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Lubis AR, Sumon MAA, Dinh-Hung N, Dhar AK, Delamare-Deboutteville J, Kim DH, Shinn AP, Kanjanasopa D, Permpoonpattana P, Doan HV, Linh NV, Brown CL. Review of quorum-quenching probiotics: A promising non-antibiotic-based strategy for sustainable aquaculture. JOURNAL OF FISH DISEASES 2024; 47:e13941. [PMID: 38523339 DOI: 10.1111/jfd.13941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 03/26/2024]
Abstract
The emergence of antibiotic-resistant bacteria (ARBs) and genes (ARGs) in aquaculture underscores the urgent need for alternative veterinary strategies to combat antimicrobial resistance (AMR). These measures are vital to reduce the likelihood of entering a post-antibiotic era. Identifying environmentally friendly biotechnological solutions to prevent and treat bacterial diseases is crucial for the sustainability of aquaculture and for minimizing the use of antimicrobials, especially antibiotics. The development of probiotics with quorum-quenching (QQ) capabilities presents a promising non-antibiotic strategy for sustainable aquaculture. Recent research has demonstrated the effectiveness of QQ probiotics (QQPs) against a range of significant fish pathogens in aquaculture. QQ disrupts microbial communication (quorum sensing, QS) by inhibiting the production, replication, and detection of signalling molecules, thereby reducing bacterial virulence factors. With their targeted anti-virulence approach, QQPs have substantial promise as a potential alternative to antibiotics. The application of QQPs in aquaculture, however, is still in its early stages and requires additional research. Key challenges include determining the optimal dosage and treatment regimens, understanding the long-term effects, and integrating QQPs with other disease control methods in diverse aquaculture systems. This review scrutinizes the current literature on antibiotic usage, AMR prevalence in aquaculture, QQ mechanisms and the application of QQPs as a sustainable alternative to antibiotics.
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Affiliation(s)
- Anisa Rilla Lubis
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Md Afsar Ahmed Sumon
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Nguyen Dinh-Hung
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Arun K Dhar
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | | | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University, Busan, Republic of Korea
| | | | - Duangkhaetita Kanjanasopa
- Agricultural Science and Technology Program, Faculty of Innovative Agriculture and Fishery Establishment Project, Prince of Songkla University, Surat Thani Campus, Surat Thani, Thailand
| | - Patima Permpoonpattana
- Agricultural Science and Technology Program, Faculty of Innovative Agriculture and Fishery Establishment Project, Prince of Songkla University, Surat Thani Campus, Surat Thani, Thailand
| | - Hien Van Doan
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
- Functional Feed Innovation Center (FuncFeed), Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Nguyen Vu Linh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
- Functional Feed Innovation Center (FuncFeed), Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Christopher L Brown
- FAO World Fisheries University Pilot Programme, Pukyong National University, Busan, South Korea
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Miranda CD, Concha C, Hurtado L, Urtubia R, Rojas R, Romero J. Occurrence of Antimicrobial-Resistant Bacteria in Intestinal Contents of Wild Marine Fish in Chile. Antibiotics (Basel) 2024; 13:332. [PMID: 38667008 PMCID: PMC11047320 DOI: 10.3390/antibiotics13040332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024] Open
Abstract
Antimicrobial-resistant bacteria (ARB) from the intestinal contents of wild fish may have a relevant ecological significance and could be used as indicators of antimicrobial-resistance dissemination in natural bacterial populations in water bodies impacted by urban contamination. Thus, the occurrence of ARB in the intestinal contents of pelagic and demersal wild fishes captured in anthropogenic-impacted Coquimbo Bay in Chile was studied. Culturable counts of total and antimicrobial-resistant bacteria were determined by a spread plate method using Trypticase soy agar and R2A media, both alone and supplemented with the antimicrobials amoxicillin, streptomycin, florfenicol, oxytetracycline and ciprofloxacin, respectively. Heterotrophic plate counts of pelagic and demersal fishes ranged from 1.72 × 106 CFU g-1 to 3.62 × 109 CFU g-1, showing variable proportions of antimicrobial resistance. Representative antimicrobial-resistant isolates were identified by 16S rRNA gene sequencing, and isolates (74) from pelagic fishes mainly belonged to Pseudomonas (50.0%) and Shewanella (17.6%) genera, whereas isolates (68) from demersal fishes mainly belonged to Vibrio (33.8%) and Pseudomonas (26.5%) genera. Antimicrobial-resistant isolates were tested for susceptibility to 12 antimicrobials by an agar disk diffusion method, showing highest resistance to streptomycin (85.2%) and amoxicillin (64.8%), and lowest resistance to oxytetracycline (23.2%) and ciprofloxacin (0.7%). Only furazolidone and trimethoprim/sulfamethoxazole were statistically different (p < 0.05) in comparisons between isolates from pelagic and demersal wild fishes. Furthermore, an important number of these isolates carried plasmids (53.5%) and produced Extended-Spectrum-β-lactamases (ESBL) (16.9%), whereas the detection of Metallo-β-Lactamases and class 1-integron was rare. This study provides evidence that wild fish are important reservoirs and spreading-vehicles of ARB, carrying plasmids and producing ESBLs in Chilean marine environments.
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Affiliation(s)
- Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Christopher Concha
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Luz Hurtado
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Rocío Urtubia
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile; (C.C.); (L.H.); (R.U.); (R.R.)
| | - Jaime Romero
- Laboratorio de Biotecnología de los Alimentos, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7830417, Chile;
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Sequino G, Valentino V, Esposito A, Volpe S, Torrieri E, De Filippis F, Ercolini D. Microbiome dynamics, antibiotic resistance gene patterns and spoilage-associated genomic potential in fresh anchovies stored in different conditions. Food Res Int 2024; 175:113788. [PMID: 38129066 DOI: 10.1016/j.foodres.2023.113788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
Fresh fish is a highly perishable product and is easily spoiled by microbiological activity and chemical oxidation of lipids. However, microbial spoilage is the main factor linked with the rapid fish sensorial degradation due to the action of specific spoilage organisms (SSOs) that have the ability to dominate over other microorganisms and produce metabolites responsible for off-flavours. We explored the microbial dynamics in fresh anchovies stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) using shotgun metagenomics, highlighting the selection of different microbial species according to the packaging type. Indeed, Pseudoalteromonas nigrifaciens, Psychrobacter cryohalolentis and Ps. immobilis, Pseudomonas deceptionensis and Vibrio splendidus have been identified as the main SSOs in aerobically stored anchovies, while Shewanella baltica, Photobacterium iliopiscarium, Ps. cryohalolentis and Ps. immobilis prevailed in VP and MAP. In addition, we identified the presence of spoilage-associated genes, leading to the potential production of biogenic amines and different off-flavors (H2S, TMA). In particular, the abundance of microbial genes leading to BA biosynthesis increased at higher storage temperature, while those related to H2S and TMA production were enriched in aerobically and VP packed anchovies, suggesting that MAP could be an effective strategy in delaying the production of these compounds. Finally, we provided evidence of the presence of a wide range of antibiotic resistance genes conferring resistance to different classes of antibiotic (β-lactams, tetracyclines, polymyxins, trimethoprims and phenicols) and highlighted that storage at higher temperature (4 and 10 °C) boosted the abundance of ARG-carrying taxa, especially in aerobically and MAP packed fish.
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Affiliation(s)
- Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Vincenzo Valentino
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Alessia Esposito
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Stefania Volpe
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Elena Torrieri
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Corso Umberto I 40, 80138 Naples, Italy.
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Corso Umberto I 40, 80138 Naples, Italy
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Xiong X, Chen R, Lai J. Comparative genomics analysis of Streptococcus iniae isolated from Trachinotus ovatus: novel insight into antimicrobial resistance and virulence differentiation. BMC Genomics 2023; 24:775. [PMID: 38097934 PMCID: PMC10720119 DOI: 10.1186/s12864-023-09882-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Streptococcus iniae is an important fish pathogen that cause significant economic losses to the global aquaculture industry every year. Although there have some reports on the genotype of S.iniae and its relationship with virulence, no genome-scale comparative analysis has been performed so far. In our previous work, we characterized 17 isolates of S.iniae from Trachinotus ovatus and divided them into two genotypes using RAPD and rep-PCR methods. Among them, BH15-2 was classified as designated genotype A (in RAPD) and genotype 1 (in rep-PCR), while BH16-24 was classified as genotype B and genotype 2. Herein, we compared the differences in growth, drug resistance, virulence, and genome between BH15-2 and BH16-24. RESULTS The results showed that the growth ability of BH16-24 was significantly faster than that of BH15-2 at the exponential stage. Antimicrobial tests revealed that BH15-2 was susceptible to most of the tested antibiotics except neomycin and gentamycin. In contrast, BH16-24 was resistant to 7 antibiotics including penicillin, sulfasomizole, compound sulfamethoxazole tablets, polymyxin B, spectinomycin, rifampin and ceftazidime. Intraperitoneal challenge of T.ovatus, showed that the LD50 value of BH15-2 was 4.0 × 102 CFU/g, while that of BH16-24 was 1.2 × 105 CFU/g. The genome of S.iniae BH15-2 was 2,175,659 bp with a GC content of 36.80%. Meanwhile, the genome of BH16-24 was 2,153,918 bp with a GC content of 36.83%. Comparative genome analysis indicated that compared with BH15-2, BH16-24 genome had a large-scale genomic inversion fragment, at the location from 502,513 bp to 1,788,813 bp, resulting in many of virulence and resistance genes differentially expression. In addition, there was a 46 kb length, intact phage sequence in BH15-2 genome, which was absent in BH16-24. CONCLUSION Comparative genomic studies of BH15-2 and BH16-24 showed that the main difference is a 1.28 Mbp inversion fragment. The inversion fragment may lead to abnormal expression of drug resistant and virulence genes, which is believed to be the main reason for the multiple resistance and weakened virulence of BH16-24. Our study revealed the potential mechanisms in underlying the differences of multidrug resistance and virulence among different genotypes of S.iniae.
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Affiliation(s)
- Xiangying Xiong
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
- Guangxi Institute of Oceanology Limited Liability Company, Beihai, 536000, Guangxi, China.
- Beibu Gulf Marine Industry Research Institute, Fangchenggang, 538000, Guangxi, China.
| | - Ruifang Chen
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
- Guangxi Institute of Oceanology Limited Liability Company, Beihai, 536000, Guangxi, China
- Beibu Gulf Marine Industry Research Institute, Fangchenggang, 538000, Guangxi, China
| | - Junxiang Lai
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
- Beibu Gulf Marine Industry Research Institute, Fangchenggang, 538000, Guangxi, China
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Say P, Nimitkul S, Bunnoy A, Na-Nakorn U, Srisapoome P. Effects of the combination of chitosan and Acinetobacter KU011TH on the growth and health performances and disease resistance of juvenile hybrid catfish (Clarias gariepinus × C. macrocephalus). FISH & SHELLFISH IMMUNOLOGY 2023; 142:109177. [PMID: 37863127 DOI: 10.1016/j.fsi.2023.109177] [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: 08/05/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 10/22/2023]
Abstract
Aquatic animal health management has become a crucial component in the goal of increasing catfish aquaculture productivity. Additionally, hybrid catfish (Clarias gariepinus × C. macrocephalus) has been promoted as a highly profitable freshwater fish in Asia. Interestingly, the crucial diseases induced by Aeromonas hydrophila have been reported to greatly impede catfish production. To overcome this challenge, the aim was to investigate the effects of the oral administration of potentially synbiotic chitosan (CH) and Acinetobacter KU011TH (AK) on the growth performance, immunological responses, and disease resistance of hybrid catfish against A. hydrophila. The control group was fed a basal diet (A), the diet fed to treatment group B was supplemented with 20 mL of CH/kg diet (B), and the experimental feed fed to groups C-D was mixed with 1 × 108, 1 × 109 and 1 × 1010 CFU/mL AK coated with 20 mL of CH/kg diet. Five different groups of juvenile hybrid catfish were continuously fed the 5 formulated feeds for 4 weeks. The results revealed that all tested feeds did not significantly enhance the hybrid catfish's average daily gain, specific growth rate, feed conversion ratio, hematocrit and erythrocyte counts. Interestingly, the application of CH and AK significantly increased the leukocyte counts, respiratory burst, lysozyme activity, alternative complement pathway hemolytic activity, and bactericidal activity (P < 0.05). The expression levels of the immune-related genes in the whole blood, head kidney, and spleen were significantly increased after CH-AK application (P < 0.05), but this finding was not observed in the liver (P > 0.05). Additionally, after 14 days of A. hydrophila peritoneal injection, the fish in group C showed significantly higher survival rates of approximately 70.0 % compared with the control fish in groups B, D, and E (52.5 %, 40.0 %, 45.0 %, and 45.0 %, respectively) (P < 0.05). These results collectively suggest that short-term application of the diet fed to group C effectively boosted the immune responses and disease resistance of hybrid catfish against A. hydrophila.
