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Gupta SS, Hamza Kh M, Sones CL, Zhang X, Sivaraman GK. The CRISPR/Cas system as an antimicrobial resistance strategy in aquatic ecosystems. Funct Integr Genomics 2024; 24:110. [PMID: 38806846 DOI: 10.1007/s10142-024-01362-7] [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: 03/13/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/30/2024]
Abstract
With the growing population, demand for food has dramatically increased, and fisheries, including aquaculture, are expected to play an essential role in sustaining demand with adequate quantities of protein and essential vitamin supplements, employment generation, and GDP growth. Unfortunately, the incidence of emerging/re-emerging AMR pathogens annually occurs because of anthropogenic activities and the frequent use of antibiotics in aquaculture. These AMR pathogens include the WHO's top 6 prioritized ESKAPE pathogens (nosocomial pathogens: Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), extended-spectrum beta lactases (ESBLs) and carbapenemase-producing E. coli, which pose major challenges to the biomagnification of both nonnative and native antibiotic-resistant bacteria in capture and cultured fishes. Although implementing the rational use of antibiotics represents a promising mitigation measure, this approach is practically impossible due to the lack of awareness among farmers about the interplay between antimicrobial use and the emergence of antimicrobial resistance (AMR). Nevertheless, to eradicate these 'superbugs,' CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR associate protein) has turned out to be a novel approach owing to its ability to perform precise site-directed targeting/knockdown/reversal of specific antimicrobial resistance genes in vitro and to distinguish AMR-resistant bacteria from a plethora of commensal aquatic bacteria. Along with highlighting the importance of virulent multidrug resistance genes in bacteria, this article aims to provide a holistic picture of CRISPR/Cas9-mediated genome editing for combating antimicrobial-resistant bacteria isolated from various aquaculture and marine systems, as well as insights into different types of CRISPR/Cas systems, delivery methods, and challenges associated with developing CRISPR/Cas9 antimicrobial agents.
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Affiliation(s)
- Sobin Sonu Gupta
- Founder & CEO at Times of Biotech, Navelim Bicholim, Goa-403505, India
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India
| | - Muneeb Hamza Kh
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India
| | - Collin L Sones
- Founder and CTO of Highfield Diagnostics, Zepler Institute of Photonics and Nanoelectronics, University of Southampton, SO17 1BJ, Southampton, UK
| | - Xunli Zhang
- School of Engineering & Institute for Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Gopalan Krishnan Sivaraman
- Microbiology, Fermentation & Biotechnology Division, ICAR- Central Institute of Fisheries Technology, Cochin-29, Kerala, India.
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Mohanty D, Das BK, Kumari P, Dey S, Bera AK, Sahoo AK, Dasgupta S, Roy S. Prevalence of Extended-Spectrum β-Lactamases (ESBLs) Producing Aeromonas spp. Isolated from Lamellidens marginalis (Lamark, 1819) of Sewage-Fed Wetland: A Phenotypic and Genotypic Approach. Microorganisms 2024; 12:723. [PMID: 38674667 PMCID: PMC11051913 DOI: 10.3390/microorganisms12040723] [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: 12/31/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 04/28/2024] Open
Abstract
The global rise of zoonotic bacteria resistant to multiple antimicrobial classes and the growing occurrence of infections caused by Aeromonas spp. resistant to β-lactam antibiotics pose a severe threat to animal and human health. However, the contribution of natural environments, particularly aquatic ecosystems, as ideal settings for the development and spread of antimicrobial resistance (AMR) is a key concern. Investigating the phenotypic antibiotic resistance and detection of β-lactamase producing Aeromonas spp. in Lamellidens marginalis, which inhabit all freshwater ecosystems of the Indian subcontinent, is essential for implications in monitoring food safety and drug resistance. In the present investigation, 92 isolates of Aeromonas spp. were recovered from 105 bivalves and screened for their antimicrobial resistance patterns. In vitro antibiotic resistance profiling showed a higher Multiple Antibiotic Resistance (MAR) index of 0.8 with the highest resistance against ampicillin/sulbactam (82%), while 58, 44, 39 and 38% of the isolates were resistant to cephalothin, erythromycin, cefoxitin and imipenem, respectively. PCR results revealed that these isolates carried the blaTEM gene (94%), which was followed by the blaCTX-M gene (51%) and the blaSHV gene (45%). A combination of blaSHV, blaCTX-M, and blaTEM genes was found in 17% of the isolates, indicating the presence of all three resistance genes. This is the first investigation which highlights the importance of multidrug-resistant Aeromonas spp. in L. marginalis. The identification of extended-spectrum-β-lactamases (ESBLs) genes demand the necessity of continuous surveillance and systematic monitoring, considering its potential health risks for both animals and human beings.
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Affiliation(s)
- Debasmita Mohanty
- ICAR-Central Inland Fisheries Research Institute, Barrackpore 700120, West Bengal, India; (D.M.); (A.K.B.); (A.K.S.); (S.D.); (S.R.)
- Department of Bioscience and Biotechnology, Fakir Mohan University, Balasore 756020, Odisha, India;
| | - Basanta Kumar Das
- ICAR-Central Inland Fisheries Research Institute, Barrackpore 700120, West Bengal, India; (D.M.); (A.K.B.); (A.K.S.); (S.D.); (S.R.)
| | - Punam Kumari
- Department of Bioscience and Biotechnology, Fakir Mohan University, Balasore 756020, Odisha, India;
| | - Saikat Dey
- National Institute of Mental Health and Neurosciences, Bangalore 5600029, Karnataka, India;
| | - Asit Kumar Bera
- ICAR-Central Inland Fisheries Research Institute, Barrackpore 700120, West Bengal, India; (D.M.); (A.K.B.); (A.K.S.); (S.D.); (S.R.)
| | - Amiya Kumar Sahoo
- ICAR-Central Inland Fisheries Research Institute, Barrackpore 700120, West Bengal, India; (D.M.); (A.K.B.); (A.K.S.); (S.D.); (S.R.)
| | - Shubhankhi Dasgupta
- ICAR-Central Inland Fisheries Research Institute, Barrackpore 700120, West Bengal, India; (D.M.); (A.K.B.); (A.K.S.); (S.D.); (S.R.)
| | - Shreya Roy
- ICAR-Central Inland Fisheries Research Institute, Barrackpore 700120, West Bengal, India; (D.M.); (A.K.B.); (A.K.S.); (S.D.); (S.R.)
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Li Y, Li R, Hou J, Sun X, Wang Y, Li L, Yang F, Yao Y, An Y. Mobile genetic elements affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance in the environment. ENVIRONMENTAL RESEARCH 2024; 243:117801. [PMID: 38043895 DOI: 10.1016/j.envres.2023.117801] [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: 10/20/2023] [Revised: 11/24/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment have not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in the environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 MGEs and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seem to play the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.
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Affiliation(s)
- Ye Li
- School of Environment Science and Engineering, Tianjin University, Tianjin, 300350, China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Ruilin Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Jie Hou
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
| | - Xuan Sun
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yajun Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Linyun Li
- Ministry of Social and Ecological Civilization, Party School of Hebei Provincial Committee of C.P.C, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yanpo Yao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
| | - Yi An
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China.
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Uhland FC, Li XZ, Mulvey MR, Reid-Smith R, Sherk LM, Ziraldo H, Jin G, Young KM, Reist M, Carson CA. Extended Spectrum β-Lactamase-Producing Enterobacterales of Shrimp and Salmon Available for Purchase by Consumers in Canada-A Risk Profile Using the Codex Framework. Antibiotics (Basel) 2023; 12:1412. [PMID: 37760708 PMCID: PMC10525137 DOI: 10.3390/antibiotics12091412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
The extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-EB) encompass several important human pathogens and are found on the World Health Organization (WHO) priority pathogens list of antibiotic-resistant bacteria. They are a group of organisms which demonstrate resistance to third-generation cephalosporins (3GC) and their presence has been documented worldwide, including in aquaculture and the aquatic environment. This risk profile was developed following the Codex Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance with the objectives of describing the current state of knowledge of ESBL-EB in relation to retail shrimp and salmon available to consumers in Canada, the primary aquacultured species consumed in Canada. The risk profile found that Enterobacterales and ESBL-EB have been found in multiple aquatic environments, as well as multiple host species and production levels. Although the information available did not permit the conclusion as to whether there is a human health risk related to ESBLs in Enterobacterales in salmon and shrimp available for consumption by Canadians, ESBL-EB in imported seafood available at the retail level in Canada have been found. Surveillance activities to detect ESBL-EB in seafood are needed; salmon and shrimp could be used in initial surveillance activities, representing domestic and imported products.
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Affiliation(s)
- F. Carl Uhland
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Xian-Zhi Li
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Richard Reid-Smith
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Lauren M. Sherk
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Hilary Ziraldo
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Grace Jin
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Kaitlin M. Young
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Mark Reist
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Carolee A. Carson
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
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Pearce R, Conrady B, Guardabassi L. Prevalence and Types of Extended-Spectrum β-Lactamase-Producing Bacteria in Retail Seafood. Foods 2023; 12:3033. [PMID: 37628032 PMCID: PMC10453871 DOI: 10.3390/foods12163033] [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: 02/01/2023] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Objectives: To assess prevalence and types of extended-spectrum β-lactamase (ESBL)-producing bacteria in retail seafood. Methods: A literature review was completed according to international guidelines for systematic reviews, except for being performed by a single reviewer. Kruskal-Wallis and Dunn tests were used to determine statistical differences between continents or seafood types. Results: Among 12,277 hits, 42 publications from 2011 to 2023 were deemed relevant to the review's objectives. The median prevalence of ESBL-contaminated products was 19.4%. A significantly lower prevalence was observed in Europe (p = 0.006) and Africa (p = 0.004) compared to Asia. Amongst the 2053 isolates analyzed in the selected studies, 44.8% were ESBL-positive. The predominant type was CTX-M (93.6%), followed by TEM (6.7%) and SHV (5.0%). Only 32.6% and 18.5% of the CTX-M-positive isolates were typed to group and gene level, respectively. While group 1 (60.2%) was prevalent over group 9 (39.8%) among Enterobacterales, the opposite trend was observed in Vibrio spp. (60.0% vs. 40.0%). Information at gene level was limited to Enterobacterales, where CTX-M-15 was the most prevalent (79.2%). Conclusions: On average, one in five seafood products sold at retail globally is contaminated with ESBL-producing Enterobacterales of clinical relevance. Our findings highlight a potential risk for consumers of raw seafood, especially in Asia.
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Affiliation(s)
- Ryan Pearce
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London NW1 0TU, UK;
- Department of Veterinary and Animal Sciences, University of Copenhagen, 2600 Copenhagen, Denmark;
| | - Beate Conrady
- Department of Veterinary and Animal Sciences, University of Copenhagen, 2600 Copenhagen, Denmark;
| | - Luca Guardabassi
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London NW1 0TU, UK;
- Department of Veterinary and Animal Sciences, University of Copenhagen, 2600 Copenhagen, Denmark;
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Akunda IK, Kariuki DW, Matulis G, Mwaura P, Maina B, Mohammed H, Paul A, Onyambu FG, Ole Kwallah A, Martins DJ, von Fricken ME, Kamau JM. Antimicrobial resistance patterns and characterisation of emerging beta-lactamase-producing Escherichia coli in camels sampled from Northern Kenya. Vet Med Sci 2023; 9:1407-1416. [PMID: 36795022 DOI: 10.1002/vms3.1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Animal husbandry practices in different livestock production systems and increased livestock-wildlife interactions are thought to be primary drivers of antimicrobial resistance (AMR) in Arid and Semi-Arid Lands (ASALs). Despite a tenfold increase in the camel population within the last decade, paired with widespread use of camel products, there is a lack of comprehensive information concerning beta-lactamase-producing Escherichia coli (E. coli) within these production systems. OBJECTIVES Our study sought to establish an AMR profile and to identify and characterise emerging beta-lactamase-producing E. coli isolated from faecal samples obtained from camel herds in Northern Kenya. METHODS The antimicrobial susceptibility profiles of E. coli isolates were established using the disk diffusion method, with beta-lactamase (bla) gene PCR product sequencing performed for phylogenetic grouping and genetic diversity assessments. RESULTS Here we show, among the recovered E. coli isolates (n = 123), the highest level of resistance was observed for cefaclor at 28.5% of isolates, followed by cefotaxime at 16.3% and ampicillin at 9.7%. Moreover, extended-spectrum beta-lactamase (ESBL)-producing E. coli harbouring the blaCTX-M-15 or blaCTX-M-27 genes were detected in 3.3% of total samples, and are associated with phylogenetic groups B1, B2 and D. Multiple variants of non-ESBL blaTEM genes were detected, the majority of which were the blaTEM-1 and blaTEM-116 genes. CONCLUSIONS Findings from this study shed light on the increased occurrence of ESBL- and non-ESBL-encoding gene variants in E. coli isolates with demonstrated multidrug resistant phenotypes. This study highlights the need for an expanded One Health approach to understanding AMR transmission dynamics, drivers of AMR development, and appropriate practices for antimicrobial stewardship in camel production systems within ASALs.
