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Liu C, Sun S, Sun Y, Li X, Gu W, Luo Y, Wang N, Wang Q. Antibiotic resistance of Escherichia coli isolated from food and clinical environment in China from 2001 to 2020. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 939:173498. [PMID: 38815827 DOI: 10.1016/j.scitotenv.2024.173498] [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: 03/26/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
Antibiotics are widely used in China's aquaculture, agricultural, and clinical settings and can lead to antibiotic resistance in various pathogens. Although the pooled prevalence estimate (PPE) and antibiotic resistance of Escherichia coli (E. coli) in food and clinical settings has been extensively studied, a comprehensive analysis of the published literature is lacking. We conducted a comprehensive search for research indicators for 2001-2020 in eight major Chinese and English literature databases. Antibiotic PPE and resistance trends of 5933 and 29,451 E. coli isolates were screened and analysed in 35 food studies (total 1821) and 62 clinical studies (total 5159). E. coli strains derived from food had the highest antibiotic resistance rate to tetracycline (TET, 71.3 %), followed by trimethoprim-sulfamethoxazole (SXT, 62.5 %) and cefazolin (CFZ, 36.2 %). E. coli strains isolated from clinical environments were highly resistant to piperacillin (PIP, 71.7 %), TET (68.3 %) and CFZ (60.9 %), consistent with foodborne E. coli drug resistance patterns. E. coli strains isolated from food and clinical samples collected in laboratories carry multiple antibiotic resistance genes (ARGs), such as blaTEM, gryA, gryB, sul1, and tetA, making E. coli a reservoir of ARGs. This study highlights the presence of drug-resistant E. coli pathogens and ARGs in food and clinical environments.
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Affiliation(s)
- Changzhen Liu
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei Engineering Research Center of Sewage Treatment and Resource Utilization, Hebei University of Engineering, Handan 056038, China
| | - Shaojing Sun
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei Engineering Research Center of Sewage Treatment and Resource Utilization, Hebei University of Engineering, Handan 056038, China
| | - Yan Sun
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei Engineering Research Center of Sewage Treatment and Resource Utilization, Hebei University of Engineering, Handan 056038, China
| | - Xuli Li
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei Engineering Research Center of Sewage Treatment and Resource Utilization, Hebei University of Engineering, Handan 056038, China
| | - Weimin Gu
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei Engineering Research Center of Sewage Treatment and Resource Utilization, Hebei University of Engineering, Handan 056038, China
| | - Yi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Na Wang
- Key Laboratory of Pesticide Environmental Assessment and Pollution Control, Nanjing Institute of Environmental Science, Ministry of Ecology and Environment of the People's Republic of China, Nanjing 210042, China
| | - Qing Wang
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact, Hebei Engineering Research Center of Sewage Treatment and Resource Utilization, Hebei University of Engineering, Handan 056038, China.
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Díaz-Torres O, Los Cobos EOVD, Kreft JU, Loge FJ, Díaz-Vázquez D, Mahlknecht J, Gradilla-Hernández MS, Senés-Guerrero C. A metagenomic study of antibiotic resistance genes in a hypereutrophic subtropical lake contaminated by anthropogenic sources. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172216. [PMID: 38583614 DOI: 10.1016/j.scitotenv.2024.172216] [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: 01/02/2024] [Revised: 03/18/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Antibiotic resistance genes (ARGs) are a major threat to human and environmental health. This study investigated the occurrence and distribution of ARGs in Lake Cajititlán, a hypereutrophic subtropical lake in Mexico contaminated by anthropogenic sources (urban wastewater and runoff from crop and livestock production). ARGs (a total of 475 genes) were detected in 22 bacterial genera, with Pseudomonas (144 genes), Stenotrophomonas (88 genes), Mycobacterium (54 genes), and Rhodococcus (27 genes) displaying the highest frequencies of ARGs. Among these, Pseudomonas aeruginosa and Stenotrophomonas maltophilia showed the highest number of ARGs. The results revealed a diverse array of ARGs, including resistance to macrolides (11.55 %), aminoglycosides (8.22 %), glycopeptides (6.22 %), tetracyclines (4 %), sulfonamides (4 %), carbapenems (1.11 %), phenicols (0.88 %), fluoroquinolones (0.44 %), and lincosamides (0.22 %). The most frequently observed ARGs were associated with multidrug resistance (63.33 %), with MexF (42 genes), MexW (36 genes), smeD (31 genes), mtrA (25 genes), and KHM-1 (22 genes) being the most common. Lake Cajititlán is a recreational area for swimming, fishing, and boating, while also supporting irrigation for agriculture and potentially acting as a drinking water source for some communities. This raises concerns about the potential for exposure to antibiotic-resistant bacteria through these activities. The presence of ARGs in Lake Cajititlán poses a significant threat to both human and environmental health. Developing strategies to mitigate the risks of antibiotic resistance, including improving wastewater treatment, and promoting strategic antibiotic use and disposal, is crucial. This study represents a significant advancement in the understanding of antibiotic resistance dynamics in a hypereutrophic subtropical lake in a developing country, providing valuable insights for the scientific community and policymakers.
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Affiliation(s)
- Osiris Díaz-Torres
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, Nuevo México, Zapopan, CP, 45138 Jalisco, México.
| | - Eric Oswaldo Valencia-de Los Cobos
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, Nuevo México, Zapopan, CP, 45138 Jalisco, México
| | - Jan-Ulrich Kreft
- Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Frank J Loge
- Department of Civil and Environmental Engineering, University of California Davis, One Shields Avenue, Davis, CA 95616, USA; Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Sada 2501 Sur, Monterrey, N.L. 64849, Mexico
| | - Diego Díaz-Vázquez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, Nuevo México, Zapopan, CP, 45138 Jalisco, México
| | - Jürgen Mahlknecht
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Sada 2501 Sur, Monterrey, N.L. 64849, Mexico
| | - Misael Sebastián Gradilla-Hernández
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, Nuevo México, Zapopan, CP, 45138 Jalisco, México.
| | - Carolina Senés-Guerrero
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Laboratorio de Sostenibilidad y Cambio Climático, Av. General Ramon Corona 2514, Nuevo México, Zapopan, CP, 45138 Jalisco, México.
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Suresh K, Pillai D. Prevalence of antimicrobial resistance, biofilm formation, efflux pump activity, and virulence capabilities in multi-drug-resistant Klebsiella pneumoniae isolated from freshwater fish farms. JOURNAL OF WATER AND HEALTH 2024; 22:721-734. [PMID: 38678425 DOI: 10.2166/wh.2024.382] [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: 12/19/2023] [Accepted: 03/25/2024] [Indexed: 04/30/2024]
Abstract
The present study aimed to determine the antibiotic resistance, underlying mechanisms, antibiotic residues, and virulence genes involved in 32 multi-drug-resistant Klebsiella pneumoniae isolates from freshwater fishes in Andhra Pradesh, India. Antibiogram studies revealed that all isolates were multi-drug-resistant, harbored tetA (96.8%), tetC (59.3%), tetD (71.9%), nfsA (59.3%), nfsB (53.1%), sul2 (68.7%), qnrC (43.7%), qnrD (50%), blaSHV (75%), blaTEM (68.7%), and blaCTX-M (93.7%) genes. Multiple antibiotic resistance index was calculated as 0.54. Sixteen isolates were confirmed to be hyper-virulent and harbored magA and rmpA genes. In total, 46.9, 31.2, and 21.9% of the isolates were categorized as strong, moderate, or weak biofilm formers, respectively. All isolates possessed an active efflux pump and harbored acrA, acrB, acrAB, and tolC genes in 94% of the isolates, followed by mdtK (56.2%). Porins such as ompK35 and ompK36 were detected in 59.3 and 62.5% of the isolates, respectively. Virulence genes fimH-1, mrkD, and entB were present in 84.3, 81.2, 87.5% of the isolates, respectively. These findings imply a potential threat that multi-drug-resistant bacterial pathogens could transmit to surrounding environments and humans through contaminated water and the aquaculture food chain.
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Affiliation(s)
- Kummari Suresh
- Department of Aquatic Animal Health Management, Faculty of Fisheries Science, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Faculty of Fisheries Science, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India E-mail: ;
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Jomehzadeh N, Ahmadi K, Ataee N, Afzali M. Molecular detection of genes encoding resistance to tetracycline and quinolones among Shigella strains isolated from children with acute diarrhea in southwest Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2023; 15:625-630. [PMID: 37941879 PMCID: PMC10628075 DOI: 10.18502/ijm.v15i5.13868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Background and Objectives An increase in the antibiotic resistance of Shigella isolates has caused major global challenges in antimicrobial therapy. Knowledge of local antibiotic resistance trends is essential for selecting appropriate antibiotic treatment regimens. This study aimed to evaluate the frequency of efflux-mediated tetracycline resistance (tet) and plasmid-mediated quinolone resistance (qnr) genes among Shigella isolates. Materials and Methods This survey investigated 91 Shigella isolates, obtained from children with acute diarrhea. The isolates were identified using standard biochemical tests and confirmed by polymerase chain reaction (PCR) assay. Besides, the susceptibility of isolates to six selected antibiotics was assessed by the disk diffusion method. All tetracycline-resistant and nalidixic acid and ciprofloxacin resistant strains were screened for tet and qnr genes by a multiplex PCR assay. Results According to the results of antibiotic susceptibility tests, the highest level of antibiotic resistance was related to tetracycline (80.2%) and doxycycline (78.1%), respectively. All isolates were sensitive to tigecycline. The PCR results showed that 40.6%, 3.1%, 21.8%, 61.6% and 28.7% of the isolates carried qnrA, qnrB, qnrS, tetA, and tetB genes, respectively. None of the isolates contained tetC and tetD genes. Conclusion The current findings revealed that tetA and qnrA genes might play a key role in conferring tetracycline and quinolone resistance.