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Affiliation(s)
- Pisey Say
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, Thailand; Center of Excellence in Aquatic Animal Health Management, Department of Aquaculture Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Sukkrit Nimitkul
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Anurak Bunnoy
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, Thailand; Center of Excellence in Aquatic Animal Health Management, Department of Aquaculture Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Uthairat Na-Nakorn
- Laboratory of Aquatic Animal Genetics, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, 50 Paholayothin Rd, Ladyao, Chatuchak, Bangkok, Thailand; Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Prapansak Srisapoome
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, Thailand; Center of Excellence in Aquatic Animal Health Management, Department of Aquaculture Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, Thailand.
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Thomson P, García P, del Río C, Castro R, Núñez A, Miranda C. Antimicrobial Resistance and Extended-Spectrum Beta-Lactamase Genes in Enterobacterales, Pseudomonas and Acinetobacter Isolates from the Uterus of Healthy Mares. Pathogens 2023; 12:1145. [PMID: 37764953 PMCID: PMC10535638 DOI: 10.3390/pathogens12091145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic-resistant bacteria are a growing concern for human and animal health. The objective of this study was to determine the antimicrobial resistance and extended-spectrum beta-lactamase genes in Enterobacterales, Pseudomonas spp. and Acinetobacter spp. isolates from the uterus of healthy mares. For this purpose, 21 mares were swabbed for samples, which were later seeded on blood agar and MacConkey agar. The isolates were identified using MALDI-TOF and the antimicrobial susceptibility test was performed using the Kirby-Bauer technique. To characterize the resistance genes, a polymerase chain reaction (PCR) scheme was performed. Of the isolates identified as Gram-negative, 68.8% were Enterobacterales, represented by E. coli, Enterobacter cloacae, Citrobacter spp., and Klebsiella pneumoniae; 28.1% belonged to the genus Acinetobacter spp.; and 3.1% to Pseudomonas aeruginosa. A 9.3% of the isolates were multidrug-resistant (MDR), presenting resistance to antibiotics from three different classes, while 18.8% presented resistance to two or more classes of different antibiotics. The diversity of three genes that code for ESBL (blaTEM, blaCTX-M and blaSHV) was detected in 12.5% of the strains. The most frequent was blaSHV, while blaTEM and blaCTX-M were present in Citrobacter spp. and Klebsiella pneumoniae. These results are an alarm call for veterinarians and their environment and suggest taking measures to prevent the spread of these microorganisms.
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Affiliation(s)
- Pamela Thomson
- Laboratorio de Microbiología Clínica y Microbioma, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370134, Chile;
| | - Patricia García
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica, Santiago 8940000, Chile;
| | - Camila del Río
- Laboratorio de Microbiología Clínica y Microbioma, Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370134, Chile;
| | - Rodrigo Castro
- Escuela de Medicina Veterinaria, Facultad de Recursos Naturales y Medicina Veterinaria, Universidad Santo Tomás, Talca 3473620, Chile
| | - Andrea Núñez
- Escuela de Medicina Veterinaria, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Curicó 3340000, Chile
- Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Santiago 7500975, Chile
| | - Carolina Miranda
- Laboratorio de Microbiología Red de Salud UC-CHRISTUS, Pontificia Universidad Católica, Santiago 8940000, Chile;
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Uhland FC, Li XZ, Mulvey MR, Reid-Smith R, Sherk LM, Ziraldo H, Jin G, Young KM, Reist M, Carson CA. Extended Spectrum β-Lactamase-Producing Enterobacterales of Shrimp and Salmon Available for Purchase by Consumers in Canada-A Risk Profile Using the Codex Framework. Antibiotics (Basel) 2023; 12:1412. [PMID: 37760708 PMCID: PMC10525137 DOI: 10.3390/antibiotics12091412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
The extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-EB) encompass several important human pathogens and are found on the World Health Organization (WHO) priority pathogens list of antibiotic-resistant bacteria. They are a group of organisms which demonstrate resistance to third-generation cephalosporins (3GC) and their presence has been documented worldwide, including in aquaculture and the aquatic environment. This risk profile was developed following the Codex Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance with the objectives of describing the current state of knowledge of ESBL-EB in relation to retail shrimp and salmon available to consumers in Canada, the primary aquacultured species consumed in Canada. The risk profile found that Enterobacterales and ESBL-EB have been found in multiple aquatic environments, as well as multiple host species and production levels. Although the information available did not permit the conclusion as to whether there is a human health risk related to ESBLs in Enterobacterales in salmon and shrimp available for consumption by Canadians, ESBL-EB in imported seafood available at the retail level in Canada have been found. Surveillance activities to detect ESBL-EB in seafood are needed; salmon and shrimp could be used in initial surveillance activities, representing domestic and imported products.
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Affiliation(s)
- F. Carl Uhland
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Xian-Zhi Li
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Richard Reid-Smith
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Lauren M. Sherk
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Hilary Ziraldo
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Grace Jin
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Kaitlin M. Young
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Mark Reist
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Carolee A. Carson
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
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8
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Ferri G, Lauteri C, Scattolini M, Vergara A. Antibiotic Resistance Profiles and ARG Detection from Isolated Bacteria in a Culture-Dependent Study at the Codfish Industry Level. Foods 2023; 12:foods12081699. [PMID: 37107494 PMCID: PMC10137873 DOI: 10.3390/foods12081699] [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: 04/04/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
The antibiotic resistance phenomenon horizontally involves numerous bacteria cultured from fresh or processed seafood matrix microbiomes. In this study, the identified bacteria from food-producing processes and industrial environments were screened for phenotypic and genotypic resistance determinants. A total of 684 bacterial strains [537 from processed codfish (Gadus morhua and Gadus macrocephalus) products as salted and seasoned and soaked and 147 from environmental samples] were isolated. Antibiotic susceptibility tests showed resistance against tetracycline, oxacillin, and clindamycin in the Staphylococcus genus (both from food and environmental samples) and against beta-lactams (cefotaxime, carbapenems, etc.) and nitrofurans (nitrofurantoin) from E. coli and Salmonella enterica serovar. Enteritidis isolates. One-thousand and ten genetic determinants-tetracycline tetC (25.17%), tetK (21.06%), tetL (11.70%), clindamycin ermC (17.23%), ermB (7.60%), linezolid cfr (8.22%), optrA (3.62%), poxtA (2.05%), and oxacillin mecA (17.37%)-were amplified from Gram-positive resistant and phenotypically susceptible bacteria. Concerning Gram-negative bacteria, the beta-lactam-resistant genes (blaTEM, blaCIT, blaCTX-M, blaIMP, blaKPC, blaOXA-48-like) represented 57.30% of the amplified ARGs. This study found high antibiotic resistance genes in circulation in the fish food industry chain from the macro- to microenvironment. The obtained data confirmed the diffusion of the "antibiotic resistance phenomenon" and its repercussions on the One-health and food-producing systems.
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Affiliation(s)
- Gianluigi Ferri
- Department of Veterinary Medicine, Post-Graduate Specialization School in Food Inspection "G. Tiecco", University of Teramo, Strada Provinciale 18, 64100 Teramo, Italy
| | - Carlotta Lauteri
- Department of Veterinary Medicine, Post-Graduate Specialization School in Food Inspection "G. Tiecco", University of Teramo, Strada Provinciale 18, 64100 Teramo, Italy
| | | | - Alberto Vergara
- Department of Veterinary Medicine, Post-Graduate Specialization School in Food Inspection "G. Tiecco", University of Teramo, Strada Provinciale 18, 64100 Teramo, Italy
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Guajardo-Leiva S, Mendez KN, Meneses C, Díez B, Castro-Nallar E. A First Insight into the Microbial and Viral Communities of Comau Fjord—A Unique Human-Impacted Ecosystem in Patagonia (42∘ S). Microorganisms 2023; 11:microorganisms11040904. [PMID: 37110327 PMCID: PMC10143455 DOI: 10.3390/microorganisms11040904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
While progress has been made in surveying the oceans to understand microbial and viral communities, the coastal ocean and, specifically, estuarine waters, where the effects of anthropogenic activity are greatest, remain partially understudied. The coastal waters of Northern Patagonia are of interest since this region experiences high-density salmon farming as well as other disturbances such as maritime transport of humans and cargo. Here, we hypothesized that viral and microbial communities from the Comau Fjord would be distinct from those collected in global surveys yet would have the distinctive features of microbes from coastal and temperate regions. We further hypothesized that microbial communities will be functionally enriched in antibiotic resistance genes (ARGs) in general and in those related to salmon farming in particular. Here, the analysis of metagenomes and viromes obtained for three surface water sites showed that the structure of the microbial communities was distinct in comparison to global surveys such as the Tara Ocean, though their composition converges with that of cosmopolitan marine microbes belonging to Proteobacteria, Bacteroidetes, and Actinobacteria. Similarly, viral communities were also divergent in structure and composition but matched known viral members from North America and the southern oceans. Microbial communities were functionally enriched in ARGs dominated by beta-lactams and tetracyclines, bacitracin, and the group macrolide–lincosamide–streptogramin (MLS) but were not different from other communities from the South Atlantic, South Pacific, and Southern Oceans. Similarly, viral communities were characterized by exhibiting protein clusters similar to those described globally (Tara Oceans Virome); however, Comau Fjord viromes displayed up to 50% uniqueness in their protein content. Altogether, our results indicate that microbial and viral communities from the Comau Fjord are a reservoir of untapped diversity and that, given the increasing anthropogenic impacts in the region, they warrant further study, specifically regarding resilience and resistance against antimicrobials and hydrocarbons.
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Affiliation(s)
- Sergio Guajardo-Leiva
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
| | - Katterinne N. Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370186, Chile
| | - Claudio Meneses
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- ANID—Millennium Science Initiative Program—Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago 8370186, Chile
| | - Beatriz Díez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
- Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 7800003, Chile
| | - Eduardo Castro-Nallar
- Departamento de Microbiología, Facultad de Ciencias de la Salud, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
- Centro de Ecología Integrativa, Campus Talca, Universidad de Talca, Avda. Lircay s/n, Talca 3465548, Chile
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10
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Cabello FC, Millanao AR, Lozano-Muñoz I, Godfrey HP. Misunderstandings and misinterpretations: Antimicrobial use and resistance in salmon aquaculture. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36934450 DOI: 10.1111/1758-2229.13147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
The exponential growth of aquaculture over the past 30 years has been accompanied by a parallel increase in the use of antimicrobials. This widespread use has had negative effects on animal, human and environmental health and affected the biodiversity of the environments where aquaculture takes place. Results showing these harmful effects have been resisted and made light of by the aquaculture industry and their scientific supporters through introduction of misunderstandings and misinterpretations of concepts developed in the evolution, genetics, and molecular epidemiology of antimicrobial resistance. We focus on a few of the most obvious scientific shortcomings and biases of two recent attempts to minimise the negative impacts of excessive antimicrobial use in Chilean salmon aquaculture on human and piscine health and on the environment. Such open debate is critical to timely implementation of effective regulation of antimicrobial usage in salmon aquaculture in Chile, if the negative local and worldwide impacts of this usage are to be avoided.
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Affiliation(s)
- Felipe C Cabello
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, New York, USA
| | - Ana R Millanao
- Instituto de Farmacia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Ivonne Lozano-Muñoz
- Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Henry P Godfrey
- Department of Pathology (retired), New York Medical College, Valhalla, New York, USA
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11
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Ferri G, Lauteri C, Vergara A. Antibiotic Resistance in the Finfish Aquaculture Industry: A Review. Antibiotics (Basel) 2022; 11:1574. [PMID: 36358229 PMCID: PMC9686606 DOI: 10.3390/antibiotics11111574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/25/2022] [Accepted: 11/06/2022] [Indexed: 11/07/2023] Open
Abstract
Significant challenges to worldwide sustainable food production continue to arise from environmental change and consistent population growth. In order to meet increasing demand, fish production industries are encouraged to maintain high growth densities and to rely on antibiotic intervention throughout all stages of development. The inappropriate administering of antibiotics over time introduces selective pressure, allowing the survival of resistant bacterial strains through adaptive pathways involving transferable nucleotide sequences (i.e., plasmids). This is one of the essential mechanisms of antibiotic resistance development in food production systems. This review article focuses on the main international regulations and governing the administering of antibiotics in finfish husbandry and summarizes recent data regarding the distribution of bacterial resistance in the finfish aquaculture food production chain. The second part of this review examines promising alternative approaches to finfish production, sustainable farming techniques, and vaccination that circumvents excessive antibiotic use, including new animal welfare measures. Then, we reflect on recent adaptations to increasingly interdisciplinary perspectives in the field and their greater alignment with the One Health initiative.