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Affiliation(s)
- Irene Karegi Akunda
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya.,One Health Center, Institute of Primate Research, Nairobi, Kenya
| | - Daniel W Kariuki
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Graham Matulis
- Department of Global and Community Health, George Mason University, Fairfax County, Virginia
| | - Patrick Mwaura
- One Health Center, Institute of Primate Research, Nairobi, Kenya
| | - Brian Maina
- Centre of Microbiology, Washington State University, Nairobi, Kenya
| | - Halima Mohammed
- Centre for Molecular Biosciences and Genomics, Nairobi, Kenya
| | - Ayieko Paul
- Regional Veterinary Investigation Laboratory, Nakuru, Kenya
| | - Frank G Onyambu
- Centre for Molecular Biosciences and Genomics, Nairobi, Kenya.,School of Health Sciences, Meru University of Science and Technology, Meru, Kenya
| | - Allan Ole Kwallah
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Dino J Martins
- Mpala Research Centre, Nanyuki, Kenya.,Turkana Basin Institute, Stony Brook University, Stony Brook, NY, USA
| | - Michael E von Fricken
- Department of Global and Community Health, George Mason University, Fairfax County, Virginia
| | - Joseph M Kamau
- One Health Center, Institute of Primate Research, Nairobi, Kenya
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Salmanov A, Shchehlov D, Artyomenko V, Svyrydiuk O, Maliarchuk R, Bortnik I, Mamonova M, Korniyenko S, Rud V, Gudym M, Shuba V, Loskutov O. Nosocomial transmission of multi-drug-resistant organisms in Ukrainian hospitals: results of a multi-centre study (2019-2021). J Hosp Infect 2023; 132:104-115. [PMID: 36565933 DOI: 10.1016/j.jhin.2022.12.008] [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: 10/24/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The increasing emergence and spread of multi-drug-resistant organisms (MDROs) in hospitals is a public health problem and continues to challenge infection control and hospital epidemiology practice worldwide. AIM The aim of this study was to characterize the epidemiology of transmission of MDROs via healthcare workers (HCWs) and the environment in the hospital wards/patient rooms. METHODS A multi-centre prospective observational study was conducted in 17 hospitals in Ukraine. Species identification was performed with standard microbial methods. β-Lactamase genes were investigated by polymerase chain reaction. Pulsed-field gel electrophoresis (PFGE) was used to determine the genetic similarity between isolates. FINDINGS Among 51,656 isolates, 19.5% were MDROs. The proportions of MDROs among isolates from patients with healthcare-associated infections, environmental surfaces and HCWs (hands, gown/gloves) were 29.2%, 16.3% and 24.2%, respectively. In 51.9% of the tested isolates, identical MDROs were found in clinical isolates, environmental samples and HCWs' hands. Meticillin resistance was found in 32.4% of Staphylococcus aureus (MRSA) isolates, and vancomycin resistance was found in 28.9% of enterococci (VRE). Resistance to third-generation cephalosporins was detected in 48.4% of Enterobacterales, and carbapenem resistance in 19.1%. Overall, 37.4% of MDROs had broad-spectrum β-lactamase genes, including extended-spectrum β-lactamase (35.8%), OXA-type (29.7%), AmpC-type (25.1%), KPC-type (25.7%) and metallo-β-lactamases, including IMP-type (5.7%), VIM-type (31.7%) and NDM-1 (21.3%). CONCLUSIONS In Ukrainian hospitals the prevalence of healthcare-associated infections caused by MDROs continues to increase, while infection control gaps in healthcare settings facilitate their transmission between patients.
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Affiliation(s)
- A Salmanov
- Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine.
| | - D Shchehlov
- Scientific-practical Centre of Endovascular Neuroradiology and Surgery of National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - V Artyomenko
- Odessa National Medical University, Odessa, Ukraine
| | - O Svyrydiuk
- Scientific-practical Centre of Endovascular Neuroradiology and Surgery of National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - R Maliarchuk
- Amosov National Institute of Cardiovascular Surgery, Kyiv, Ukraine
| | - I Bortnik
- Scientific-practical Centre of Endovascular Neuroradiology and Surgery of National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - M Mamonova
- Bogomolets National Medical University, Kyiv, Ukraine
| | - S Korniyenko
- Odessa National Medical University, Odessa, Ukraine
| | - V Rud
- National Pirogov Memorial Medical University, Vinnytsia, Ukraine
| | - M Gudym
- Scientific-practical Centre of Endovascular Neuroradiology and Surgery of National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
| | - V Shuba
- Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
| | - O Loskutov
- Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
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"If You Do Not Take the Medicine and Complete the Dose…It Could Cause You More Trouble": Bringing Awareness, Local Knowledge and Experience into Antimicrobial Stewardship in Tanzania. Antibiotics (Basel) 2023; 12:antibiotics12020243. [PMID: 36830154 PMCID: PMC9952761 DOI: 10.3390/antibiotics12020243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global health issue disproportionately affecting low- and middle-income countries. In Tanzania, multi-drug-resistant bacteria (MDR) are highly prevalent in clinical and community settings, inhibiting effective treatment and recovery from infection. The burden of AMR can be alleviated if antimicrobial stewardship (AMS) programs are coordinated and incorporate local knowledge and systemic factors. AMS includes the education of health providers to optimise antimicrobial use to improve patient outcomes while minimising AMR risks. For programmes to succeed, it is essential to understand not just the awareness of and receptiveness to AMR education, but also the opportunities and challenges facing health professionals. We conducted in-depth interviews (n = 44) with animal and human health providers in rural northern Tanzania in order to understand their experiences around AMR. In doing so, we aimed to assess the contextual factors surrounding their practices that might enable or impede the translation of knowledge into action. Specifically, we explored their motivations, training, understanding of infections and AMR, and constraints in daily practice. While providers were motivated in supporting their communities, clear issues emerged regarding training and understanding of AMR. Community health workers and retail drug dispensers exhibited the most variation in training. Inconsistencies in understandings of AMR and its drivers were apparent. Providers cited the actions of patients and other providers as contributing to AMR, perpetuating narratives of blame. Challenges related to AMR included infrastructural constraints, such as a lack of diagnostic testing. While health and AMR-specific training would be beneficial to address awareness, equally important, if not more critical, is tackling the challenges providers face in turning knowledge into action.
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Mwakyoma AA, Kidenya BR, Minja CA, Mushi MF, Sandeman A, Sabiti W, Holden MTG, Mshana SE. Comparison of Horizontal blaCTX-M Gene Transfer via Conjugation among Extended Spectrum β-Lactamases Producing Escherichia coli Isolates from Patients with Urinary Tract Infection, Their Animals, and Environment. ARCHIVES OF MOLECULAR BIOLOGY AND GENETICS 2023; 2:1-8. [PMID: 37250807 PMCID: PMC7614579 DOI: 10.33696/genetics.2.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Background The dissemination of the extended spectrum β-lactamases (ESBL) producing E. coli poses a significant public health problem. Understanding the efficiency and frequency of horizontal gene transfer via conjugation of ESBL producing E. coli is imperative towards devising prevention and control measures. This study compared the frequencies and efficiencies of horizontal blaCTX-M gene transfer via conjugation among Escherichia coli isolates from urine and gastrointestinal tract (GIT) of patients with urinary tract infection (UTI), their animals and environment. Methods Horizontal blaCTX-M gene transfer via conjugation by a broth mating experiment was performed using 50 confirmed ESBL producing E. coli isolates as donors and Escherichia coli J53 (F-, met, pro, Azr), as the recipient. The transconjugants were detected and their frequencies and efficiencies of conjugation were measured and compared between ESBL producing E. coli isolates multi-sourced from urine, GIT, animals and environment. Antimicrobial susceptibility testing of all resulting transconjugants was performed. DNA was extracted from all transconjugants to confirm the presence and the acquisition of blaCTX-M gene. Results Out of 50 ESBL producing E. coli isolates harboring blaCTX-M gene, 37 (74.0%) successfully exercised horizontal gene transfer through conjugation. All transconjugants were confirmed phenotypically and genotypically by PCR. Of note, all of the isolates from environment 100.0% (7/7) performed conjugation, exhibiting the highest transfer efficiency, followed by isolates from urine and animals, with the conjugation transfer efficiency of 77.8% (14/18) and 76.1% (10/13), respectively. The isolates from the environment conjugated with a significant more efficiency than those from the GIT [Two-sample test of proportions; p-value = 0.0119]. The overall conjugation transfer frequencies ranged from 0.4 × 10-14 - 5.5 × 10-11 per donor cells with the highest median conjugation transfer frequency observed among isolates from animal (3.23 × 10-12 [IQR: 0.70 × 10-12 - 7.22 × 10-12]) followed by that of isolates from the environment (1.60 × 10-12 [IQR: 0.30 × 10-12 - 5.0 × 10-12]). Conclusion ESBL producing E. coli from human, animals and environment exercises horizontal blaCTX-M gene transfer efficiently with the highest occurrence among isolates from the environment and animals. The antimicrobial resistance control and prevention strategies should be widened up to explore strategies to prevent horizontal AMR gene transfer.
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Affiliation(s)
- Adam A. Mwakyoma
- Department of Bochemistry and Molecular Biology, Catholic University of Health and Allied Sciences, P. O. Box 1464, Bugando, Mwanza, Tanzania
- Department of Clinical Microbiology, Kilimanjaro Christian Medical Centre, P. O. Box 3010 Moshi, Kilimanjaro, Tanzania
| | - Benson R. Kidenya
- Department of Bochemistry and Molecular Biology, Catholic University of Health and Allied Sciences, P. O. Box 1464, Bugando, Mwanza, Tanzania
| | - Caroline A. Minja
- Department of Bochemistry and Molecular Biology, Catholic University of Health and Allied Sciences, P. O. Box 1464, Bugando, Mwanza, Tanzania
| | - Martha F. Mushi
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, P. O. Box 1464, Bugando, Mwanza, Tanzania
| | - Alison Sandeman
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Wilber Sabiti
- School of Medicine, University of St Andrews, St Andrews, UK
| | | | - Stephen E. Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, P. O. Box 1464, Bugando, Mwanza, Tanzania
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10
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Whole Genome Sequencing Reveals Presence of High-Risk Global Clones of Klebsiella pneumoniae Harboring Multiple Antibiotic Resistance Genes in Multiple Plasmids in Mwanza, Tanzania. Microorganisms 2022; 10:microorganisms10122396. [PMID: 36557648 PMCID: PMC9785957 DOI: 10.3390/microorganisms10122396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is an important multidrug-resistant (MDR) pathogen, causing both community- and healthcare-associated infections. The resistance is due to the continuous accumulation of multiple antibiotic-resistance-genes (ARGs) through spontaneous genomic mutations and the acquisition of conjugative plasmids. This study presents antibiotics resistance genes, plasmids replicons, and virulence genes of K. pneumoniae isolates from clinical specimens in a tertiary hospital, Mwanza, Tanzania. METHODS Whole genome sequencing (WGS) of 34 K. pneumoniae was performed, using an Illumina NextSeq 500, followed by in silco analysis. RESULTS A total of 34 extended-spectrum beta-lactamase-producing K. pneumoniae, isolated from blood samples from neonatal units were whole-genome sequenced. Of these, 28 (82.4%) had an identified sequence type (ST), with ST14 (39.3%, n = 11) being frequently identified. Moreover, 18 (52.9%) of the bacteria harbored at least one plasmid, from which a total of 25 plasmid replicons were identified with a predominance of IncFIB(K) 48.0% (n = 12). Out of 34 sequenced K. pneumoniae, 32 (94.1%) were harboring acquired antibiotic/biocides-resistance-genes (ARGs) with a predominance of blaCTX-M-15 (90.6%), followed by oqxB (87.5%), oqxA (84.4%), blaTEM-1B (84.4%) and sul2 (84.4%). Interestingly, we observed the ColRNAI plasmid-replicon (n = 1) and qacE gene (n = 4) for the first time in this setting. CONCLUSION Global high-risk clones of K. pneumoniae isolates carry multiple ARGs in multiple plasmid-replicons. Findings from this study warrant genomic-based surveillance to monitor high-risk global clones, epidemic plasmids and ARGs in low- and middle-income countries.
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11
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Ogunlaja A, Ogunlaja OO, Olukanni OD, Taylor GO, Olorunnisola CG, Dougnon VT, Mousse W, Fatta-Kassinos D, Msagati TAM, Unuabonah EI. Antibiotic resistomes and their chemical residues in aquatic environments in Africa. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 312:119783. [PMID: 35863703 DOI: 10.1016/j.envpol.2022.119783] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The aquatic environment is a hotspot for the transfer of antibiotic resistance to humans and animals. Several reviews have put together research efforts on the presence and distribution of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic chemical residue (ACRs) in food, hospital wastewater, and even in other aquatic environments. However, these reports are largely focused on data from developed countries, while data from developing countries and especially those in Africa, are only marginally discussed. This review is the first effort that distills information on the presence and distribution of ARGs and ACRs in the African aquatic environments (2012-2021). This review provides critical information on efforts put into the study of ARB, ARGs, and ACRs in aquatic environments in Africa through the lens of the different sub-regions in the continent. The picture provided is compared with those from some other continents in the world. It turns out that the large economies in Africa (South Africa, Nigeria, Tunisia, Kenya) all have a few reports of ARB and ARGs in their aquatic environment while smaller economies in the continent could barely provide reports of these in their aquatic environment (in most cases no report was found) even though they have some reports on resistomes from clinical studies. Interestingly, the frequency of these reports of ARB and ARGs in aquatic environments in Africa suggests that the continent is ahead of the South American continent but behind Europe and Asia in relation to providing information on these contaminants. Common ARGs found in African aquatic environment encode resistance to sulfonamide, tetracycline, β-lactam, and macrolide classes of antibiotics. The efforts and studies from African scientists in eliminating ARB and ARGs from the aquatic environment in Africa are also highlighted. Overall, this document is a ready source of credible information for scientists, policy makers, governments, and regional bodies on ARB, ARGs, and ACRs in aquatic environments in Africa. Hopefully, the information provided in this review will inspire some necessary responses from all stakeholders in the water quality sector in Africa to put in more effort into providing more scientific evidence of the presence of ARB, ARGs, and ACRs in their aquatic environment and seek more efficient ways to handle them to curtail the spread of antibiotic resistance among the population in the continent. This will in turn, put the continent on the right path to meeting the United Nations Sustainable Development Goals #3 and #6, which at the moment, appears to be largely missed by most countries in the continent.