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Affiliation(s)
- Nabi Jomehzadeh
- Department of Microbiology, School of Medicine, Abadan University of Medical Sciences, Abadan, Iran
| | - Khadijeh Ahmadi
- Department of Microbiology, School of Medicine, Abadan University of Medical Sciences, Abadan, Iran
| | - Nazanin Ataee
- Department of Biology, Kavian Institute of Higher Education, Mashhad, Iran
| | - Maryam Afzali
- Department of Microbiology, Faculty of Medicine, Mashhad Medical Sciences, Islamic Azad University, Mashhad, Iran
- Department of Laboratory Sciences, Faculty of Paramedicine, Mashhad Medical Sciences, Islamic Azad University, Mashhad, Iran
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Mkangara M. Prevention and Control of Human Salmonella enterica Infections: An Implication in Food Safety. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2023; 2023:8899596. [PMID: 37727836 PMCID: PMC10506869 DOI: 10.1155/2023/8899596] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 08/19/2023] [Accepted: 08/26/2023] [Indexed: 09/21/2023]
Abstract
Salmonella is a foodborne zoonotic pathogen causing diarrhoeal disease to humans after consuming contaminated water, animal, and plant products. The bacterium is the third leading cause of human death among diarrhoeal diseases worldwide. Therefore, human salmonellosis is of public health concern demanding integrated interventions against the causative agent, Salmonella enterica. The prevention of salmonellosis in humans is intricate due to several factors, including an immune-stable individual infected with S. enterica continuing to shed live bacteria without showing any clinical signs. Similarly, the asymptomatic Salmonella animals are the source of salmonellosis in humans after consuming contaminated food products. Furthermore, the contaminated products of plant and animal origin are a menace in food industries due to Salmonella biofilms, which enhance colonization, persistence, and survival of bacteria on equipment. The contaminated food products resulting from bacteria on equipment offset the economic competition of food industries and partner institutions in international business. The most worldwide prevalent broad-range Salmonella serovars affecting humans are Salmonella Typhimurium and Salmonella Enteritidis, and poultry products, among others, are the primary source of infection. The broader range of Salmonella serovars creates concern over multiple strategies for preventing and controlling Salmonella contamination in foods to enhance food safety for humans. Among the strategies for preventing and controlling Salmonella spread in animal and plant products include biosecurity measures, isolation and quarantine, epidemiological surveillance, farming systems, herbs and spices, and vaccination. Other measures are the application of phages, probiotics, prebiotics, and nanoparticles reduced and capped with antimicrobial agents. Therefore, Salmonella-free products, such as beef, pork, poultry meat, eggs, milk, and plant foods, such as vegetables and fruits, will prevent humans from Salmonella infection. This review explains Salmonella infection in humans caused by consuming contaminated foods and the interventions against Salmonella contamination in foods to enhance food safety and quality for humans.
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Affiliation(s)
- Mwanaisha Mkangara
- Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, P.O. Box 2958, Dar es Salaam, Tanzania
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Boraei-Nezhad G, Saadati D, Jahantigh M, Saadat-Jou S. Prevalence of Salmonella infection in village chickens and determination of the tetracycline resistance genes in the Salmonella isolates in the Sistan region, Iran. Braz J Microbiol 2023; 54:2375-2382. [PMID: 37418110 PMCID: PMC10484867 DOI: 10.1007/s42770-023-01033-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
Recently, an increasing number of multi drug resistant Salmonella species have been emerged due to overuse of antibiotics in veterinary and human medicine which has adverse consequences on public health. The present study was conducted with the aim of investigating the prevalence of Salmonella infection in village chickens in Sistan region and determining the prevalence of the antibiotic resistance genes in Salmonella isolated from these birds. In this study, 100 chickens were randomly selected from five counties of Sistan region. A cloacal swab sample was taken from each bird and also information about age, gender, breed, proximity with other birds, proximity with waterfowl, proximity with livestock, and receiving different antibiotics especially tetracycline were obtained using a questionnaire. Conventional culture methods used for Salmonella detection and isolation. Then, amplification of invA gene by PCR was used to confirm Salmonella colonies. Finally, 27 samples were confirmed to be infected with Salmonella by both culture and PCR methods. Disk diffusion method was used to determine the sensitivity to 4 antibiotics including; tetracycline, gentamicin, cefepime, and difloxacin. The results of the present study showed that proximity to waterfowl (OR = 0.273) significantly mitigates the risk of Salmonella infection. For the isolates, the highest resistance was recorded against cefepime and the highest susceptibility was to difloxacin. The presence proportion of tetA and tetB in tetracycline resistant isolates was higher than that in susceptible ones but this difference was not statistically significant.
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Affiliation(s)
| | - Dariush Saadati
- Department of Food Hygiene, Faculty of Veterinary Medicine, University of Zabol, Bonjar Road, Zabol, 9861335856, Iran.
| | - Mohammad Jahantigh
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Zabol, Zabol, Iran
| | - Samira Saadat-Jou
- DVM Graduated, Faculty of Veterinary Medicine, University of Tehran Veterinarian, Zabol, Iran
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Zaatout N, Al-Mustapha AI, Bouaziz A, Ouchene R, Heikinheimo A. Prevalence of AmpC, ESBL, and colistin resistance genes in Enterobacterales isolated from ready-to-eat food in Algeria. Braz J Microbiol 2023; 54:2205-2218. [PMID: 37526891 PMCID: PMC10484844 DOI: 10.1007/s42770-023-01082-3] [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: 02/24/2023] [Accepted: 07/23/2023] [Indexed: 08/02/2023] Open
Abstract
Antimicrobial resistance among bacteria present in ready-to-eat foods is an emerging concern. Hence, this study investigated the presence of extended-spectrum and AmpC β-lactamases (ESBL/AmpC)-producing Enterobacterales (ESBL-E) and the dissemination of mcr-1 in ESBL-E from ready-to-eat food samples (RTE) in Algeria. RTE food samples (n = 204) were aseptically collected and selectively cultured using MacConkey agar. The isolates were screened for ESBL production using the DDST test, confirmed ESBL-E isolates were identified using different conventional methods and MALDI-TOF MS, antibiotic susceptibility was determined using the disc diffusion and broth microdilution assay, ESBL-E isolates were analyzed for colistin and ESBL/AmpC encoding genes by PCR, and food samples were analyzed by univariate and multiple logistic regression. Overall, 48 (17.4%) of the 276 Enterobacterales were confirmed as ESBL producers, with a high prevalence in soups (40%), salads (25%), and cream-filled pastries (23.8%). Antibiotic susceptibility testing revealed that all the ESBL-E isolates were found multi-drug resistant. PCR revealed that blaTEM, blaCTX-M, blaCMY-2, blaOXA-1, and blaSHV were the most frequently detected. blaCTX-M-9 and blaCTX-M-1 were the predominant CTX-M types. Furthermore, four isolates were positive for mcr-1; three of them harbored the colistin resistance gene and ESBL/AmpC genes (2 E. cloacae and 1 S. enterica). To the best of our knowledge, this is the first report that detects the presence of the mcr-1 gene in ESBL-E strains isolated from RTE foods in Algeria. These findings suggest an urgent need for strict policies that prevent the spread and transmission of ESBL-E in food.
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Affiliation(s)
- Nawel Zaatout
- Faculty of Natural and Life Sciences, University of Batna 2, 05000, Batna, Algeria.
| | - Ahmad I Al-Mustapha
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ibadan, State, Oyo, Nigeria
- Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Services, Ilorin, Nigeria
| | - Amira Bouaziz
- Faculty of Natural and Life Sciences, University of Batna 2, 05000, Batna, Algeria
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Batna, Algeria
| | - Rima Ouchene
- Laboratory of Applied Microbiology, Faculty of Nature and Life Sciences, University of Bejaia, 06000, Bejaia, Algeria
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Finnish Food Authority, Seinäjoki, Finland
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Almansour AM, Alhadlaq MA, Alzahrani KO, Mukhtar LE, Alharbi AL, Alajel SM. The Silent Threat: Antimicrobial-Resistant Pathogens in Food-Producing Animals and Their Impact on Public Health. Microorganisms 2023; 11:2127. [PMID: 37763971 PMCID: PMC10537193 DOI: 10.3390/microorganisms11092127] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 09/29/2023] Open
Abstract
The emergence of antimicrobial resistance (AMR) is a global health problem without geographic boundaries. This increases the risk of complications and, thus, makes it harder to treat infections, which can result in higher healthcare costs and a greater number of deaths. Antimicrobials are often used to treat infections from pathogens in food-producing animals, making them a potential source of AMR. Overuse and misuse of these drugs in animal agriculture can lead to the development of AMR bacteria, which can then be transmitted to humans through contaminated food or direct contact. It is therefore essential to take multifaceted, comprehensive, and integrated measures, following the One Health approach. To address this issue, many countries have implemented regulations to limit antimicrobial use. To our knowledge, there are previous studies based on AMR in food-producing animals; however, this paper adds novelty related to the AMR pathogens in livestock, as we include the recent publications of this field worldwide. In this work, we aim to describe the most critical and high-risk AMR pathogens among food-producing animals, as a worldwide health problem. We also focus on the dissemination of AMR genes in livestock, as well as its consequences in animals and humans, and future strategies to tackle this threat.
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Affiliation(s)
- Ayidh M. Almansour
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia; (M.A.A.); (K.O.A.); (A.L.A.)
| | - Meshari A. Alhadlaq
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia; (M.A.A.); (K.O.A.); (A.L.A.)
| | - Khaloud O. Alzahrani
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia; (M.A.A.); (K.O.A.); (A.L.A.)
| | - Lenah E. Mukhtar
- Antimicrobial Resistance Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia;
| | - Abdulmohsen L. Alharbi
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia; (M.A.A.); (K.O.A.); (A.L.A.)
| | - Sulaiman M. Alajel
- Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh 11671, Saudi Arabia;
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Espinoza LL, Huamán DC, Cueva CR, Gonzales CD, León YI, Espejo TS, Monge GM, Alcántara RR, Hernández LM. Genomic analysis of multidrug-resistant Escherichia coli strains carrying the mcr-1 gene recovered from pigs in Lima-Peru. Comp Immunol Microbiol Infect Dis 2023; 99:102019. [PMID: 37473695 DOI: 10.1016/j.cimid.2023.102019] [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: 04/01/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/22/2023]
Abstract
Antibiotic resistance is a current problem that significantly impacts overall health. The dissemination of antibiotic resistance genes (ARGs) to urban areas primarily occurs through ARG-carrying bacteria present in the gut microbiota of animals raised in intensive farming settings, such as pig production. Hence, this study aimed to isolate and analyzed 87 Escherichia coli strains from pig fecal samples obtained from intensive farms in Lima Department. The isolates were subjected to Kirby-Bauer-Disk Diffusion Test and PCR for mcr-1 gene identification. Disk-diffusion assay revealed a high level of resistance among these isolates to oxytetracycline, ampicillin, cephalothin, chloramphenicol, ciprofloxacin, and doxycycline. PCR analysis identified the mcr-1 gene in 8% (7/87) E. coli isolates. Further, whole genome sequencing was conducted on 17 isolates, including multidrug resistance (MDR) E. coli and/or mcr-1 gene carriers. This analysis unveiled a diverse array of ARGs. Alongside the mcr-1 gene, the blaCTX-M55 gene was particularly noteworthy as it confers resistance to third generation cephalosporins, including ceftriaxone. MDR E. coli genomes exhibited other ARGs encoding resistance to fosfomycin (fosA3), quinolones (qnrB19, qnrS1, qnrE1), tetracyclines (tetA, tetB, tetD, tetM), sulfonamides (sul1, sul2, sul3), amphenicols (cmlA1, floR), lincosamides (inuE), as well as various aminoglycoside resistance genes. Additionally, Multi Locus Sequence Typing (MLST) revealed a high diversity of E. coli strains, including ST10, a pandemic clone. This information provides evidence of the dissemination of highly significant ARGs in public health. Therefore, it is imperative to implement measures aimed at mitigating and preventing the transmission of MDR bacteria carrying ARGs to urban environments.
