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da Silva SKSM, Fuentes-Castillo DA, Ewbank AC, Sacristán C, Catão-Dias JL, Sevá AP, Lincopan N, Deem SL, Feitosa LCS, Catenacci LS. ESBL-Producing Enterobacterales at the Human-Domestic Animal-Wildlife Interface: A One Health Approach to Antimicrobial Resistance in Piauí, Northeastern Brazil. Vet Sci 2024; 11:195. [PMID: 38787167 PMCID: PMC11125940 DOI: 10.3390/vetsci11050195] [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: 03/18/2024] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
The use, misuse, and overuse of antimicrobials is one of the main public health threats of the 21st century. We investigated the risk factor of the presence of extended-spectrum, cephalosporin-resistant Enterobacterales in feces of non-domestic and domestic birds and other domestic animals in Piauí State, northeast Brazil. We collected a total of 387 cloacal and rectal swab samples of free-living birds, domestic birds, and domestic mammals in five municipalities: Amarante, Água Branca, Lagoa Alegre, Parnaíba, and Teresina. A total of 59/387 (15.2%) of these samples harbored extended spectrum beta-lactamase (ESBL)-producing Enterobacterales. Using the MALDI-TOF technique, we identified fifty-seven samples as Escherichia coli and two samples as Klebsiella pneumoniae. Teresina and Parnaíba had the highest prevalence of animals with resistant bacteria (32.1% and 27.1%, respectively) and highest exposure risk factor (OR of 16.06 and 8.58, respectively, and p < 0.001 for all). Multidrug-resistant, ESBL-producing Enterobacterales were observed in 72.8% of the samples (43/59). For the free-living birds, the positive samples belonged to a great kiskadee (Pitangus sulphuratus) and a semipalmated sandpiper (Calidris pusilla) in migratory and resident species, respectively. For domestic animals, the swine samples showed the highest prevalence of antimicrobial resistance. The lack of access to veterinary care and information regarding antimicrobial therapy, along with the easy access to antimicrobials without medical prescription, favors the inadequate use of antimicrobials in Piauí.
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Affiliation(s)
- Sandy Kelly S. M. da Silva
- Programa de Pós-Graduação Saúde Animal na Amazônia, Universidade Federal do Pará (UFPA), Belém 66075-110, Brazil
| | - Danny A. Fuentes-Castillo
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción (UDEC), Concepción 4070409, Chile;
| | - Ana Carolina Ewbank
- Centro de Investigación en Sanidad Animal (CISA-INIA), Consejo Superior de Investigaciones Científicas (CSIC), 28130 Valdeolmos, Spain; (A.C.E.)
| | - Carlos Sacristán
- Centro de Investigación en Sanidad Animal (CISA-INIA), Consejo Superior de Investigaciones Científicas (CSIC), 28130 Valdeolmos, Spain; (A.C.E.)
