromosomal mutation(s) and transferable plasmid-mediated colistin resistance (encoded by mcr genes). Perhaps unexpectedly, mcr-variants have exhibited rapid emergence and spread across most African regions. The genetic variant mcr-1 is predominant in humans, animals, and the natural environment, and is primarily carried by IncHI2- type plasmid. The highest numbers of studies reporting the dissemination of colistin-resistant Gram-negative bacteria were conducted in the North African region.
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Affiliation(s)
- B Hassen
- University of Tunis El Manar, Laboratory of Bacteriological Research, Institute of Veterinary Research of Tunisia, 20 street Jebel Lakhdhar, Bab Saadoun, Tunis, 1006, Tunisia
| | - S Hammami
- University of Manouba, IRESA, School of Veterinary Medicine of Sidi-Thabet, Ariana, Tunis, Tunisia
| | - A Hassen
- Laboratoire de Traitement et de Valorisation des rejets hydriques, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP, 273, 8020, Soliman, Tunisia
| | - M S Abbassi
- University of Tunis El Manar, Laboratory of Bacteriological Research, Institute of Veterinary Research of Tunisia, 20 street Jebel Lakhdhar, Bab Saadoun, Tunis, 1006, Tunisia.,University of Tunis El Manar, Faculty de Medicine of Tunis, Laboratory of antibiotic resistance LR99ES09, Tunis, Tunisia
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Ohene Larbi R, Adeapena W, Ayim-Akonor M, Ansa EDO, Tweya H, Terry RF, Labi AK, Harries AD. Antimicrobial, Multi-Drug and Colistin Resistance in Enterobacteriaceae in Healthy Pigs in the Greater Accra Region of Ghana, 2022: A Cross-Sectional Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10449. [PMID: 36012083 PMCID: PMC9408530 DOI: 10.3390/ijerph191610449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
There is little published information on antimicrobial resistance (AMR) in animals in Ghana. We determined the prevalence and factors associated with AMR, multi-drug resistance (MDR-resistance to ≥3 antimicrobial classes) and colistin resistance in Enterobacteriaceae in healthy pigs in Accra, Ghana. Rectal swabs obtained from the pigs on 20 farms from January to March 2022, were examined for Escherichia coli, Enterobacter spp. and Klebsiella pneumoniae. AMR was determined using standard microbiological techniques and the mcr-1 gene detected through molecular analysis. Enterobacteriaceae were isolated from 197 of 200 pigs: these comprised 195 E. coli isolates, 38 Enterobacter spp. and 3 K. pneumoniae, either singly or combined. Over 60% of E. coli were resistant to tetracycline, with 27% and 34% being resistant to amoxicillin/clavulanic acid and ampicillin, respectively; 23% of E. coli and 5% of Enterobacter spp. exhibited MDR phenotypes. Phenotypic colistin resistance was found in 8% of E. coli and Enterobacter spp., with the mcr-1 gene detected in half. Our study findings should be incorporated into on-going AMR, MDR and colistin resistance surveillance programs in Ghana. We further advocate for tailored-specific education for pig farmers on animal antimicrobial use and for strengthened regulatory policy on antimicrobial usage and monitoring in the animal production industry.
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Affiliation(s)
- Rita Ohene Larbi
- CSIR—Animal Research Institute, P.O. Box AH 20 Achimota-Accra, Greater Accra Region, Ghana
| | - Wisdom Adeapena
- Kintampo Health Research Centre, P.O. Box 200, Kintampo, Bono East Region, Ghana
| | - Matilda Ayim-Akonor
- CSIR—Animal Research Institute, P.O. Box AH 20 Achimota-Accra, Greater Accra Region, Ghana
| | - Ebenezer D. O. Ansa
- CSIR—Animal Research Institute, P.O. Box AH 20 Achimota-Accra, Greater Accra Region, Ghana
| | - Hannock Tweya
- Malawi International Training and Education Center for Health (Malawi-I-TECH), Lilongwe P.O. Box 30369, Malawi
| | - Robert Fraser Terry
- Special Programme for Research and Training in Tropical Diseases, World Health Organization, 1211 Geneva, Switzerland
| | - Appiah-Korang Labi
- WHO Country Office, P.O. Box MB 142, 7 Ameda Street, Roman Ridge-Accra, Greater Accra Region, Ghana
| | - Anthony D. Harries
- Centre for Operational Research, International Union Against Tuberculosis and Lung Disease (The Union), 75001 Paris, France
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Bakry N, Awad W, Ahmed S, Kamel M. The role of Musca domestica and milk in transmitting pathogenic multidrug-resistant Escherichia coli and associated phylogroups to neonatal calves. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:39593-39609. [PMID: 35107727 DOI: 10.1007/s11356-022-18747-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Escherichia coli, as a global source of antimicrobial resistance, is a serious veterinary and public health concern. The transmission of pathogenic multidrug-resistant (MDR) E. coli within diarrheic calves and its correlation with Musca domestica and milk strains have been investigated. In total, 110, 80, and 26 E. coli strains were obtained from 70 rectal swabs from diarrheic calves, 60 milk samples and 20 M. domestica, respectively. Molecular pathotyping of E. coli revealed the presence of pathogenic E. coli with a higher percentage of shigatoxigenic strains within diarrheic calves and M. domestica at 46.4% and 34.6%, respectively. Phenotypic antimicrobial resistance revealed higher β-lactams resistance except for cefquinome that exhibited low resistance in M.domestica and milk strains at 30.8% and 30%, respectively. The extended-spectrum cephalosporin (ESC) resistant strains were detected within fecal, M. domestica, and milk strains at 69.1%, 73.1%, and 71.3%, respectively. All E. coli strains isolated from M. domestica exhibited MDR, while fecal and milk strains were harboring MDR at 99.1% and 85%, respectively. Molecular detection of resistant genes revealed the predominance of the blaTEM gene, while none of these strains harbored the blaOXA gene. The highest percentages for blaCTXM and blaCMYII genes were detected in M. domestica strains at 53.8% and 61.5%, respectively. Regarding colistin resistance, the mcr-1 gene was detected only in fecal and milk strains at 35.5% and 15%, respectively. A high frequency of phylogroup B2 was detected within fecal and M. domestica strains, while milk strains were mainly assigned to the B1 phylogroup. Pathogenic E. coli strains with the same phenotypic and genotypic antimicrobial resistance and phylogroups were identified for both diarrheic calves and M. domestica, suggesting that the possible role of M. domestica in disseminating pathogenic strains and antimicrobial resistance in dairy farms.