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Affiliation(s)
- Luis Luna Espinoza
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Dennis Carhuaricra Huamán
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru; Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão 1010, São Paulo 05508-090, Brazil
| | - Carmen Rodríguez Cueva
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Carla Durán Gonzales
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Yennifer Ignación León
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Thalía Silvestre Espejo
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Geraldine Marcelo Monge
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Raúl Rosadio Alcántara
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Lenin Maturrano Hernández
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation [SANIGEN], Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru.
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Soares GG, Campanini EB, Ferreira RL, Damas MSF, Rodrigues SH, Campos LC, Galvão JD, Fuentes ASDC, Freire CCDM, Malavazi I, Pitondo-Silva A, da Cunha AF, Pranchevicius MCDS. Brevundimonas brasiliensis sp. nov.: a New Multidrug-Resistant Species Isolated from a Patient in Brazil. Microbiol Spectr 2023; 11:e0441522. [PMID: 37067439 PMCID: PMC10269605 DOI: 10.1128/spectrum.04415-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/17/2023] [Indexed: 04/18/2023] Open
Abstract
To increase knowledge on Brevundimonas pathogens, we conducted in-depth genomic and phenotypic characterization of a Brevundimonas strain isolated from the cerebrospinal fluid of a patient admitted in a neonatal intensive care unit. The strain was identified as a member of the genus Brevundimonas based on Vitek 2 system results and 16S rRNA gene sequencing and presented a multidrug resistance profile (MDR). Several molecular and biochemical tests were used to characterize and identify the species for in-depth results. The draft genome assembly of the isolate has a total length of 3,261,074 bp and a G+C of 66.86%, similar to other species of the genus. Multilocus sequence analysis, Type (Strain) Genome Server, digital DNA-DNA hybridization, and average nucleotide identity confirmed that the Brevundimonas sp. studied represents a distinct species, for which we propose the name Brevundimonas brasiliensis sp. nov. In silico analysis detected antimicrobial resistance genes (AMRGs) mediating resistance to β-lactams (penP, blaTEM-16, and blaBKC-1) and aminoglycosides [strA, strB, aac(6')-Ib, and aac(6')-Il]. We also found AMRGs encoding the AcrAB efflux pump that confers resistance to a broad spectrum of antibiotics. Colistin and quinolone resistance can be attributed to mutation in qseC and/or phoP and GyrA/GyrB, respectively. The Brevundimonas brasiliensis sp. nov. genome contained copies of type IV secretion system (T4SS)-type integrative and conjugative elements (ICEs); integrative mobilizable elements (IME); and Tn3-type and IS3, IS6, IS5, and IS1380 families, suggesting an important role in the development and dissemination of antibiotic resistance. The isolate presented a range of virulence-associated genes related to biofilm formation, adhesion, and invasion that can be relevant for its pathogenicity. Our findings provide a wealth of data to hinder the transmission of MDR Brevundimonas and highlight the need for monitoring and identifying new bacterial species in hospital environments. IMPORTANCE Brevundimonas species is considered an opportunistic human pathogen that can cause multiple types of invasive and severe infections in patients with underlying pathologies. Treatment of these pathogens has become a major challenge because many isolates are resistant to most antibiotics used in clinical practice. Furthermore, there are no consistent therapeutic results demonstrating the efficacy of antibacterial agents. Although considered a rare pathogen, recent studies have provided evidence of the emergence of Brevundimonas in clinical settings. Hence, we identified a novel pathogenic bacterium, Brevundimonas brasiliensis sp. nov., that presented a multidrug resistance (MDR) profile and carried diverse genes related to drug resistance, virulence, and mobile genetic elements. Such data can serve as a baseline for understanding the genomic diversity, adaptation, evolution, and pathogenicity of MDR Brevundimonas.
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Affiliation(s)
- Gabriela Guerrera Soares
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Roumayne Lopes Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | - Saulo Henrique Rodrigues
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | | | | | | | - Caio César de Melo Freire
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Iran Malavazi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - André Pitondo-Silva
- Programas de Pós-graduação em Odontologia e Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | | | - Maria-Cristina da Silva Pranchevicius
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Centro de Ciências Biológicas e da Saúde, Biodiversidade Tropical - BIOTROP, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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Mudenda S, Malama S, Munyeme M, Matafwali SK, Kapila P, Katemangwe P, Mainda G, Mukubesa AN, Hadunka MA, Muma JB. Antimicrobial resistance profiles of Escherichia coli isolated from laying hens in Zambia: implications and significance on one health. JAC Antimicrob Resist 2023; 5:dlad060. [PMID: 37223392 PMCID: PMC10202439 DOI: 10.1093/jacamr/dlad060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 04/27/2023] [Indexed: 05/25/2023] Open
Abstract
Background Antimicrobial resistance (AMR) has been deepening in the layer poultry sector in Zambia partly due to the inappropriate use of antimicrobials. Escherichia coli (E. coli), a commensal and zoonotic bacterium, can potentially be a source of AMR. Objectives This study assessed the phenotypic AMR profiles of E. coli isolated from the apparent health-laying hens in Lusaka and Copperbelt provinces of Zambia. Methods A cross-sectional study was conducted between September 2020 and April 2021 in which 365 cloacal swabs were collected from 77-layer farms based in Lusaka and Copperbelt provinces of Zambia. E. coli isolation and identification were done using cultural and biochemical properties and confirmed using the 16S rRNA gene sequencing. Antimicrobial susceptibility testing (AST) was done using the Kirby-Bauer disc-diffusion method. Data analysis was done using WHONET 2020 and Stata v.16.1. Results Of the 365 samples, E. coli was isolated from 92.9% (n = 339). The AMR was detected in 96.5% (n = 327) of the isolates, of which 64.6% (n = 219) were multidrug-resistant (MDR). E. coli was highly resistant to tetracycline (54.6%) and ampicillin (54%) but showed low resistance to meropenem (0.9%), ceftazidime (6.2%) and chloramphenicol (8.8%). Conclusion This study found a high prevalence of E. coli resistant to some commonly used antibiotics in poultry, which is a public health concern because of the potential contamination of eggs and layers of chicken meat that enter the food chain. Urgent attention is needed, including strengthening antimicrobial stewardship and surveillance programmes in layer poultry production in Zambia.
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Affiliation(s)
| | - Sydney Malama
- Department of Biological Sciences, School of Natural Sciences, University of Zambia, Lusaka, Zambia
| | - Musso Munyeme
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Scott Kaba Matafwali
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Penjaninge Kapila
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Patrick Katemangwe
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Geoffrey Mainda
- Department of Veterinary Services, Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka, Zambia
| | | | - Mwendalubi Albert Hadunka
- Department of Animal Health, Centre for Infectious Disease Research in Zambia (CIDRZ), Lusaka, Zambia
| | - John Bwalya Muma
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
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12
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Monyama MC, Taioe OM, Nkhebenyane JS, van Wyk D, Ramatla T, Thekisoe OMM. Bacterial Communities Associated with Houseflies ( Musca domestica L.) Inhabiting Hospices in South Africa. Microorganisms 2023; 11:1440. [PMID: 37374941 DOI: 10.3390/microorganisms11061440] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Houseflies are alleged reservoirs as well as vectors of human and animal pathogens, including bacteria, because they frequently have contact with animal excreta and decaying organic substances. The rapid adaptation process of ingested microbes in the insect gut may involve gene transfer, including antibiotic resistance determinants among different bacterial strains. Six hundred and fifty-seven (n = 657) houseflies were collected from hospices and were identified morphologically and genetically using the 16S rRNA, CO1, and ITS2 barcoding genes. This study also characterized the bacterial communities harboured by the captured houseflies using 16S rRNA metabarcoding on the next-generation sequencing (NGS) platform and further sought to detect antibiotic resistance traits by using gene-specific PCR assays. Generated sequences for the targeted gene fragments matched with Musca domestica and all the sequences were deposited to the GenBank database. The 16S rRNA metabarcoding analysis revealed that the most abundant phyla detected with variable abundance observed among all the houseflies were Proteobacteria, followed by Firmicutes, and Bacteroidetes. Furthermore, the NGS data revealed the presence of multiple bacterial genera, including Providencia, Enterobacter, Dysgonomonas, Escherichia-Shigella, Klebsiella, Pseudomonas, and Streptococcus, which are known to harbour potentially pathogenic species of animals and humans. Antibiotic resistance genes detected from the housefly DNA in this study included ermB, tetA, blaSHV, and blaTEM. Moreover, these genes are associated with resistance to erythromycin, tetracycline, and beta-lactams antibiotics, respectively. The presence of bacterial pathogens and the detection of antibiotic resistance genes from the houseflies collected from the hospices indicates the possible health risk to patients in hospices and the surrounding community. Therefore, it is imperative to keep high standards of hygiene, food preparation, safety, and control of houseflies in hospices.
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Affiliation(s)
- Maropeng C Monyama
- Department of Life and Consumer Sciences, University of South Africa, Florida 1710, South Africa
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Oriel M Taioe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
- Epidemiology, Parasites and Vectors, Agricultural Research Council-Onderstepoort Veterinary Research, Pretoria 0110, South Africa
| | - Jane S Nkhebenyane
- Department of Life Sciences, Central University of Technology, Bloemfontein 9300, South Africa
| | - Deidre van Wyk
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Tsepo Ramatla
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Oriel M M Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
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13
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My TT, Thien LV, Manh VD, My BTP, Lan DTM, Binh DX, Duc VM. Antimicrobial resistance and molecular characterization of Escherichia coli isolated from bovine mastitis samples in Nghe An province, Vietnam. Vet World 2023; 16:743-751. [PMID: 37235152 PMCID: PMC10206968 DOI: 10.14202/vetworld.2023.743-751] [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: 01/13/2023] [Accepted: 03/06/2023] [Indexed: 05/28/2023] Open
Abstract
Background and Aim Vietnam's dairy sector is in its early phase of large-scale farming development. Therefore, mastitis in cows is always a concern to farm owners. This study aimed to determine the antimicrobial susceptibility, resistance, and virulence-related genes of Escherichia coli isolated from bovine mastitis in Nghe An province of Vietnam. Materials and Methods Fifty E. coli strains were isolated from the clinical cases and subjected to this study. All isolates were tested for antimicrobial susceptibility by the disk-diffusion method, as described by the Clinical and Laboratory Standards Institute. Antimicrobial and virulence genes were confirmed by polymerase chain reaction with specific primers. Results All isolates were resistant to lincomycin and sulfamethoxazole and sensitive to gentamicin, while other antimicrobials showed resistance from 2% to 90%. Multidrug resistance was confirmed in 46% of isolates, and none of them were identified as extended-spectrum beta-lactamase producers. From fifty strains tested for antimicrobial and virulence genes, six isolates harbored tetA, 6 tetB, 13 sul1, 15 sul2, 2 Intimin (eae), 1 iutA, and 3 stx2. Conclusion Antimicrobial and multidrug resistances are the main virulence factors of E. coli isolated from bovine mastitis in Vietnam. The virulence genes encoding adhesion, siderophore, Shiga-toxin-producing, and antimicrobials resistant were first reported in Vietnam with low prevalence and contributed to the pathogenesis.