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Affiliation(s)
- Aemere Ogunlaja
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, P.M.B 230, Ede, Osun State, Nigeria.
| | - Olumuyiwa O Ogunlaja
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Chemical Sciences, Faculty of Natural and Applied Sciences, Lead City University, Ibadan, Nigeria
| | - Olumide D Olukanni
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Biochemistry, Faculty of Basic Medical Sciences, Redeemer's University, P.M.B. 230, Ede, Nigeria
| | - Gloria O Taylor
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, P.M.B 230, Ede, Osun State, Nigeria
| | - Chidinma G Olorunnisola
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Chemical Sciences, Faculty of Natural Sciences, Redeemer's University, P.M.B 230, Ede, Osun State, Nigeria
| | - Victorien T Dougnon
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Benin
| | - Wassiyath Mousse
- Research Unit in Applied Microbiology and Pharmacology of Natural Substances, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Benin
| | - Despo Fatta-Kassinos
- Department of Civil and Environmental Engineering and Nireas-International Water Research Centre, School of Engineering, University of Cyprus, PO Box 20537, 1678 Nicosia, Cyprus
| | - Titus A M Msagati
- Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science Engineering and Technology, University of South Africa, South Africa
| | - Emmanuel I Unuabonah
- African Centre of Excellence for Water and Environmental Research (ACEWATER), Redeemer's University, P.M.B 230, Ede, 232101, Osun State, Nigeria; Department of Chemical Sciences, Faculty of Natural Sciences, Redeemer's University, P.M.B 230, Ede, Osun State, Nigeria
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12
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Altayb HN, Elbadawi HS, Alzahrani FA, Baothman O, Kazmi I, Nadeem MS, Hosawi S, Chaieb K. Co-Occurrence of β-Lactam and Aminoglycoside Resistance Determinants among Clinical and Environmental Isolates of Klebsiella pneumoniae and Escherichia coli: A Genomic Approach. Pharmaceuticals (Basel) 2022; 15:1011. [PMID: 36015159 PMCID: PMC9416466 DOI: 10.3390/ph15081011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 12/04/2022] Open
Abstract
The presence of antimicrobial-resistance genes (ARGs) in mobile genetic elements (MGEs) facilitates the rapid development and dissemination of multidrug-resistant bacteria, which represents a serious problem for human health. This is a One Health study which aims to investigate the co-occurrence of antimicrobial resistance determinants among clinical and environmental isolates of K. pneumoniae and E. coli. Various bioinformatics tools were used to elucidate the bacterial strains' ID, resistome, virulome, MGEs, and phylogeny for 42 isolates obtained from hospitalized patients (n = 20) and environmental sites (including fresh vegetables, fruits, and drinking water) (n = 22). The multilocus sequence typing (MLST) showed that K. pneumoniae belonged to ten sequence types (STs) while the E. coli belonged to seventeen STs. Multidrug-resistant isolates harbored β-lactam, aminoglycoside resistance determinants, and MGE were detected circulating in the environment (drinking water, fresh vegetables, and fruits) and in patients hospitalized with postoperative infections, neonatal sepsis, and urinary tract infection. Four K. pneumoniae environmental isolates (7E, 16EE, 1KE, and 19KE) were multidrug-resistant and were positive for different beta-lactam and aminoglycoside resistance determinants. blaCTX-M-15 in brackets of ISEc 9 and Tn 3 transposases was detected in isolates circulating in the pediatrics unit of Soba hospital and the environment. This study documented the presence of bacterial isolates harboring a similar pattern of antimicrobial resistance determinants circulating in hospitals and environments. A rapid response is needed from stakeholders to initiate a program for infection prevention and control measures to detect such clones disseminated in the communities and hospitals.
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Affiliation(s)
- Hisham N. Altayb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hana S. Elbadawi
- Microbiology and Parasitology Department, Soba University Hospital, University of Khartoum, Khartoum 11115, Sudan
| | - Faisal A. Alzahrani
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Embryonic Stem Cells Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Othman Baothman
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Kamel Chaieb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environmental and Products, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
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13
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Mondain V, Retur N, Bertrand B, Lieutier-Colas F, Carenco P, Diamantis S. Advocacy for Responsible Antibiotic Production and Use. Antibiotics (Basel) 2022; 11:antibiotics11070980. [PMID: 35884234 PMCID: PMC9311909 DOI: 10.3390/antibiotics11070980] [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: 06/11/2022] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022] Open
Abstract
Antibiotic-resistant bacteria have become one of humankind’s major challenges, as testified by the UN’s Call to Action on Antimicrobial Resistance in 2021. Our knowledge of the underlying processes of antibiotic resistance is steadily improving. Beyond the inappropriate use of antimicrobials in human medicine, other causes have been identified, raising ethical issues and requiring an approach to the problem from a “One Health” perspective. Indeed, it is now clear that the two main issues regarding the subject of antibiotics are their misuse in the global food industry and their method of production, both leading to the emergence and spread of bacterial resistance.
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Affiliation(s)
- Véronique Mondain
- Centre Hospitalo-Universitaire de Nice, Service des Maladies Infectieuses et Tropicales, Hôpital Archet 1, 06202 Nice, France
- Correspondence:
| | - Nicolas Retur
- Centre Hospitalo-Universitaire de Nice, Pharmacie, Hôpital Archet 1, 06202 Nice, France;
| | | | - Florence Lieutier-Colas
- AntibioEst, Regional Antibiotic Therapy Centre, Nancy University Hospital, Brabois Hospital, 54511 Vandoeuvre-les-Nancy, France;
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14
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Sola M, Mani Y, Saras E, Drapeau A, Grami R, Aouni M, Madec JY, Haenni M, Mansour W. Prevalence and Characterization of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Enterobacterales from Tunisian Seafood. Microorganisms 2022; 10:microorganisms10071364. [PMID: 35889085 PMCID: PMC9323973 DOI: 10.3390/microorganisms10071364] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 02/01/2023] Open
Abstract
Aquaculture is a rapidly expanding sector in which it is important to monitor the occurrence of multi-drug resistant (MDR) bacteria. The presence of extended-spectrum β-lactamase (ESBL-) or carbapenemase-producing Enterobacterales is a commonly used indicator of the resistance burden in a given sector. In this study, 641 pieces of farmed fish (sea bream and sea bass), as well as 1075 Mediterranean clams, were analyzed. All ESBL- and carbapenemase-producing Enterobacterales collected were whole-genome sequenced. The proportion of ESBL-producing Enterobacterales was 1.4% in fish and 1.6% in clams, carried by Escherichia coli (n = 23) and Klebsiella pneumoniae (n = 4). The ESBL phenotype was exclusively due to the presence of blaCTX-M genes, the most frequent one being blaCTX-M-15. The blaCTX-M-1 gene was also identified in six E. coli, among which four were carried by IncI1/pST3 plasmids, possibly betraying an animal origin. Carbapenemases were absent in fish but identified in two K. pneumoniae isolates from clams (blaNDM-1 and blaOXA-48). Several sequence types (STs) identified were associated with human MDR clones such as E. coli ST131 and ST617, or K. pneumoniae ST307 and ST147. Our results might indicate that bacteria from hospital or farm effluents can reach the open sea and contaminate seafood and fish that are living or raised nearby. Therefore, monitoring the quality of water discharged to the sea and the presence of MDR bacteria in seafood is mandatory to ensure the quality of fishery products.
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Affiliation(s)
- Mehdi Sola
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée (LR12ES02), Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, Sousse 4002, Tunisia; (M.S.); (Y.M.); (R.G.); (W.M.)
| | - Yosra Mani
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée (LR12ES02), Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, Sousse 4002, Tunisia; (M.S.); (Y.M.); (R.G.); (W.M.)
| | - Estelle Saras
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon, Université de Lyon, 69007 Lyon, France; (E.S.); (A.D.); (J.-Y.M.)
| | - Antoine Drapeau
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon, Université de Lyon, 69007 Lyon, France; (E.S.); (A.D.); (J.-Y.M.)
| | - Raoudha Grami
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée (LR12ES02), Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, Sousse 4002, Tunisia; (M.S.); (Y.M.); (R.G.); (W.M.)
| | - Mahjoub Aouni
- Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives, Faculté de Pharmacie de Monastir, Université de Monastir, Monastir 5000, Tunisia;
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon, Université de Lyon, 69007 Lyon, France; (E.S.); (A.D.); (J.-Y.M.)
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Laboratoire de Lyon, Université de Lyon, 69007 Lyon, France; (E.S.); (A.D.); (J.-Y.M.)
- Correspondence:
| | - Wejdene Mansour
- Laboratoire de Recherche Biophysique Métabolique et Pharmacologie Appliquée (LR12ES02), Faculté de Médecine Ibn Al Jazzar Sousse, Université de Sousse, Sousse 4002, Tunisia; (M.S.); (Y.M.); (R.G.); (W.M.)
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15
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Abdallah R, Kuete Yimagou E, Hadjadj L, Mediannikov O, Ibrahim A, Davoust B, Barciela A, Hernandez-Aguilar RA, Diatta G, Sokhna C, Raoult D, Rolain JM, Baron SA. Population Diversity of Antibiotic Resistant Enterobacterales in Samples From Wildlife Origin in Senegal: Identification of a Multidrug Resistance Transposon Carrying blaCTX–M–15 in Escherichia coli. Front Microbiol 2022; 13:838392. [PMID: 35369484 PMCID: PMC8971907 DOI: 10.3389/fmicb.2022.838392] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/18/2022] [Indexed: 01/08/2023] Open
Abstract
Introduction The role of wildlife in the transmission of antimicrobial resistant (AMR) is suspected but scarcely reported in current studies. Therefore, we studied the dynamics and prevalence of antibiotic-resistant Enterobacterales in antibiotic-limited areas of Senegal. Materials and Methods We collected fecal samples from monkeys and apes (N = 226) and non-fecal environmental samples (N = 113) from Senegal in 2015 and 2019. We grew the samples on selective media, subsequently isolated AMR Enterobacterales, and then sequenced their genomes. Results We isolated 72 different Enterobacterales among which we obtained a resistance rate of 65% for colistin (N = 47/72) and 29% for third generation-cephalosporin (C3G) (29%, N = 21/72). Interestingly, almost 46% of our isolates, among Enterobacter sp., Citrobacter cronae and Klebsiella aerogenes, belong to 34 new STs. Moreover, the genes blaCTX–M–15, blaTEM1B, sul2, dfrA14, qnrs, aph(3′′), aph(6), tetA, and tetR harbored within a transposon on the IncY plasmid of ST224 Escherichia coli were transferred and inserted into a ST10 E. coli phage coding region. Conclusion Wildlife constitutes a rich, unexplored reservoir of natural microbial diversity, AMR genes and international resistant clones pathogenic in humans. The presence of a transposon that carries AMR genes is intriguing since no antibiotics are used in the non-human primates we studied.
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Affiliation(s)
- Rim Abdallah
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Edmond Kuete Yimagou
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Linda Hadjadj
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Oleg Mediannikov
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ahmad Ibrahim
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard Davoust
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Amanda Barciela
- Dindefelo Biological Station, Jane Goodall Institute Spain and Senegal, Kedougou, Senegal
| | - R. Adriana Hernandez-Aguilar
- Dindefelo Biological Station, Jane Goodall Institute Spain and Senegal, Kedougou, Senegal
- Department of Social Psychology and Quantitative Psychology, Faculty of Psychology, Serra Hunter Programme, University of Barcelona, Barcelona, Spain
| | - Georges Diatta
- VITROME IRD 257, Campus International de Recherche IRD-UCAD de Hann, Dakar, Senegal
| | - Cheikh Sokhna
- IHU Méditerranée Infection, Marseille, France
- VITROME IRD 257, Campus International de Recherche IRD-UCAD de Hann, Dakar, Senegal
| | - Didier Raoult
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- *Correspondence: Sophie Alexandra Baron,
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16
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Nüesch‐Inderbinen M, Hänni C, Zurfluh K, Hartnack S, Stephan R. Antimicrobial resistance profiles of
Escherichia coli
and prevalence of extended‐spectrum beta‐lactamase‐producing Enterobacteriaceae in calves from organic and conventional dairy farms in Switzerland. Microbiologyopen 2022; 11:e1269. [PMID: 35478290 PMCID: PMC8924695 DOI: 10.1002/mbo3.1269] [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: 12/13/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 11/22/2022] Open
Abstract
This study compared the antimicrobial resistance (AMR) among commensal Escherichia coli in the fecal microbiota of young calves raised on organic and on conventional dairy farms in Switzerland. Further, fecal carriage of extended‐spectrum beta‐lactamase (ESBL) producing Enterobacteriaceae was assessed for calves from both farming systems. Where possible, data on antimicrobial usage (AMU) were obtained. Antimicrobial susceptibility testing was performed on a total of 71 isolates using the disk diffusion method. ESBL producers were characterized by polymerase chain reaction‐based multilocus sequence typing and sequencing of the blaESBL genes. Organically raised calves were significantly more likely to harbor E. coli that showed AMR to ampicillin (odds ratio [OR]: 2.78, 95% confidence interval [CI]: 1.02–7.61, p = 0.046), streptomycin (OR: 3.22, 95% CI: 1.17–8.92, p = 0.046), kanamycin (OR: 11.3, 95% CI: 2.94–43.50, p < 0.001), and tetracycline (OR: 3.25, 95% CI: 1.13–9.31, p = 0.028). Calves with reported AMU were significantly more likely to harbor E. coli with resistance to ampicillin (OR: 3.91, 95% CI: 1.03–14.85, p = 0.045), streptomycin (OR: 4.35, 95% CI: 1.13–16.7, p = 0.045), and kanamycin (OR: 8.69, 95% CI: 2.01–37.7, p = 0.004). ESBL‐producing Enterobacteriaceae (18 E. coli and 3 Citrobacter braakii) were detected exclusively among samples from conventionally farmed calves (OR: infinity [∞], 95% CI: 2.3–∞, p < 0.0013). The observations from this study suggest that AMR is highly prevalent among commensal E. coli in young dairy calves, irrespective of the farm management system, with proportions of certain resistance phenotypes higher among organic calves. By contrast, the occurrence of ESBL producers among young dairy calves may be linked to factors associated with conventional farming.