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Affiliation(s)
- Gianluigi Ferri
- Faculty of Veterinary Medicine, Post-Graduate Specialization School in Food Inspection “G. Tiecco”, University of Teramo, Strada Provinciale 18, 64100 Teramo, Italy
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12
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Ballash GA, Baesu A, Lee S, Mills MC, Mollenkopf DF, Sullivan SMP, Lee J, Bayen S, Wittum TE. Fish as sentinels of antimicrobial resistant bacteria, epidemic carbapenemase genes, and antibiotics in surface water. PLoS One 2022; 17:e0272806. [PMID: 36054112 PMCID: PMC9439226 DOI: 10.1371/journal.pone.0272806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/26/2022] [Indexed: 12/01/2022] Open
Abstract
Surface waters, especially those receiving wastewater flows, can disseminate antimicrobial resistant bacteria (ARB), antimicrobial resistance genes (ARG), and antibiotics. In the Scioto River of central Ohio, United States, we evaluated fishes as potential sentinels of ARB and antimicrobial contamination and investigated the influence of antimicrobial exposure on the fish intestinal resistome. Seventy-seven fish were collected from river reaches receiving inputs from two wastewater treatment plants that serve the greater Columbus Metropolitan Area. Fish were screened for the presence of cephalosporin-resistant (CeRO) and carbapenem-resistant (CRO) organisms, epidemic carbapenemase genes, and antibiotic drugs and metabolites using culture methods, droplet digital PCR, and ultra-high performance liquid chromatography tandem mass spectroscopy (UHPLC-MS/MS). Nearly 21% of fish harbored a CeRO in their resistome, with 19.4% exhibiting bacteria expressing an AmpC genotype encoded by blaCMY, and 7.7% with bacteria expressing an extended-spectrum β-lactamase phenotype encoded by blaCTX-M.blaKPC and blaNDM were present in 87.7% (57/65) and 80.4% (37/46) of the intestinal samples at an average abundance of 104 copies. Three antibiotics–lincomycin (19.5%), azithromycin (31.2%) and sulfamethoxazole (3.9%)–were found in hepatic samples at average concentrations between 25–31 ng/g. Fish harboring blaCTX-M and those exposed to azithromycin were at greater odds of being downstream of a wastewater treatment plant. Fish that bioconcentrated antibiotics in their liver were not at greater odds of harboring CeRO, CRO, or epidemic carbapenemase gene copies in their resistome. Our findings confirm that fishes can be effective bioindicators of surface waters contaminated with ARB, ARG, and antibiotics. Moreover, our findings highlight the varying importance of different mechanisms that facilitate establishment of ARB in aquatic ecosystems.
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Affiliation(s)
- Gregory A. Ballash
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Anca Baesu
- Department of Food Science and Agricultural Chemistry, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Seungjun Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
| | - Molly C. Mills
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
| | - Dixie F. Mollenkopf
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - S. Mažeika P. Sullivan
- Schiermeier Olentangy River Wetland Research Park, School of Environment and Natural Resources, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
- Department of Food Science and Technology, The Ohio State University, Columbus, Ohio, United States of America
| | - Stephen Bayen
- Department of Food Science and Agricultural Chemistry, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Thomas E. Wittum
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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13
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A NLP Pipeline for the Automatic Extraction of a Complete Microorganism’s Picture from Microbiological Notes. J Pers Med 2022; 12:jpm12091424. [PMID: 36143209 PMCID: PMC9504513 DOI: 10.3390/jpm12091424] [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: 07/10/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/21/2022] Open
Abstract
The Italian “Istituto Superiore di Sanità” (ISS) identifies hospital-acquired infections (HAIs) as the most frequent and serious complications in healthcare. HAIs constitute a real health emergency and, therefore, require decisive action from both local and national health organizations. Information about the causative microorganisms of HAIs is obtained from the results of microbiological cultures of specimens collected from infected body sites, but microorganisms’ names are sometimes reported only in the notes field of the culture reports. The objective of our work was to build a NLP-based pipeline for the automatic information extraction from the notes of microbiological culture reports. We analyzed a sample composed of 499 texts of notes extracted from 1 month of anonymized laboratory referral. First, our system filtered texts in order to remove nonmeaningful sentences. Thereafter, it correctly extracted all the microorganisms’ names according to the expert’s labels and linked them to a set of very important metadata such as the translations into national/international vocabularies and standard definitions. As the major result of our pipeline, the system extracts a complete picture of the microorganism.
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14
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Hutchison C. Wars and sweets: microbes, medicines and other moderns in and beyond the(ir) antibiotic era. MEDICAL HUMANITIES 2022; 48:medhum-2021-012366. [PMID: 35948395 PMCID: PMC9411908 DOI: 10.1136/medhum-2021-012366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Once upon a time, many of us moderns dreamt that our future was bright, squeaky clean, germ-free. Now, we increasingly fear that bacterial resistance movements and hordes of viruses are cancelling our medicated performances, and threatening life as many of us have come to know it. In order for our modern antibiotic theatre of war to go on, we pray for salvation through our intensive surveillance of microbes, crusades for more rational antibiotic wars, increased recruitment of resistance fighters and development of antibiotic armaments through greater investment in our medical-industrial-war complex. But not all of us are in favour of the promise of perpetual antimicrobial wars, no matter how careful or rational their proponents aspire to be. An increasing vocal and diverse opposition has amassed in academic journals, newspapers and other fields of practice denouncing medicalisation and pharamceuticalisation of our daily lives, as well as our modern medicine as overly militaristic. In this paper, rather than simply rehearsing many of these well-made and meaning debates to convert you to yet another cause, I enrol them in redescriptions of our modern medical performances in the hope of awakening you from your aseptic dream. What follows is my invitation for you to re-enact our mythic antibiotic era in all its martial g(l)ory. I promise that it will bring you no physically harm, yet I can't promise it will leave your beliefs unscathed, as you follow its playful redescription of how our objective scientific descriptions, clinical prescriptions, economic strategies, political mandates and military orders, not to mention our warspeak, have always been deeply entangled with triumphs and devastations of The(ir) Great anti-Microbial Wars (aka our antibiotic era).
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Affiliation(s)
- Coll Hutchison
- Global Health and Development, London School of Hygiene and Tropical Medicine Faculty of Public Health and Policy, London, UK
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15
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Díaz-Gavidia C, Barría C, Weller DL, Salgado-Caxito M, Estrada EM, Araya A, Vera L, Smith W, Kim M, Moreno-Switt AI, Olivares-Pacheco J, Adell AD. Humans and Hoofed Livestock Are the Main Sources of Fecal Contamination of Rivers Used for Crop Irrigation: A Microbial Source Tracking Approach. Front Microbiol 2022; 13:768527. [PMID: 35847115 PMCID: PMC9279616 DOI: 10.3389/fmicb.2022.768527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/19/2022] [Indexed: 12/01/2022] Open
Abstract
Freshwater bodies receive waste, feces, and fecal microorganisms from agricultural, urban, and natural activities. In this study, the probable sources of fecal contamination were determined. Also, antibiotic resistant bacteria (ARB) were detected in the two main rivers of central Chile. Surface water samples were collected from 12 sampling sites in the Maipo (n = 8) and Maule Rivers (n = 4) every 3 months, from August 2017 until April 2019. To determine the fecal contamination level, fecal coliforms were quantified using the most probable number (MPN) method and the source of fecal contamination was determined by Microbial Source Tracking (MST) using the Cryptosporidium and Giardia genotyping method. Separately, to determine if antimicrobial resistance bacteria (AMB) were present in the rivers, Escherichia coli and environmental bacteria were isolated, and the antibiotic susceptibility profile was determined. Fecal coliform levels in the Maule and Maipo Rivers ranged between 1 and 130 MPN/100-ml, and 2 and 30,000 MPN/100-ml, respectively. Based on the MST results using Cryptosporidium and Giardia host-specific species, human, cattle, birds, and/or dogs hosts were the probable sources of fecal contamination in both rivers, with human and cattle host-specific species being more frequently detected. Conditional tree analysis indicated that coliform levels were significantly associated with the river system (Maipo versus Maule), land use, and season. Fecal coliform levels were significantly (p < 0.006) higher at urban and agricultural sites than at sites immediately downstream of treatment centers, livestock areas, or natural areas. Three out of eight (37.5%) E. coli isolates presented a multidrug-resistance (MDR) phenotype. Similarly, 6.6% (117/1768) and 5.1% (44/863) of environmental isolates, in Maipo and Maule River showed and MDR phenotype. Efforts to reduce fecal discharge into these rivers should thus focus on agriculture and urban land uses as these areas were contributing the most and more frequently to fecal contamination into the rivers, while human and cattle fecal discharges were identified as the most likely source of this fecal contamination by the MST approach. This information can be used to design better mitigation strategies, thereby reducing the burden of waterborne diseases and AMR in Central Chile.
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Affiliation(s)
- Constanza Díaz-Gavidia
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Carla Barría
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Daniel L. Weller
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, United States
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, United States
| | - Marilia Salgado-Caxito
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Erika M. Estrada
- Department of Food Science and Technology, Eastern Shore Agricultural Research and Extension Center, Virginia Tech, Painter, Virginia
| | - Aníbal Araya
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaiso, Chile
| | - Leonardo Vera
- Escuela Ingeniería Ambiental, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Woutrina Smith
- One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Minji Kim
- Department of Civil and Environmental Engineering, University of California, Davis, Davis, CA, United States
| | - Andrea I. Moreno-Switt
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge Olivares-Pacheco
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaiso, Chile
| | - Aiko D. Adell
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- *Correspondence: Aiko D. Adell,
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16
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Loest D, Uhland FC, Young KM, Li XZ, Mulvey MR, Reid-Smith R, Sherk LM, Carson CA. Carbapenem-resistant Escherichia coli from shrimp and salmon available for purchase by consumers in Canada: a risk profile using the Codex framework. Epidemiol Infect 2022; 150:e148. [PMID: 35968840 PMCID: PMC9386791 DOI: 10.1017/s0950268822001030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/28/2022] [Accepted: 05/21/2022] [Indexed: 11/05/2022] Open
Abstract
Resistance to carbapenems in human pathogens is a growing clinical and public health concern. The carbapenems are in an antimicrobial class considered last-resort, they are used to treat human infections caused by multidrug-resistant Enterobacterales, and they are classified by the World Health Organization as 'High Priority Critically Important Antimicrobials'. The presence of carbapenem-resistant Enterobacterales (CREs) of animal-origin is of concern because targeted studies of Canadian retail seafood revealed the presence of carbapenem resistance in a small number of Enterobacterales isolates. To further investigate this issue, a risk profile was developed examining shrimp and salmon, the two most important seafood commodities consumed by Canadians and Escherichia coli, a member of the Enterobacterales order. Carbapenem-resistant E. coli (CREc) isolates have been identified in shrimp and other seafood products. Although carbapenem use in aquaculture has not been reported, several classes of antimicrobials are utilised globally and co-selection of antimicrobial-resistant microorganisms in an aquaculture setting is also of concern. CREs have been identified in retail seafood purchased in Canada and are currently thought to be uncommon. However, data concerning CRE or CREc occurrence and distribution in seafood are limited, and argue for implementation of ongoing or periodic surveillance.
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Affiliation(s)
- Daleen Loest
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - F. Carl Uhland
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Kaitlin M. Young
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Xian-Zhi Li
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Richard Reid-Smith
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Lauren M. Sherk
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
| | - Carolee A. Carson
- Centre for Food-borne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, Ontario, Canada
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17
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Delannoy S, Hoffer C, Youf R, Dauvergne E, Webb HE, Brauge T, Tran ML, Midelet G, Granier SA, Haenni M, Fach P, Brisabois A. High Throughput Screening of Antimicrobial Resistance Genes in Gram-Negative Seafood Bacteria. Microorganisms 2022; 10:microorganisms10061225. [PMID: 35744743 PMCID: PMC9230514 DOI: 10.3390/microorganisms10061225] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 01/24/2023] Open
Abstract
From a global view of antimicrobial resistance over different sectors, seafood and the marine environment are often considered as potential reservoirs of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs); however, there are few studies and sparse results on this sector. This study aims to provide new data and insights regarding the content of resistance markers in various seafood samples and sources, and therefore the potential exposure to humans in a global One Health approach. An innovative high throughput qPCR screening was developed and validated in order to simultaneously investigate the presence of 41 ARGs and 33 MGEs including plasmid replicons, integrons, and insertion sequences in Gram-negative bacteria. Analysis of 268 seafood isolates from the bacterial microflora of cod (n = 24), shellfish (n = 66), flat fishes (n = 53), shrimp (n = 10), and horse mackerel (n = 115) show the occurrence of sul-1, ant(3″)-Ia, aph(3')-Ia, strA, strB, dfrA1, qnrA, and blaCTX-M-9 genes in Pseudomonas spp., Providencia spp., Klebsiella spp., Proteus spp., and Shewanella spp. isolates and the presence of MGEs in all bacterial species investigated. We found that the occurrence of MGE may be associated with the seafood type and the environmental, farming, and harvest conditions. Moreover, even if MGE were detected in half of the seafood isolates investigated, association with ARG was only identified for twelve isolates. The results corroborate the hypothesis that the incidence of antimicrobial-resistant bacteria (ARB) and ARG decreases with increasing distance from potential sources of fecal contamination. This unique and original high throughput micro-array designed for the screening of ARG and MGE in Gram-negative bacteria could be easily implementable for monitoring antimicrobial resistance gene markers in diverse contexts.