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Affiliation(s)
- Tran Trung My
- Department of Animal Science and Veterinary Medicine, Thai Nguyen University of Agriculture and Forestry, Thai Nguyen University, Quyet Thang, Thai Nguyen City, Vietnam
- Department of Quality Assurance, TH Dairy Institute, Nghia Son, Nghia Dan, Nghe An, Vietnam
| | - Le Van Thien
- Department of Quality Assurance, TH Dairy Institute, Nghia Son, Nghia Dan, Nghe An, Vietnam
- Department of Veterinary Medicine, The Vietnam National University of Agriculture, Trau Quy, Gia Lam, Ha Noi, Vietnam
| | - Vu Duy Manh
- TH Milk Food Joint Stock Company, Nghia Son, Nghia Dan, Nghe An, Vietnam
| | - Bui Thi Phuong My
- TH Milk Food Joint Stock Company, Nghia Son, Nghia Dan, Nghe An, Vietnam
| | - Dang Thi Mai Lan
- Department of Animal Science and Veterinary Medicine, Thai Nguyen University of Agriculture and Forestry, Thai Nguyen University, Quyet Thang, Thai Nguyen City, Vietnam
| | - Dang Xuan Binh
- Department of Animal Science and Veterinary Medicine, Thai Nguyen University of Agriculture and Forestry, Thai Nguyen University, Quyet Thang, Thai Nguyen City, Vietnam
| | - Vu Minh Duc
- Department of Agro-forestry Technology, College of Economics and Technology, Thai Nguyen University, Thinh Dan, Thai Nguyen City, Vietnam
- Laboratory of Veterinary Public Health, Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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14
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Antimicrobial resistance in bacteria isolated from peridomestic Rattus species: A scoping literature review. One Health 2023. [DOI: 10.1016/j.onehlt.2023.100522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
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15
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Antibiotic-Resistant Bacteria, Antimicrobial Resistance Genes, and Antibiotic Residue in Food from Animal Sources: One Health Food Safety Concern. Microorganisms 2023; 11:microorganisms11010161. [PMID: 36677453 PMCID: PMC9863624 DOI: 10.3390/microorganisms11010161] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Antibiotic-resistant bacteria causing foodborne serious illnesses can be found in contaminated food. Therefore, this study aimed to identify the pathogens, genes, and antimicrobial residues present in raw milk and meat. We collected 40 raw milk and 40 beef samples using the aseptic method from various parts of the Faisalabad metropolis, Pakistan. The samples were cultured on blood, MacConkey, and UTI chrome agar. The VITEK 2 compact system was used for microbial identification and determination of minimum inhibitory concentrations. Antimicrobial resistance genes for extended-spectrum β-lactamases, methicillin resistance in Staphylococcus aureus, and carbapenem resistance were identified using molecular techniques. ELISA was used to determine the tetracycline residue level in each sample. The beef samples showed polymicrobial contamination with 64 bacterial isolates, with Escherichia coli (29; 45.3%) and Klebsiella pneumoniae (11; 17.1%) predominating. The milk samples showed polymicrobial contamination with 73 bacterial isolates, with E. coli (22; 30%), K. pneumoniae (12; 16.4%), and S. aureus (10; 13.6%) forming the majority. Twenty-eight (43.7%) isolates from beef harbored tet genes, nineteen (29.6%) blaCTX-M, and fourteen (21.8%) blaNDM-1, and twenty-six (35.6%) isolates from milk harbored tet genes, nineteen (26%) blaTEM and blaCTX-M, and three (4%) blaNDM-1. Twenty-two (55%) each of the beef and milk samples exceeded the maximum residue limit for tetracycline. Polymicrobial contamination by bacteria possessing blaCTX-M, blaTEM, blaNDM-1, blaOXA, mecA, and tet genes was identified in food samples. The high tetracycline residue levels pose a serious health risk to consumers.
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Bhowmick S, Pal S, Sunder J, Sujatha T, De AK, Mondal T, Singh AD, Joardar SN, Batabyal K, Dutta TK, Bandyopadhyay S, Tiwari A, Samanta I. Exploring broilers and native fowls of Andaman and Nicobar Islands as a source of β-lactamase-producing Enterobacteriaceae even with limited anthropogenic activities and docking-based identification of catalytic domains in novel β-lactamase variants. Front Vet Sci 2023; 9:1075133. [PMID: 36686169 PMCID: PMC9849777 DOI: 10.3389/fvets.2022.1075133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023] Open
Abstract
Objectives The present study was conducted to detect the occurrence of β-lactamase and biofilm-producing Escherichia coli, Salmonella, and Klebsiella in broilers and native fowl reared in the Andaman and Nicobar Islands, India. The study also included molecular docking experiments to confirm the nature of the catalytic domains found in the β-lactamase variants obtained and to reveal the clonal relationship of the isolates with human clinical strains from the database. Materials and methods A total of 199 cloacal swabs were collected from five poultry breeds/varieties (broiler, Vanraja, Desi, Nicobari, and layer) in three districts of the Andaman and Nicobar Islands. E. coli, Salmonella enterica, and Klebsiella pneumoniae were isolated by standard techniques and confirmed by PCR. Phenotypical β-lactamase producers were identified by a double-disc test. The genes (bla CTX, bla SHV, bla TEM , and bla AmpC) were screened, and selected sequences of β-lactamase variants were submitted to DDBJ. Homology modeling, model validation, and active site identification of different β-lactamase variants were done by the SWISS-MODEL. Molecular docking was performed to identify the catalytic domains of the β-lactamase variants. The selected β-lactamase sequences were compared with the Indian ESBL sequences from human clinical strains in NCBI-GenBank. Results In total, 425 Enterobacteriaceae strains were isolated from the collected samples. Klebsiella pneumoniae (42.58%) was found to be the most prevalent, followed by Salmonella enterica (30.82%) and E. coli (26.58%). The phenotypical antibiogram of all 425 isolates showed the highest resistance against oxytetracycline (61-76%) and the lowest against gentamicin (15-20%). Phenotypical production of β-lactamase enzymes was observed in 141 (33.38%) isolates. The isolation rate of β-lactamase producing E. coli, Salmonella enterica, and Klebsiella pneumoniae was significantly higher (p < 0.05) in the birds reared in the South Andaman district (25.6, 17.5, and 18.7%, respectively) than in Nicobar (11.5, 7.6, 7.1%, respectively). Genotyping of the β-lactamase-producing isolates revealed the maximum possession of bla TEM, followed by bla SHV and bla CTX - M. The nucleotide sequences were found to be similar with bla CTX - M-15, bla SHV - 11, bla SHV - 27, bla SHV - 228, bla TEM - 1, and bla AmpC in BLAST search. Distribution of studied biofilm-associated genes in Enterobacteriaceae strains from different varieties of the birds revealed that the layer birds had the maximum possession, followed by Vanraja, Desi, broilers, and Nicobari fowls. The phylogenetic analysis of selected sequences revealed a partial clonal relationship with human clinical strains of the Indian subcontinent. Molecular docking depicted the Gibbs free energy release for 10 different macromolecules (proteins) and ligand (antibiotic) complexes, ranging from -8.1 (SHV-27 + cefotaxime) to -7 (TEM-1 + cefotaxime) kcal/mol. Conclusion and relevance The study revealed β-lactamase variants circulating in the fowl population of the Andaman and Nicobar Islands (India), even in remote places with low anthropogenic activity. Most of the strains possessed bla TEM - 1, followed by bla CTX - M-15. Possession of bla SHV - 11, bla SHV - 27, and bla SHV - 228 in poultry Enterobacteriaceae strains was not reported earlier from any part of the world. The phylogenetic analysis revealed a partial clonal relationship of β-lactamase sequences with the human clinical strains isolated from the Indian subcontinent.
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Affiliation(s)
- Sneha Bhowmick
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India,Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Surajit Pal
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Jai Sunder
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - T. Sujatha
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Arun Kumar De
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Tousif Mondal
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Abhishek D. Singh
- Department of Veterinary Public Health, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Siddhartha Narayan Joardar
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Kunal Batabyal
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Tapan Kumar Dutta
- Department of Veterinary Microbiology, Central Agricultural University, Aizawl, Mizoram, India
| | - Samiran Bandyopadhyay
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, West Bengal, India
| | - Ananda Tiwari
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland,Ananda Tiwari ✉
| | - Indranil Samanta
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India,*Correspondence: Indranil Samanta ✉; ✉
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Tohmaz M, Askari Badouei M, Kalateh Rahmani H, Hashemi Tabar G. Antimicrobial resistance, virulence associated genes and phylogenetic background versus plasmid replicon types: the possible associations in avian pathogenic Escherichia coli (APEC). BMC Vet Res 2022; 18:421. [PMID: 36447231 PMCID: PMC9710092 DOI: 10.1186/s12917-022-03496-x] [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: 12/27/2021] [Accepted: 10/27/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) in bacterial isolates from food producing animals not only challenges the preventive and therapeutic strategies in veterinary medicine, but also threatens public health. Genetic elements placed on both chromosome and plasmids could be involved in AMR. In the present study, the associations of genomic backbone and plasmids with AMR were evaluated. We also provided some primary evidences that which genetic lineages potentially host certain groups of plasmids. RESULTS In the current study, 72 avian pathogenic Escherichia coli (APEC) strains were examined. Isolates resistant to tetracycline and trimethoprim-sulfamethoxazole (87.5%; each), and harboring blaTEM (61.1%) were dominant. Moreover, phylogroup D was the most prevalent phylogroup in total (23.6%), and among multidrug-resistant (MDR) isolates (14/63). The most prevalent Inc-types were also defined as follows: IncP (65.2%), IncI1 (58.3%), and IncF group (54.1%). Significant associations among phylogroups and AMR were observed such as group C to neomycin (p = 0.002), gentamicin (p = 0.017) and florfenicol (p = 0.036). Furthermore, group D was associated with blaCTX. In terms of associations among Inc-types and AMR, resistance to aminoglycoside antibiotics was considerably linked with IncP (p = 0.012), IncI1 (p = 0.038) and IncA/C (p = 0.005). The blaTEM and blaCTX genes presence were connected with IncI1 (p = 0.003) and IncFIC (p = 0.013), respectively. It was also shown that members of the D phylogroup frequently occured in replicon types FIC (8/20), P (13/47), I1 (13/42), HI2 (5/14) and L/M (3/3). CONCLUSIONS Accorging to the results, it seems that group D strains have a great potential to host a variety of plasmids (Inc-types) carrying different AMR genes. Thus, based on the results of the current study, phyogroup D could be a potential challenge in dealing with AMR in poultry. There were more strong correlations among Inc-types and AMR compared to phylotypes and AMR. It is suggested that in epidemiological studies on AMR both genomic backbone and major plasmid types should be investigated.