| | - José L. Catão-Dias
- Laboratório de Patologia Comparada de Animais Selvagens (LAPCOM), Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo (USP), São Paulo 05508-270, Brazil
| | - Anaiá P. Sevá
- Departamento de Ciências Agrárias e Ambientais, Universidade Estadual de Santa Cruz (UESC), Bahia 45662-900, Brazil
| | - Nilton Lincopan
- Laboratório de Resistência Bacteriana e Alternativas Terapêuticas, Instituto de Ciências Biomédicas, Universidade de São Paulo (USP), São Paulo 05508-220, Brazil
| | - Sharon L. Deem
- Saint Loius Zoo, Institute for Conservation Medicine, St. Louis, MO 63110, USA
| | - Lauro C. S. Feitosa
- Centro de Inteligência em Agravos Tropicais Emergentes e Negligenciados (CIATEN) e Centro de Ciências Agrárias (CCA), Universidade Federal do Piauí (UFPI), Piauí 64049-550, Brazil;
| | - Lilian S. Catenacci
- Programa de Pós-Graduação Saúde Animal na Amazônia, Universidade Federal do Pará (UFPA), Belém 66075-110, Brazil
- Saint Loius Zoo, Institute for Conservation Medicine, St. Louis, MO 63110, USA
- Centro de Inteligência em Agravos Tropicais Emergentes e Negligenciados (CIATEN) e Centro de Ciências Agrárias (CCA), Universidade Federal do Piauí (UFPI), Piauí 64049-550, Brazil;
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Wang C, Wu S, Zhou W, Hu L, Hu Q, Cao Y, Wang L, Chen X, Zhang Q. Effects of Neolamarckia cadamba leaves extract on microbial community and antibiotic resistance genes in cecal contents and feces of broilers challenged with lipopolysaccharides. Appl Environ Microbiol 2024; 90:e0110723. [PMID: 38231769 PMCID: PMC10880616 DOI: 10.1128/aem.01107-23] [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: 07/07/2023] [Accepted: 10/20/2023] [Indexed: 01/19/2024] Open
Abstract
The effects of Neolamarckia cadamba leaves extract (NCLE), with effective ingredients of flavonoids, on antibiotic resistance genes (ARGs) and relevant microorganisms in cecal contents and feces of broilers treated with or without lipopolysaccharide stimulation (LPS) were investigated. LPS stimulation increased (P < 0.05) the relative abundance of ARGs and mobile genetic elements (MGEs), such as tet(W/N/W), APH(3')-IIIa, ErmB, tet (44), ANT (6)-Ia, tet(O), tet (32), Vang_ACT_CHL, myrA, ANT (6)-Ib, IncQ1, tniB, and rep2 in cecal contents. However, the difference disappeared (P > 0.05) when NCLE was added at the same time. These differential ARGs and MGEs were mainly correlated (P < 0.01) with Clostridiales bacterium, Lachnospiraceae bacterium, and Candidatus Woodwardibium gallinarum. These species increased in LPS-stimulated broilers and decreased when NCLE was applied at the same time. In feces, LPS stimulation decreased (P < 0.05) the relative abundance of tet(Q), adeF, ErmF, Mef(En2), OXA-347, tet (40), npmA, tmrB, CfxA3, and ISCrsp1, while the LPS + NCLE treated group showed no significant effect (P > 0.05) on these ARGs. These differential ARGs and MGEs in feces were mainly correlated (P < 0.01) with Clostridiales bacterium, Pseudoflavonifractor sp. An184, Flavonifractor sp. An10, Ruminococcaceae bacterium, etc. These species increased in LPS-stimulated broilers and increased when NCLE was applied at the same time. In conclusion, LPS stimulation and NCLE influenced microbial communities and associated ARGs in both cecal contents and feces of broilers. NCLE alleviated the change of ARGs and MGEs in LPS-induced broilers by maintaining the microbial balance.IMPORTANCEAntibiotics showed a positive effect on gut health regulation and growth performance improvement in livestock breeding, but the antimicrobial resistance threat and environment pollution problem are increasingly severe with antibiotics abuse. As alternatives, plant extract containing bioactive substances are increasingly used to improve immunity and promote productivity. However, little is known about their effects on diversity and abundance of ARGs. Here, we investigated the effects of NCLE, with effective ingredients of flavonoids, on ARGs and relevant microorganisms in cecal contents and feces of broilers treated with or without lipopolysaccharide stimulation. We found that NCLE reduced the abundance of ARGs in cecal contents of lipopolysaccharide-induced broilers by maintaining the microbial balance. This study provides a comprehensive view of cecal and fecal microbial community, ARGs, and MGEs of broiler following LPS stimulation and NCLE treatment. It might be used to understand and control ARGs dissemination in livestock production.