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Affiliation(s)
- Noha Bakry
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Walid Awad
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Samia Ahmed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
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10
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Antibiotics Resistance in Escherichia coli Isolated from Livestock in the Emirate of Abu Dhabi, UAE, 2014–2019. Int J Microbiol 2022; 2022:3411560. [PMID: 35519508 PMCID: PMC9064518 DOI: 10.1155/2022/3411560] [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: 11/08/2021] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Escherichia coli (E. coli) is a zoonotic pathogen that showed growing resistance to antibiotics. No descriptive analysis highlights the threat of antimicrobial-resistant (AMR) of E. coli among livestock in the United Arab Emirates (UAE). Herein, we conducted phenotypic and genotypic resistance studies on E. coli isolates from livestock samples in the Emirate of Abu Dhabi based on routine diagnosis between the periods 2014–2019. Bacterial culture and disk diffusion methods were used for bacterial isolation and phenotypic resistance analysis. Resistance mechanism was studied by PCR targeting the most commonly resistance genes: ampicillin (blaSHV, blaCMY, and blaTEM-1B), tetracyclines (tetA and tetB), co-trimoxazole [sulfamethoxazole (sul1, sul2, and sul3) + trimethoprim (dfrA1 and dfrA17)], aminoglycosides [aph(3'')-Ia, aph(6)-Id, and aac(3)-IV], and fluoroquinolones (qnrA and aac(6’)-Ib-cr). Analysis of 165 E. coli isolates showed resistant to ampicillin, tetracycline, co-trimoxazole, gentamicin, and enrofloxacin by 157/165 (95.4%), 154/165 (93.6%), 141/165 (86%), 139/165 (85%), and 135/165 (82.7%), respectively. Predominant resistance gene/s detected by PCR were blaCMY (119/160, 72%) and blaTEM-1B (154/160, 96.3%) for ampicillin; tetA (162/164, 98.8%) and tetB (112/164, 68.3%) for tetracyclines; sul2 (156/164, 95%), sul3 (138/164, 84%), and dfra17 (74/164, 44.5%) for co-trimoxazole; aph(3'')-Ia (134/164, 82.1%) and aph(6)-Id (161/164, 98.2%) for aminoglycosides; and aac(6’)-Ib-cr (61/61, 100%) for enrofloxacin. Both phenotypic and genotypic analyses revealed that all E. coli isolates were multidrug-resistant (resistance to 3, 4, and 5 antibiotics classes by 3.6%, 57.6%, and 38.8%, respectively) carrying one or more resistance gene/s for the same antibiotic. PCR profiling confirmed the presence of resistance genes corresponding to their antibiotic profile. Results of the study will highlight the knowledge based on E. coli AMR related to livestock in UAE that may call for interventions.
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11
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Geographic and Socioeconomic Influence on Knowledge and Practices Related to Antimicrobial Resistance among Smallholder Pig Farmers in Uganda. Antibiotics (Basel) 2022; 11:antibiotics11020251. [PMID: 35203853 PMCID: PMC8868422 DOI: 10.3390/antibiotics11020251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
To mitigate the development of antimicrobial resistance (AMR), antibiotic use (ABU) in the livestock sector needs to be reduced. In low- and middle-income countries, regulations have shown to be less successful in reducing ABU. Here, a bottom-up approach can complement legal frameworks, which requires an understanding of the drivers for ABU. In this study, we investigated the influence of geographic and socioeconomic settings on determinants for ABU among pig farmers in Uganda. The data were collected through a questionnaire in two districts, Lira and Mukono, and comparative statistical analyses were performed. Farmers in Lira had less access to animal health services, applied disease prevention measures less and used antibiotics more. In Mukono, it was more common to consult a veterinarian in response to disease, while in Lira it was more common to consult an animal health worker. There was no difference in how many farmers followed treatment instructions from a veterinarian, but it was more common in Lira to follow instructions from pharmacies. The findings support the need for locally tailored AMR-reducing interventions to complement regulations. To accomplish this tailoring, systematic collection of knowledge of farm structures, farm practices and access to animal health services and veterinary drugs is necessary.