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Affiliation(s)
- Maad Tohmaz
- grid.411301.60000 0001 0666 1211Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahdi Askari Badouei
- grid.411301.60000 0001 0666 1211Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Hamideh Kalateh Rahmani
- grid.411301.60000 0001 0666 1211Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Gholamreza Hashemi Tabar
- grid.411301.60000 0001 0666 1211Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
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Knowledge, Attitudes, and Practices of Community Pharmacy Professionals on Poultry Antibiotic Dispensing, Use, and Bacterial Antimicrobial Resistance in Zambia: Implications on Antibiotic Stewardship and WHO AWaRe Classification of Antibiotics. Antibiotics (Basel) 2022; 11:antibiotics11091210. [PMID: 36139990 PMCID: PMC9495135 DOI: 10.3390/antibiotics11091210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Globally, the inappropriate dispensing and use of antibiotics in animals has contributed to the development of bacterial antimicrobial resistance (AMR). In Zambia, there is insufficient information among community pharmacy professionals on antibiotic use (ABU) and AMR in food-producing animals. This study assessed community pharmacy professionals’ knowledge, attitudes, and practices regarding poultry antibiotic dispensing, use, and bacterial AMR in the Lusaka district of Zambia. A cross-sectional study was conducted among 178 community pharmacy professionals between February and April 2022 using a semi-structured questionnaire. Data were analyzed using Stata version 17. Of the total participants (n = 178), 51.1% (n = 91) were pharmacists. The most dispensed antibiotic was oxytetracycline, a Watch antibiotic, mainly without prescriptions. Good knowledge of ABU and AMR was associated with work experience for more than one year (p = 0.016), while good practices were associated with male gender (p = 0.039) and work experience of more than one year (p = 0.011). The study found moderate knowledge, positive attitudes, and moderate practices of pharmacy professionals on poultry ABU and AMR. There was high dispensing of poultry antibiotics without prescriptions, which calls for strict implementation of antimicrobial stewardship and surveillance programs in poultry production in Zambia to reduce AMR.
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Antibiotic Resistance in Bacteria—A Review. Antibiotics (Basel) 2022; 11:antibiotics11081079. [PMID: 36009947 PMCID: PMC9404765 DOI: 10.3390/antibiotics11081079] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 12/03/2022] Open
Abstract
Background: A global problem of multi-drug resistance (MDR) among bacteria is the cause of hundreds of thousands of deaths every year. In response to the significant increase of MDR bacteria, legislative measures have widely been taken to limit or eliminate the use of antibiotics, including in the form of feed additives for livestock, but also in metaphylaxis and its treatment, which was the subject of EU Regulation in 2019/6. Numerous studies have documented that bacteria use both phenotypis and gentic strategies enabling a natural defence against antibiotics and the induction of mechanisms in increasing resistance to the used antibacterial chemicals. The mechanisms presented in this review developed by the bacteria have a significant impact on reducing the ability to combat bacterial infections in humans and animals. Moreover, the high prevalence of multi-resistant strains in the environment and the ease of transmission of drug-resistance genes between the different bacterial species including commensal flora and pathogenic like foodborne pathogens (E. coli, Campylobacter spp., Enterococcus spp., Salmonella spp., Listeria spp., Staphylococcus spp.) favor the rapid spread of multi-resistance among bacteria in humans and animals. Given the global threat posed by the widespread phenomenon of multi-drug resistance among bacteria which are dangerous for humans and animals, the subject of this study is the presentation of the mechanisms of resistance in most frequent bacteria called as “foodborne pathoges” isolated from human and animals. In order to present the significance of the global problem related to multi-drug resistance among selected pathogens, especially those danger to humans, the publication also presents statistical data on the percentage range of occurrence of drug resistance among selected bacteria in various regions of the world. In addition to the phenotypic characteristics of pathogen resistance, this review also presents detailed information on the detection of drug resistance genes for specific groups of antibiotics. It should be emphasized that the manuscript also presents the results of own research i.e., Campylobacter spp., E. coli or Enetrococcus spp. This subject and the presentation of data on the risks of drug resistance among bacteria will contribute to initiating research in implementing the prevention of drug resistance and the development of alternatives for antimicrobials methods of controlling bacteria.
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Deekshit VK, Srikumar S. 'To be, or not to be' - the dilemma of 'silent' antimicrobial resistance genes in bacteria. J Appl Microbiol 2022; 133:2902-2914. [PMID: 35882476 DOI: 10.1111/jam.15738] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Antimicrobial resistance is a serious threat to public health that dramatically undermines our ability to treat bacterial infections. Microorganisms exhibit resistance to different drug classes by acquiring resistance determinants through multiple mechanisms including horizontal gene transfer. The presence of drug resistance genotypes is mostly associated with corresponding phenotypic resistance against the particular antibiotic. However, bacterial communities harboring silent antimicrobial resistance genes - genes whose presence is not associated with a corresponding resistant phenotype, do exist. Under suitable conditions, the expression pattern of such genes often revert and regain resistance, and could potentially lead to therapeutic failure. We often miss the presence of silent genes, since the current experimental paradigms are focused on resistant strains. Therefore, the knowledge on the prevalence, importance, and mechanism of silent antibiotic resistance genes in bacterial pathogens is very limited. Silent genes, therefore, provide an additional level of complexity in the war against drug-resistant bacteria, reminding us that not only phenotypically resistant strains but also susceptible strains should be carefully investigated. In this review, we discuss the presence of silent antimicrobial resistance genes in bacteria, their relevance, and their importance in public health.
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Affiliation(s)
- Vijaya Kumar Deekshit
- Nitte (Deemed to be University), Nitte University Center for Science Education and Research, Division of Infectious Diseases, Paneer Campus, Deralakatte, Mangaluru - 575018, Karnataka, India
| | - Shabarinath Srikumar
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, UAE
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Nguyen TD, Itayama T, Ramaraj R, Iwami N, Shimizu K, Dao TS, Pham TL, Maseda H. Physiological response of Simocephalus vetulus to five antibiotics and their mixture under 48-h acute exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154585. [PMID: 35306083 DOI: 10.1016/j.scitotenv.2022.154585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 05/20/2023]
Abstract
Antibiotics, widely known as major environmental xenobiotics, are increasingly being released into ecosystems due to their essential functions in human health and production. During the COVID-19 pandemic waves, antibiotic use increases remarkably in treating bacterial coinfections. Antibiotics were initially expected only to affect prokaryotes, but recent research has shown that they can disturb the biological systems of eukaryotes, especially vulnerable aquatic creatures, through both direct and indirect processes. However, their toxicity to the freshwater cladoceran Simocephalus vetulus, an essential link in the aquatic food web, has never been evaluated. The effects of four fluoroquinolones (ciprofloxacin: CFX, ofloxacin: OFX, gatifloxacin: GFX, delafloxacin: DFX), tetracycline (TET), and a mixture of these medicines (MIX) on S. vetulus thoracic limb rate (TLR) were examined in this study. After S. vetulus was exposed to 20 and 40 mg GFX L-1, 90% and 100% mortality rates were recorded. At 2.5-10 mg L-1, GFX dramatically lowered the TLR of S. vetulus, resulting in a median effective concentration of 9.69 mg L-1. TLRs increased when the organisms were exposed to 10-40 mg L-1 of CFX and 1.25-40 mg L-1 of OFX. However, DFX and TET exposures did not affect TLRs. Exposure to MIX reduced TLR only at 40 mg L-1, suggesting an antagonistic interaction among the five pharmaceuticals. This study demonstrated that S. vetulus physiological responses to antibiotics, even in the same class, are complex and elusive. Beyond a common additive concentration principle, the antagonistic interaction of antibiotic mixture indicates a high level of uncertainty in terms of ecological dangers. We initially introduce S. vetulus to ecotoxicological studies of antibiotics, presenting the species as a low-cost model for physiological investigations of environmental xenobiotics.
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Affiliation(s)
- Tan-Duc Nguyen
- Graduate school of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Japan
| | - Tomoaki Itayama
- Graduate school of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki-shi, Japan.
| | - Rameshprabu Ramaraj
- School of Renewable Energy, Maejo University, Sansai, Chiang Mai 50290, Thailand
| | - Norio Iwami
- School of Science and Engineering, Meise University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan
| | - Kazuya Shimizu
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki, Japan
| | - Thanh-Son Dao
- Faculty of Environment and Natural Resources, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam; Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
| | - Thanh Luu Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Street, Cau Giay District, Hanoi 100000, Viet Nam; Institute of Tropical Biology, Vietnam Academy of Science and Technology (VAST), 85 Tran Quoc Toan Street, District 3, Ho Chi Minh City 700000, Viet Nam
| | - Hideaki Maseda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
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Tetracycline-Resistant Genes in Escherichia coli from Clinical and Nonclinical Sources in Rivers State, Nigeria. Int J Microbiol 2022; 2022:9192424. [PMID: 35855811 PMCID: PMC9288291 DOI: 10.1155/2022/9192424] [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: 05/02/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
Background Monitoring the occurrence of tetracycline resistance and its determinants in both clinical and nonclinical settings is essential in understanding the role played by continuous usage of this drug in animal husbandry and the withdrawal of this drug from clinical practice. Limited information is available on this from our locale. This study, therefore, set out to explore the occurrence of specific tetracycline-resistant genes in Escherichia coli from clinical and nonclinical sources in Rivers State, Nigeria. Methods Two hundred clinical and nonclinical samples were analyzed for the presence of E. coli using standard phenotypic and genotypic tests. Susceptibility testing was carried out using the Kirby–Bauer disc diffusion method, and specific tetracycline-resistant genes (tetA, tetB, tetG, and tetM) were assayed. Results Results showed that stool samples had the highest occurrence of E. coli (39, 78%), and soil had the lowest (13, 26%). Tetracycline resistance was observed in 80.7% of total isolates. The tetA genes were the most commonly occurring (n = 80, 89.9%) detected in confirmed E. coli isolates, and tetG, the least commonly occurring (n = 16,18%) of isolates. The combined presence of tetA-tetM was the highest (n = 14, 15.7%), followed by tetA-tetB (n = 13, 14.8%). Conclusion The present study reports on the occurrence and distribution of four tetracycline-resistant determinants in E. coli from clinical and nonclinical sources in Rivers State, Nigeria. The high-level occurrence of the most commonly occurring tetracycline gene even in nonclinical isolates could be indicative of a potential reservoir of this resistance. And, this could limit the reintroduction of tetracycline even in combination therapy.