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Affiliation(s)
- Sabine Delannoy
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
- Correspondence:
| | - Corine Hoffer
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Raphaëlle Youf
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Emilie Dauvergne
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Hattie E. Webb
- Department of Animal and Food Sciences, International Center for Food Safety Excellence, Texas Tech University, Lubbock, TX 79409, USA;
| | - Thomas Brauge
- Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Laboratory for Food Safety, ANSES, 62200 Boulogne-sur-Mer, France; (T.B.); (G.M.)
| | - Mai-Lan Tran
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Graziella Midelet
- Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Laboratory for Food Safety, ANSES, 62200 Boulogne-sur-Mer, France; (T.B.); (G.M.)
| | - Sophie A. Granier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, ANSES, 35306 Fougères, France;
| | - Marisa Haenni
- Antimicrobial Resistance and Bacterial Virulence Unit, Lyon Laboratory, Université de Lyon, ANSES, 69364 Lyon, France;
| | - Patrick Fach
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Anne Brisabois
- Strategy and Programs Department, ANSES, 94700 Maisons-Alfort, France;
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18
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Bardhan A, Abraham TJ, Singha J, Saha S, Sarker S, Patil PK. The effects of extended feeding of florfenicol coated medicated diets on the safety, serum biomarkers and blood cells morphology of Nile tilapia Oreochromis niloticus (L.). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:39914-39927. [PMID: 35112251 DOI: 10.1007/s11356-021-18418-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Tilapia is one of the most consumed farmed fish, which requires the use of antibiotics in certain phases of its production. This study assessed the safety of 30 days of oral florfenicol (FFC) dosing at 0-10 times the therapeutic dose (1 × : 10 mg/kg biomass/day) in Oreochromis niloticus juveniles. Behavioural changes, feed consumption, mortality and biomass were evaluated. Besides, the levels of serum glucose, calcium, chloride, creatinine, alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase and blood cell morphology were determined at scheduled intervals. The 30 days of oral FFC dosing caused 3.33% (1 ×) to 18.33% (10 ×) mortalities, reduced feed intake and biomass in a dose-dependent manner. The fish fed the therapeutic dose recorded 1.25-fold increase in biomass, while the control group recorded 1.45-fold increase in 30 days. No significant erythrocyte morphological alterations were observed in the 1 × group compared to the control. However, marked morphological alterations like tear-shaped, spindle-shaped and degenerative erythrocytes in higher dosing groups indicated FFC cytotoxicity. All the serum biomarkers of O. niloticus increased significantly on day 10 and day 30 FFC dosing in a dose-dependent manner, except for calcium and chloride, which reduced significantly during the dosing period. Within 2 weeks of suspension of FFC dosing, the serum biomarker levels became normal except for alkaline phosphatase and creatinine. The recovery of biomass, feed intake, serum biomarker levels and erythrocyte morphological changes suggested that the FFC-induced changes are reversible. This study has, thus, proclaimed the safety of FFC at the therapeutic dose in O. niloticus.
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Affiliation(s)
- Avishek Bardhan
- Department of Aquatic Animal Health, Faculty of Fishery Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata, 700094, West Bengal, India
| | - Thangapalam Jawahar Abraham
- Department of Aquatic Animal Health, Faculty of Fishery Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata, 700094, West Bengal, India.
| | - Jasmine Singha
- Department of Aquatic Animal Health, Faculty of Fishery Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata, 700094, West Bengal, India
| | - Suchismita Saha
- Department of Aquatic Animal Health, Faculty of Fishery Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata, 700094, West Bengal, India
| | - Sudeshna Sarker
- Department of Aquatic Animal Health, Faculty of Fishery Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata, 700094, West Bengal, India
| | - Prasanna Kumar Patil
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Raja Annamalai Puram, Chennai, 600028, Tamil Nadu, India
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Qualitative Risk Assessment for Antimicrobial Resistance among Humans from Salmon Fillet Consumption Due to the High Use of Antibiotics against Bacterial Infections in Farmed Salmon. Antibiotics (Basel) 2022; 11:antibiotics11050662. [PMID: 35625306 PMCID: PMC9137906 DOI: 10.3390/antibiotics11050662] [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: 03/31/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Worldwide, aquaculture is considered as a hotspot environment for antimicrobial resistance (AMR) due to the intense use of antibiotics in its productive systems. Chile is the second largest producer of farmed salmon worldwide, and tons of antibiotics are used to control bacterial diseases, such as Salmon Rickettsial Syndrome (SRS) and Bacterial Kidney Disease (BKD). However, studies determining the risk of consuming salmon fillets that have been treated with antibiotics during the salmon production are limited. Consulting leading experts in the field could provide a knowledge base to identify and address this question and research gaps. Methods: Multisectoral risk perception of AMR through salmon fillet consumption was evaluated by eliciting expert data obtained through discussions during a workshop and from questionnaires given to experts from academia (n = 15, 63%), the public sector (n = 5, 21%), and the salmon industry (n = 4, 17%). Results: The qualitative risk analysis suggested an overall ‘low’ probability of AMR acquisition by consumption of salmon fillet that had been treated during the production cycle. The risk perception varied slightly between production stages in freshwater and seawater. In consensus with all sectors, this overall ‘low’, but existing, risk was probably associated with bacterial infections and the use of antibiotics. Conclusions: As it is essential to reduce the use of antibiotics in the Chilean salmon industry, this intersectoral approach and consensual results could favor effective implementation of targeted initiatives for the control and prevention of major bacterial diseases.
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Strategies for Enzymatic Inactivation of the Veterinary Antibiotic Florfenicol. Antibiotics (Basel) 2022; 11:antibiotics11040443. [PMID: 35453195 PMCID: PMC9029715 DOI: 10.3390/antibiotics11040443] [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: 03/07/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
Large quantities of the antibiotic florfenicol are used in animal farming and aquaculture, contaminating the ecosystem with antibiotic residues and promoting antimicrobial resistance, ultimately leading to untreatable multidrug-resistant pathogens. Florfenicol-resistant bacteria often activate export mechanisms that result in resistance to various structurally unrelated antibiotics. We devised novel strategies for the enzymatic inactivation of florfenicol in different media, such as saltwater or milk. Using a combinatorial approach and selection, we optimized a hydrolase (EstDL136) for florfenicol cleavage. Reaction kinetics were followed by time-resolved NMR spectroscopy. Importantly, the hydrolase remained active in different media, such as saltwater or cow milk. Various environmentally-friendly application strategies for florfenicol inactivation were developed using the optimized hydrolase. As a potential filter device for cost-effective treatment of waste milk or aquacultural wastewater, the hydrolase was immobilized on Ni-NTA agarose or silica as carrier materials. In two further application examples, the hydrolase was used as cell extract or encapsulated with a semi-permeable membrane. This facilitated, for example, florfenicol inactivation in whole milk, which can help to treat waste milk from medicated cows, to be fed to calves without the risk of inducing antibiotic resistance. Enzymatic inactivation of antibiotics, in general, enables therapeutic intervention without promoting antibiotic resistance.
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21
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Ramírez C, Gutiérrez MS, Venegas L, Sapag C, Araya C, Caruffo M, López P, Reyes-Jara A, Toro M, González-Rocha G, Yáñez JM, Navarrete P. Microbiota composition and susceptibility to florfenicol and oxytetracycline of bacterial isolates from mussels (Mytilus spp.) reared on different years and distance from salmon farms. ENVIRONMENTAL RESEARCH 2022; 204:112068. [PMID: 34547250 DOI: 10.1016/j.envres.2021.112068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/05/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Chilean aquaculture mainly produces salmonids and molluscs. Salmonid production has been questioned by its excessive use of antimicrobials. This study aimed to investigate the bacterial microbiota composition of Mytilus spp. cultivated near salmonid farms and to determine the minimum inhibitory concentration (MIC) to florfenicol and oxytetracycline of its culturable bacteria. Seven Mytilus farming sites classified according to their proximity to salmon farms as close (CSF) or distant (DSF) were sampled in two years. We analyzed Mytilus microbiota composition through culture-independent methods, and isolated culturable bacteria, and identified those isolates with MIC values ≥ 64 μg mL-1 to florfenicol or oxytetracycline. Results revealed that the alpha diversity was affected by sampling year but not by Mytilus farming site location or its interaction. Nevertheless, in 2018, we observed a significant negative correlation between the alpha diversity of Mytilus microbiota in each farm sites and the tonnes of florfenicol reported for each phytosanitary management area. We detected significant differences in beta diversity and relative abundance of specific bacterial taxa in Mytilus microbiota depending on the proximity to salmon farms and years. A higher proportion of isolates with MIC values ≥ 64 μg mL-1 to both antibiotics was detected in 2019 compared to 2018, but not significant differences were detected according to Mytilus farming site location. However, in 2019, isolates from CSF sites showed higher MIC values for both antibiotics than those from DSF. Bacterial genera corresponding to isolates with MIC values ≥ 64 μg mL-1 represented a low proportion of Mytilus microbiota identified with the culture-independent approach, reflecting the need to implement new methodologies in the study of antimicrobial resistance. These results suggest that the proximity to salmonid farms and sampling year influence the Mytilus microbiota and MIC values of their bacterial isolates; however, other environmental variables should be considered in further studies.
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Affiliation(s)
- Carolina Ramírez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - María Soledad Gutiérrez
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile; ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Chile
| | - Lucas Venegas
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | | | - Carolina Araya
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Mario Caruffo
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Paulina López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Angélica Reyes-Jara
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Magaly Toro
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Chile; Millennium Nucleus for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - José Manuel Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile; Núcleo Milenio INVASAL, Concepción, Chile
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Chile; ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Chile.
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22
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Gavric D, Knezevic P. Optimized Method for Pseudomonas aeruginosa Integrative Filamentous Bacteriophage Propagation. Front Microbiol 2022; 12:707815. [PMID: 35095778 PMCID: PMC8790315 DOI: 10.3389/fmicb.2021.707815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Filamentous bacteriophages frequently infect Pseudomonas aeruginosa and alter its phenotypic traits, including virulence factors. The first step in examination of these phages is to obtain suspensions with high virus titer, but as there are no methods for integrative filamentous phage multiplication, the aim was to design, describe, and compare two methods for this purpose. As models, three strains of Pseudomonas aeruginosa, containing (pro)phages Pf4, Pf5, and PfLES were used (PAO1, UCBPP-PA14, and LESB58, respectively). Method 1 comprised propagation of phages in 6 L of bacterial culture for 48 h, and method 2 applied 600 mL culture and incubation for 6 days with centrifugation and addition of new medium and inoculum at 2-day intervals. In method 1, phages were propagated by culture agitation, followed by centrifugation and filtration (0.45 and 0.22 μm), and in method 2, cultures were agitated and centrifuged several times to remove bacteria without filtration. Regardless of the propagation method, supernatants were subjected to concentration by PEG8000 and CsCl equilibrium density gradient centrifugation, and phage bands were removed after ultracentrifugation and dialyzed. In the obtained suspensions, phage titer was determined, and concentration of isolated ssDNA from virions was measured. When propagation method 2 was compared with method 1, the phage bands in CsCl were much thicker, phage number was 3.5–7.4 logs greater, and concentration of ssDNA was 7.6–22.4 times higher. When phage count was monitored from days 2 to 6, virion numbers increased for 1.8–5.6 logs, depending on phage. We also observed that filamentous phage plaques faded after 8 h of incubation when the double layer agar spot method was applied, whereas the plaques were visible for 24 h on single-layer agar. Finally, for the first time, we confirmed existence of replicative form and virions of PfLES (pro)phage as well as its ability to produce plaques. Similarly, for the first time, we confirmed plaque production of Pf5 (pro)phage present in P. aeruginosa strain UCBPP-PA14. The described method 2 has many advantages and can be further improved and adopted for filamentous phages of other hosts.