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Affiliation(s)
| | - Claudia Hänni
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich Zurich Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich Zurich Switzerland
| | - Sonja Hartnack
- Section of Epidemiology, Vetsuisse Faculty, University of Zurich Zurich Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich Zurich Switzerland
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17
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Kimera ZI, Mgaya FX, Mshana SE, Karimuribo ED, Matee MIN. Occurrence of Extended Spectrum Beta Lactamase (ESBL) Producers, Quinolone and Carbapenem Resistant Enterobacteriaceae Isolated from Environmental Samples along Msimbazi River Basin Ecosystem in Tanzania. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18168264. [PMID: 34444027 PMCID: PMC8394723 DOI: 10.3390/ijerph18168264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/24/2021] [Accepted: 07/28/2021] [Indexed: 12/18/2022]
Abstract
We conducted environmental surveillance of antimicrobial resistance (AMR) bacteria in the Msimbazi river basin in Tanzania to determine the occurrence of extended-spectrum β-lactamase (ESBL)-producing, carbapenem resistant Enterobacteriaceae (CRE) and quinolone resistant Escherichia coli and Klebsiella spp. A total of 213 Enterobacteriaceae isolates were recovered from 219 samples. Out of the recovered isolates, 45.5% (n = 97) were Klebsiella pneumoniae and 29.6% (n = 63) were Escherichia coli. K. pneumoniae isolates were more resistant in effluent (27.9%) compared to the E. coli (26.6%). The E. coli had a higher resistance in river water, sediment and crop soil than the K. pneumoniae (35 versus 25%), respectively. Higher resistance in K. pneumoniae was found in nalidixic acid (54.6%) and ciprofloxacin (33.3%) while the E. coli isolates were highly resistant to ciprofloxacin (39.7%) and trimethoprim/sulfamethoxazole (38%). Resistance increased from 28.3% in Kisarawe, where the river originates, to 59.9% in Jangwani (the middle section) and 66.7% in Upanga West, where the river enters the Indian Ocean. Out of 160 E. coli and K. pneumoniae isolates, 53.2% (n = 85) were resistant to more than three classes of the antibiotic tested, occurrence being higher among ESBL producers, quinolone resistant and carbapenem resistant strains. There is an urgent need to curb environmental contamination with antimicrobial agents in the Msimbazi Basin.
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Affiliation(s)
- Zuhura I. Kimera
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam 11103, Tanzania; (F.X.M.); (M.I.N.M.)
- Ministry of Livestock and Fisheries, Mtumba Area, P.O. Box 2182, Dodoma 40487, Tanzania
- Correspondence:
| | - Fauster X. Mgaya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam 11103, Tanzania; (F.X.M.); (M.I.N.M.)
| | - Stephen E. Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, P.O. Box 1464, Mwanza 33109, Tanzania;
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania;
| | - Esron D. Karimuribo
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania;
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, P.O. Box 3021, Morogoro 67125, Tanzania
| | - Mecky I. N. Matee
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam 11103, Tanzania; (F.X.M.); (M.I.N.M.)
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania;
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Minja CA, Shirima G, Mshana SE. Conjugative Plasmids Disseminating CTX-M-15 among Human, Animals and the Environment in Mwanza Tanzania: A Need to Intensify One Health Approach. Antibiotics (Basel) 2021; 10:antibiotics10070836. [PMID: 34356757 PMCID: PMC8300620 DOI: 10.3390/antibiotics10070836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 11/30/2022] Open
Abstract
Background: Globally, blaCTX-M-15 beta-lactamases are the most popular extended spectrum beta-lactamase alleles that are widely distributed due its mobilisation by mobile genetic elements in several compartments. We aimed to determine the conjugation frequencies and replicon types associated with plasmids carrying blaCTX-M-15 gene from Extended Spectrum Beta-lactamase producing isolates in order to understand the dissemination of resistance genes in different compartments. Material and methods: A total of 51 archived isolates carrying blaCTX-M-15 beta-lactamases were used as donors in this study. Antibiotic susceptibility tests were performed as previously described for both donors and transconjugants. Conjugation experiment was performed by a modified protocol of the plate mating experiment, and plasmid replicon types were screened among donor and transconjugant isolates by multiplex Polymerase Chain Reaction in a set of three primer panels. Results: The conjugation efficiency of plasmids carrying blaCTX-M-15 was 88.2% (45/51) with conjugation frequencies in the order of 10−1 to 10−9 and a 100% transfer efficiency observed among E. coli of animal origin. Majority of donors (n = 21) and transconjugants (n = 14) plasmids were typed as either Inc FIA or Inc FIB. Resistance to non-beta-lactam antibiotics was transferrable in 34/45 (75.6%) of events. Ciprofloxacin, tetracycline and sulphamethoxazole-trimethoprim resistance was co-transferred in 29/34 (85.3%) such events. Gentamicin resistance was transferred in 17/34 (50%) of events. Conclusions: Majority of plasmids carrying blaCTX-M-15 were conjugatively transferred by IncF plasmids along with non-beta lactam resistance. There is a need for more research on plasmids to understand how plasmids especially multi replicon plasmids interact and the effect of such interaction on conjugation. One Health approach is to be intensified to address antimicrobial resistance which is a public health threat.
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Affiliation(s)
- Caroline A. Minja
- School of Life Sciences, Department of Global Health and Biomedical Sciences, Nelson Mandela African Institution of Science and Technology, Arusha 23306, Tanzania;
- Correspondence:
| | - Gabriel Shirima
- School of Life Sciences, Department of Global Health and Biomedical Sciences, Nelson Mandela African Institution of Science and Technology, Arusha 23306, Tanzania;
| | - Stephen E. Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza 33109, Tanzania;
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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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Sangeda RZ, Baha A, Erick A, Mkumbwa S, Bitegeko A, Sillo HB, Fimbo AM, Chambuso M, Mbugi EV. Consumption Trends of Antibiotic for Veterinary Use in Tanzania: A Longitudinal Retrospective Survey From 2010-2017. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.694082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BackgroundWith increased livestock keeping, multiple prevailing infections, antimicrobial agents’ use and pattern in Tanzania, the development of antimicrobial resistance (AMR) becomes inevitable. Antibiotic-resistant pathogens have increasingly become a major challenge in human and animal medicine. Although inappropriate use of antibiotics in humans is the principal cause of resistance, antibiotic-resistant bacteria originating from animals contribute to the emergence and spread of these bacteria. Antibiotics help control a multitude of bacterial infections that are major causes of diseases in both animals and humans. Rational use in animals is crucial to control any development and transfer of AMR to humans. This study aimed to create quantitative evidence of animal antimicrobial usage patterns in Tanzania to serve as a baseline for surveillance of antimicrobial use and antimicrobial resistance control.MethodologyThis descriptive longitudinal retrospective study was conducted to explore the trend of veterinary-antibiotics consumed in the eight years, from 1st January 2010 to 31st December 2017 in Tanzania mainland. The data source was records of all antibiotics imported for veterinary use into Tanzania’s mainland according to the Tanzania Medicines and Medical Devices Authority (TMDA) records. The analysis employed the World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology using Anatomical Therapeutic and Chemical (ATC) classification. Regression and time series analysis was used to establish trends in antibiotics consumption.ResultsA total of 12,147,491 kg of antibiotics were consumed in Tanzania from 2010 to 2017. Tetracycline, sulfonamides and trimethoprim, quinolones, aminoglycosides, beta-lactams and antibacterial combinations were the most commonly used antibacterial agents in Tanzania. Tetracycline class topped the list with about 8,090,798 kg (66.6%) out of 12,147,491 kg total quantity of antimicrobials consumed. Non-significant, linear curve estimations and time series analysis indicate a decline in the quantities of veterinary antibiotics used in the eight years from 2010 to 2017.ConclusionsThis study suggests that tetracycline is the most used antibiotic class for veterinary medicine in Tanzania. The trend of antimicrobial use is generally decreasing compared to other countries in Africa. Even though some antibiotics have the lowest consumption rate, they are also prone to AMR, prompting follow-up by the relevant regulatory authorities.
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Kurittu P, Khakipoor B, Brouwer MS, Heikinheimo A. Plasmids conferring resistance to extended-spectrum beta-lactamases including a rare IncN+IncR multireplicon carrying blaCTX-M-1 in Escherichia coli recovered from migrating barnacle geese ( Branta leucopsis). OPEN RESEARCH EUROPE 2021; 1:46. [PMID: 37645149 PMCID: PMC10446048 DOI: 10.12688/openreseurope.13529.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 08/31/2023]
Abstract
Background: Increasing antimicrobial resistance (AMR) is a global threat and wild migratory birds may act as mediators of resistant bacteria across country borders. Our objective was to study extended-spectrum beta-lactamase (ESBL) and plasmid-encoded AmpC (pAmpC) producing Escherichia coli in barnacle geese using whole genome sequencing (WGS) and to identify plasmids harboring bla genes. Methods: Barnacle geese feces (n=200) were collected during fall 2017 and spring 2018 from an urban area in Helsinki, Finland. ESBL/AmpC-producing E. coli were recovered from nine samples (4.5%) and isolates were subjected to WGS on both short- and long-read sequencers, enabling hybrid assembly and determination of the genomic location of bla genes. Results: A rare multireplicon IncN+IncR was recovered from one isolate carrying bla CTX-M-1 in addition to aadA2b, lnu(F), and qnrS1. Moreover, rarely detected IncY plasmids in two isolates were found to harbor multiple resistance genes in addition to the human-associated bla CTX-M-15. Poultry-associated bla CMY-2 was identified from the widely distributed IncI1 and IncK plasmids from four different isolates. One isolate harbored an IncI1 plasmid with bla CTX-M-1 and flor. A chromosomal point mutation in the AmpC promoter was identified in one of the isolates. WGS analysis showed isolates carried multiple resistance and virulence genes and harbored multiple different plasmid replicons in addition to bla-carrying plasmids. Conclusions: Our findings suggest that wild migratory birds serve as a limited source of ESBL/AmpC-producing E. coli and may act as disseminators of the epidemic plasmid types IncI1 and IncK but also rarely detected plasmid types carrying multidrug resistance. Human and livestock-associated ESBL enzyme types were recovered from samples, suggesting a potential for interspecies transmission. WGS offers a thorough method for studying AMR from different sources and should be implemented more widely in the future for AMR surveillance and detection. Understanding plasmid epidemiology is vital for efforts to mitigate global AMR spread.
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Affiliation(s)
- Paula Kurittu
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Banafsheh Khakipoor
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Laboratory and Research Division, Microbiology Unit, Finnish Food Authority, Seinäjoki, Finland
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Incompatibility Group I1 (IncI1) Plasmids: Their Genetics, Biology, and Public Health Relevance. Microbiol Mol Biol Rev 2021; 85:85/2/e00031-20. [PMID: 33910982 DOI: 10.1128/mmbr.00031-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial plasmids are extrachromosomal genetic elements that often carry antimicrobial resistance (AMR) genes and genes encoding increased virulence and can be transmissible among bacteria by conjugation. One key group of plasmids is the incompatibility group I1 (IncI1) plasmids, which have been isolated from multiple Enterobacteriaceae of food animal origin and clinically ill human patients. The IncI group of plasmids were initially characterized due to their sensitivity to the filamentous bacteriophage If1. Two prototypical IncI1 plasmids, R64 and pColIb-P9, have been extensively studied, and the plasmids consist of unique regions associated with plasmid replication, plasmid stability/maintenance, transfer machinery apparatus, single-stranded DNA transfer, and antimicrobial resistance. IncI1 plasmids are somewhat unique in that they encode two types of sex pili, a thick, rigid pilus necessary for mating and a thin, flexible pilus that helps stabilize bacteria for plasmid transfer in liquid environments. A key public health concern with IncI1 plasmids is their ability to carry antimicrobial resistance genes, including those associated with critically important antimicrobials used to treat severe cases of enteric infections, including the third-generation cephalosporins. Because of the potential importance of these plasmids, this review focuses on the distribution of the plasmids, their phenotypic characteristics associated with antimicrobial resistance and virulence, and their replication, maintenance, and transfer.
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Existence of Multiple ESBL Genes among Phenotypically Confirmed ESBL Producing Klebsiella pneumoniae and Escherichia coli Concurrently Isolated from Clinical, Colonization and Contamination Samples from Neonatal Units at Bugando Medical Center, Mwanza, Tanzania. Antibiotics (Basel) 2021; 10:antibiotics10050476. [PMID: 33919117 PMCID: PMC8143173 DOI: 10.3390/antibiotics10050476] [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: 03/25/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
The proportions and similarities of extended-spectrum β-lactamase (ESBL) producing K. pneumoniae (ESBL-KP) and E. coli (ESBL-EC) carrying multiple ESBL genes is poorly known at our setting. This study investigated the existence of multiple ESBL genes (blaCTX-M, blaTEM, and blaSHV) among ESBL-KP and ESBL-EC concurrently isolated from clinical, colonization, and contamination samples from neonatology units in Mwanza-Tanzania. Twenty and 55 presumptive ESBL-EC and ESBL-KP, respectively, from a previous study archived at −80 °C were successfully recovered for this study. Isolates were screened and confirmed for production of ESBLs by phenotypic methods followed by multiplex PCR assay to determine ESBL genes. All (100%) and 97.3% of presumptive ESBL isolates were phenotypically confirmed by Clinical and Laboratory Standards Institute (CLSI) and modified double-disc synergy methods, respectively. About 93.3% (70/75) of phenotypically confirmed ESBL isolates had at least one ESBL gene, whereby for 62.9% (44/70), all ESBL genes (blaCTX-M, blaTEM, and blaSHV) were detected. Eight pairs of ESBL bacteria show similar patterns of antibiotics susceptibility and ESBL genes. ESBL-KP and ESBL-EC, concurrently isolated from clinical, colonization and contamination samples, harbored multiple ESBL genes. Further, eight pairs of ESBL isolates had similar patterns of antibiotics susceptibility and ESBL genes, suggesting transmission of and/or sharing of mobile genetic elements (MGEs) among ESBL-KP and ESBL-EC.