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12
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Dione MM, Amia WC, Ejobi F, Ouma EA, Wieland B. Supply Chain and Delivery of Antimicrobial Drugs in Smallholder Livestock Production Systems in Uganda. Front Vet Sci 2021; 8:611076. [PMID: 34568469 PMCID: PMC8455991 DOI: 10.3389/fvets.2021.611076] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 07/27/2021] [Indexed: 11/15/2022] Open
Abstract
This study assessed the veterinary drug supply chain in Uganda, the constraints faced by the actors, and how the challenges influence the use of antimicrobial (AMs) by livestock farmers. We carried out stakeholder consultation workshops, key informant interviews and a knowledge, practices, and awareness survey with actors of the veterinary drug supply chain. We also profiled drugs stored in 23 urban and peri-urban drug shops in Lira and Mukono districts to record the commonly sold drugs. The veterinary drug supply chain is made of several actors including wholesalers, retailers, Animal Health Service Providers (AHSP) and farmers. Nearly ninety per cent of drug retailers and veterinary practitioners did not receive specialized training in veterinary medicine, and most of veterinary practitioners have been in the drug business market for more than 10 years. Antibiotics and anti-helminthics were the most stocked drugs by retailers, with antibiotics ranking highest in terms of contribution to annual financial profits, accounting for 33%. The choice of a drug by veterinary practitioners was mainly informed by past success with efficacy of the drug, and financial capacity of the client (the farmer) to meet the treatment cost. Many veterinary practitioners were not conversant with veterinary drug policies of the country, with Mukono having a higher number (72%) compared to Lira (37%). Veterinary practitioners from Lira district compared to Mukono and those mainly serving small scale farmers relative to large scale smallholders were more knowledgeable about antibiotics and AMR. Several supply chain constraints were identified as potential drivers of misuse of antibiotics that could contribute to AMR. These included low level of education of supply chain actors, particularly drug retailers, poor handling of drugs at purchase and administration practices, low enforcement of policies and regulations, and lack of awareness of stakeholders about policies that regulate drug use. Thus, future interventions to reduce misuse of AM drugs in livestock production systems in Uganda such as capacity building, should also target veterinary input suppliers, and deliberately involve a strong policy advocacy component.
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Affiliation(s)
- Michel Mainack Dione
- Animal and Human Health Program, International Livestock Research Institute, Dakar, Senegal
| | - Winfred Christine Amia
- Animal and Human Health Program, International Livestock Research Institute, Kampala, Uganda
| | - Francis Ejobi
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Emily Awuor Ouma
- Animal and Human Health Program, International Livestock Research Institute, Kampala, Uganda
| | - Barbara Wieland
- Animal and Human Health Program, International Livestock Research Institute, Addis Ababa, Ethiopia.,Institute of Virology and Immunology, Mittelhaeusern, Switzerland
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13
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Büdel T, Kuenzli E, Campos-Madueno EI, Mohammed AH, Hassan NK, Zinsstag J, Hatz C, Endimiani A. On the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat. J Antimicrob Chemother 2021; 75:2432-2441. [PMID: 32562537 DOI: 10.1093/jac/dkaa198] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES Intestinal colonization with extended-spectrum cephalosporin-resistant (ESC-R) and colistin-resistant (CST-R) Enterobacterales (Ent) can be driven by contact with colonized animals and/or contamination of the food chain. We studied the ESC-R-Ent and COL-R-Ent colonizing poultry as well as contaminating chicken meat in Zanzibar (Tanzania). Results were compared with recently published data obtained from rectal swabs of people in the community. METHODS During June and July 2018, we collected poultry faecal material (n = 62) and retail chicken meat (n = 37) samples. ESC-R and CST-R strains were isolated implementing selective approaches and characterized with different molecular methods, including WGS coupled with core-genome analyses. RESULTS The prevalence of ESC-R-Ent and CST-R-Ent, respectively, were: 88.7% and 48.4% in poultry; and 43.2% and 18.9% in chicken meat. Overall, the following strains and main resistance mechanisms were found in the two settings: 69 ESC-R Escherichia coli (CTX-M-15 subgroup, 75%), 34 ESC-R Klebsiella pneumoniae (CTX-M-9 group, 54.5%), 24 non-ESC-R but CST-R E. coli (mcr-1, 95.8%) and 17 non-ESC-R but CST-R K. pneumoniae (D150G substitution in PhoQ). Several clones (differing by only 0-13 single nucleotide variants) were concomitantly and frequently found in human and non-human settings: mcr-1-carrying E. coli ST46; CTX-M-15-producing E. coli ST361; CTX-M-14-producing K. pneumoniae ST17; and CTX-M-15-producing K. pneumoniae ST1741. CONCLUSIONS This is one of the few studies that have assessed the occurrence of identical MDR Enterobacterales in human and non-human settings. The frequent human gut colonization observed in the community might be favoured by the spread of ESC-R-Ent and CST-R-Ent in poultry and chicken meat. Further studies with a One Health approach should be carried out to better investigate this phenomenon.