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Affiliation(s)
- Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
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23
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González-Gaya B, García-Bueno N, Buelow E, Marin A, Rico A. Effects of aquaculture waste feeds and antibiotics on marine benthic ecosystems in the Mediterranean Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151190. [PMID: 34710419 DOI: 10.1016/j.scitotenv.2021.151190] [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: 05/26/2021] [Revised: 09/20/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Intensive aquaculture is an important source of organic waste and antibiotics into the marine environment. Yet, their impacts on benthic marine ecosystems are poorly understood. Here, we investigated the ecological impacts of fish feed waste alone and in combination with three different antibiotics (i.e., oxytetracycline, florfenicol and flumequine) in benthic ecosystems of the Mediterranean Sea by performing a field experiment. We assessed the fate of the antibiotics in the sediment and their accumulation in wild fauna after two weeks of exposure. Moreover, we investigated the impact of the feed waste alone and in combination with the antibiotics on sediment physico-chemical properties, on benthic invertebrates, as well as on the microbiota and resistome of the sampled sediments. One week after the last antibiotic application, average oxytetracycline and flumequine concentrations in the sediment were <1% and 15% of the applied dose, respectively, while florfenicol was not detected. Flumequine concentrations in wild invertebrates reached 3 μg g-1, while concentrations of oxytetracycline were about an order of magnitude lower, and florfenicol was not detected. Feed waste, with and without antibiotics, increased the concentration of fine particulate matter, affected the pH and redox conditions, and significantly reduced the biodiversity and abundance of benthic invertebrates. Feed waste also had a significant influence on the structure of sediment microbial communities, while specific effects related to the different antibiotics ranged from insignificant to mild. The presence of antibiotics significantly influenced the normalized abundance of the measured antibiotic resistance genes. Florfenicol and oxytetracycline contributed to an increase of genes conferring resistance to macrolides, tetracyclines, aminoglycosides and chloramphenicol, while flumequine had a less clear impact on the sediment resistome. This study demonstrates that feed waste from aquaculture farms can rapidly alter the habitat and biodiversity of Mediterranean benthic ecosystems, while antibiotic residual concentrations can contribute to the enrichment of bacterial genes resistant to antibiotic classes that are of high relevance for human medicine.
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Affiliation(s)
- Belén González-Gaya
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805 Alcalá de Henares, Madrid, Spain; Research Centre for Experimental Marine Biology and Biotechnology, University of the Basque Country (PiE-UPV/EHU), Areatza Pasealekua 47, 48620 Plentzia, Basque Country, Spain; Department of Analytical Chemistry, Science and Technology Faculty, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, 48940 Leioa, Basque Country, Spain
| | - Nuria García-Bueno
- Murcia University, Ecology and Hydrology department, Biology Faculty, University campus of Espinardo, 30100 Murcia, Spain
| | - Elena Buelow
- University Limoges, INSERM, CHU Limoges, RESINFIT, U1092, F-87000 Limoges, France; University Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Institut Jean Roget, Domaine de la Merci, BP170, 38042 Grenoble Cedex 9, Grenoble, France
| | - Arnaldo Marin
- Murcia University, Ecology and Hydrology department, Biology Faculty, University campus of Espinardo, 30100 Murcia, Spain
| | - Andreu Rico
- IMDEA Water Institute, Science and Technology Campus of the University of Alcalá, Avenida Punto Com 2, 28805 Alcalá de Henares, Madrid, Spain; Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, c/ Catedrático José Beltrán 2, 46980 Paterna, Valencia, Spain.
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24
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Vásquez-Ponce F, Higuera-Llantén S, Parás-Silva J, Gamboa-Acuña N, Cortés J, Opazo-Capurro A, Ugalde JA, Alcalde-Rico M, Olivares-Pacheco J. Genetic characterization of clinically relevant class 1 integrons carried by multi-drug resistant bacteria (MDRB) isolated from the gut microbiota of highly antibiotic treated Salmo salar. J Glob Antimicrob Resist 2022; 29:55-62. [DOI: 10.1016/j.jgar.2022.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/08/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
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25
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Kaszab E, Farkas M, Radó J, Micsinai A, Nyírő-Fekete B, Szabó I, Kriszt B, Urbányi B, Szoboszlay S. Novel members of bacterial community during a short-term chilled storage of common carp (Cyprinus carpio). Folia Microbiol (Praha) 2021; 67:299-310. [PMID: 34877630 PMCID: PMC8933370 DOI: 10.1007/s12223-021-00935-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022]
Abstract
This work aimed to identify the key members of the bacterial community growing on common carp (Cyprinus carpio) fillets during chilled storage with next-generation sequencing (NGS) and cultivation-dependent methods. Carp fillets were stored for 96 h at 2 °C and 6 °C with and without a vacuum package, and an additional frozen-thawed storage experiment was set for 120 days. Community profiles of the initial and stored fish samples were determined by amplicon sequencing. Conventional microbial methods were used parallelly for the enumeration and cultivation of the dominant members of the microbial community. Cultivated bacteria were identified with 16S rRNA sequencing and the MALDI-TOF MS method. Based on our results, the vacuum package greatly affected the diversity and composition of the forming microbial community, while temperature influenced the cell counts and consequently the microbiological criteria for shelf-life of the examined raw fish product. Next-generation sequencing revealed novel members of the chilled flesh microbiota such as Vagococcus vulneris or Rouxiella chamberiensis in the vacuum-packed samples. With traditional cultivation, 161 bacterial strains were isolated and identified at the species level, but the identified bacteria overlapped with only 45% of the dominant operational taxonomic units (OTUs) revealed by NGS. Next-generation sequencing is a promising and highly reliable tool recommended to reach a higher resolution of the forming microbial community of stored fish products. Knowledge of the initial microbial community of the flesh enables further optimization and development of processing and storage technology.
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Affiliation(s)
- Edit Kaszab
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 1 Páter Károly, 2100, Gödöllő, Hungary.
| | - Milán Farkas
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 1 Páter Károly, 2100, Gödöllő, Hungary
| | - Júlia Radó
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 1 Páter Károly, 2100, Gödöllő, Hungary
| | | | | | - István Szabó
- Department of Environmental Toxicology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 1 Páter Károly, 2100, Gödöllő, Hungary
| | - Balázs Kriszt
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 1 Páter Károly, 2100, Gödöllő, Hungary
| | - Béla Urbányi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 1 Páter Károly, 2100, Gödöllő, Hungary
| | - Sándor Szoboszlay
- Department of Environmental Safety, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, 1 Páter Károly, 2100, Gödöllő, Hungary
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26
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Behera BK, Dehury B, Rout AK, Patra B, Mantri N, Chakraborty HJ, Sarkar DJ, Kaushik NK, Bansal V, Singh I, Das BK, Rao AR, Rai A. Metagenomics study in aquatic resource management: Recent trends, applied methodologies and future needs. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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27
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Álvarez de Haro N, Van AP, Robb CT, Rossi AG, Desbois AP. Release of chromatin extracellular traps by phagocytes of Atlantic salmon, Salmo salar (Linnaeus, 1758). FISH & SHELLFISH IMMUNOLOGY 2021; 119:209-219. [PMID: 34438058 PMCID: PMC8653909 DOI: 10.1016/j.fsi.2021.08.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 05/05/2023]
Abstract
Neutrophils release chromatin extracellular traps (ETs) as part of the fish innate immune response to counter the threats posed by microbial pathogens. However, relatively little attention has been paid to this phenomenon in many commercially farmed species, despite the importance of understanding host-pathogen interactions and the potential to influence ET release to reduce disease outbreaks. The aim of this present study was to investigate the release of ETs by Atlantic salmon (Salmo salar L.) immune cells. Extracellular structures resembling ETs of different morphology were observed by fluorescence microscopy in neutrophil suspensions in vitro, as these structures stained positively with Sytox Green and were digestible with DNase I. Immunofluorescence studies confirmed the ET structures to be decorated with histones H1 and H2A and neutrophil elastase, which are characteristic for ETs in mammals and other organisms. Although the ETs were released spontaneously, release in neutrophil suspensions was stimulated most significantly with 5 μg/ml calcium ionophore (CaI) for 1 h, whilst the fish pathogenic bacterium Aeromonas salmonicida (isolates 30411 and Hooke) also exerted a stimulatory effect. Microscopic observations revealed bacteria in association with ETs, and fewer bacterial colonies of A. salmonicida Hooke were recovered at 3 h after co-incubation with neutrophils that had been induced to release ETs. Interestingly, spontaneous release of ETs was inversely associated with fish mass (p < 0.05), a surrogate for age. Moreover, suspensions enriched for macrophages and stimulated with 5 μg/ml CaI released ET-like structures that occasionally led to the formation of large clumps of cells. A deeper understanding for the roles and functions of ETs within innate immunity of fish hosts, and their interaction with microbial pathogens, may open new avenues towards protecting cultured stocks against infectious diseases.
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Affiliation(s)
- Neila Álvarez de Haro
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Andre P Van
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Calum T Robb
- University of Edinburgh, Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, United Kingdom
| | - Adriano G Rossi
- University of Edinburgh, Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, United Kingdom
| | - Andrew P Desbois
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom.
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28
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Ortiz-Severín J, Stuardo CJ, Jiménez NE, Palma R, Cortés MP, Maldonado J, Maass A, Cambiazo V. Nutrient Scarcity in a New Defined Medium Reveals Metabolic Resistance to Antibiotics in the Fish Pathogen Piscirickettsia salmonis. Front Microbiol 2021; 12:734239. [PMID: 34707589 PMCID: PMC8542936 DOI: 10.3389/fmicb.2021.734239] [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: 06/30/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Extensive use of antibiotics has been the primary treatment for the Salmonid Rickettsial Septicemia, a salmonid disease caused by the bacterium Piscirickettsia salmonis. Occurrence of antibiotic resistance has been explored in various P. salmonis isolates using different assays; however, P. salmonis is a nutritionally demanding intracellular facultative pathogen; thus, assessing its antibiotic susceptibility with standardized and validated protocols is essential. In this work, we studied the pathogen response to antibiotics using a genomic, a transcriptomic, and a phenotypic approach. A new defined medium (CMMAB) was developed based on a metabolic model of P. salmonis. CMMAB was formulated to increase bacterial growth in nutrient-limited conditions and to be suitable for performing antibiotic susceptibility tests. Antibiotic resistance was evaluated based on a comprehensive search of antibiotic resistance genes (ARGs) from P. salmonis genomes. Minimum inhibitory concentration assays were conducted to test the pathogen susceptibility to antibiotics from drug categories with predicted ARGs. In all tested P. salmonis strains, resistance to erythromycin, ampicillin, penicillin G, streptomycin, spectinomycin, polymyxin B, ceftazidime, and trimethoprim was medium-dependent, showing resistance to higher antibiotic concentrations in the CMMAB medium. The mechanism for antibiotic resistance to ampicillin in the defined medium was further explored and was proven to be associated to a decrease in the bacterial central metabolism, including the TCA cycle, the pentose-phosphate pathway, energy production, and nucleotide metabolism, and it was not associated with decreased growth rate of the bacterium or with the expression of any predicted ARG. Our results suggest that nutrient scarcity plays a role in the bacterial antibiotic resistance, protecting against the detrimental effects of antibiotics, and thus, we propose that P. salmonis exhibits a metabolic resistance to ampicillin when growing in a nutrient-limited medium.