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Affiliation(s)
- Cheng Wang
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
- State key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shuo Wu
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
| | - Wei Zhou
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
| | - Lei Hu
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
| | - Qi Hu
- Bioinformation Center, NEOMICS Institute, Shenzhen, China
| | - Yong Cao
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Li Wang
- State key Laboratory of Swine and Poultry Breeding Industry, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoyang Chen
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
| | - Qing Zhang
- College of Forestry and Landscape Architecture, Guangdong Province Research Center of Woody Forage Engineering Technology, South China Agricultural University, Guangzhou, China
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Panyako PM, Ommeh SC, Kuria SN, Lichoti JK, Musina J, Nair V, Nene V, Munir M, Oyola SO. Metagenomic Characterization of Poultry Cloacal and Oropharyngeal Swabs in Kenya Reveals Bacterial Pathogens and Their Antimicrobial Resistance Genes. Int J Microbiol 2024; 2024:8054338. [PMID: 38374958 PMCID: PMC10876313 DOI: 10.1155/2024/8054338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/28/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
Poultry enteric bacterial diseases are of significant economic importance because they are responsible for production losses due to weight loss, increased morbidity and mortality, and increased cost of production arising from poor feed conversion and treatment. This cross-sectional purposive study characterized enteric bacterial pathogens in poultry from selected agroclimatic regions in Kenya and investigated their antimicrobial resistance gene profiles. Cloacal (n = 563) and oropharyngeal (n = 394) swabs were collected and pooled into 16 and 14 samples, respectively, to characterize bacterial pathogens and their antimicrobial resistance gene profiles. We report that Proteobacteria, Chlamydiae, and Firmicutes are the most dominant phyla present in both cloacal and oropharyngeal swabs of the six poultry species studied, indicating the colonization of the poultry gut by many pathogenic bacteria. Using KEGG and COG databases, some pathways related to metabolism, genetic information, and cellular processing were detected. We also report the abundance of antimicrobial resistance genes that confer resistance to β-lactamases, aminoglycosides, and tetracycline in most of the poultry analyzed, raising concern about the dangers associated with continuous and inappropriate use of these antibiotics in poultry production. The antimicrobial resistance gene data generated in this study provides a valuable indicator of the use of antimicrobials in poultry in Kenya. The information generated is essential for managing bacterial diseases, especially in backyard poultry raised under scavenging conditions.
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Affiliation(s)
- Philip M. Panyako
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Sheila C. Ommeh
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Stephen N. Kuria
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Jacqueline K. Lichoti
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture, Livestock and Fisheries, Nairobi, Kenya
| | - Johns Musina
- Department of Zoology, National Museums of Kenya, Nairobi, Kenya
| | | | - Vish Nene
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Muhammad Munir
- Department: Biomedical and Life Sciences, Lancaster University, Bailrigg, UK
| | - Samuel O. Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
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Hahaj-Siembida A, Nowakiewicz A, Korzeniowska-Kowal A, Szecówka K, Trościańczyk A, Zięba P, Kania MG. Red foxes (Vulpes vulpes) as a specific and underappreciated reservoir of resistant and virulent coagulase-positive Staphylococcus spp. strains. Res Vet Sci 2024; 166:105111. [PMID: 38113638 DOI: 10.1016/j.rvsc.2023.105111] [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: 06/18/2023] [Revised: 12/03/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
The aim of the study was to analyze the presence of coagulase-positive Staphylococcus in swabs collected from red foxes and to characterize the drug resistance and virulence of these bacteria. In total, 415 rectal and oral swabs were collected, and coagulase-positive strains of S. pseudintermedius (n = 104) and S. aureus (n = 27) were identified using multiplex-PCR and MALDI TOF MS. Subsequent analyses showed the highest phenotypic resistance of the strains to penicillin (16.8%) and tetracycline (30.5%) confirmed by the presence of the blaZ, tetM, and tetK genes. Slightly lower resistance to erythromycin (6.9%), clindamycin (9.2%), gentamicin, streptogramins, rifampicin, nitrofurantoin, and sulphamethoxazol/trimetophrim was exhibited by single strains. Several virulence genes in a few different combinations were detected in S. aureus; LukE-LukD, and seB were the most frequent genes (37%), LukE-LukD, seB, and seC were detected in 11% of the strains, and PVL, etA, etB, and tst genes were present in two or single strains. The results of our research have confirmed that the red fox is an underestimated reservoir of coagulase-positive Staphylococcus strains, with approximately 50% of carriers of at least one resistance gene. In turn, 88.8% of the S. aureus strains had one or more virulence genes; therefore, this species of wildlife animals should be monitored as part of epidemiological surveillance.