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Affiliation(s)
- Thomas Büdel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Esther Kuenzli
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | | | | | | | - Jakob Zinsstag
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Christoph Hatz
- Department of Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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14
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Kakooza S, Muwonge A, Nabatta E, Eneku W, Ndoboli D, Wampande E, Munyiirwa D, Kayaga E, Tumwebaze MA, Afayoa M, Ssajjakambwe P, Tayebwa DS, Tsuchida S, Okubo T, Ushida K, Sakurai K, Mutebi F. A retrospective analysis of antimicrobial resistance in pathogenic Escherichia coli and Salmonella spp. isolates from poultry in Uganda. Int J Vet Sci Med 2021; 9:11-21. [PMID: 34104644 PMCID: PMC8158283 DOI: 10.1080/23144599.2021.1926056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
There are increasing reports of antimicrobial treatment failures for bacterial diseases of poultry in Uganda. The paucity of data on antimicrobial resistance (AMR) of pathogenic bacteria in Uganda is a major setback to AMR control. This study investigated the occurrence of fowl typhoid, colibacillosis, and AMR in associated pathogens from 2012 to 2018. Laboratory records from the Central Diagnostic Laboratory (CDL), a National Veterinary Diagnostic Facility located at Makerere University, were reviewed. Archived isolates of the causative bacteria for the two diseases were also evaluated for AMR. The frequencies of the two disease conditions, their clinical and necropsy presentations and the demographic data of the diagnostic samples were summarized from the records. Archived bacterial isolates were revived before antimicrobial susceptibility testing. This was done on Mueller Hinton agar using the disk diffusion method, against 16 antimicrobials of medical and veterinary importance according to the Clinical Laboratory Standards Institute guidelines. A total of 697 poultry cases were presented for bacteriological investigations in the review period. Colibacillosis and salmonellosis had prevalence rates of 39.7% (277/697) and 16.2% (113/697), respectively. A total of 63 and 92 isolates of Escherichia coli and Salmonella spp., respectively, were archived but 43 (68.3%) E. coli and 47 (51.1%) Salmonella spp. isolates were recovered and evaluated for AMR. Multidrug resistance was more frequent in E. coli (38; 88.4%) than salmonellae (25; 53.2%), (p < 0.001). The high prevalence of colibacillosis, salmonellosis and the AMR of associated pathogens warrants immediate institution of appropriate disease control measures.
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Affiliation(s)
- Steven Kakooza
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Adrian Muwonge
- Department of Genetics and Genomics, the Roslin Institute, University of Edinburgh, Edinburgh, Scotland
| | - Esther Nabatta
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Wilfred Eneku
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Dickson Ndoboli
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Eddie Wampande
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Damian Munyiirwa
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Edrine Kayaga
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Maria Agnes Tumwebaze
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Mathias Afayoa
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Paul Ssajjakambwe
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Dickson Stuart Tayebwa
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Sayaka Tsuchida
- Chubu University, Academy of Emerging Sciences, Kasugai, Japan
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Sapporo, Japan
| | - Kazunari Ushida
- Chubu University, Academy of Emerging Sciences, Kasugai, Japan
| | - Ken'ichi Sakurai
- Faculty of Life and Environmental Sciences, Department of Animal Sciences, Teikyo University of Science, Tokyo, Japan
| | - Francis Mutebi
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
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15
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Tsuchida S, Hattori T, Sawada A, Ogata K, Watanabe J, Ushida K. Fecal metabolite analysis of Japanese macaques in Yakushima by LC-MS/MS and LC-QTOF-MS. J Vet Med Sci 2021; 83:1012-1015. [PMID: 33952783 PMCID: PMC8267200 DOI: 10.1292/jvms.21-0076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We performed a comprehensive fecal metabolite analysis using LC-MS/MS and LC-QTOF-MS
approaches as a preliminary study. Feces of Japanese macaques on Yakushima Island were
collected from five monkeys at two separate locations. Using the former methodology, 59
substances such as free amino acids, nucleotides, nucleosides and nucleic acid bases, and
organic acids in the citrate cycle were quantitatively detected and successfully
differentiated in two different monkey groups by the concentrations of nucleic acid
metabolites and free amino acids. In the latter, around 12,000 substances were detected
both by positive and negative mode in each sample. Differences in signal intensities were
observed between two monkey groups in the concentrations of plant secondary metabolites
such as cyanogenic glycosides, flavonoids, and phenolics.