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Affiliation(s)
- Javiera Ortiz-Severín
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Fondap Center for Genome Regulation (Fondap 15200002), Universidad de Chile, Santiago, Chile
| | - Camila J Stuardo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Natalia E Jiménez
- Fondap Center for Genome Regulation (Fondap 15200002), Universidad de Chile, Santiago, Chile.,Centro de Modelamiento Matemático (AFB170001), Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile and UMI-CNRS 2807, Santiago, Chile
| | - Ricardo Palma
- Fondap Center for Genome Regulation (Fondap 15200002), Universidad de Chile, Santiago, Chile.,Centro de Modelamiento Matemático (AFB170001), Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile and UMI-CNRS 2807, Santiago, Chile
| | - María P Cortés
- Fondap Center for Genome Regulation (Fondap 15200002), Universidad de Chile, Santiago, Chile.,Centro de Modelamiento Matemático (AFB170001), Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile and UMI-CNRS 2807, Santiago, Chile
| | - Jonathan Maldonado
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Fondap Center for Genome Regulation (Fondap 15200002), Universidad de Chile, Santiago, Chile
| | - Alejandro Maass
- Fondap Center for Genome Regulation (Fondap 15200002), Universidad de Chile, Santiago, Chile.,Centro de Modelamiento Matemático (AFB170001), Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile and UMI-CNRS 2807, Santiago, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile.,Fondap Center for Genome Regulation (Fondap 15200002), Universidad de Chile, Santiago, Chile
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Díaz-Gavidia C, Barría C, Rivas L, García P, Alvarez FP, González-Rocha G, Opazo-Capurro A, Araos R, Munita JM, Cortes S, Olivares-Pacheco J, Adell AD, Moreno-Switt AI. Isolation of Ciprofloxacin and Ceftazidime-Resistant Enterobacterales From Vegetables and River Water Is Strongly Associated With the Season and the Sample Type. Front Microbiol 2021; 12:604567. [PMID: 34594307 PMCID: PMC8477802 DOI: 10.3389/fmicb.2021.604567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 08/12/2021] [Indexed: 12/03/2022] Open
Abstract
The dissemination of antibiotic-resistant bacteria (ARB) from water used for crop irrigation to vegetables is poorly studied. During a year, five farmer markets in a city in Central Chile were visited, and 478 vegetable samples (parsleys, corianders, celeries, lettuces, chards, and beets) were collected. Simultaneously, 32 water samples were collected from two rivers which are used to irrigate the vegetables produced in the area. Resistant Enterobacterales were isolated and identified. Colistin resistance gene mcr-1 and extended spectrum β-lactamases (ESBL) were molecularly detected. The association of environmental factors was evaluated, with the outcomes being the presence of Enterobacterales resistant to four antibiotic families and the presence of multidrug resistance (MDR) phenotypes. Parsley, coriander, and celery showed the highest prevalence of resistant Enterobacterales (41.9% for ciprofloxacin and 18.5% for ceftazidime). A total of 155 isolates were obtained, including Escherichia coli (n=109), Citrobacter sp. (n=20), Enterobacter cloacae complex (n=8), Klebsiella pneumoniae (n=8), and Klebsiella aerogenes (n=1). Resistance to ampicillin (63.2%) and ciprofloxacin (74.2%) was most frequently found; 34.5% of the isolates showed resistance to third-generation cephalosporins, and the MDR phenotype represented 51.6% of the isolates. In two E. coli isolates (1.29%), the gene mcr-1 was found and ESBL genes were found in 23/62 isolates (37%), with blaCTX-M being the most frequently found in 20 isolates (32%). Resistant Enterobacterales isolated during the rainy season were less likely to be MDR as compared to the dry season. Understanding environmental associations represent the first step toward an improved understanding of the public health impact of ARB in vegetables and water.
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Affiliation(s)
- Constanza Díaz-Gavidia
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Carla Barría
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Lina Rivas
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile.,Genomics and Resistant Microbes Group, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Patricia García
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile.,Escuela de Medicina, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisca P Alvarez
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Gerardo González-Rocha
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile.,Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Andrés Opazo-Capurro
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile.,Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Rafael Araos
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile.,Genomics and Resistant Microbes Group, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - José M Munita
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile.,Genomics and Resistant Microbes Group, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Sandra Cortes
- Escuela de Medicina, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Advance Center for Chronic Diseases (ACCDiS), Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Centro de Desarrollo Urbano Sustentable, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jorge Olivares-Pacheco
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile.,Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Aiko D Adell
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Andrea I Moreno-Switt
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile.,Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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30
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 7: Amphenicols: florfenicol and thiamphenicol. EFSA J 2021; 19:e06859. [PMID: 34729087 PMCID: PMC8546524 DOI: 10.2903/j.efsa.2021.6859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The specific concentrations of florfenicol and thiamphenicol in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield, were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. The FARSC for florfenicol was estimated. However, due to the lack of data, the calculation of the FARSC for thiamphenicol was not possible until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for florfenicol, whilst for thiamphenicol no suitable data for the assessment were available. Uncertainties and data gaps associated to the levels reported were addressed. For florfenicol, it was recommended to perform further studies to supply more diverse and complete data related to the requirements for calculation of the FARSC, whereas for thiamphenicol, the recommendation was to generate the data required to fill the gaps which prevented the FARSC calculation.
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31
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Abdelraheem WM, Khairy RMM, Zaki AI, Zaki SH. Effect of ZnO nanoparticles on methicillin, vancomycin, linezolid resistance and biofilm formation in Staphylococcus aureus isolates. Ann Clin Microbiol Antimicrob 2021; 20:54. [PMID: 34419054 PMCID: PMC8379777 DOI: 10.1186/s12941-021-00459-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/12/2021] [Indexed: 12/25/2022] Open
Abstract
Background Multidrug resistant (MDR) and biofilm producing Staphylococcus aureus strains are usually associated with serious infections. This study aimed to evaluate the antibacterial and antibiofilm-formation effects of zinc oxide nanoparticles (ZnO-NPs) against staphylococcus aureus (S. aureus) isolates. Methods A total of 116 S. aureus isolates were recovered from 250 burn wound samples. The antimicrobial/antibiofilm effects of ZnO-NPs against methicillin, vancomycin and linezolid resistant S. aureus (MRSA, VRSA and LRSA) isolates were examined using phenotypic and genotypic methods. The minimum inhibitory concentration (MIC) of ZnO-NPs was determined by microdilution method. The effects of sub-MIC concentrations of ZnO-NPs on biofilm formation and drug resistance in S. aureus were determined by the microtiter plate method. The change in the expression levels of the biofilm encoding genes and resistance genes in S. aureus isolates after treatment with ZnO-NPs was assessed by real time reverse transcriptase PCR (rt-PCR). Results MICs of ZnO-NPs in S. aureus isolates were (128–2048 µg/ml). The sub-MIC of ZnO-NPs significantly reduced biofilm formation rate (the highest inhibition rate was 76.47% at 1024 µg/ml) and the expression levels of biofilm genes (ica A, ica D and fnb A) with P < 0.001. Moreover, Sub-MIC of ZnO-NPs significantly reduced the rates of MRSA from 81.9 (95 isolates) to 13.30% (15 isolates), VRSA from 33.60 (39 isolates) to 0% and LARSA from 29.30 (34) to 0% as well as the expression levels of resistance genes (mec A, van A and cfr) with P value < 0.001. Conclusion ZnO-NPs can be used as antibiofilm and potent antimicrobial against MRSA, VRSA and LRSA isolates. Supplementary Information The online version contains supplementary material available at 10.1186/s12941-021-00459-2.
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Affiliation(s)
- Wedad M Abdelraheem
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
| | - Rasha M M Khairy
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt.
| | - Alaa I Zaki
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
| | - Shaimaa H Zaki
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
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Bornbusch SL, Drea CM. Antibiotic Resistance Genes in Lemur Gut and Soil Microbiota Along a Gradient of Anthropogenic Disturbance. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.704070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The overuse of man-made antibiotics has facilitated the global propagation of antibiotic resistance genes in animals, across natural and anthropogenically disturbed environments. Although antibiotic treatment is the most well-studied route by which resistance genes can develop and spread within host-associated microbiota, resistomes also can be acquired or enriched via more indirect routes, such as via transmission between hosts or via contact with antibiotic-contaminated matter within the environment. Relatively little is known about the impacts of anthropogenic disturbance on reservoirs of resistance genes in wildlife and their environments. We therefore tested for (a) antibiotic resistance genes in primate hosts experiencing different severities and types of anthropogenic disturbance (i.e., non-wildlife animal presence, human presence, direct human contact, and antibiotic treatment), and (b) covariation between host-associated and environmental resistomes. We used shotgun metagenomic sequencing of ring-tailed lemur (Lemur catta) gut resistomes and associated soil resistomes sampled from up to 10 sites: seven in the wilderness of Madagascar and three in captivity in Madagascar or the United States. We found that, compared to wild lemurs, captive lemurs harbored greater abundances of resistance genes, but not necessarily more diverse resistomes. Abundances of resistance genes were positively correlated with our assessments of anthropogenic disturbance, a pattern that was robust across all ten lemur populations. The composition of lemur resistomes was site-specific and the types of resistance genes reflected antibiotic usage in the country of origin, such as vancomycin use in Madagascar. We found support for multiple routes of ARG enrichment (e.g., via human contact, antibiotic treatment, and environmental acquisition) that differed across lemur populations, but could result in similar degrees of enrichment. Soil resistomes varied across natural habitats in Madagascar and, at sites with greater anthropogenic disturbance, lemurs and soil resistomes covaried. As one of the broadest, single-species investigations of wildlife resistomes to date, we show that the transmission and enrichment of antibiotic resistance genes varies across environments, thereby adding to the mounting evidence that the resistance crisis extends outside of traditional clinical settings.
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33
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Effects of elderflower extract enriched with polyphenols on antioxidant defense of salmon leukocytes. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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34
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Lozano-Muñoz I, Wacyk J, Kretschmer C, Vásquez-Martínez Y, Martin MCS. Antimicrobial resistance in Chilean marine-farmed salmon: Improving food safety through One Health. One Health 2021; 12:100219. [PMID: 33553565 PMCID: PMC7856317 DOI: 10.1016/j.onehlt.2021.100219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/17/2021] [Accepted: 01/21/2021] [Indexed: 12/25/2022] Open
Abstract
Aquaculture is seen as an essential requirement for improving food security and nutrition. Fish such as salmonids are a primary source of protein and essential nutrients. Aquaculture provide income for communities across the world and have a smaller carbon footprint than terrestrial animal-production systems. However, fish diseases are a constant threat, and the use of antibiotics is a source of concern due to its adverse impacts on the environment and human health. Chilean salmon farming has made several efforts to reduce the use of antibiotics for the eradication of piscirickettsiosis, a disease caused by the gram-negative bacteria Piscirickettsia salmonis. Excessive amounts of antibiotics continue to be used in Chilean aquaculture, playing an important role in the emerging public health crisis of antimicrobial resistance. Without doubt, P. salmonis is becoming increasingly resistant to important frontline antimicrobial classes, with severe implications for the future treatment of infectious human and animal diseases. Antimicrobial-resistant bacteria as well as antibiotic residues from salmon production are spreading in the environment, and thus both salmon food commodities and wild organisms can become a source of resistant bacteria that can be transmitted to humans as foodborne contaminants. This urgent threat needs to be addressed by implementing national strategies in compliance with international standards that include both prudent antimicrobial use in marine salmon farms and the investment towards a One Health approach, which combines human, animal and environmental health.
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Affiliation(s)
- Ivonne Lozano-Muñoz
- Laboratorio de Nutrición, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Región Metropolitana CP 8820808, Chile
| | - Jurij Wacyk
- Laboratorio de Nutrición, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Región Metropolitana CP 8820808, Chile
| | - Cristina Kretschmer
- Laboratorio de Nutrición, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Región Metropolitana CP 8820808, Chile
| | - Yesseny Vásquez-Martínez
- Laboratorio de Virología Molecular y Control de Patógenos, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’higgins 3363, Santiago, Región Metropolitana CP 9170022, Chile
- Programa Centro de Investigación Biomédica Aplicada, Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Av. Libertador Bernardo O’Higgins 3363, Santiago, Región Metropolitana CP 9170022, Chile
| | - Marcelo Cortez-San Martin
- Laboratorio de Virología Molecular y Control de Patógenos, Facultad de Química y Biología, Universidad de Santiago de Chile, Av. Libertador Bernardo O’higgins 3363, Santiago, Región Metropolitana CP 9170022, Chile
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Manure Microbial Communities and Resistance Profiles Reconfigure after Transition to Manure Pits and Differ from Those in Fertilized Field Soil. mBio 2021; 12:mBio.00798-21. [PMID: 33975936 PMCID: PMC8262906 DOI: 10.1128/mbio.00798-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, we collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons. We used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms. We found that as the microbiome transitions from fresh dairy cow manure to manure pits, microbial taxonomic compositions and resistance profiles experience distinct restructuring, including decreases in alpha diversity and shifts in specific ARG abundances that potentially correspond to fresh manure going from a gut-structured community to an environment-structured community. Further, we did not find evidence of shared microbial community or a transfer of ARGs between manure and field soil microbiomes. Our results suggest that fresh manure experiences a compositional change in manure pits during storage and that the storage of manure in manure pits does not result in a depletion of ARGs. We did not find evidence of taxonomic or ARG restructuring of soil microbiota with the application of manure to field soils, as soil communities remained resilient to manure-induced perturbation.