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Firoozeh F, Zibaei M, Badmasti F, Khaledi A. Virulence factors, antimicrobial resistance and the relationship between these characteristics in uropathogenic Escherichia coli. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Plasmid profile analysis of Escherichia coli and Salmonella enterica isolated from pigs, pork, and humans. Epidemiol Infect 2022; 150:e110. [PMID: 35535461 PMCID: PMC9214845 DOI: 10.1017/s0950268822000814] [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] [Indexed: 11/17/2022] Open
Abstract
This study aimed to determine the epidemiology and association of antimicrobial resistance (AMR) among Escherichia coli and Salmonella in Thailand. The E. coli (n = 1047) and Salmonella (n = 816) isolates from pigs, pork and humans were screened for 18 replicons including HI1, HI2, I1-γ, X, L/M, N, FIA, FIB, W, Y, P, FIC, A/C, T, FIIAs, F, K and B/O using polymerase chain reaction-based replicon typing. The E. coli (n = 26) and Salmonella (n = 3) isolates carrying IncF family replicons, ESBL and/or mcr genes were determined for FAB formula. IncF represented the major type of plasmids. Sixteen and eleven Inc groups were identified in E. coli (85.3%) and Salmonella (25.7%), respectively. The predominant replicon patterns between E. coli and Salmonella were IncK-F (23.7%) and IncF (46.2%). Significant correlations (P < 0.05) were observed between plasmid-replicon type and resistance phenotype. Plasmid replicon types were significantly different among sources of isolates and sampling periods. The most common FAB types between E. coli and Salmonella were F2:A-:B- (30.8%) and S1:A-:B- (66.7%), respectively. In conclusion, various plasmids present in E. coli and Salmonella. Responsible and prudent use of antimicrobials is suggested to reduce the selective pressures that favour the spread of AMR determinants. Further studies to understand the evolution of R plasmids and their contribution to the dissemination of AMR genes are warranted.
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Gurnani M, Chauhan A, Ranjan A, Tuli HS, Alkhanani MF, Haque S, Dhama K, Lal R, Jindal T. Filamentous Thermosensitive Mutant Z: An Appealing Target for Emerging Pathogens and a Trek on Its Natural Inhibitors. BIOLOGY 2022; 11:biology11050624. [PMID: 35625352 PMCID: PMC9138142 DOI: 10.3390/biology11050624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/18/2022] [Accepted: 04/01/2022] [Indexed: 12/14/2022]
Abstract
Simple Summary Antimicrobial resistance (AMR) is a pressing issue worldwide that must be addressed swiftly. It is driven by spontaneous evolution, bacterial mutation, and the dissemination of resistant genes via horizontal gene transfer. Researchers are working on many novel targets, which can become a pathway to inhibit harmful bacteria. Filamentous Thermosensitive mutant-Z (Fts-Z) is one such bacterial target that has gained popularity amongst scientists due to its conserved nature in bacteria and absence in eukaryotes. The aim of this work was to review the Fts-Z mechanism of action along with current studies on natural inhibitors for Fts-Z. Abstract Antibiotic resistance is a major emerging issue in the health care sector, as highlighted by the WHO. Filamentous Thermosensitive mutant Z (Fts-Z) is gaining significant attention in the scientific community as a potential anti-bacterial target for fighting antibiotic resistance among several pathogenic bacteria. The Fts-Z plays a key role in bacterial cell division by allowing Z ring formation. Several in vitro and in silico experiments have demonstrated that inhibition of Fts-Z can lead to filamentous growth of the cells, and finally, cell death occurs. Many natural compounds that have successfully inhibited Fts-Z are also studied. This review article intended to highlight the structural–functional aspect of Fts-Z that leads to Z-ring formation and its contribution to the biochemistry and physiology of cells. The current trend of natural inhibitors of Fts-Z protein is also covered.
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Affiliation(s)
- Manisha Gurnani
- Amity Institute of Environmental Science, Amity University, Noida 201301, India;
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida 201303, India;
- Correspondence: (A.C.); (A.R.)
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
- Correspondence: (A.C.); (A.R.)
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Ambala 133207, India;
| | - Mustfa F. Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Faculty of Medicine, Görükle Campus, Bursa Uludağ University, Nilüfer, Bursa 16059, Turkey
| | - Kuldeep Dhama
- Division of Pathology, ICAR—Indian Veterinary Research Institute, Bareilly 243122, India;
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi 110021, India;
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida 201303, India;
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Prevalence and characterisation of antimicrobial resistance genes and class 1 and 2 integrons in multiresistant Escherichia coli isolated from poultry production. Sci Rep 2022; 12:6062. [PMID: 35410349 PMCID: PMC9001716 DOI: 10.1038/s41598-022-09996-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/29/2022] [Indexed: 12/29/2022] Open
Abstract
A global increase in the populations of drug resistant bacteria exerts negative effects on animal production and human health. Our study has been focused on the assessment of resistance determinants in relation to phenotypic resistance of the 74 commensal E. coli isolates present in different ecological environments. The samples were collected from poultry litter, feces, and neck skin. Among the microorganisms isolated from the poultry litter (group A), the highest resistance was noted against AMP and DOX (100%). In the E. coli extracts from the cloacal swabs (group B), the highest resistance was observed against AMP (100%) and CIP (92%). The meat samples (group C) were characterized by resistance to AMP (100%) and STX (94.7%). Genes encoding resistance to β-lactams (blaTEM, blaCTX-M), fluoroquinolones (qnrA, qnrB, qnrS), aminoglycosides (strA-strB, aphA1, aac(3)-II), sulfonamides (sul1, sul2, sul3), trimethoprim (dfr1, dfr5, dfr7/17) and tetracyclines (tetA, tetB) were detected in the studied bacterial isolates. The presence of class 1 and 2 integrons was confirmed in 75% of the MDR E. coli isolates (plasmid DNA), of which 60% contained class 1 integrons, 15% contained class 2 integrons, and 11.7% carried integrons of both classes. Thus, it may be concluded that integrons are the common mediators of antimicrobial resistance among commensal multidrug resistant Escherichia coli at important stages of poultry production.
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Kim SW, Kim K, Lee YJ. Comparative analysis of antimicrobial resistance and genetic characteristics of Escherichia coli from broiler breeder farms in Korea. CANADIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1139/cjas-2021-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Broiler breeder farms could be a reservoir of Escherichia coli, disseminating antimicrobial resistance and virulence factors. We investigated the antimicrobial resistance of E. coli from nine broiler breeder farms and characterised their resistance and virulence genes. A total of 256 E. coli showed a high level of resistance to tetracycline, nalidixic acid, ampicillin, and cephalothin, followed by trimethoprim-sulfamethoxazole and chloramphenicol. The resistance to nalidixic acid, ampicillin, trimethoprim–sulfamethoxazole, and chloramphenicol showed significant differences among the farms. Among 202 β-lactam-resistant E. coli, 138 carried β-lactamase genes. The most prevalent β-lactamase gene was blaTEM-1, of which the presence differed significantly across the farms. Out of 197 tetracycline-resistant E. coli isolates, tetA and tetB were detected in 164 and 50, with significant differences among the farms. Also, 45 of 196 nalidixic acid-resistant E. coli carried qnrS while 67 of 149 trimethoprim–sulfamethoxazole-resistant E. coli carried sul2. Among the five virulence genes tested, ompT was the most prevalent, and all genes except for iutA distributed significantly different among the farms. The phenotypic and genotypic characteristics of E. coli were significantly different among the farms; therefore, management at the breeder level is required to control the vertical transmission of E. coli.
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Affiliation(s)
- Shin-Woo Kim
- Kyungpook National University College of Veterinary Medicine, 579998, Daegu, Korea (the Republic of), 41566
| | - Koeun Kim
- Kyungpook National University College of Veterinary Medicine, 579998, Daegu, Korea (the Republic of), 41566
| | - Young Ju Lee
- Kyungpook National University, 34986, Daegu, Korea (the Republic of), 41566
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Virulence and antimicrobial resistance profile of non-typhoidal Salmonella enterica serovars recovered from poultry processing environments at wet markets in Dhaka, Bangladesh. PLoS One 2022; 17:e0254465. [PMID: 35130286 PMCID: PMC8820648 DOI: 10.1371/journal.pone.0254465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 01/13/2022] [Indexed: 11/19/2022] Open
Abstract
The rapid emergence of virulent and multidrug-resistant (MDR) non-typhoidal Salmonella (NTS) enterica serovars is a growing public health concern globally. The present study focused on the assessment of the pathogenicity and antimicrobial resistance (AMR) profiling of NTS enterica serovars isolated from the chicken processing environments at wet markets in Dhaka, Bangladesh. A total of 870 samples consisting of carcass dressing water (CDW), chopping board swabs (CBS), and knife swabs (KS) were collected from 29 wet markets. The prevalence of Salmonella was found to be 20% in CDW, 19.31% in CBS, and 17.58% in KS, respectively. Meanwhile, the MDR Salmonella was found to be 72.41%, 73.21%, and 68.62% in CDW, CBS, and KS, respectively. All isolates were screened by polymerase chain reaction (PCR) for eight virulence genes, namely invA, agfA, IpfA, hilA, sivH, sefA, sopE, and spvC. The S. Enteritidis and untyped Salmonella isolates harbored all virulence genes while S. Typhimurium isolates carried six virulence genes, except sefA and spvC. Phenotypic resistance revealed decreased susceptibility to ciprofloxacin, streptomycin, ampicillin, tetracycline, gentamicin, sulfamethoxazole-trimethoprim, amoxicillin-clavulanic acid, and azithromycin. Genotypic resistance showed a higher prevalence of plasmid-mediated blaTEM followed by tetA, sul1, sul2, sul3, and strA/B genes. The phenotypic and genotypic resistance profiles of the isolates showed a harmonic and symmetrical trend. According to the findings, MDR and virulent NTS enterica serovars predominate in wet market conditions and can easily enter the human food chain. The chi-square analysis showed significantly higher associations among the phenotypic resistance, genotypic resistance and virulence genes in CDW, CBS, and KS respectively (p < 0.05).