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Affiliation(s)
- Sayaka Tsuchida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.,Present address: Department of Environmental Biology, College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | | | - Akiko Sawada
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.,Present address: Kyoto University Primate Research Institute, Kanrin 41-2, Inuyama, Aichi 484-8506, Japan
| | | | | | - Kazunari Ushida
- Chubu University Academy of Emerging Sciences, Kasugai, Aichi 487-8501, Japan.,Present address: Department of Environmental Biology, College of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
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16
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Manishimwe R, Moncada PM, Musanayire V, Shyaka A, Scott HM, Loneragan GH. Antibiotic-Resistant Escherichia coli and Salmonella from the Feces of Food Animals in the East Province of Rwanda. Animals (Basel) 2021; 11:1013. [PMID: 33916794 PMCID: PMC8067188 DOI: 10.3390/ani11041013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022] Open
Abstract
In Rwanda, information on antibiotic resistance in food animals is scarce. This study was conducted to detect and phenotypically characterize antibiotic-resistant Escherichia coli and Salmonella in feces of cattle, goats, pigs, and poultry in the East province of Rwanda. We isolated non-type-specific (NTS) E. coli and Salmonella using plain culture media. In addition, we used MacConkey agar media supplemented with cefotaxime at 1.0 μg/mL and ciprofloxacin at 0.5 μg/mL to increase the probability of detecting E. coli with low susceptibility to third-generation cephalosporins and quinolones, respectively. Antibiotic susceptibility testing was performed using the disk diffusion test. Among 540 NTS E. coli isolates, resistance to tetracycline was the most frequently observed (35.6%), followed by resistance to ampicillin (19.6%) and streptomycin (16.5%). Percentages of NTS E. coli resistant to all three antibiotics and percentages of multidrug-resistant strains were higher in isolates from poultry. All isolated Salmonella were susceptible to all antibiotics. The sample-level prevalence for resistance to third-generation cephalosporins was estimated at 35.6% with all third-generation cephalosporin-resistant E. coli, expressing an extended-spectrum beta-lactamase phenotype. The sample-level prevalence for quinolone resistance was estimated at 48.3%. These results provided a baseline for future research and the development of integrated surveillance initiatives.
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Affiliation(s)
- Rosine Manishimwe
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX 79415, USA;
- Department of Veterinary Medicine, University of Rwanda, Nyagatare 56, Rwanda;
| | - Paola M. Moncada
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX 79415, USA;
| | - Vestine Musanayire
- Rwanda Veterinary Service Department, Rwanda Agriculture and Animal Resources Development Board, Ministry of Agriculture, Kigali 5016, Rwanda;
| | - Anselme Shyaka
- Department of Veterinary Medicine, University of Rwanda, Nyagatare 56, Rwanda;
| | - H. Morgan Scott
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA;
| | - Guy H. Loneragan
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX 79106, USA;
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17
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Ikwap K, Gertzell E, Hansson I, Dahlin L, Selling K, Magnusson U, Dione M, Jacobson M. The presence of antibiotic-resistant Staphylococcus spp. and Escherichia coli in smallholder pig farms in Uganda. BMC Vet Res 2021; 17:31. [PMID: 33461527 PMCID: PMC7814613 DOI: 10.1186/s12917-020-02727-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The development of antimicrobial resistance is of global concern, and is commonly monitored by the analysis of certain bacteria. The aim of the present study was to study the antibiotic susceptibility in isolates of Staphylococcus spp. and Escherichia (E.) coli obtained from healthy pigs originating from nineteen herds enrolled in a study on herd health management in Lira district, northern Uganda. Skin and nasal swabs were analyzed for the presence of Staphylococcus spp., and selectively cultivated to investigate the presence of methicillin-resistant Staphylococcus (S.) aureus (MRSA), and rectal swabs were analyzed for the presence of E. coli. Antibiotic susceptibility was tested by broth micro-dilution. Information on the antibiotic usage and treatment regimens during the previous year was gathered using structured interviews and longitudinal data. RESULTS In Staphylococcus spp., resistance to penicillin (10/19 isolates; 53%), fusidic acid (42%) and tetracycline (37%) were most commonly found. In E. coli, resistance to sulfamethoxazole (46/52 isolates; 88%), tetracycline (54%) and trimethoprim (17%) was most frequent. Methicillin-resistant S. aureus was found in one sample (1/50; 2%). Multi-drug resistant isolates of Staphylococcus spp. and E. coli were found in 54 and 47% of the herds, respectively. At the herd level, no associations could be made between antibiotic resistance and herd size or treatment regimens for either of the bacteria. CONCLUSION In conclusion, resistance to important antibiotics frequently used in animals in Uganda was common, and the presence of MRSA was demonstrated, in Ugandan pig herds.
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Affiliation(s)
- K Ikwap
- Makerere University, College of Veterinary Medicine, Animal Resources and Biosecurity, Kampala, Uganda
| | - E Gertzell
- Swedish University of Agricultural Sciences, Faculty of Veterinary Medicine and Animal Science, Uppsala, Sweden.