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Crescenzo G, Tinelli A, Centoducati G, Zizzadoro C, Leone R, Piccinno M, Lai O. Residue depletion and histopathological alterations in gilthead sea bream (Sparus aurata) after oral administration of oxytetracycline. JOURNAL OF APPLIED ANIMAL RESEARCH 2021. [DOI: 10.1080/09712119.2021.1921779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Giuseppe Crescenzo
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Bari 70010, Italy
| | - Antonella Tinelli
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Bari 70010, Italy
| | - Gerardo Centoducati
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Bari 70010, Italy
| | - Claudia Zizzadoro
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Bari 70010, Italy
| | - Rosa Leone
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Bari 70010, Italy
| | - Mariagrazia Piccinno
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Bari 70010, Italy
| | - Olimpia Lai
- Department of Veterinary Medicine, University of Bari “Aldo Moro”, Bari 70010, Italy
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Sazykin IS, Khmelevtsova LE, Seliverstova EY, Sazykina MA. Effect of Antibiotics Used in Animal Husbandry on the Distribution of Bacterial Drug Resistance (Review). APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821010166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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38
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Castañeda PS, Olvera LG, Bernad MJB, López HS, Escobar-Chávez JJ. Development of a Spectrophotometric Method for the Determination of Florfenicol in Eudragit Nanocapsules. Pharm Chem J 2021. [DOI: 10.1007/s11094-021-02340-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Salgueiro V, Manageiro V, Bandarra NM, Reis L, Ferreira E, Caniça M. Bacterial Diversity and Antibiotic Susceptibility of Sparus aurata from Aquaculture. Microorganisms 2020; 8:E1343. [PMID: 32887439 PMCID: PMC7564983 DOI: 10.3390/microorganisms8091343] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 02/02/2023] Open
Abstract
In a world where the population continues to increase and the volume of fishing catches stagnates or even falls, the aquaculture sector has great growth potential. This study aimed to contribute to the depth of knowledge of the diversity of bacterial species found in Sparus aurata collected from a fish farm and to understand which profiles of diminished susceptibility to antibiotics would be found in these bacteria that might be disseminated in the environment. One hundred thirty-six bacterial strains were recovered from the S. aurata samples. These strains belonged to Bacillaceae, Bacillales Family XII. Incertae Sedis, Comamonadaceae, Enterobacteriaceae, Enterococcaceae, Erwiniaceae, Micrococcaceae, Pseudomonadaceae and Staphylococcaceae families. Enterobacter sp. was more frequently found in gills, intestine and skin groups than in muscle groups (p ≤ 0.01). Antibiotic susceptibility tests found that non-susceptibility to phenicols was significantly higher in gills, intestine and skin samples (45%) than in muscle samples (24%) (p ≤ 0.01) and was the most frequently found non-susceptibility in both groups of samples. The group of Enterobacteriaceae from muscles presented less decreased susceptibility to florfenicol (44%) than in the group of gills, intestine and skin samples (76%). We found decreased susceptibilities to β-lactams and glycopeptides in the Bacillaceae family, to quinolones and mupirocin in the Staphylococcaceae family, and mostly to β-lactams, phenicols and quinolones in the Enterobacteriaceae and Pseudomonadaceae families. Seven Enterobacter spp. and five Pseudomonas spp. strains showed non-susceptibility to ertapenem and meropenem, respectively, which is of concern because they are antibiotics used as a last resort in serious clinical infections. To our knowledge, this is the first description of species Exiguobacterium acetylicum, Klebsiella michiganensis, Lelliottia sp. and Pantoea vagans associated with S. aurata (excluding cases where these bacteria are used as probiotics) and of plasmid-mediated quinolone resistance qnrB19-producing Leclercia adecarboxylata strain. The non-synonymous G385T and C402A mutations at parC gene (within quinolone resistance-determining regions) were also identified in a Klebsiella pneumoniae, revealing decreased susceptibility to ciprofloxacin. In this study, we found not only bacteria from the natural microbiota of fish but also pathogenic bacteria associated with fish and humans. Several antibiotics for which decreased susceptibility was found here are integrated into the World Health Organization list of "critically important antimicrobials" and "highly important antimicrobials" for human medicine.
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Affiliation(s)
- Vanessa Salgueiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR-HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (V.S.); (V.M.); (L.R.); (E.F.)
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4051-401 Oporto, Portugal
| | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR-HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (V.S.); (V.M.); (L.R.); (E.F.)
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4051-401 Oporto, Portugal
| | - Narcisa M. Bandarra
- Department of Sea and Marine Resources, Portuguese Institute for the Sea and Atmosphere (IPMA, IP), 1749-077 Lisbon, Portugal;
| | - Lígia Reis
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR-HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (V.S.); (V.M.); (L.R.); (E.F.)
| | - Eugénia Ferreira
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR-HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (V.S.); (V.M.); (L.R.); (E.F.)
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4051-401 Oporto, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR-HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (V.S.); (V.M.); (L.R.); (E.F.)
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4051-401 Oporto, Portugal
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Sustainable aquaculture through the One Health lens. ACTA ACUST UNITED AC 2020; 1:468-474. [PMID: 37128071 DOI: 10.1038/s43016-020-0127-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 07/07/2020] [Indexed: 01/08/2023]
Abstract
Aquaculture is predicted to supply the majority of aquatic dietary protein by 2050. For aquaculture to deliver significantly enhanced volumes of food in a sustainable manner, appropriate account needs to be taken of its impacts on environmental integrity, farmed organism health and welfare, and human health. Here, we explore increased aquaculture production through the One Health lens and define a set of success metrics - underpinned by evidence, policy and legislation - that must be embedded into aquaculture sustainability. We provide a framework for defining, monitoring and averting potential negative impacts of enhanced production - and consider interactions with land-based food systems. These metrics will inform national and international science and policy strategies to support improved aquatic food system design.
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Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota. Anim Microbiome 2020; 2:26. [PMID: 33499964 PMCID: PMC7807502 DOI: 10.1186/s42523-020-00046-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery and examination of these communities in fish of commercial importance is not well documented. Examining the impacts of antibiotics on farmed fish microbiota is fundamental for improving our understanding and management of healthy farmed fish. This work assessed yellowtail kingfish (Seriola lalandi) skin and gut bacterial communities after an oral antibiotic combination therapy in poor performing fish that displayed signs of enteritis over an 18-day period. In an attempt to promote improved bacterial re-establishment after antibiotic treatment, faecal microbiota transplantation (FMT) was also administered via gavage or in the surrounding seawater, and its affect was evaluated over 15 days post-delivery. RESULTS Antibiotic treatment greatly perturbed the global gut bacterial communities of poor-performing fish - an effect that lasted for up to 18 days post treatment. This perturbation was marked by a significant decrease in species diversity and evenness, as well as a concomitant increase in particular taxa like an uncultured Mycoplasmataceae sp., which persisted and dominated antibiotic-treated fish for the entire 18-day period. The skin-associated bacterial communities were also perturbed by the antibiotic treatment, notably within the first 3 days; however, this was unlike the gut, as skin microbiota appeared to shift towards a more 'normal' (though disparate) state after 5 days post antibiotic treatment. FMT was only able to modulate the impacts of antibiotics in some individuals for a short time period, as the magnitude of change varied substantially between individuals. Some fish maintained certain transplanted gut taxa (i.e. present in the FMT inoculum; namely various Aliivibrio related ASVs) at Day 2 post FMT, although these were lost by Day 8 post FMT. CONCLUSION As we observed notable, prolonged perturbations induced by antibiotics on the gut bacterial assemblages, further work is required to better understand the processes/dynamics of their re-establishment following antibiotic exposure. In this regard, procedures like FMT represent a novel approach for promoting improved microbial recovery, although their efficacy and the factors that support their success requires further investigation.
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Changes in the Microbiome of Mariculture Feed Organisms after Treatment with a Potentially Probiotic Strain of Phaeobacter inhibens. Appl Environ Microbiol 2020; 86:AEM.00499-20. [PMID: 32385083 DOI: 10.1128/aem.00499-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/03/2020] [Indexed: 01/04/2023] Open
Abstract
The Phaeobacter genus has been explored as probiotics in mariculture as a sustainable strategy for the prevention of bacterial infections. Its antagonistic effect against common fish pathogens is predominantly due to the production of the antibacterial compound tropodithietic acid (TDA), and TDA-producing strains have repeatedly been isolated from mariculture environments. Despite many in vitro trials targeting pathogens, little is known about its impact on host-associated microbiomes in mariculture. Hence, the purpose of this study was to investigate how the addition of a TDA-producing Phaeobacter inhibens strain affects the microbiomes of live feed organisms and fish larvae. We used 16S rRNA gene sequencing to characterize the bacterial diversity associated with live feed microalgae (Tetraselmis suecica), live feed copepod nauplii (Acartia tonsa), and turbot (Scophthalmus maximus) eggs/larvae. The microbial communities were unique to the three organisms investigated, and the addition of the probiotic bacterium had various effects on the diversity and richness of the microbiomes. The structure of the live feed microbiomes was significantly changed, while no effect was seen on the community structure associated with turbot larvae. The changes were seen primarily in particular taxa. The Rhodobacterales order was indigenous to all three microbiomes and decreased in relative abundance when P. inhibens was introduced in the copepod and turbot microbiomes, while it was unaffected in the microalgal microbiome. Altogether, the study demonstrates that the addition of P. inhibens in higher concentrations, as part of a probiotic regime, does not appear to cause major imbalances in the microbiome, but the effects were specific to closely related taxa.IMPORTANCE This work is an essential part of the risk assessment of the application of roseobacters as probiotics in mariculture. It provides insights into the impact of TDA-producing Phaeobacter inhibens on the commensal bacteria related to mariculture live feed and fish larvae. Also, the study provides a sequencing-based characterization of the microbiomes related to mariculture-relevant microalga, copepods, and turbot larvae.
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High performance of Mn2(BDC)2(DMF)2-derived MnO@C nanocomposite as superior remediator for a series of emergent antibiotics. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113038] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Bhute SS, Escobedo B, Haider M, Mekonen Y, Ferrer D, Hillyard SD, Friel AD, van Breukelen F, Hedlund BP. The gut microbiome and its potential role in paradoxical anaerobism in pupfishes of the Mojave Desert. Anim Microbiome 2020; 2:20. [PMID: 33499968 PMCID: PMC7807710 DOI: 10.1186/s42523-020-00037-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/27/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Pupfishes frequently enter paradoxical anaerobism in response to endogenously produced or exogenously supplied ethanol in a dose-dependent manner. To decipher the role of the gut microbiota in ethanol-associated paradoxical anaerobism, gut microbial communities were depleted using a cocktail of antibiotics and profiled using 16S rRNA gene sequencing. RESULTS Compared to the control group (n = 12), microbiota-depleted fish (n = 12) spent more time in paradoxical anaerobism. Our analysis indicated that the bacterial phyla Proteobacteria, Fusobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Patescibacteria, and Dependentiae dominated the pupfish gut, which is consistent with other fish gut microbiota. Although the gut microbial communities with and without antibiotic treatment were similarly diverse, they were distinct and the greatest contribution to the dissimilarity (27.38%) was the common fish commensal Cetobacterium. CONCLUSIONS This study reports the first characterization of gut microbial communities of pupfish and suggests the microbiome may play a critical role in regulating metabolic strategies that are critical for survival in extremes of temperature and oxygen concentration. We speculate that Cetobacterium, a primary fermenter, also consumes ethanol through secondary fermentation via an alcohol dehydrogenase and therefore regulates the transition from paradoxical anaerobism to aerobic respiration in fish. Given the wide distribution and abundance of Cetobacterium in warm-water fishes, this process may be of broad importance, and suggests that the microbiome be carefully considered for both conservation and aquaculture.
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Affiliation(s)
- Shrikant S Bhute
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Brisa Escobedo
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Mina Haider
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Yididya Mekonen
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Dafhney Ferrer
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Stanley D Hillyard
- School of Dental Medicine, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Ariel D Friel
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Frank van Breukelen
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA.
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA.
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Silva EN, Martins TVF, Miyauchi-Tavares TM, Miranda BAE, Dos Santos GDA, Rosa CP, Santos JA, Novaes RD, de Almeida LA, Corsetti PP. Amoxicillin-induced gut dysbiosis influences estrous cycle in mice and cytokine expression in the ovary and the caecum. Am J Reprod Immunol 2020; 84:e13247. [PMID: 32304259 DOI: 10.1111/aji.13247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/03/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022] Open
Abstract
PROBLEM Gut dysbiosis is caused by several factors, including the use of antibiotics. Since intestinal dysbiosis is associated with a wide range of immunopathological and reproductive conditions, the main goal of this study was to evaluate amoxicillin-induced gut dysbiosis and its influence on the oestrous cycle in mice. METHOD OF STUDY Mice were treated with amoxicillin or PBS, and faecal microbiota was evaluated by 16S rDNA metagenomic sequencing. The oestrous cycle was evaluated by vaginal cytology, vaginal opening and flow cytometry. After the induction of gut dysbiosis, the ovaries and the caecum were analysed to differential expression of IL-1β and IL-10 genes and histological analysis. RESULTS Amoxicillin-treated mice presented differing bacterial groups in the faecal microbiota when compared to the PBS-treated group indicating that amoxicillin treatment-induced gut dysbiosis and they gained weight. The vaginal cytology analysis showed that amoxicillin-induced gut dysbiosis decreased the number of cells but increased the relative number of leucocytes and altered the oestrous cycle. IL-1β was shown to be upregulated in the caecum and in the ovary of the dysbiotic mice. On the other hand, IL-10 expression was shown to be diminished in both organs of the dysbiotic mice. The oocyte area from dysbiotic group presented lower than non-dysbiotic mice with increasing thickness of the pellucid zone. The follicular teak from dysbiotic mice showed lower thickness than non-dysbiotic mice. CONCLUSION The results indicate that amoxicillin induces gut dysbiosis and influences the oestrous cycle and the inflammatory status of the ovary and the caecum.