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Affiliation(s)
- Agata Hahaj-Siembida
- Sub-Department of Veterinary Microbiology, Department of Preclinical Veterinary Sciences, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland.
| | - Aneta Nowakiewicz
- Sub-Department of Veterinary Microbiology, Department of Preclinical Veterinary Sciences, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland.
| | - Agnieszka Korzeniowska-Kowal
- Polish Collection of Microorganisms (PCM), Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland.
| | - Kamila Szecówka
- Polish Collection of Microorganisms (PCM), Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland.
| | - Aleksandra Trościańczyk
- Sub-Department of Veterinary Microbiology, Department of Preclinical Veterinary Sciences, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland.
| | - Przemysław Zięba
- State Veterinary Laboratory, Droga Męczenników Majdanka 50, 20-325 Lublin, Poland
| | - Monika Greguła Kania
- Department of Animal Breeding and Agricultural Advisory, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland.
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Zhu L, Wang J. Editorial: Community series in the wildlife gut microbiome and its implication for conservation biology, volume II. Front Microbiol 2023; 14:1329928. [PMID: 38173679 PMCID: PMC10761474 DOI: 10.3389/fmicb.2023.1329928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Affiliation(s)
- Lifeng Zhu
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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Afonso CL, Afonso AM. Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Vet Sci 2023; 10:690. [PMID: 38133241 PMCID: PMC10747646 DOI: 10.3390/vetsci10120690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.
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Ameer A, Cheng Y, Saleem F, Uzma, McKenna A, Richmond A, Gundogdu O, Sloan WT, Javed S, Ijaz UZ. Temporal stability and community assembly mechanisms in healthy broiler cecum. Front Microbiol 2023; 14:1197838. [PMID: 37779716 PMCID: PMC10534011 DOI: 10.3389/fmicb.2023.1197838] [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: 03/31/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
In recent years, there has been an unprecedented advancement in in situ analytical approaches that contribute to the mechanistic understanding of microbial communities by explicitly incorporating ecology and studying their assembly. In this study, we have analyzed the temporal profiles of the healthy broiler cecal microbiome from day 3 to day 35 to recover the stable and varying components of microbial communities. During this period, the broilers were fed three different diets chronologically, and therefore, we have recovered signature microbial species that dominate during each dietary regime. Since broilers were raised in multiple pens, we have also parameterized these as an environmental condition to explore microbial niches and their overlap. All of these analyses were performed in view of different parameters such as body weight (BW-mean), feed intake (FI), feed conversion ratio (FCR), and age (days) to link them to a subset of microbes that these parameters have a bearing upon. We found that gut microbial communities exhibited strong and statistically significant specificity for several environmental variables. Through regression models, genera that positively/negatively correlate with the bird's age were identified. Some short-chain fatty acids (SCFAs)-producing bacteria, including Izemoplasmatales, Gastranaerophilales, and Roseburia, have a positive correlation with age. Certain pathogens, such as Escherichia-Shigella, Sporomusa, Campylobacter, and Enterococcus, negatively correlated with the bird's age, which indicated a high disease risk in the initial days. Moreover, the majority of pathways involved in amino acid biosynthesis were also positively correlated with the bird's age. Some probiotic genera associated with improved performance included Oscillospirales; UCG-010, Shuttleworthia, Bifidobacterium, and Butyricicoccaceae; UCG-009. In general, predicted antimicrobial resistance genes (piARGs) contributed at a stable level, but there was a slight increase in abundance when the diet was changed. To the best of the authors' knowledge, this is one of the first studies looking at the stability, complexity, and ecology of natural broiler microbiota development in a temporal setting.