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Multidrug-Resistant, Including Extended-Spectrum Beta Lactamase-Producing and Quinolone-Resistant, Escherichia coli Isolated from Poultry and Domestic Pigs in Dar es Salaam, Tanzania. Antibiotics (Basel) 2021; 10:antibiotics10040406. [PMID: 33918543 PMCID: PMC8069735 DOI: 10.3390/antibiotics10040406] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/21/2021] [Accepted: 03/23/2021] [Indexed: 12/30/2022] Open
Abstract
We determined the phenotypic profile of multidrug-resistant (MDR) Escherichia coli isolated from 698 samples (390 and 308 from poultry and domestic pigs, respectively). In total, 562 Enterobacteria were isolated. About 80.5% of the isolates were E. coli. Occurrence of E. coli was significantly higher among domestic pigs (73.1%) than in poultry (60.5%) (p = 0.000). In both poultry and domestic pigs, E. coli isolates were highly resistant to tetracycline (63.5%), nalidixic acid (53.7%), ampicillin (52.3%), and trimethoprim/sulfamethoxazole (50.9%). About 51.6%, 65.3%, and 53.7% of E. coli were MDR, extended-spectrum beta lactamase-producing enterobacteriaceae (ESBL-PE), and quinolone-resistant, respectively. A total of 68% of the extended-spectrum beta lactamase (ESBL) producers were also resistant to quinolones. For all tested antibiotics, resistance was significantly higher in ESBL-producing and quinolone-resistant isolates than the non-ESBL producers and non-quinolone-resistant E. coli. Eight isolates were resistant to eight classes of antimicrobials. We compared phenotypic with genotypic results of 20 MDR E. coli isolates, ESBL producers, and quinolone-resistant strains and found 80% harbored blaCTX-M, 15% aac(6)-lb-cr, 10% qnrB, and 5% qepA. None harbored TEM, SHV, qnrA, qnrS, qnrC, or qnrD. The observed pattern and level of resistance render this portfolio of antibiotics ineffective for their intended use.
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Moremi N, Silago V, Mselewa EG, Chifwaguzi AP, Mirambo MM, Mushi MF, Matemba L, Seni J, Mshana SE. Extended-spectrum β-lactamase bla CTX-M-1 group in gram-negative bacteria colonizing patients admitted at Mazimbu hospital and Morogoro Regional hospital in Morogoro, Tanzania. BMC Res Notes 2021; 14:77. [PMID: 33640022 PMCID: PMC7913416 DOI: 10.1186/s13104-021-05495-x] [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] [Received: 12/15/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Objective The objective of this study was to determine the proportion of extended spectrum β-lactamase producing gram-negative bacteria (ESBL-GNB) colonizing patients admitted at Mazimbu hospital and Morogoro Regional hospital, in Morogoro, Tanzania. Rectal colonization with ESBL-GNB increases the risks of developing bacterial infections by extra-intestinal pathogenic ESBL-GNB. Results Of the 285 patients investigated, 123 (43.2%) carried ESBL-GNB in their intestines. Five of the 123 ESBL positive patients were colonized with two different bacteria, making a total of 128 ESBL producing isolates. Escherichia coli (n = 95, 74.2%) formed the majority of ESBL isolates. The proportion of CTX-M-1 group genes among ESBL isolates tested was 94.9% (93/98). History of antibiotic use (OR: 1.83, 95% CI: 1.1–3.2, P = 0.03), being on antibiotic treatment (OR: 2.61, 95% CI: 1.5–4.53, P = 0.001), duration of hospital stay (OR: 1.2, 95% CI: 1.1–1.3, P < 0.001) and history of previous admission (OR: 2.24, 95% CI: 1.2–4.1, P = 0.009) independently predicted ESBL-GNB carriage.
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Affiliation(s)
- Nyambura Moremi
- Quality Assurance & Training Centre, National Health Laboratory, P. O. Box 9083, Dar Es Salaam, Tanzania
| | - Vitus Silago
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences-Bugando, P. O. Box 1464, Mwanza, Tanzania.
| | - Erick G Mselewa
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences-Bugando, P. O. Box 1464, Mwanza, Tanzania
| | - Ashery P Chifwaguzi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences-Bugando, P. O. Box 1464, Mwanza, Tanzania
| | - Mariam M Mirambo
- Quality Assurance & Training Centre, National Health Laboratory, P. O. Box 9083, Dar Es Salaam, Tanzania
| | - Martha F Mushi
- Quality Assurance & Training Centre, National Health Laboratory, P. O. Box 9083, Dar Es Salaam, Tanzania
| | - Lucas Matemba
- National Institute for Medical Research, P. O. Box 805, Dodoma, Tanzania
| | - Jeremiah Seni
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences-Bugando, P. O. Box 1464, Mwanza, Tanzania
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences-Bugando, P. O. Box 1464, Mwanza, Tanzania
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Sindato C, Mboera LEG, Katale BZ, Frumence G, Kimera S, Clark TG, Legido-Quigley H, Mshana SE, Rweyemamu MM, Matee M. Knowledge, attitudes and practices regarding antimicrobial use and resistance among communities of Ilala, Kilosa and Kibaha districts of Tanzania. Antimicrob Resist Infect Control 2020; 9:194. [PMID: 33287878 PMCID: PMC7720393 DOI: 10.1186/s13756-020-00862-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/22/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) represents one of the biggest threats to health globally. This cross-sectional study determined knowledge, attitudes and practices (KAP) regarding antimicrobial use (AMU) and AMR among communities of Ilala, Kilosa and Kibaha in Tanzania. METHOD A semi-structured questionnaire was used to collect socio-demographic and KAP data through face-to-face interviews. Responses related to the triad of KAP were assigned scores that were aggregated for each participant. Linear regression analysis was conducted to determine predictors of KAP scores. RESULTS The study enrolled 828 participants from the three districts. A total of 816 (98.6%) were aware of antimicrobials, and 808 (99%, n = 816) reported to have used them. Antimicrobials were mainly used to treat cough (68.0%), urinary tract infections (53.4%), diarrhoea (48.5%) and wounds (45.2%). The most frequent sources of antimicrobials were health facility (65.0%, n = 820) and pharmacies/basic drug shops (53.7%). The median AMU knowledge score was 5 (IQR = 4, 7) and that of AMR was 26 (IQR=23, 29). The median AMU attitudes score was 32 (IQR: 29, 35) and that of AMR was 19 (IQR=17, 22). The median AMU practice score was 3 (IQR: 3, 3). The KAP scores were significantly influenced by increased participant's age (βadj=0.10; 95% CI: 0.05, 0.15) and level of education, being lower among those with primary education (βadj=5.32; 95% CI: 3.27, 7.37) and highest among those with college/university education (βadj=9.85; 95% CI: 6.04, 13.67). CONCLUSION The study documented a moderate level of KAP regarding AMU and AMR in the study districts. The participant's age and level of education were significantly associated with participant's KAP scores. The observed inadequate knowledge, inappropriate attitude, and practices of AMU and AMR should be considered as alarming problems that require immediate actions including policy formulation and planning of community-based mitigation measures.
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Affiliation(s)
- Calvin Sindato
- National Institute for Medical Research, Tabora Research Centre, Tabora, Tanzania.
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania.
| | - Leonard E G Mboera
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Bugwesa Z Katale
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
- Tanzania Commission for Science and Technology, Dar es Salaam, Tanzania
| | - Gasto Frumence
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Sharadhuli Kimera
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
- College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Stephen E Mshana
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
- Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Mark M Rweyemamu
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Mecky Matee
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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Kimera ZI, Frumence G, Mboera LEG, Rweyemamu M, Mshana SE, Matee MIN. Assessment of Drivers of Antimicrobial Use and Resistance in Poultry and Domestic Pig Farming in the Msimbazi River Basin in Tanzania. Antibiotics (Basel) 2020; 9:antibiotics9120838. [PMID: 33255152 PMCID: PMC7760815 DOI: 10.3390/antibiotics9120838] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/23/2020] [Accepted: 10/28/2020] [Indexed: 11/22/2022] Open
Abstract
Uncontrolled use of drugs both in humans and animals coupled with environmental contamination exacerbate the development and spread of antimicrobial resistance. This paper assessed the drivers of antimicrobial use and resistance in poultry and domestic pig farming and the environment. Questionnaires, in-depth interviews, and focus group discussions (FGDs) were used to collect information regarding demographic characteristics, knowledge, practices, attitudes, and perceptions of the drivers of antimicrobial use and resistance in animal farming and the environment. We found a higher proportion of usage of veterinary antimicrobials for prophylactic purposes (87.6%) in animal farming, than for therapeutic purposes (80.5%). The degree of farming experience was significantly (p < 0.05) related to the knowledge on the source of antimicrobial use, methods used in disease diagnosis, access to veterinary services, stocking of antimicrobials at home, and presence of agriculture activities that involve the use of manure. Uncontrolled disposal of wastes from households, disposal of human and veterinary drugs, and weak implementation of the legal framework was identified as the major contributors to the environment. The high usage of veterinary antimicrobials and the environmental contamination identified requires multisectoral interventions, as well as a review of government strategies, policies, and regulations on antimicrobial use.
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Affiliation(s)
- Zuhura I. Kimera
- Muhimbili University of Health and Allied Sciences, P.O. Box 65001, 11103 Dar es Salaam, Tanzania; (G.F.); (M.I.N.M.)
- Ministry of Livestock and Fisheries, Mtumba Area, P.O. Box 2182, 40487 Dodoma, Tanzania
- Correspondence:
| | - Gasto Frumence
- Muhimbili University of Health and Allied Sciences, P.O. Box 65001, 11103 Dar es Salaam, Tanzania; (G.F.); (M.I.N.M.)
| | - Leonard E. G. Mboera
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297, 67125 Morogoro, Tanzania; (L.E.G.M.); (M.R.)
| | - Mark Rweyemamu
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297, 67125 Morogoro, Tanzania; (L.E.G.M.); (M.R.)
| | - Stephen E. Mshana
- Catholic University of Health and Allied Sciences, P.O. Box 1464, 33109 Mwanza, Tanzania;
| | - Mecky I. N. Matee
- Muhimbili University of Health and Allied Sciences, P.O. Box 65001, 11103 Dar es Salaam, Tanzania; (G.F.); (M.I.N.M.)
- SACIDS Africa Centre of Excellence for Infectious Diseases, Sokoine University of Agriculture, P.O. Box 3297, 67125 Morogoro, Tanzania; (L.E.G.M.); (M.R.)
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Divya PS, Thajudeen J, Yousuf J, Madavan A, Abdulla MH. Genetic relatedness, phylogenetic groups, antibiotic resistance, and virulence genes associated with ExPEC in
Escherichia coli
isolates from finfish and shellfish. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Puthenkandathil Sukumaran Divya
- Department of Marine Biology, Microbiology and Biochemistry School of Marine Sciences Cochin University of Science and Technology Cochin India
| | - Jabir Thajudeen
- Department of Marine Biology, Microbiology and Biochemistry School of Marine Sciences Cochin University of Science and Technology Cochin India
| | - Jesmi Yousuf
- Department of Marine Biology, Microbiology and Biochemistry School of Marine Sciences Cochin University of Science and Technology Cochin India
| | - Anand Madavan
- School of Environmental Studies Cochin University of Science and Technology Cochin India
| | - Mohamed Hatha Abdulla
- Department of Marine Biology, Microbiology and Biochemistry School of Marine Sciences Cochin University of Science and Technology Cochin India
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Sivaraman GK, Sudha S, Muneeb KH, Shome B, Holmes M, Cole J. Molecular assessment of antimicrobial resistance and virulence in multi drug resistant ESBL-producing Escherichia coli and Klebsiella pneumoniae from food fishes, Assam, India. Microb Pathog 2020; 149:104581. [PMID: 33080358 DOI: 10.1016/j.micpath.2020.104581] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023]
Abstract
The present study investigated the prevalence of Extended-Spectrum Beta Lactamase (ESBL) -producing E. coli and K. pneumoniae from the food fishes in retail markets in Assam, India. A total of 54 ESBL-producing E. coli and 12 K. pneumoniae isolates were recovered from 79 fish samples and were analyzed for antimicrobial resistance genes (ARGs) and virulence genes. E. coli isolates were categorized as multi drug resistant with resistance up to 12 different antibiotics with multiple antibiotic resistances (MAR) index ranging from 0.26 to 0.63. In E. coli, 100% resistance to cefotaxime along with 6% resistance to ceftazidime (third-generation cephalosporins) was observed. Moreover, 85% of the E. coli isolates were resistant to cefepime, a fourth-generation cephalosporin. K. pneumoniae showed resistance to 11 different antibiotics with MAR index value ranging from 0.21 to 0.57. All K. pneumoniae isolates showed 100% resistance to cefotaxime, 67% resistance to ceftazidime and 75% resistance to cefepime. Molecular characterization of ARGs revealed the presence of CTX-M group 1(CTX-M-15) in almost all E. coli isolates (98%, n = 53) and 100% in K. pneumoniae. A combination of uniplex and multiplex PCRs revealed fewer ARGs in E. coli isolates, with each isolate carrying 3 to 5 genes (tetA, dfrA1, sul1, sul2, qnrB, qnrS, aac(6')-Ib-cr). Majority of the E. coli were assigned to low-virulence phylogroup B1 and A while 8% of them belonged to pathogenic phylogroup D. 31 unique genetic profiles were identified for E. coli isolates by Pulsed-Field Gel Electrophoresis (PFGE) typing. K. pneumoniae isolates were highly diverse with 11 unique genetic profiles and a substantial ARG profile (blaTEM, blaSHV, blaOXA-1-like, tetA, strA, strB, dfrA1, sul1, sul2, qnrB, qnrS, aac(6')-Ib-cr, oqxA, oqxB). The frequency of ARGs ranged between 4 and 11. All K. pneumoniae isolates belonged to capsular serotype with wzi gene. Virulence gene iutA was prominent in all isolates while ybtS and kfu were confirmed in two isolates. Our findings raise concerns that fishes bought for consumption may serve as potential reservoirs of AMR genes and pose serious threat to public health. The study emphasizes the need for extensive surveillance of resistant strains in aquaculture and related settings, their in-depth analysis of population structure and transmission dynamics.