| | - I Hansson
- Swedish University of Agricultural Sciences, Faculty of Veterinary Medicine and Animal Science, Uppsala, Sweden
| | - L Dahlin
- Swedish University of Agricultural Sciences, Faculty of Veterinary Medicine and Animal Science, Uppsala, Sweden
| | - K Selling
- Swedish University of Agricultural Sciences, Faculty of Veterinary Medicine and Animal Science, Uppsala, Sweden
| | - U Magnusson
- Swedish University of Agricultural Sciences, Faculty of Veterinary Medicine and Animal Science, Uppsala, Sweden
| | - M Dione
- International Livestock Research Institute, Dakar, Senegal
| | - M Jacobson
- Swedish University of Agricultural Sciences, Faculty of Veterinary Medicine and Animal Science, Uppsala, Sweden
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18
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El Zowalaty ME, Hickman RA, Gambushe SM, Zishiri OT, El Zowalaty AE, Järhult JD. Genome sequences of two multidrug-resistant Escherichia coli strains MEZEC8 and MEZEC10 isolated from livestock in South Africa. J Glob Antimicrob Resist 2020; 23:445-449. [PMID: 33246212 DOI: 10.1016/j.jgar.2020.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/30/2020] [Accepted: 11/10/2020] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVES The emergence of antimicrobial-resistant livestock-associated Escherichia coli represents a great public health concern. Here we report the draft genome sequences of two multidrug-resistant livestock-associated E. coli strains MEZEC8 and MEZEC10 isolated from sheep in South Africa. METHODS Genomic DNA of E. coli strains MEZEC8 and MEZEC10 was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids, and the sequence type (ST) was determined by multilocus sequence typing (MLST). To compare strains MEZEC8 and MEZEC10 with other previously published sequences of E. coli strains, raw read sequences of E. coli from livestock were downloaded from the NCBI's Sequence Read Archive and all sequence files were treated identically to generate a core genome bootstrapped maximum likelihood phylogenetic tree. RESULTS Antimicrobial resistance genes were detected in MEZEC8 and MEZEC10 conferring resistance to tetracycline and macrolides. MEZEC10 harboured two extrachromosomal plasmids (pO111 and Incl2), while MEZEC8 did not contain any extrachromosomal plasmids. Strain MEZEC8 belonged to serotype H25:O9 and ST58, whereas strain MEZEC10 belonged to serotype H49:O8 and ST1844. CONCLUSION The genome sequences of E. coli strains MEZEC8 and MEZEC10 will serve as a reference point for molecular epidemiological studies of antimicrobial-resistant livestock-associated E. coli in Africa. In addition, this study allows in-depth analysis of genomic structure and will provide valuable information enabling us understand the antimicrobial resistance of livestock-associated E. coli.
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Affiliation(s)
- Mohamed E El Zowalaty
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates; Sharjah Institute of Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-75 123, Sweden.
| | - Rachel A Hickman
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-75 123, Sweden
| | - Sydney M Gambushe
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Oliver T Zishiri
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Ahmed E El Zowalaty
- Sahlgrenska Center for Cancer Research, Department of Surgery, Institute of Clinical Sciences, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Josef D Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, SE-75 185, Sweden
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19
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Chen J, Li H, Xie H, Xu D. A novel method combining aptamer-Ag 10NPs based microfluidic biochip with bright field imaging for detection of KPC-2-expressing bacteria. Anal Chim Acta 2020; 1132:20-27. [PMID: 32980107 DOI: 10.1016/j.aca.2020.07.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/04/2020] [Accepted: 07/24/2020] [Indexed: 12/23/2022]
Abstract
The β-lactam drugs resistance poses a serious threat to human health throughout the world. Klebsiella pneumoniae carbapenemase 2 (KPC-2) is a carbapenemase that produced in bacteria can hydrolyze carbapenems, which typically considered as the antibiotics of last resort. Therefore, there is an urgent need to quickly and accurately detect whether bacteria express KPC-2. In this paper, a PDMS/glass microfluidic biochip integrated with aptamer-modified Ag10NPs nano-biosensors was developed for rapid, simple and specific pathogenic bacteria detection, more importantly, the biochip was combined with bright field imaging, then the captured bacteria could be observed and counted directly without using extra chemical labeling. KPC-2-expressing Escherichia coli (KPC-2 E.coli) was used as the target bacterium with a detected limit of 102 CFU and capture efficiency exceeded 90%. This method is remarkably specific towards KPC-2 E.coli over other non-resistant bacteria, and pathogen assay only takes ∼1 h to complete in a ready-to-use microfluidic biochip. Furthermore, the effective capture and fast counting of microfluidic biochip system demonstrates its potential for the rapid detection of antibiotic-resistant bacteria.
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Affiliation(s)
- Jing Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, PR China
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, PR China
| | - Hexin Xie
- State Key Laboratory of Bioreactor Engineering Shanghai Key Laboratory of New Drug Design School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry Engineering, Nanjing University, No 163, Xianlin Avenue, Nanjing, 210023, PR China.
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20
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Isolation and genomic characterization of a pathogenic Providencia rettgeri strain G0519 in turtle Trachemys scripta. Antonie van Leeuwenhoek 2020; 113:1633-1662. [PMID: 32951105 DOI: 10.1007/s10482-020-01469-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023]
Abstract
Providencia rettgeri infection has occurred occasionally in aquaculture, but is rare in turtles. Here, a pathogenic P. rettgeri strain G0519 was isolated from a diseased slider turtle (Trachemys scripta) in China, and qPCR assay was established for the RTX toxin (rtxD) gene. Histopathological examination showed that many inflammatory cells were infiltrated into heart, liver and intestine, as well as the necrosis of liver, kidney and spleen. The genome consisted of one circular chromosome (4.493 Mb) and one plasmid (18.8 kb), and predicted to contain 4170 and 19 protein-coding genes, respectively. Multiple pathogenic and virulence factors (e.g., fimbria, adhesion, invasion, toxin, hemolysin, chemotaxis, secretion system), multidrug-resistant genes (e.g., ampC, per-1, oxa-1, sul1, tetR) and a novel genomic resistance island PRI519 were identified. Comparative genome analysis revealed the closest relationship was with P. rettgeri, and with P. heimbachae closer than with other Providencia spp. To our knowledge, this was first report on genomic characterization of multidrug-resistant pathogenic P. rettgeri in cultured turtles.