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Lozica L, Villumsen KR, Li G, Hu X, Maljković MM, Gottstein Ž. Genomic Analysis of Escherichia coli Longitudinally Isolated from Broiler Breeder Flocks after the Application of an Autogenous Vaccine. Microorganisms 2022; 10:microorganisms10020377. [PMID: 35208834 PMCID: PMC8879504 DOI: 10.3390/microorganisms10020377] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/29/2022] [Accepted: 02/03/2022] [Indexed: 11/24/2022] Open
Abstract
Escherichia coli is the main bacterial cause of major economic losses and animal welfare issues in poultry production. In this study, we investigate the effect of an autogenous vaccine on E. coli strains longitudinally isolated from broiler breeder flocks on two farms. In total, 115 E. coli isolates were sequenced using Illumina technologies, and compared based on a single-nucleotide polymorphism (SNP) analysis of the core-genome and antimicrobial resistance (AMR) genes they carried. The results showed that SNP-based phylogeny corresponds to a previous multilocus-sequence typing (MLST)-based phylogeny. Highly virulent sequence types (STs), including ST117-F, ST95-B2, ST131-B2 and ST390-B2, showed a higher level of homogeneity. On the other hand, less frequent STs, such as ST1485, ST3232, ST7013 and ST8573, were phylogenetically more distant and carried a higher number of antimicrobial resistance genes in most cases. In total, 25 antimicrobial genes were detected, of which the most prevalent were mdf(A) (100%), sitABCD (71.3%) and tet(A) (13.91%). The frequency of AMR genes showed a decreasing trend over time in both farms. The highest prevalence was detected in strains belonging to the B1 phylogenetic group, confirming the previous notion that commensal strains act as reservoirs and carry more resistance genes than pathogenic strains that are mostly associated with virulence genes.
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Affiliation(s)
- Liča Lozica
- Department of Poultry Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia;
| | - Kasper Rømer Villumsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Dyrlægevej 88, 1870 Copenhagen, Denmark;
| | - Ganwu Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China;
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA;
| | - Xiao Hu
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA;
| | - Maja Maurić Maljković
- Department of Animal Breeding and Livestock Production, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia;
| | - Željko Gottstein
- Department of Poultry Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia;
- Correspondence: ; Tel.: +385-1239-0280
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Uddin MB, Alam MN, Hasan M, Hossain SMB, Debnath M, Begum R, Samad MA, Hoque SF, Chowdhury MSR, Rahman MM, Hossain MM, Hassan MM, Lundkvist Å, Järhult JD, El Zowalaty ME, Ahmed SSU. Molecular Detection of Colistin Resistance mcr-1 Gene in Multidrug-Resistant Escherichia coli Isolated from Chicken. Antibiotics (Basel) 2022; 11:antibiotics11010097. [PMID: 35052973 PMCID: PMC8772701 DOI: 10.3390/antibiotics11010097] [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: 03/16/2021] [Revised: 08/12/2021] [Accepted: 08/27/2021] [Indexed: 11/29/2022] Open
Abstract
Zoonotic and antimicrobial-resistant Escherichia coli (hereafter, E. coli) is a global public health threat which can lead to detrimental effects on human health. Here, we aim to investigate the antimicrobial resistance and the presence of mcr-1 gene in E. coli isolated from chicken feces. Ninety-four E. coli isolates were obtained from samples collected from different locations in Bangladesh, and the isolates were identified using conventional microbiological tests. Phenotypic disk diffusion tests using 20 antimicrobial agents were performed according to CLSI-EUCAST guidelines, and minimum inhibitory concentrations (MICs) were determined for a subset of samples. E. coli isolates showed high resistance to colistin (88.30%), ciprofloxacin (77.66%), trimethoprim/sulfamethoxazole (76.60%), tigecycline (75.53%), and enrofloxacin (71.28%). Additionally, the pathotype eaeA gene was confirmed in ten randomly selected E. coli isolates using primer-specific polymerase chain reaction (PCR). The presence of mcr-1 gene was confirmed using PCR and sequencing analysis in six out of ten E. coli isolates. Furthermore, sequencing and phylogenetic analyses revealed a similarity between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, indicating that the six tested isolates were colistin resistant. Finally, the findings of the present study showed that E. coli isolated from chicken harbored mcr-1 gene, and multidrug and colistin resistance. These findings accentuate the need to implement strict measures to limit the imprudent use of antibiotics, particularly colistin, in agriculture and poultry farms.
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Affiliation(s)
- Md Bashir Uddin
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
- Correspondence: (M.B.U.); (M.E.E.Z.); (S.S.U.A.)
| | - Mohammad Nurul Alam
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.H.); (S.F.H.)
| | - S. M. Bayejed Hossain
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mita Debnath
- Kazi Farms Poultry Laboratory, Gazipur 1700, Bangladesh;
| | - Ruhena Begum
- Bangladesh Livestock Research Institute (BLRI), Savar 1341, Bangladesh; (R.B.); (M.A.S.)
| | - Mohammed A. Samad
- Bangladesh Livestock Research Institute (BLRI), Savar 1341, Bangladesh; (R.B.); (M.A.S.)
| | - Syeda Farjana Hoque
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.H.); (S.F.H.)
| | - Md. Shahidur Rahman Chowdhury
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Md. Mahfujur Rahman
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Md. Mukter Hossain
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mohammad Mahmudul Hassan
- Department of Physiology, Biochemistry and Pharmacology, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh;
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE 75 123 Uppsala, Sweden;
| | - Josef D. Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, SE 75 123 Uppsala, Sweden;
| | - Mohamed E. El Zowalaty
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE 75 123 Uppsala, Sweden;
- Correspondence: (M.B.U.); (M.E.E.Z.); (S.S.U.A.)
| | - Syed Sayeem Uddin Ahmed
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet 3100, Bangladesh
- Correspondence: (M.B.U.); (M.E.E.Z.); (S.S.U.A.)
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Ma L, Yang H, Guan L, Liu X, Zhang T. Risks of antibiotic resistance genes and antimicrobial resistance under chlorination disinfection with public health concerns. ENVIRONMENT INTERNATIONAL 2022; 158:106978. [PMID: 34784521 DOI: 10.1016/j.envint.2021.106978] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/23/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
As a widely used disinfection technology, the effects of chlorination on antibiotic resistome and bacterial community received great scientific concerns, while the pathogens associated health risks kept largely unknown. With this concern, the present study used metagenomic analysis combined with culture method to reveal chlorination effects on antibiotic resistance genes (ARGs) and their bacterial hosts (total microbes and Escherichia coli) through simulating the chlorination dosage with human health concerns (drinking water and swimming pool). The resistome profiling showed that chlorination process could significantly decrease both abundance and diversity of total ARGs, while with limited removal rates of 6.0-8.7% for opportunistic pathogens E. coli isolates. Of all the observed 515 ARG subtypes, 105 core subtypes were identified and persistent during chlorination for both total microbes and E. coli. Antibiotic susceptibility test showed that chlorination treatment could efficiently remove multi-resistant E. coli isolates but select for tetracycline resistant isolates. Five ARG-carrying genomes (assigned to Bacteroidetes, Firmicutes, Actinobacteria) enriched by 18.1-102% after chlorination were retrieved by using metagenomic binning strategies. Bray-Curtis dissimilarity, network and procrustes analyses all indicated the remained antibiotic resistome and bacterial community were mainly chlorination-driven. Furthermore, a systematic pipeline for monitoring chlorination-associated antimicrobial resistance risks was proposed. These together enhance our knowledge of chlorination treatment associated public concerns, as important reference and guidance for surveillance and control of antibiotic resistance.
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Affiliation(s)
- Liping Ma
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.
| | - Huiying Yang
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Lei Guan
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Xiaoyu Liu
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong Special Administrative Region
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Rezatofighi SE, Najafifar A, Askari Badouei M, Peighambari SM, Soltani M. An Integrated Perspective on Virulence-Associated Genes (VAGs), Antimicrobial Resistance (AMR), and Phylogenetic Clusters of Pathogenic and Non-pathogenic Avian Escherichia coli. Front Vet Sci 2021; 8:758124. [PMID: 34901248 PMCID: PMC8651559 DOI: 10.3389/fvets.2021.758124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/15/2021] [Indexed: 12/05/2022] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is an important bacterial pathogen that causes avian colibacillosis and leads to huge economic losses in the poultry industry. Different virulence traits contribute to pathogenesis of APEC infections, and antimicrobial resistance (AMR) has also been an overwhelming issue in poultry worldwide. In the present study, we aimed to investigate and compare the presence of virulence-associated genes (VAGs), AMR, and phylogenetic group's distribution among APEC and avian fecal E. coli (AFEC) strains. E. coli from birds with colisepticemia and yolk sac infection (YSI) (APEC) plus E. coli strains from the feces of healthy birds (AFEC) were compared by the aforementioned traits. In addition, the clonal relatedness was compared using Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Although all strains were susceptible to fosfomycin, ceftriaxone, and cefixime, almost all strains (98%) were multi-drug resistant (MDR). All strains (except two) harbored at least three or more VAGs, and the virulence scores tended to be higher in pathogenic strains especially in the colisepticemic group. All phylogenetic groups were found in isolates from YSI, colisepticemia, and the feces of healthy birds; however, the frequency of phylogroups varied according to the source of the isolate. B1 and C phylogroups were statistically more likely to be found among APEC from YSI and colisepticemic E. coli groups, respectively, while phylogroup A was the most frequently occurring phylogroup among AFEC strains. Our findings also revealed that AMR and VAGs are not essentially co-evolved traits as in some instances AMR strains were more prevalent among AFEC. This reflects the divergent evolutionary pathways of resistance acquisition in pathogenic or non-pathogenic avian E. coli strains. Importantly, strains related to phylogenetic group C showed higher virulence score and AMR that requires further attention. To some extent, ERIC-PCR was able to group strains by isolation source, phylogroup, or virulence genes. Further integrated studies along with assessment of more detailed genotypic and phenotypic features could potentially lead to better understanding of virulence, resistance, and evolution of ExPEC.