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Affiliation(s)
- G K Sivaraman
- Microbiology Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Kochi, India.
| | - S Sudha
- Microbiology Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Kochi, India
| | - K H Muneeb
- Microbiology Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Kochi, India
| | - Bibek Shome
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bangalore, India
| | - Mark Holmes
- Department of Veterinary Medicine, University of Cambridge, UK
| | - Jennifer Cole
- Department of Geography, Royal Holloway, University of London, UK.PhD Principal Scientist & Principal Investigator, Microbiology Fermentation and Biotechnology Division ICAR-Central Institute of Fisheries Technology, Matsyapuri P. O, Willingdon Island Kochi, 682 029, India
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Ayeni FA, Falgenhauer J, Schmiedel J, Schwengers O, Chakraborty T, Falgenhauer L. Detection of blaCTX-M-27-encoding Escherichia coli ST206 in Nigerian poultry stocks. J Antimicrob Chemother 2020; 75:3070-3072. [PMID: 32688376 DOI: 10.1093/jac/dkaa293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Funmilola A Ayeni
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Judith Schmiedel
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Oliver Schwengers
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany.,Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University, Giessen, Germany.,German Center for Infection Research, Partner site Giessen-Marburg-Langen, Giessen, Germany
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Katale BZ, Misinzo G, Mshana SE, Chiyangi H, Campino S, Clark TG, Good L, Rweyemamu MM, Matee MI. Genetic diversity and risk factors for the transmission of antimicrobial resistance across human, animals and environmental compartments in East Africa: a review. Antimicrob Resist Infect Control 2020; 9:127. [PMID: 32762743 PMCID: PMC7409632 DOI: 10.1186/s13756-020-00786-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/21/2020] [Indexed: 12/30/2022] Open
Abstract
Background The emergence and spread of antimicrobial resistance (AMR) present a challenge to disease control in East Africa. Resistance to beta-lactams, which are by far the most used antibiotics worldwide and include the penicillins, cephalosporins, monobactams and carbapenems, is reducing options for effective control of both Gram-positive and Gram-negative bacteria. The World Health Organization, Food and Agricultural Organization and the World Organization for Animal Health have all advocated surveillance of AMR using an integrated One Health approach. Regional consortia also have strengthened collaboration to address the AMR problem through surveillance, training and research in a holistic and multisectoral approach. This review paper contains collective information on risk factors for transmission, clinical relevance and diversity of resistance genes relating to extended-spectrum beta-lactamase-producing (ESBL) and carbapenemase-producing Enterobacteriaceae, and Methicillin-resistant Staphylococcus aureus (MRSA) across the human, animal and environmental compartments in East Africa. Main body The review of the AMR literature (years 2001 to 2019) was performed using search engines such as PubMed, Scopus, Science Direct, Google and Web of Science. The search terms included ‘antimicrobial resistance and human-animal-environment’, ‘antimicrobial resistance, risk factors, genetic diversity, and human-animal-environment’ combined with respective countries of East Africa. In general, the risk factors identified were associated with the transmission of AMR. The marked genetic diversity due to multiple sequence types among drug-resistant bacteria and their replicon plasmid types sourced from the animal, human and environment were reported. The main ESBL, MRSA and carbapenem related genes/plasmids were the blaCTX-Ms (45.7%), SCCmec type III (27.3%) and IMP types (23.8%), respectively. Conclusion The high diversity of the AMR genes suggests there may be multiple sources of resistance bacteria, or the possible exchange of strains or a flow of genes amongst different strains due to transfer by mobile genetic elements. Therefore, there should be harmonized One Health guidelines for the use of antibiotics, as well as regulations governing their importation and sale. Moreover, the trend of ESBLs, MRSA and carbapenem resistant (CAR) carriage rates is dynamic and are on rise over time period, posing a public health concern in East Africa. Collaborative surveillance of AMR in partnership with regional and external institutions using an integrated One Health approach is required for expert knowledge and technology transfer to facilitate information sharing for informed decision-making.
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Affiliation(s)
- Bugwesa Z Katale
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania. .,Tanzania Commission for Science and Technology, Dar es Salaam, Tanzania. .,SACIDS Foundation for One Health (SACIDS), Sokoine University of Agriculture, Morogoro, Tanzania.
| | - Gerald Misinzo
- SACIDS Foundation for One Health (SACIDS), Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Stephen E Mshana
- SACIDS Foundation for One Health (SACIDS), Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Harriet Chiyangi
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,SACIDS Foundation for One Health (SACIDS), Sokoine University of Agriculture, Morogoro, Tanzania
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.,Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Liam Good
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | - Mark M Rweyemamu
- SACIDS Foundation for One Health (SACIDS), Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Mecky I Matee
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,SACIDS Foundation for One Health (SACIDS), Sokoine University of Agriculture, Morogoro, Tanzania
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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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Silago V, Kovacs D, Msanga DR, Seni J, Matthews L, Oravcová K, Zadoks RN, Lupindu AM, Hoza AS, Mshana SE. Bacteremia in critical care units at Bugando Medical Centre, Mwanza, Tanzania: the role of colonization and contaminated cots and mothers' hands in cross-transmission of multidrug resistant Gram-negative bacteria. Antimicrob Resist Infect Control 2020; 9:58. [PMID: 32375857 PMCID: PMC7201549 DOI: 10.1186/s13756-020-00721-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022] Open
Abstract
Background Multidrug resistance (MDR) is a major clinical problem in tertiary hospitals in Tanzania and jeopardizes the life of neonates in critical care units (CCUs). To better understand methods for prevention of MDR infections, this study aimed to determine, among other factors, the role of MDR-Gram-negative bacteria (GNB) contaminating neonatal cots and hands of mothers as possible role in transmission of bacteremia at Bugando Medical Centre (BMC), Mwanza, Tanzania. Methods This cross-sectional, hospital-based study was conducted among neonates and their mothers in a neonatal intensive care unit and a neonatology unit at BMC from December 2018 to April 2019. Blood specimens (n = 200) were sub-cultured on 5% sheep blood agar (SBA) and MacConkey agar (MCA) plates. Other specimens (200 neonatal rectal swabs, 200 maternal hand swabs and 200 neonatal cot swabs) were directly inoculated on MCA plates supplemented with 2 μg/ml cefotaxime (MCA-C) for screening of GNB resistant to third generation cephalosporins, r-3GCs. Conventional biochemical tests, Kirby-Bauer technique and resistance to cefoxitin 30 μg were used for identification of bacteria, antibiotic susceptibility testing and detection of MDR-GNB and screening of potential Amp-C beta lactamase producing GNB, respectively. Results The prevalence of culture confirmed bacteremia was 34.5% of which 85.5% were GNB. Fifty-five (93.2%) of GNB isolated from neonatal blood specimens were r-3GCs. On the other hand; 43% of neonates were colonized with GNB r-3GCs, 32% of cots were contaminated with GNB r-3GCs and 18.5% of hands of neonates’ mothers were contaminated with GNB r-3GCs. The prevalences of MDR-GNB isolated from blood culture and GNB r-3GCs isolated from neonatal colonization, cots and mothers’ hands were 96.6, 100, 100 and 94.6%, respectively. Significantly, cyanosis (OR[95%CI]: 3.13[1.51–6.51], p = 0.002), jaundice (OR[95%CI]: 2.10[1.07–4.14], p = 0.031), number of invasive devices (OR[95%CI]: 2.52[1.08–5.85], p = 0.031) and contaminated cot (OR[95%CI]: 2.39[1.26–4.55], p = 0.008) were associated with bacteremia due to GNB. Use of tap water only (OR[95%CI]: 2.12[0.88–5.09], p = 0.040) was protective for bacteremia due to GNB. Conclusion High prevalence of MDR-GNB bacteremia and intestinal colonization, and MDR-GNB contaminating cots and mothers’ hands was observed. Improved cots decontamination strategies is crucial to limit the spread of MDR-GNB. Further, clinical presentations and water use should be considered in administration of empirical therapy whilst awaiting culture results.
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Affiliation(s)
- Vitus Silago
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P. O. Box 1464, Bugando, Mwanza, Tanzania. .,Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P. O. Box 3000, Morogoro, Tanzania.
| | - Dory Kovacs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Delfina R Msanga
- Department of Pediatrics and Child Health, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P. O. Box 1464, Bugando, Mwanza, Tanzania
| | - Jeremiah Seni
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P. O. Box 1464, Bugando, Mwanza, Tanzania
| | - Louise Matthews
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Katarina Oravcová
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.,Sydney School of Veterinary Science, University of Sydney, Sydney, Australia
| | - Athumani M Lupindu
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P. O. Box 3000, Morogoro, Tanzania
| | - Abubakar S Hoza
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P. O. Box 3000, Morogoro, Tanzania
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, P. O. Box 1464, Bugando, Mwanza, Tanzania
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Ebomah KE, Okoh AI. An African perspective on the prevalence, fate and effects of carbapenem resistance genes in hospital effluents and wastewater treatment plant (WWTP) final effluents: A critical review. Heliyon 2020; 6:e03899. [PMID: 32420480 PMCID: PMC7215200 DOI: 10.1016/j.heliyon.2020.e03899] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/30/2020] [Accepted: 04/28/2020] [Indexed: 01/04/2023] Open
Abstract
This article provides an overview of the antibiotic era and discovery of earliest antibiotics until the present day state of affairs, coupled with the emergence of carbapenem-resistant bacteria. The ways of response to challenges of antibiotic resistance (AR) such as the development of novel strategies in the search of new antibiotics, designing more effective preventive measures as well as the ecology of AR have been discussed. The applications of plant extract and chemical compounds like nanomaterials which are based on recent developments in the field of antimicrobials, antimicrobial resistance (AMR), and chemotherapy were briefly discussed. The agencies responsible for environmental protection have a role to play in dealing with the climate crisis which poses an existential threat to the planet, and contributes to ecological support towards pathogenic microorganisms. The environment serves as a reservoir and also a vehicle for transmission of antimicrobial resistance genes hence, as dominant inhabitants we have to gain a competitive advantage in the battle against AMR.
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Affiliation(s)
- Kingsley Ehi Ebomah
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice 5700, South Africa
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, South Africa
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Kimera ZI, Mshana SE, Rweyemamu MM, Mboera LEG, Matee MIN. Antimicrobial use and resistance in food-producing animals and the environment: an African perspective. Antimicrob Resist Infect Control 2020; 9:37. [PMID: 32122406 PMCID: PMC7053060 DOI: 10.1186/s13756-020-0697-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/07/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The overuse of antimicrobials in food animals and the subsequent contamination of the environment have been associated with development and spread of antimicrobial resistance. This review presents information on antimicrobial use, resistance and status of surveillance systems in food animals and the environment in Africa. METHODS Information was searched through PubMed, Google Scholar, Web of Science, and African Journal Online databases. Full-length original research and review articles on antimicrobial use, prevalence of AMR from Africa covering a period from 2005 to 2018 were examined. The articles were scrutinized to extract information on the antimicrobial use, resistance and surveillance systems. RESULTS A total of 200 articles were recovered. Of these, 176 studies were included in the review while 24 articles were excluded because they were not relevant to antimicrobial use and/or resistance in food animals and the environment. The percentage of farms using antimicrobials in animal production ranged from 77.6% in Nigeria to 100% in Tanzania, Cameroon, Zambia, Ghana and Egypt. The most antibiotics used were tetracycline, aminoglycoside and penicillin groups. The percentage of multi drug resistant isolates ranged from 20% in Nigeria to 100% in South Africa, Zimbabwe and Tunisia. In the environment, percentage of multi drug resistant isolates ranged from 33.3% in South Africa to 100% in Algeria. None of the countries documented national antimicrobial use and resistance surveillance system in animals. CONCLUSION There is high level of antimicrobial use, especially tetracycline, aminoglycoside and penicillin in animal production systems in Africa. This is likely to escalate the already high prevalence of antimicrobial resistance and multi drug resistance in the continent. This, coupled with weak antimicrobial resistance surveillance systems in the region is a great concern to the animals, environment and humans as well.
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Affiliation(s)
- Zuhura I Kimera
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.
- Ministry of Livestock and Fisheries, Dodoma, Tanzania.
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Mark M Rweyemamu
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Chuo Kikuu Morogoro, Tanzania
| | - Leonard E G Mboera
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Chuo Kikuu Morogoro, Tanzania
| | - Mecky I N Matee
- Department of Microbiology and Immunology, School of Medicine, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Chuo Kikuu Morogoro, Tanzania
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Silago V, Mukama Y, Haule AL, Chacha F, Igenge J, Mushi MF, Mshana SE. Bacteriospermia, extended spectrum beta lactamase producing Gram-negative bacteria and other factors associated with male infertility in Mwanza, Tanzania: a need of diagnostic bacteriology for management of male infertility. Afr Health Sci 2020; 20:4-13. [PMID: 33402887 PMCID: PMC7750055 DOI: 10.4314/ahs.v20i1.4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Infections caused by Extended spectrum beta lactamase (ESBL) producing bacterial are global challenge. There is limited information on the magnitude of bacteriospermia, ESBL producing Gram-negative bacteria (GNB) causing bacteriospermia and factors associated with male infertility. This study determined magnitude of bacteriospermia, ESBL-GNB and other factors association with infertility among presumptive infertile men in Mwanza, Tanzania. Methods A cross-sectional hospital-based study was conducted between May 2017 and July 2018 among 137 presumptive infertile men. Semen specimens were self-collected by masturbation into clean, sterile and none-spermicidal containers and processed following laboratory standard operating procedures (SOPs). Data analysis was done using STATA 13.0. Results Gram-negative bacteria were predominantly isolated (86.4%), of which 31.6% were ESBL producers. In a total 44 bacteria were isolated from semen culture. The blaCTX-M gene was detected in 75% of phenotypically confirmed ESBL producers. Infertility was independently found to be associated with abnormal spermatozoa morphology (OR (95%CI): 14.48(3.17–66.05)) and abnormal spermatozoa motility (OR (95%CI): 0.05(0.01–0.24)). However, neither bacteriospermia (OR (95%CI): 0.86(0.29–2.59)) nor ESBL bacteriospermia (OR (95%CI): 0.13(0.01–1.22)) was found to be associated with infertility. Conclusion One third of bacteriospermia is due to ESBL-producers with history of antibiotic use being protective factor for infertility. Abnormal spermatozoa morphology and poor spermatozoa forward motility independently predicted infertility.