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21
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Okubo T, Yossapol M, Ikushima S, Kakooza S, Wampande EM, Asai T, Tsuchida S, Ohya K, Maruyama F, Kabasa JD, Ushida K. Isolation and Characterization of Antimicrobial-Resistant Escherichia coli from Retail Meats from Roadside Butcheries in Uganda. Foodborne Pathog Dis 2020; 17:666-671. [PMID: 32551973 DOI: 10.1089/fpd.2020.2796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Retail meats are one of the main routes for spreading antimicrobial-resistant bacteria (ARB) from livestock to humans through the food chain. In African countries, retail meats are often sold at roadside butcheries without chilling or refrigeration. Retail meats in those butcheries are suspected to be contaminated by ARB, but it was not clear. In this study, we tested for the presence of antimicrobial-resistant Escherichia coli from retail meats (n = 64) from roadside butcheries in Kampala, Uganda. The meat surfaces were swabbed and inoculated on PetriFilm SEC agar to isolate E. coli. We successfully isolated E. coli from 90.6% of these retail meat samples. We identified the phylogenetic type, antimicrobial susceptibility, and antimicrobial resistance genes prevalence between retail meat isolates (n = 89). Phylogenetic type B1 was identified from 70.8% of the retail meat isolates, suggesting that the isolates originated primarily from fecal contamination during meat processing. Tetracycline (TET)-resistant isolates with tetA and/or tetB gene(s) were the most frequently detected (28.1%), followed by ampicillin (AMP) resistance genes with blaTEM (15.7%,) and sulfamethoxazole-trimethoprim (SXT) resistance genes with sul2 (15.7%). No extended-spectrum beta-lactamase-producing isolates were detected. A conjugation assay showed that resistance to AMP, TET, and SXT could be simultaneously transferred to recipients. These findings suggest that antimicrobial-resistant E. coli can easily be transferred from farms to tables from retail meats obtained from roadside butcheries.
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Affiliation(s)
- Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Sapporo, Japan
| | - Montira Yossapol
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Office of Academic Affairs, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham, Thailand
| | - Shiori Ikushima
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Steven Kakooza
- Department of Veterinary Pharmacy, Clinics and Comparative Medicine, School of Veterinary Medicine and Animal Resources, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Eddie M Wampande
- Department of Veterinary Pharmacy, Clinics and Comparative Medicine, School of Veterinary Medicine and Animal Resources, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Tetsuo Asai
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - Sayaka Tsuchida
- Chubu University Academy of Emerging Sciences, Kasugai, Japan.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Kenji Ohya
- Department of Applied Veterinary Sciences, United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan.,Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
| | - Fumito Maruyama
- Microbial Genomics and Ecology, Office of Academic Research and Industry-Government Collaboration, Academy of Hiroshima University, Hiroshima, Japan
| | - John D Kabasa
- Department of Pharmacy, Clinical and Comparative Medicine, School of Veterinary Medicine and Animal Resources, Makerere University, Kampala, Uganda
| | - Kazunari Ushida
- Chubu University Academy of Emerging Sciences, Kasugai, Japan.,Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
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22
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Weil AA, Debela MD, Muyanja DM, Kakuhikire B, Baguma C, Bangsberg DR, Tsai AC, Lai PS. Gut carriage of antimicrobial resistance genes in women exposed to small-scale poultry farms in rural Uganda: A feasibility study. PLoS One 2020; 15:e0229699. [PMID: 32525954 PMCID: PMC7289395 DOI: 10.1371/journal.pone.0229699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/19/2020] [Indexed: 01/21/2023] Open
Abstract
Background Antibiotic use for livestock is presumed to be a contributor to the acquisition of antimicrobial resistance (AMR) genes in humans, yet studies do not capture AMR data before and after livestock introduction. Methods We performed a feasibility study by recruiting a subset of women in a delayed-start randomized controlled trial of small-scale chicken farming to examine the prevalence of clinically-relevant AMR genes. Stool samples were obtained at baseline and one year post-randomization from five intervention women who received chickens at the start of the study, six control women who did not receive chickens until the end of the study, and from chickens provided to the control group at the end of the study. Stool was screened for 87 clinically significant AMR genes using a commercially available qPCR array (Qiagen). Results Chickens harbored 23 AMR genes from classes found in humans as well as additional vancomycin and β-lactamase resistance genes. AMR patterns between intervention and control women appeared more similar at baseline than one year post randomization (PERMANOVA R2 = 0.081, p = 0.61 at baseline, R2 = 0.186, p = 0.09 at 12 months) Women in the control group who had direct contact with the chickens sampled in the study had greater similarities in AMR gene patterns to chickens than those in the intervention group who did not have direct contact with chickens sampled (p = 0.01). However, at one year there was a trend towards increased similarity in AMR patterns between humans in both groups and the chickens sampled (p = 0.06). Conclusions Studies designed to evaluate human AMR genes in the setting of animal exposure should account for high baseline AMR rates. Concomitant collection of animal, human, and environmental samples over time is recommended to determine the directionality and source of AMR genes. Trial registration ClinicalTrials.gov Identifier NCT02619227.