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Affiliation(s)
- Evandro Neves Silva
- Laboratório de Imunologia das Doenças Infecciosas e Crônicas, Universidade José do Rosário Vellano, Alfenas, Brazil
| | - Thaís Viana Fialho Martins
- Laboratório de Imunologia das Doenças Infecciosas e Crônicas, Universidade José do Rosário Vellano, Alfenas, Brazil
| | | | | | - Gabriela de Assis Dos Santos
- Laboratório de Imunologia das Doenças Infecciosas e Crônicas, Universidade José do Rosário Vellano, Alfenas, Brazil
| | - Caio Pupin Rosa
- Departamento de Microbiologia e Imunologia, Universidade Federal de Alfenas, Alfenas, Brazil
| | - Jeferson Antônio Santos
- Laboratório de Imunologia das Doenças Infecciosas e Crônicas, Universidade José do Rosário Vellano, Alfenas, Brazil
| | - Rômulo Dias Novaes
- Departamento de Biologia Estrutural, Universidade Federal de Alfenas, Alfenas, Brazil
| | | | - Patrícia Paiva Corsetti
- Laboratório de Imunologia das Doenças Infecciosas e Crônicas, Universidade José do Rosário Vellano, Alfenas, Brazil
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Hurtado L, Miranda CD, Rojas R, Godoy FA, Añazco MA, Romero J. Live Feeds Used in the Larval Culture of Red Cusk Eel, Genypterus chilensis, Carry High Levels of Antimicrobial-Resistant Bacteria and Antibiotic-Resistance Genes (ARGs). Animals (Basel) 2020; 10:ani10030505. [PMID: 32197370 PMCID: PMC7142716 DOI: 10.3390/ani10030505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/29/2020] [Accepted: 03/10/2020] [Indexed: 11/27/2022] Open
Abstract
Simple Summary The culture of the marine fish red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture but low larval survival rates have prompted the need for the continuous use of antibiotics, mainly florfenicol. In this study, the role of live prey (rotifers and the brine shrimp Artemia franciscana) used to feed fish larvae as a source of antibacterial-resistant bacteria in a commercial culture of G. chilensis was investigated. Samples of live feeds were collected during the larval growth period and their bacterial contents were determined. High levels of potentially opportunistic pathogens, such as Vibrio spp., as well as florfenicol-resistant bacteria, were detected. Sixty-five florfenicol-resistant isolates were recovered from these cultures and identified as Vibrio (81.5%) and Pseudoalteromonas (15.4%), which exhibited a high incidence of co-resistance to the antibiotics streptomycin, oxytetracycline, co-trimoxazole, and kanamycin. The majority of them carried the florfenicol-resistance encoding genes floR and fexA. The high prevalence of antibiotic-resistant bacteria and the associated genetic elements in live feed administered to reared fish larvae requires the prompt implementation of efficient management strategies to prevent future therapy failures in fish larval cultures and the spread of antibiotic-resistant bacteria to associated aquatic environments. Abstract The culture of red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture but low larval survival rates have prompted the need for the continuous use of antibacterials. The main aim of this study was to evaluate the role of live feed as a source of antibacterial-resistant bacteria in a commercial culture of G. chilensis. Samples of rotifer and Artemia cultures used as live feed were collected during the larval growth period and culturable bacterial counts were performed using a spread plate method. Rotifer and Artemia cultures exhibited high levels of resistant bacteria (8.03 × 104 to 1.79 × 107 CFU/g and 1.47 × 106 to 3.50 × 108 CFU/g, respectively). Sixty-five florfenicol-resistant isolates were identified as Vibrio (81.5%) and Pseudoalteromonas (15.4%) using 16S rRNA gene sequence analysis. A high incidence of resistance to streptomycin (93.8%), oxytetracycline (89.2%), co-trimoxazole (84.6%), and kanamycin (73.8%) was exhibited by resistant isolates. A high proportion of isolates (76.9%) carried the florfenicol-resistance encoding genes floR and fexA, as well as plasmid DNA (75.0%). The high prevalence of multiresistant bacteria in live feed increases the incidence of the resistant microbiota in reared fish larvae, thus proper monitoring and management strategies for live feed cultures appear to be a priority for preventing future therapy failures in fish larval cultures.
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Affiliation(s)
- Luz Hurtado
- Programa Cooperativo de Doctorado en Acuicultura, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile;
| | - Claudio D. Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile;
- Centro AquaPacífico, Universidad Católica del Norte, Coquimbo 1780000, Chile
- Correspondence: ; Tel.: +56-512209762
| | - Rodrigo Rojas
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Coquimbo 1780000, Chile;
- Centro AquaPacífico, Universidad Católica del Norte, Coquimbo 1780000, Chile
| | - Félix A. Godoy
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile; (F.A.G.); (M.A.A.)
| | - Mark A. Añazco
- Centro i~mar, Universidad de Los Lagos, Puerto Montt 5480000, Chile; (F.A.G.); (M.A.A.)
| | - Jaime Romero
- Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Macul, Santiago 7810000, Chile;
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Niu G, Khattiya R, Zhang T, Boonyayatra S, Wongsathein D. Phenotypic and genotypic characterization of Streptococcus spp. isolated from tilapia (Oreochromis spp.) cultured in river-based cage and earthen ponds in Northern Thailand. JOURNAL OF FISH DISEASES 2020; 43:391-398. [PMID: 31984538 DOI: 10.1111/jfd.13137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Streptococcus spp. are major pathogenic bacteria associated with massive mortality in tilapia. This study investigated the phenotypic and genotypic characterization of Streptococcus agalactiae (GBS) and Streptococcus iniae (S. iniae) isolated from tilapia in river-based floating cage and earthen pond farms in northern Thailand. Isolates were identified by biochemical and molecular analyses. Capsular typing, enterobacterial repetitive intergenic consensus polymerase chain reaction and multilocus sequence typing were performed to investigate the genetic relatedness. Six and one isolates were confirmed as GBS and S. iniae, respectively. All Streptococcus spp. isolates were obtained from 4 river-based cage farms (4/33), while samples collected from earthen pond farms (N = 28) were negative for streptococcosis. All GBS with serotype Ⅲ and sequence type (ST) 283 was observed. The β-haemolytic GBS isolates were resistant to five antimicrobials, while the S. iniae was susceptible to all antimicrobials. This study indicates both GBS and S. iniae are the major bacterial pathogens responsible for streptococcosis infection in farmed tilapia of northern Thailand with GBS as dominant species. This survey highlights that the river-based cage farms seriously impact on the healthy development of the tilapia industry.
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Affiliation(s)
- Guoyi Niu
- Graduate Degree Program in Veterinary Science, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Department of Food Animal Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Rutch Khattiya
- Department of Food Animal Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Tingrui Zhang
- Department of Food Animal Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Sukolrat Boonyayatra
- Department of Food Animal Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Dilok Wongsathein
- Department of Food Animal Clinic, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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Cabello FC, Godfrey HP, Ivanova L, Shah SQA, Sørum H, Tomova A. Freshwater salmon aquaculture in Chile and transferable antimicrobial resistance. Environ Microbiol 2019; 22:559-563. [PMID: 31828945 DOI: 10.1111/1462-2920.14891] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 02/03/2023]
Abstract
Large amounts of antimicrobials are used in salmonid aquaculture in Chile. Most are used in marine aquaculture, but appreciable amounts are also employed in freshwater aquaculture. Much research and many publications have examined transferable antimicrobial resistance in bacteria isolated from marine salmon farms, but much less attention has been paid to this area in freshwater salmon farming. A recent paper by Domínguez et al. (2019) has as least in part remedied this situation. We now comment on some of its interpretations and have attempted to point out its areas of strength and weakness in light of the published scientific literature. Seen in this setting, the important results presented by Domínguez et al. (2019) underline the need for increased awareness of the challenge to animal and human health posed by excessive use of antimicrobials in aquaculture.
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Affiliation(s)
- Felipe C Cabello
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | - Henry P Godfrey
- Department of Pathology, New York Medical College, Valhalla, NY, USA
| | - Larisa Ivanova
- Department of Pediatrics, New York Medical College, Valhalla, NY, USA
| | - Syed Q A Shah
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Henning Sørum
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Alexandra Tomova
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
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Costa JMD, Moura CSD, Pádua CAMD, Vegi ASF, Magalhães SMS, Rodrigues MB, Ribeiro AQ. Restrictive measure for the commercialization of antimicrobials in Brazil: results achieved. Rev Saude Publica 2019; 53:68. [PMID: 31432930 PMCID: PMC6705550 DOI: 10.11606/s1518-8787.2019053000879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 10/06/2018] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE To assess whether the incidence of hospital infection by a resistant microorganism decreased after the implementation of the restrictive measure of the National Health Surveillance Agency for the commercialization of antimicrobials. METHODS A historical cohort study of medical records of adult patients admitted to a general and public hospital from May 2010 to July 2011. A cohort was formed with patients admitted in the period before the restrictive measure for the commercialization of antimicrobials (Phase I) and a second cohort was formed with patients admitted after the implementation of the restrictive measure (Phase II). RESULTS The instantaneous risk of hospital infection by a resistant microorganism was estimated at seven by 1,000 people-time (95%CI 0.006–0.008) in Phase I, and four by 1,000 people-time (95%CI 0.003–0.005) in Phase II of the study. The differences between the survival curves in the different phases of the study and stratified by age group were also significant (p < 0.05). CONCLUSIONS The results suggest that the implementation of the restrictive measure of the commercialization of antimicrobials by the National Health Surveillance Agency reduced the incidence of hospital infection by a resistant microorganism.
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Affiliation(s)
- Josiane Moreira da Costa
- Universidade Federal de Minas Gerais. Faculdade de Farmácia. Programa de Pós-Graduação em Medicamentos e Assistência Farmacêutica. Belo Horizonte, MG, Brasil
| | - Cristiano Soares de Moura
- McGill University. Division of Clinical Epidemiology. Department of Epidemiology. Montreal, Quebec, Canada
| | | | - Aline Siqueira Fogal Vegi
- McGill University. Division of Clinical Epidemiology. Department of Epidemiology. Montreal, Quebec, Canada
| | | | - Marina Barra Rodrigues
- Universidade Federal de Minas Gerais. Faculdade de Farmácia. Departamento de Farmácia Social. Belo Horizonte, MG, Brasil
| | - Andréia Queiroz Ribeiro
- Universidade Federal de Viçosa. Centro de Ciências Biológicas e da Saúde. Departamento de Nutrição e Saúde. Viçosa, MG, Brasil
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Gupta S, Fernandes J, Kiron V. Antibiotic-Induced Perturbations Are Manifested in the Dominant Intestinal Bacterial Phyla of Atlantic Salmon. Microorganisms 2019; 7:E233. [PMID: 31382431 PMCID: PMC6723382 DOI: 10.3390/microorganisms7080233] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/26/2019] [Accepted: 07/28/2019] [Indexed: 12/25/2022] Open
Abstract
The intestinal microbiota of certain farmed fish are often exposed to antimicrobial substances, such as antibiotics, that are used to prevent and treat bacterial diseases. Antibiotics that kill or inhibit the growth of harmful microbes can rapidly alter intestinal microbial diversity and composition, with potential effects on the host health. In this study, we have elucidated the impact of two antibiotics, florfenicol and oxolinic acid, by employing a high-throughput 16S rRNA gene amplicon sequencing technique on the distal and mid intestinal microbial communities of Atlantic salmon (Salmo salar). For this, Atlantic salmon were offered diets with or without antibiotics. We then investigated the bacterial communities in the intestinal mucus of the fish. Our results showed that antibiotic exposure shifts the intestinal microbial profile differentially. In addition, the bacterial compositions of the control and antibiotic-fed groups were significantly different. Antibiotic feeding altered the composition and abundance of the dominant bacterial phyla, namely Proteobacteria, Actinobacteria, Firmicutes, Spirochaetes, Bacteroidetes, Tenericutes, and Thermotogae. The bacterial association network analysis also indicated the differential pattern of co-occurrence of bacteria in the three study groups. The results regarding the differences in the structure and association of the intestinal microbiota of Atlantic salmon after florfenicol and oxolinic acid feeding can be employed to attenuate the adverse effects of antibiotic feeding on fish.
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Affiliation(s)
- Shruti Gupta
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Jorge Fernandes
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
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