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Affiliation(s)
- Vitus Silago
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Bugando. P. O. Box 1464 Mwanza, Tanzania
| | - Yusuph Mukama
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Bugando. P. O. Box 1464 Mwanza, Tanzania
| | - Anna L Haule
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Bugando. P. O. Box 1464 Mwanza, Tanzania
| | - Frank Chacha
- Department of Urology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Bugando. P. O. Box 1464 Mwanza, Tanzania
| | - John Igenge
- Department of Urology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Bugando. P. O. Box 1464 Mwanza, Tanzania
| | - Martha F Mushi
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Bugando. P. O. Box 1464 Mwanza, Tanzania
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Bugando. P. O. Box 1464 Mwanza, Tanzania
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Baniga Z, Hounmanou YMG, Kudirkiene E, Kusiluka LJM, Mdegela RH, Dalsgaard A. Genome-Based Analysis of Extended-Spectrum β-Lactamase-Producing Escherichia coli in the Aquatic Environment and Nile Perch ( Lates niloticus) of Lake Victoria, Tanzania. Front Microbiol 2020; 11:108. [PMID: 32153519 PMCID: PMC7046833 DOI: 10.3389/fmicb.2020.00108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL)-producing bacteria constitute an emerging global health issue with food products being vehicles of transmission and the aquatic environments serving as potential reservoirs. This study aimed to characterize ESBL-producing Escherichia coli in Nile perch and water from Lake Victoria in Tanzania. A total of 180 samples of Nile perch and 60 water samples were screened for ESBL-producing E. coli on MacConkey agar supplemented with 2 μg/ml of cefotaxime and confirmed by blaCTX–M and blaTEM PCR. Antimicrobial resistance was determined by the disk diffusion method, and the ESBL-producing isolates were whole genome sequencing (WGS). ESBL-producing E. coli were detected in eight of the 180 analyzed Nile perch samples, and only one water sample was positive (1.7%, n = 60). Isolates were resistant to sulfamethoxazole–trimethoprim (100%), ampicillin/cloxacillin (100%), erythromycin 72.7% (8/11), tetracycline 90.9% (10/11), and nalidixic acid 63.6% (7/11). This mostly corroborates the resistance genes that they carried for sulfonamides (sul1 and sul2), trimethoprim (dfrA and dfrB), aminoglycosides [aac(3)-IId, strA, and strB], tetracycline [tet(B) and tet(D)], and fluoroquinolones (qepA4). They harbored plasmid replicon types IncF, IncX, IncQ, and Col and carried blaCTX–M–15 and blaTEM–1B genes generally found on the same contigs as the IncF plasmid replicon. Although epidemiologically unrelated, the strains formed three separate sequence type–phylogroup–serotype-specific clusters: C1, C2, and C3. Cluster C1 included five strains (3 to 13 SNPs) belonging to ST167, phylogroup A, and serotype O9:H21; the two C2 strains (11 SNPs) belong to ST156, phylogroup B1, and serotype ONT:H28; and C3 was made up of four strains (SNPs ranged from 4 to 17) of ST636, phylogroup B2, and serotype O45:H7. The common virulence gene gad was reported in all strains. In addition, strains in C2 and C3 possessed iss, lpfA, and nfaE virulence genes, and the vat gene was found only in C3. The present study reports the occurrence of multidrug-resistant ESBL-producing E. coli carrying plasmid-mediated ESBL genes in offshore water and Nile perch in Lake Victoria. Strains formed three clonal clusters of unknown origin. This study reveals that the Lake may serve as reservoir for ESBL-producing bacteria that can be transmitted by fish as a food chain hazard of One-Health concern.
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Affiliation(s)
- Zebedayo Baniga
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Fisheries Development, National Fish Quality Control Laboratory-Nyegezi, Mwanza, Tanzania
| | - Yaovi M Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Egle Kudirkiene
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lughano J M Kusiluka
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania.,Mzumbe University, Mzumbe, Tanzania
| | - Robinson H Mdegela
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
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Characterization of ESBL-Producing Enterobacteria from Fruit Bats in an Unprotected Area of Makokou, Gabon. Microorganisms 2020; 8:microorganisms8010138. [PMID: 31963801 PMCID: PMC7022737 DOI: 10.3390/microorganisms8010138] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 01/09/2023] Open
Abstract
In Gabon, terrestrial mammals of protected areas have been identified as a possible source of antibiotic-resistant bacteria. Some studies on antibiotic resistance in bats have already been carried out. The main goal of our study was to detect extended-spectrum beta-lactamases (ESBLs) that are produced by enterobacteria from bats in the Makokou region in Gabon. Sixty-eight fecal samples were obtained from 68 bats caught in the forests located 1 km from the little town of Makokou. After culture and isolation, 66 Gram-negative bacterial colonies were obtained. The double-disk diffusion test confirmed the presence of ESBLs in six (20.69%) Escherichia coli isolates, four (13.79%) Klebsiella pneumoniae isolates, and one (3.45%) Enterobacter cloacae isolate. The analysis based on the nucleotide sequences of the ESBL resistance genes showed that all cefotaximase-Munichs (CTX-Ms) were CTX-M-15 and that all sulfhydryl variables (SHVs) were SHV-11: 41.67% CTX-M-15-producing E. coli, 16.67% CTX-M-15+SHV-11-producing E. coli, 8.33% CTX-M-15-producing K. pneumoniae, 25% CTX-M-15+SHV-11-producing K. pneumoniae, and 8.33% CTX-M-15-produced E. cloacae. This study shows for the first time the presence of multiresistant ESBL-producing enterobacteria in fruit bats in Makokou.
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Abstract
While the description of resistance to quinolones is almost as old as these antimicrobial agents themselves, transferable mechanisms of quinolone resistance (TMQR) remained absent from the scenario for more than 36 years, appearing first as sporadic events and afterward as epidemics. In 1998, the first TMQR was soundly described, that is, QnrA. The presence of QnrA was almost anecdotal for years, but in the middle of the first decade of the 21st century, there was an explosion of TMQR descriptions, which definitively changed the epidemiology of quinolone resistance. Currently, 3 different clinically relevant mechanisms of quinolone resistance are encoded within mobile elements: (i) target protection, which is mediated by 7 different families of Qnr (QnrA, QnrB, QnrC, QnrD, QnrE, QnrS, and QnrVC), which overall account for more than 100 recognized alleles; (ii) antibiotic efflux, which is mediated by 2 main transferable efflux pumps (QepA and OqxAB), which together account for more than 30 alleles, and a series of other efflux pumps (e.g., QacBIII), which at present have been sporadically described; and (iii) antibiotic modification, which is mediated by the enzymes AAC(6')Ib-cr, from which different alleles have been claimed, as well as CrpP, a newly described phosphorylase.
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Mainda G, Lupolova N, Sikakwa L, Richardson E, Bessell PR, Malama SK, Kwenda G, Stevens MP, Bronsvoort BMD, Muma JB, Gally DL. Whole Genome Sequence Analysis Reveals Lower Diversity and Frequency of Acquired Antimicrobial Resistance (AMR) Genes in E. coli From Dairy Herds Compared With Human Isolates From the Same Region of Central Zambia. Front Microbiol 2019; 10:1114. [PMID: 31214130 PMCID: PMC6555227 DOI: 10.3389/fmicb.2019.01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/02/2019] [Indexed: 11/19/2022] Open
Abstract
Antibiotic treatment of sick dairy cattle is critical for the sustainability of this production system which is vital for food security and societal prosperity in many low and middle-income countries. Given the increasingly high levels of antibiotic resistance worldwide and the challenge this presents for the treatment of bacterial infections, the rational use of antibiotics in humans and animals has been emphatically recommended in the spirit of a “One Health” approach. The aim of this study was to characterize antimicrobial resistance (AMR) genes and their frequencies from whole genome sequences of Escherichia coli isolated from both dairy cattle and human patients in central Zambia. Whole genome sequences of E. coli isolates from dairy cattle (n = 224) and from patients at a local hospital (n = 73) were compared for the presence of acquired AMR genes. In addition we analyzed the publicly available genomes of 317 human E. coli isolates from over the wider African continent. Both acquired antibiotic resistance genes and phylogroups were identified from de novo assemblies and SNP based phylogenetic analyses were used to visualize the distribution of resistance genes in E. coli isolates from the two hosts. Greater acquired AMR gene diversity was detected in human compared to bovine E. coli isolates across multiple classes of antibiotics with particular resistance genes for extended-spectrum beta lactamases (ESBL), quinolones, macrolides and fosfomycin only detected in E. coli genomes of human origin. The striking difference was that the Zambian or wider African human isolates were significantly more likely to possess multiple acquired AMR genes compared to the Zambian dairy cattle isolates. The median number of resistance genes in the Zambian cattle cohort was 0 (0–1 interquartile range), while in the Zambian human and wider African cohorts the medians and interquartile ranges were 6 (4–9) and 6 (0–8), respectively. The lower frequency and reduced diversity of acquired AMR genes in the dairy cattle isolates is concordant with relatively limited antibiotic use that we have documented in this region, especially among smallholder farmers. The relatively distinct resistant profiles in the two host populations also indicates limited sharing of strains or genes.
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Affiliation(s)
- Geoffrey Mainda
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.,Department of Veterinary Services, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | - Nadejda Lupolova
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Linda Sikakwa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Emily Richardson
- MicrobesNG, University of Birmingham, Birmingham, United Kingdom
| | - Paul R Bessell
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Sydney K Malama
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Geoffrey Kwenda
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Mark P Stevens
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Barend M deC Bronsvoort
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - John B Muma
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - David L Gally
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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Zou H, Zheng B, Sun M, Ottoson J, Li Y, Berglund B, Chi X, Ji X, Li X, Stålsby Lundborg C, Nilsson LE. Evaluating Dissemination Mechanisms of Antibiotic-Resistant Bacteria in Rural Environments in China by Using CTX-M-Producing Escherichia coli as an Indicator. Microb Drug Resist 2019; 25:975-984. [PMID: 30942653 DOI: 10.1089/mdr.2018.0431] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
It is becoming increasingly recognized that the environment plays an important role both in the emergence and in dissemination of antibiotic-resistant bacteria (ARB), Mechanisms and factors facilitating this development are, however, not yet well understood. The high detection rate of CTX-M genes in environmental sources provides an opportunity to explore this issue. In this study, 88 CTX-M-producing Escherichia coli were isolated from 30 pig feces samples from 30 pig farms and 201 environmental samples. CTX-M-producing E. coli was detected with the following frequencies in the different types of samples: pig feces, 73%; river water, 64%; river sediment, 52%; wastewater, 31%; drinking water, 23%; outlet sediment, 21%; soil, 17%; and vegetables, 4.4%. Dissemination of CTX-M-producing E. coli to different environmental matrices was evaluated by analyzing the genetic relatedness of isolates from different environmental sources, and putative transmission routes through bird feces, pig feces, drinking water, river sediment, river water, and wastewater were hypothesized. Dissemination through these routes is likely facilitated by anthropogenic activities and environmental factors. Wild birds as potential vectors for dissemination of CTX-M-producing E. coli have the capacity to spread ARB across long distances. Regional dissemination between different environmental matrices of CTX-M-producing E. coli increases the exposure risk of humans and animals in the area.
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Affiliation(s)
- Huiyun Zou
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Mingli Sun
- Center of Disease Prevention and Control, Zhucheng City, Shandong Province, China
| | - Jakob Ottoson
- National Food Agency, Department of Risk and Benefit Assessment, Uppsala, Sweden
| | - Yubo Li
- Center of Disease Prevention and Control, Zhucheng City, Shandong Province, China
| | - Björn Berglund
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Xiaohui Chi
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Xiang Ji
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Cecilia Stålsby Lundborg
- Global Health-Health Systems and Policy: Medicines, Focusing Antibiotics, Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Lennart E Nilsson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
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Guo S, Tay MY, Aung KT, Seow KL, Ng LC, Purbojati RW, Drautz-Moses DI, Schuster SC, Schlundt J. Phenotypic and genotypic characterization of antimicrobial resistant Escherichia coli isolated from ready-to-eat food in Singapore using disk diffusion, broth microdilution and whole genome sequencing methods. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.12.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Bollache L, Bardet E, Depret G, Motreuil S, Neuwirth C, Moreau J, Hartmann A. Dissemination of CTX-M-Producing Escherichia coli in Freshwater Fishes From a French Watershed (Burgundy). Front Microbiol 2019; 9:3239. [PMID: 30671043 PMCID: PMC6331413 DOI: 10.3389/fmicb.2018.03239] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/13/2018] [Indexed: 01/13/2023] Open
Abstract
The burden of extended-spectrum β-lactamases producing Escherichia coli (ESBL-Ec), has increased over several decades. Freshwater ecosystems are suspected to play an important ecological and evolutionary role in driving the dissemination of antimicrobial resistance. The aim of our study was to decipher the occurrence of ESBL-Ec in a small watershed (Ouche river, Burgundy, France), targeting environmental matrices and fishes. Among cefotaxime resistant E. coli (ctxR Ec) isolates, we detected and characterized 36 ESBL-Ec from water, biofilm and fish guts. ctxR Ec and ESBL-Ec were found in samples from sites near the first small town, located downstream from the watershed which was studied. Treatment of urban wastewater by waste water treatment plants (WWTP), might therefore be a major potential source of ctxR Ec and thus of ESBL-Ec. Prevalence of total E. coli and ctxR Ec in fish guts ranged between 0 to 92% and 0 to 85%; respectively, depending on the sampling site and the fish species. The diet of fish (predator or omnivore) seems to strongly influence the prevalence of total E. coli and ESBL-Ec. Extended spectrum beta-lactamases produced by the isolates from this study belonged to the CTX-M family (CTX-M group 1 and 9). Moreover, some environmental ESBL-Ec proved to share genotypic features (MLST types) with isolates which originated from 8 WWTP effluents discharged in the Ouche river and with the sequence type ST131, which is widely described in clinical isolates. Ninety-seven % (97%) of ESBL-Ec from the study harbored additional antibiotic resistances and can thus be considered as multi drug resistant (MDR) bacteria. Finally, 53% of the ESBL-Ec strains harbored class 1 integron-integrase (intl1). These results are discussed with the perspective of defining indicators of antibiotic resistance contamination in freshwater ecosystems.