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Affiliation(s)
| | - Arash Najafifar
- Private Veterinary Practitioner, Independent Researcher, Tehran, Iran
| | - Mahdi Askari Badouei
- Faculty of Veterinary Medicine, Department of Pathobiology, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Soltani
- Faculty of Veterinary Medicine, Department of Avian Diseases, University of Tehran, Tehran, Iran
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Liu W, Ying N, Mo Q, Li S, Shao M, Sun L, Zhu L. Machine learning for identifying resistance features of Klebsiella pneumoniae using whole-genome sequence single nucleotide polymorphisms. J Med Microbiol 2021; 70. [PMID: 34812714 DOI: 10.1099/jmm.0.001474] [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: 11/18/2022] Open
Abstract
Introduction. Klebsiella pneumoniae, a gram-negative bacterium, is a common pathogen causing nosocomial infection. The drug-resistance rate of K. pneumoniae is increasing year by year, posing a severe threat to public health worldwide. K. pneumoniae has been listed as one of the pathogens causing the global crisis of antimicrobial resistance in nosocomial infections. We need to explore the drug resistance of K. pneumoniae for clinical diagnosis. Single nucleotide polymorphisms (SNPs) are of high density and have rich genetic information in whole-genome sequencing (WGS), which can affect the structure or expression of proteins. SNPs can be used to explore mutation sites associated with bacterial resistance.Hypothesis/Gap Statement. Machine learning methods can detect genetic features associated with the drug resistance of K. pneumoniae from whole-genome SNP data.Aims. This work used Fast Feature Selection (FFS) and Codon Mutation Detection (CMD) machine learning methods to detect genetic features related to drug resistance of K. pneumoniae from whole-genome SNP data.Methods. WGS data on resistance of K. pneumoniae strains to four antibiotics (tetracycline, gentamicin, imipenem, amikacin) were downloaded from the European Nucleotide Archive (ENA). Sequence alignments were performed with MUMmer 3 to complete SNP calling using K. pneumoniae HS11286 chromosome as the reference genome. The FFS algorithm was applied to feature selection of the SNP dataset. The training set was constructed based on mutation sites with mutation frequency >0.995. Based on the original SNP training set, 70% of SNPs were randomly selected from each dataset as the test set to verify the accuracy of the training results. Finally, the resistance genes were obtained by the CMD algorithm and Venny.Results. The number of strains resistant to tetracycline, gentamicin, imipenem and amikacin was 931, 1048, 789 and 203, respectively. Machine learning algorithms were applied to the SNP training set and test set, and 28 and 23 resistance genes were predicted, respectively. The 28 resistance genes in the training set included 22 genes in the test set, which verified the accuracy of gene prediction. Among them, some genes (KPHS_35310, KPHS_18220, KPHS_35880, etc.) corresponded to known resistance genes (Eef2, lpxK, MdtC, etc). Logistic regression classifiers were established based on the identified SNPs in the training set. The area under the curves (AUCs) of the four antibiotics was 0.939, 0.950, 0.912 and 0.935, showing a strong ability to predict bacterial resistance.Conclusion. Machine learning methods can effectively be used to predict resistance genes and associated SNPs. The FFS and CMD algorithms have wide applicability. They can be used for the drug-resistance analysis of any microorganism with genomic variation and phenotypic data. This work lays a foundation for resistance research in clinical applications.
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Affiliation(s)
- Wenjia Liu
- College of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China
| | - Nanjiao Ying
- College of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China.,Institute of Biomedical Engineering, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China
| | - Qiusi Mo
- College of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China
| | - Shanshan Li
- College of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China
| | - Mengjie Shao
- College of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China
| | - Lingli Sun
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, Zhejiang, 310012, PR China.,NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, Zhejiang, 310012, PR China
| | - Lei Zhu
- College of Automation, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China.,Institute of Biomedical Engineering, Hangzhou Dianzi University, Hangzhou, Zhejiang, 310018, PR China
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Goudarztalejerdi A, Mohammadzadeh A, Niazi K, Mohammad Mirzaei M. High Prevalence of Multidrug Resistance and Biofilm-Formation Ability Among Avian Escherichia coli Isolated from Broilers in Iran. Microb Drug Resist 2021; 28:244-254. [PMID: 34756121 DOI: 10.1089/mdr.2021.0091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The present study was conducted to determine the antimicrobial resistance pattern and biofilm-formation ability in 100 Avian-Pathogenic Escherichia coli (APEC) isolated from colibacillosis-suspected broilers and 100 Avian Fecal E. coli (AFEC) isolates from healthy broilers in Hamedan, Iran. All isolates were screened by polymerase chain reaction for antimicrobial resistance genes, class 1 and 2 integrons, and biofilm-associated genes. Besides, we assessed the possible relationship between biofilm-formation ability antibiotic resistance patterns, genetic background, and the pathogenicity of APEC strains. 81% of APEC and 73% of AFEC isolates showed multidrug resistance (MDR) phenotype; in addition, 45% of the APEC and 21% of the AFEC strains showed biofilm-formation ability. This is the first report of the biofilm formation ability in E. coli isolated from broilers in Iran. The most prevalent antibiotic resistance gene in APEC strains was tetA (68%), followed by sul1 (63%), dfrA1-like (51%), and blaTEM (30%), whereas in AFEC strains, the frequencies of the antibiotic resistance genes were tetA (63%), sul1 (58%), dfrA1-like (49%), and blaTEM (22%). Out of 81 MDR APEC isolates, 53 (65.4%) and 38 (46.91%) isolates were positive for intI1 and intI2 genes, respectively. In the AFEC strains intI1 and intI2 genes were presented in 57 and 33 isolates, respectively. All APEC isolates belonging to phylogenetic groups B1, B2, and C were MDR. The results of the present study indicate that isolates with biofilm-forming ability show more MDR properties and probably have more pathogenicity to broilers.
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Affiliation(s)
- Ali Goudarztalejerdi
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran
| | - Abdolmajid Mohammadzadeh
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran
| | - Khalid Niazi
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran
| | - Mostafa Mohammad Mirzaei
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran
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Hamed EA, Abdelaty MF, Sorour HK, Roshdy H, AbdelRahman MAA, Magdy O, Ibrahim WA, Sayed A, Mohamed H, Youssef MI, Hassan WM, Badr H. Monitoring of Antimicrobial Susceptibility of Bacteria Isolated from Poultry Farms from 2014 to 2018. Vet Med Int 2021; 2021:6739220. [PMID: 34540194 PMCID: PMC8448596 DOI: 10.1155/2021/6739220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/25/2021] [Indexed: 11/24/2022] Open
Abstract
The current situation of antibiotic resistance of most bacterial pathogens was a threat to the poultry and public health with increasing economic losses. Regarding this problem, monitoring of the circulating microorganisms occurred with the antibiotic resistance profile. A total of 657 different samples from internal organs (liver, heart, lung, and yolk) and paper-lining chick boxes were collected from native chicken farms which were submitted to the Reference Laboratory for Veterinary Quality Control on Poultry Production in the period from 2014 to 2018 for the detection of Salmonella, Escherichia coli (E. coli), and Staphylococcus. The bacterial isolates were tested for their antimicrobial susceptibility by disk diffusion technique. Salmonella was isolated from 128 out of 657 (19.5%), E. coli was isolated from 496 out of 657 (75.5%), and Staphylococcus species was isolated from 497 out of 657 (75.6%). All Salmonella positive samples were examined for antibiotic resistance against 10 different antibiotics, and the highest percentage all over the five years was against penicillin, ampicillin, and tetracycline. All E. coli positive samples were examined for antibiotic resistance against 14 different antibiotics, and the highest percentage all over the five years was with ampicillin, tetracycline, norfloxacin, streptomycin, and danofloxacin. All Staphylococcus positive sample species were examined for antibiotic resistance against 14 different antibiotics, and the highest percentage of resistance all over the five years was shown with tetracycline, streptomycin, ampicillin, and nalidixic acid.
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Affiliation(s)
- Engy Ahmed Hamed
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - May Fathy Abdelaty
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - Hend Karam Sorour
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - Heba Roshdy
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - Mona Aly Abdelhalim AbdelRahman
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - Ola Magdy
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - Waleed Abdelfatah. Ibrahim
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - Ahmed Sayed
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - Hytham Mohamed
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - Mohammed Iraqi Youssef
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - Wafaa Mohamed Hassan
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
| | - Heba Badr
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agricultural Research Center (ARC), Nadi El-Seid Street, Dokki P.O. Box 246, Giza 12618, Egypt
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Siddiky NA, Sarker MS, Khan MSR, Begum R, Kabir ME, Karim MR, Rahman MT, Mahmud A, Samad MA. Virulence and Antimicrobial Resistance Profiles of Salmonella enterica Serovars Isolated from Chicken at Wet Markets in Dhaka, Bangladesh. Microorganisms 2021; 9:952. [PMID: 33924919 PMCID: PMC8145576 DOI: 10.3390/microorganisms9050952] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/28/2021] [Accepted: 04/18/2021] [Indexed: 01/06/2023] Open
Abstract
Virulent and multi drug resistant (MDR) Salmonellaenterica is a foremost cause of foodborne diseases and had serious public health concern globally. The present study was undertaken to identify the pathogenicity and antimicrobial resistance (AMR) profiles of Salmonellaenterica serovars recovered from chicken at wet markets in Dhaka, Bangladesh. A total of 870 cecal contents of broiler, sonali, and native chickens were collected from 29 wet markets. The overall prevalence of S. Typhimurium, S. Enteritidis, and untyped Salmonella spp., were found to be 3.67%, 0.57%, and 1.95% respectively. All isolates were screened by polymerase chain reaction (PCR) for eight virulence genes, namely invA, agfA, IpfA, hilA, sivH, sefA, sopE, and spvC. S. Enteritidis isolates carried all virulence genes whilst S. Typhimurium isolates carried six virulence genes except sefA and spvC. A diverse phenotypic and genotypic AMR pattern was found. Harmonic descending trends of resistance patterns were observed among the broiler, sonali, and native chickens. Interestingly, virulent and MDR Salmonella enterica serovars were found in native chicken, although antimicrobials were not used in their production cycle. The research findings anticipate that virulent and MDR Salmonella enterica are roaming in the wet markets which can easily anchor to the vendor, consumers, and in the food chain.
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Affiliation(s)
- Nure Alam Siddiky
- Antimicrobial Resistance Action Center, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh; (N.A.S.); (M.S.S.); (R.B.); (M.E.K.); (M.R.K.); (A.M.)
| | - Md Samun Sarker
- Antimicrobial Resistance Action Center, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh; (N.A.S.); (M.S.S.); (R.B.); (M.E.K.); (M.R.K.); (A.M.)
| | - Md. Shahidur Rahman Khan
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.S.R.K.); (M.T.R.)
| | - Ruhena Begum
- Antimicrobial Resistance Action Center, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh; (N.A.S.); (M.S.S.); (R.B.); (M.E.K.); (M.R.K.); (A.M.)
| | - Md. Ehsanul Kabir
- Antimicrobial Resistance Action Center, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh; (N.A.S.); (M.S.S.); (R.B.); (M.E.K.); (M.R.K.); (A.M.)
| | - Md. Rezaul Karim
- Antimicrobial Resistance Action Center, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh; (N.A.S.); (M.S.S.); (R.B.); (M.E.K.); (M.R.K.); (A.M.)
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.S.R.K.); (M.T.R.)
| | - Asheak Mahmud
- Antimicrobial Resistance Action Center, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh; (N.A.S.); (M.S.S.); (R.B.); (M.E.K.); (M.R.K.); (A.M.)
| | - Mohammed A. Samad
- Antimicrobial Resistance Action Center, Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh; (N.A.S.); (M.S.S.); (R.B.); (M.E.K.); (M.R.K.); (A.M.)
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37
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Antimicrobial resistance in fecal Escherichia coli isolated from poultry chicks in northern Iran. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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