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Affiliation(s)
- Ana A. Weil
- Department of Medicine, Massachusetts General Hospital Boston, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Meti D. Debela
- Department of Medicine, Massachusetts General Hospital Boston, Boston, Massachusetts, United States of America
| | | | | | - Charles Baguma
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - David R. Bangsberg
- Mbarara University of Science and Technology, Mbarara, Uganda
- Oregon Health & Science University, Portland State University School of Public Health, Portland, Oregon, United States of America
| | - Alexander C. Tsai
- Harvard Medical School, Boston, Massachusetts, United States of America
- Mbarara University of Science and Technology, Mbarara, Uganda
- Harvard Center for Population and Development Studies, Cambridge, Massachusetts, United States of America
- Center for Global Health and Mongan Institute, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Peggy S. Lai
- Department of Medicine, Massachusetts General Hospital Boston, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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23
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Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes. PLoS One 2020; 15:e0231852. [PMID: 32469885 PMCID: PMC7259651 DOI: 10.1371/journal.pone.0231852] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/11/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The crisis of antimicrobial resistance is already here with us, affecting both humans and animals alike and very soon, small cuts and surgeries will become life threatening. This study aimed at determine the whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: phylogenomic changes, virulence and resistant genes. METHODS This was a laboratory based cross sectional study. Bacterial isolates analyzed in this study were 42 multidrug resistant E. coli isolated from stool samples from both humans (n = 30) and cattle (n = 12) in pastoralist communities collected between January 2018-March 2019. Most of the isolates (41/42) were resistant to three or more antibiotics (multi-drug resistant) and 21/42 isolates were ESBL producers; 13/30 from human and 8/12 from cattle. Whole Genome Sequencing (WGS) was carried out at the facilities of Kenya Medical Research Institute-Wellcome trust, Kilifi, to determine the phylogenomic changes, virulence and resistant genes. RESULTS At household level, the genomes from both human and animals clustered away from one another except for one instance where two human isolates from the same household clustered together. However, 67% of the E. coli isolated from cattle were closely related to those found in humans. The E. coli isolates were assigned to eight different phylogroups: A, B1, B2, Cladel, D, E, F and G, with a majority being assigned to phylogroup A; while most of the animal isolates were assigned to phylogroup B1. The carriage of multiple AMR genes was higher from the E. coli population from humans than those from cattle. Among these were Beta-lactamase; blaOXA-1: Class D beta-lactamases; blaTEM-1, blaTEM-235: Beta-lactamase; catA1: chloramphenicol acetyl transferase; cmlA1: chloramphenicol efflux transporter; dfrA1, dfrA12, dfrA14, dfrA15, dfrA17, dfrA5, dfrA7, dfrA8: macrolide phosphotransferase; oqxB11: RND efflux pump conferring resistance to fluoroquinolone; qacL, qacEdelta1: quinolone efflux pump; qnrS1: quinolone resistance gene; sul1, sul2, sul3: sulfonamide resistant; tet(A), tet(B): tetracycline efflux pump. A high variation of virulence genes was registered among the E. coli genomes from humans than those of cattle origin. CONCLUSION From the analysis of the core genome and phenotypic resistance, this study has demonstrated that the E. coli of human origin and those of cattle origin may have a common ancestry. Limited sharing of virulence genes presents a challenge to the notion that AMR in humans is as a result of antibiotic use in the farm and distorts the picture of the directionality of transmission of AMR at a human-animal interface and presents a task of exploring alternative routes of transmission of AMR.
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24
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Okubo T, Hasegawa T, Fukuda A, Thapa J, Usui M, Tamura Y, Yamaguchi H. Screening of hospital-manhole sewage using MacConkey agar with cefotaxime reveals extended-spectrum β-lactamase (ESBL)-producing Escherichia coli. Int J Antimicrob Agents 2019; 54:831-833. [PMID: 31398479 DOI: 10.1016/j.ijantimicag.2019.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/26/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Nishi-5 Kita-12 Jo Kitaku, Sapporo 060-0812, Japan
| | - Takaki Hasegawa
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Nishi-5 Kita-12 Jo Kitaku, Sapporo 060-0812, Japan
| | - Akira Fukuda
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan; Osaka Institute of Public Health Microbiology Section, 8-34 Tojotyo, Tennoji, Osaka 543-0026, Japan
| | - Jeewan Thapa
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Nishi-5 Kita-12 Jo Kitaku, Sapporo 060-0812, Japan
| | - Masaru Usui
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan
| | - Yutaka Tamura
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Nishi-5 Kita-12 Jo Kitaku, Sapporo 060-0812, Japan.
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