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Affiliation(s)
- Loic Bollache
- UMR CNRS 6249, Laboratoire Chrono-Environnement, Besançon, France
- Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne, Université de Bourgogne Franche-Comté, Dijon, France
| | - Emeline Bardet
- Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne, Université de Bourgogne Franche-Comté, Dijon, France
| | - Géraldine Depret
- Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne, Université de Bourgogne Franche-Comté, Dijon, France
| | | | - Catherine Neuwirth
- Bacteriology Department, University Hospital, Université de Bourgogne Franche-Comté, Dijon, France
| | - Jérome Moreau
- UMR CNRS 6282 Biogéosciences, Laboratoire Biogéosciences, Dijon, France
| | - Alain Hartmann
- Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne, Université de Bourgogne Franche-Comté, Dijon, France
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44
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Isolation, molecular characterization and antimicrobial resistance of enterobacteriaceae isolated from fish and seafood. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.01.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Oniciuc EA, Likotrafiti E, Alvarez-Molina A, Prieto M, Santos JA, Alvarez-Ordóñez A. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes (Basel) 2018; 9:E268. [PMID: 29789467 PMCID: PMC5977208 DOI: 10.3390/genes9050268] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.
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Affiliation(s)
- Elena A Oniciuc
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati 800008, Romania.
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Technology, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki T.K. 57400, Greece.
| | - Adrián Alvarez-Molina
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Miguel Prieto
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
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Bandyopadhyay S, Banerjee J, Bhattacharyya D, Samanta I, Mahanti A, Dutta TK, Ghosh S, Nanda PK, Dandapat P, Bandyopadhyay S. Genomic Identity of Fluoroquinolone-Resistant blaCTX-M-15-Type ESBL and pMAmpC β-Lactamase Producing Klebsiella pneumoniae from Buffalo Milk, India. Microb Drug Resist 2018; 24:1345-1353. [PMID: 29565231 DOI: 10.1089/mdr.2017.0368] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
We investigated the occurrence of extended-spectrum β-lactamase (ESBL) and AmpC-type β-lactamase (ACBL) producing quinolone-resistant Klebsiella pneumoniae (KP) in milk samples of apparently healthy buffaloes (n = 348) and buffaloes (n = 19) with evidence of subclinical mastitis from seven districts of West Bengal, India. In total, 12 ESBL producing KP were isolated with blaCTX-M-15 gene and 7 of them were ACBL producers, as well. The blaCTX-M-15 genes were carried by transposable element ISEcp1. The plasmid-mediated quinolone resistance genes-qnrS, qnrA, qnrB, qepA, and aac(6')-Ib-cr were detected in five, one, three, four, and one isolate (s), respectively. In addition, eight isolates carried mutation in gyrase (gyrA) and six in topoisomerase IV (parC). Resistance markers/genes for sulfonamide (sul1), tetracycline [tet(A) and tet(B)], and aminoglycoside (aacC2) were also detected in eight, four, and one isolate(s), respectively. The class I integrons identified in five isolates carried aad2/aad5 and dfrA12/dfrA17 gene cassettes. The enterobacterial repetitive intergenic consensus-PCR revealed that all the isolates were genetically diverse and comprised a heterogeneous population. Isolation of multidrug-resistant KP, a typical nosocomial pathogen from buffalo milk, reiterates the need to monitor farm animals for ESBL producing Enterobacteriaceae and emphasizes on judicious use of antibiotics in animal husbandry sector.
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Affiliation(s)
| | - Jaydeep Banerjee
- 1 ICAR-Indian Veterinary Research Institute , ERS, Kolkata, India
| | | | | | | | - Tapan K Dutta
- 3 Department of Veterinary Microbiology, CAU , Selesih, Aizawl, Mizoram, India
| | - Sarbaswarup Ghosh
- 4 Sasya Shyamala Krishi Vigyan Kendra, Ramakrishna Mission Vivekananda Educational and Research Institute , Arapanch, Sonarpur, Kolkata, India
| | - Pramod K Nanda
- 1 ICAR-Indian Veterinary Research Institute , ERS, Kolkata, India
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Emergence of an Extensively Drug-Resistant Salmonella enterica Serovar Typhi Clone Harboring a Promiscuous Plasmid Encoding Resistance to Fluoroquinolones and Third-Generation Cephalosporins. mBio 2018; 9:mBio.00105-18. [PMID: 29463654 PMCID: PMC5821095 DOI: 10.1128/mbio.00105-18] [Citation(s) in RCA: 349] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibiotic resistance is a major problem in Salmonella enterica serovar Typhi, the causative agent of typhoid. Multidrug-resistant (MDR) isolates are prevalent in parts of Asia and Africa and are often associated with the dominant H58 haplotype. Reduced susceptibility to fluoroquinolones is also widespread, and sporadic cases of resistance to third-generation cephalosporins or azithromycin have also been reported. Here, we report the first large-scale emergence and spread of a novel S Typhi clone harboring resistance to three first-line drugs (chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole) as well as fluoroquinolones and third-generation cephalosporins in Sindh, Pakistan, which we classify as extensively drug resistant (XDR). Over 300 XDR typhoid cases have emerged in Sindh, Pakistan, since November 2016. Additionally, a single case of travel-associated XDR typhoid has recently been identified in the United Kingdom. Whole-genome sequencing of over 80 of the XDR isolates revealed remarkable genetic clonality and sequence conservation, identified a large number of resistance determinants, and showed that these isolates were of haplotype H58. The XDR S Typhi clone encodes a chromosomally located resistance region and harbors a plasmid encoding additional resistance elements, including the blaCTX-M-15 extended-spectrum β-lactamase, and carrying the qnrS fluoroquinolone resistance gene. This antibiotic resistance-associated IncY plasmid exhibited high sequence identity to plasmids found in other enteric bacteria isolated from widely distributed geographic locations. This study highlights three concerning problems: the receding antibiotic arsenal for typhoid treatment, the ability of S Typhi to transform from MDR to XDR in a single step by acquisition of a plasmid, and the ability of XDR clones to spread globally.IMPORTANCE Typhoid fever is a severe disease caused by the Gram-negative bacterium Salmonella enterica serovar Typhi. Antibiotic-resistant S Typhi strains have become increasingly common. Here, we report the first large-scale emergence and spread of a novel extensively drug-resistant (XDR) S Typhi clone in Sindh, Pakistan. The XDR S Typhi is resistant to the majority of drugs available for the treatment of typhoid fever. This study highlights the evolving threat of antibiotic resistance in S Typhi and the value of antibiotic susceptibility testing and whole-genome sequencing in understanding emerging infectious diseases. We genetically characterized the XDR S Typhi to investigate the phylogenetic relationship between these isolates and a global collection of S Typhi isolates and to identify multiple genes linked to antibiotic resistance. This S Typhi clone harbored a promiscuous antibiotic resistance plasmid previously identified in other enteric bacteria. The increasing antibiotic resistance in S Typhi observed here adds urgency to the need for typhoid prevention measures.
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48
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Jørgensen SB, Søraas AV, Arnesen LS, Leegaard TM, Sundsfjord A, Jenum PA. A comparison of extended spectrum β-lactamase producing Escherichia coli from clinical, recreational water and wastewater samples associated in time and location. PLoS One 2017; 12:e0186576. [PMID: 29040337 PMCID: PMC5645111 DOI: 10.1371/journal.pone.0186576] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/03/2017] [Indexed: 01/09/2023] Open
Abstract
Extended spectrum β-lactamase producing Escherichia coli (ESBL-EC) are excreted via effluents and sewage into the environment where they can re-contaminate humans and animals. The aim of this observational study was to detect and quantify ESBL-EC in recreational water and wastewater, and perform a genetic and phenotypic comparative analysis of the environmental strains with geographically associated human urinary ESBL-EC. Recreational fresh- and saltwater samples from four different beaches and wastewater samples from a nearby sewage plant were filtered and cultured on differential and ESBL-selective media. After antimicrobial susceptibility testing and multi-locus variable number of tandem repeats assay (MLVA), selected ESBL-EC strains from recreational water were characterized by whole genome sequencing (WGS) and compared to wastewater and human urine isolates from people living in the same area. We detected ESBL-EC in recreational water samples on 8/20 occasions (40%), representing all sites. The ratio of ESBL-EC to total number of E. coli colony forming units varied from 0 to 3.8%. ESBL-EC were present in all wastewater samples in ratios of 0.56-0.75%. ST131 was most prevalent in urine and wastewater samples, while ST10 dominated in water samples. Eight STs and identical ESBL-EC MLVA-types were detected in all compartments. Clinical ESBL-EC isolates were more likely to be multidrug-resistant (p<0.001). This study confirms that ESBL-EC, including those that are capable of causing human infection, are present in recreational waters where there is a potential for human exposure and subsequent gut colonisation and infection in bathers. Multidrug-resistant E. coli strains are present in urban aquatic environments even in countries where antibiotic consumption in both humans and animals is highly restricted.
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Affiliation(s)
- Silje B. Jørgensen
- Section for Medical Microbiology, Department of Laboratory Medicine, Vestre Viken Hospital Trust, Bærum, Norway
- Department of Clinical Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- * E-mail:
| | - Arne V. Søraas
- Section for Medical Microbiology, Department of Laboratory Medicine, Vestre Viken Hospital Trust, Bærum, Norway
| | | | - Truls M. Leegaard
- Department of Clinical Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
| | - Pål A. Jenum
- Section for Medical Microbiology, Department of Laboratory Medicine, Vestre Viken Hospital Trust, Bærum, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Moremi N, Claus H, Vogel U, Mshana SE. Faecal carriage of CTX-M extended-spectrum beta-lactamase-producing Enterobacteriaceae among street children dwelling in Mwanza city, Tanzania. PLoS One 2017; 12:e0184592. [PMID: 28898269 PMCID: PMC5595323 DOI: 10.1371/journal.pone.0184592] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/25/2017] [Indexed: 01/20/2023] Open
Abstract
Background Data on ESBL carriage of healthy people including children are scarce especially in developing countries. We analyzed the prevalence and genotypes of ESBL-producing Enterobacteriaceae (EPE) in Tanzanian street children with rare contact to healthcare facilities but significant interactions with the environment, animals and other people. Methodology/ Principle findings Between April and July 2015, stool samples of 107 street children, who live in urban Mwanza were analyzed for EPE. Intestinal carriage of EPE was found in 34 (31.8%, 95% CI; 22.7–40.3) children. Of the 36 isolates from 34 children, 30 (83.3%) were Escherichia coli (E. coli) and six Klebsiella pneumoniae (K. pneumoniae). Out of 36 isolates, 36 (100%), 35 (97%), 25 (69%) and 16 (44%) were resistant to tetracycline, trimethoprim-sulfamethoxazole, ciprofloxacin and gentamicin, respectively. Beta-lactamase genes and the multilocus sequence types of E. coli and K. pneumoniae were characterized. ESBL gene blaCTX-M-15 was detected in 75% (27/36) of ESBL isolates. Sequence types (STs) 131, 10, 448 and 617 were the most prevalent in E. coli. Use of local herbs (OR: 3.5, 95% CI: 1.51–8.08, P = 0.003) and spending day and night on streets (OR: 3.6, 95% CI: 1.44–8.97, P = 0.005) were independent predictors of ESBL carriage. Conclusions/ Significance We observed a high prevalence of blaCTX-M-15 in EPE collected from street children in Tanzania. Detection of E. coli STs 131, 10, 38 and 648, which have been observed worldwide in animals and people, highlights the need for multidisciplinary approaches to understand the epidemiology and drivers of antimicrobial resistance in low-income countries.
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Affiliation(s)
- Nyambura Moremi
- Department of Microbiology and Immunology, Catholic University of Health and Allied SciencesBugando, Mwanza, Tanzania
- Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
- * E-mail: ,
| | - Heike Claus
- Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
| | - Ulrich Vogel
- Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
| | - Stephen E. Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied SciencesBugando, Mwanza, Tanzania
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50
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Seni J, Moremi N, Matee M, van der Meer F, DeVinney R, Mshana SE, D Pitout JD. Preliminary insights into the occurrence of similar clones of extended-spectrum beta-lactamase-producing bacteria in humans, animals and the environment in Tanzania: A systematic review and meta-analysis between 2005 and 2016. Zoonoses Public Health 2017; 65:1-10. [PMID: 28834351 DOI: 10.1111/zph.12387] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 11/26/2022]
Abstract
The emergence and spread of extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-PE) are complex and of the public health concern across the globe. This review aimed at assessing the ESBL-PE clones circulating in humans, animals and the environment to provide evidence-based insights for combating ESBL-PE using One Health approach. Systematic search from Medline/PubMed, Google Scholar and African Journals Online was carried out and retrieved nine eligible articles (of 131) based on phenotypic and genotypic detection of ESBL-PE between 2005 and 2016 in Tanzania. Analysis was performed using STATA 11.0 software to delineate the prevalence of ESBL-PE, phenotypic resistance profiles and clones circulating in the three interfaces. The overall prevalence of ESBL-PE in the three interfaces was 22.6% (95% CI: 21.1-24.2) with the predominance of Escherichia coli (E. coli) strains (51.6%). The majority of ESBL-PE were resistant to the commonly used antimicrobials such as trimethoprim-sulfamethoxazole and tetracycline/doxycycline, 38%-55% were resistant to ciprofloxacin and all were sensitive to meropenem/imipenem. ESBL-PE infections were more associated with deaths compared to non-ESBL-PE infections. Strikingly, E. coli ST38, ST131 and ST2852 were found to intersect variably across the three interfaces. The predominant allele, blaCTX-M-15, was found mostly in the conjugative IncF plasmids connoting transmission potential. The high prevalence of ESBL-PE and shared clones across the three interfaces, including the global E. coli ST131 clone, indicates wide and inter-compartmental spread that calls for One Health genomic-driven studies to track the resistome flow.
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Affiliation(s)
- J Seni
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania.,Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - N Moremi
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - M Matee
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es salaam, Tanzania
| | - F van der Meer
- Faculty of Veterinary Medicine: Ecosystem and Public Health, University of Calgary, Calgary, AB, Canada
| | - R DeVinney
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - S E Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - J D D Pitout
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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