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Affiliation(s)
- Aqsa Ameer
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Youqi Cheng
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Farrukh Saleem
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Uzma
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - William T. Sloan
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Sundus Javed
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Umer Zeeshan Ijaz
- Water and Environment Research Group, Mazumdar-Shaw Advanced Research Centre, University of Glasgow, Glasgow, United Kingdom
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
- College of Science and Engineering, University of Galway, Galway, Ireland
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Nam NN, Do HDK, Loan Trinh KT, Lee NY. Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions. Foods 2023; 12:foods12112140. [PMID: 37297385 DOI: 10.3390/foods12112140] [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: 04/21/2023] [Revised: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 72820, Vietnam
| | - Kieu The Loan Trinh
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Republic of Korea
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Ribeiro J, Silva V, Monteiro A, Vieira-Pinto M, Igrejas G, Reis FS, Barros L, Poeta P. Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli. Animals (Basel) 2023; 13:1362. [PMID: 37106925 PMCID: PMC10135345 DOI: 10.3390/ani13081362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.
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Affiliation(s)
- Jessica Ribeiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2829-516 Lisbon, Portugal
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2829-516 Lisbon, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Andreia Monteiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Madalena Vieira-Pinto
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Veterinary Science, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2829-516 Lisbon, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Filipa S. Reis
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Lillian Barros
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
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10
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Despotovic M, de Nies L, Busi SB, Wilmes P. Reservoirs of antimicrobial resistance in the context of One Health. Curr Opin Microbiol 2023; 73:102291. [PMID: 36913905 DOI: 10.1016/j.mib.2023.102291] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/13/2023] [Indexed: 03/15/2023]
Abstract
The emergence and spread of antimicrobial resistance (AMR) and resistant bacteria, are a global public health challenge. Through horizontal gene transfer, potential pathogens can acquire antimicrobial resistance genes (ARGs) that can subsequently be spread between human, animal, and environmental reservoirs. To understand the dissemination of ARGs and linked microbial taxa, it is necessary to map the resistome within different microbial reservoirs. By integrating knowledge on ARGs in the different reservoirs, the One Health approach is crucial to our understanding of the complex mechanisms and epidemiology of AMR. Here, we highlight the latest insights into the emergence and spread of AMR from the One Health perspective, providing a baseline of understanding for future scientific investigations into this constantly growing global health threat.
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Affiliation(s)
- Milena Despotovic
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, 7 Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Laura de Nies
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, 7 Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, 7 Avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6, avenue du Swing, Belvaux, L-4367, Luxembourg.
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11
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Antibiotic Susceptibility, Resistance Gene Determinants and Corresponding Genomic Regions in Lactobacillus amylovorus Isolates Derived from Wild Boars and Domestic Pigs. Microorganisms 2022; 11:microorganisms11010103. [PMID: 36677394 PMCID: PMC9863647 DOI: 10.3390/microorganisms11010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Restrictions on the use of antibiotics in pigs lead to the continuous search for new probiotics serving as an alternative to antibiotics. One of the key parameters for probiotic bacteria selection is the absence of horizontally transmissible resistance genes. The aim of our study was to determine antibiotic susceptibility profiles in 28 Lactobacillus amylovorus isolates derived from the digestive tract of wild boars and farm pigs by means of the broth microdilution method and whole genome sequencing (WGS). We revealed genetic resistance determinants and examined sequences flanking resistance genes in these strains. Our findings indicate that L. amylovorus strains from domestic pigs are predominantly resistant to tetracycline, erythromycin and ampicillin. WGS analysis of horizontally transmissible genes revealed only three genetic determinants (tetW, ermB and aadE) of which all tetW and ermB genes were present only in strains derived from domestic pigs. Sequence analysis of coding sequences (CDS) in the neighborhood of the tetW gene revealed the presence of site-specific recombinase (xerC/D), site-specific DNA recombinase (spoIVCA) or DNA-binding transcriptional regulator (xre), usually directly downstream of the tetW gene. In the case of ermB, CDS for omega transcriptional repressor or mobilization protein were detected upstream of the ermB gene.
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12
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Fogliano C, Motta CM, Avallone B. Salicylate attenuates gentamicin-induced ototoxicity and facilitates the recovery in the basilar papilla of the lizard Podarcis siculus. Neurotoxicology 2022; 93:301-310. [DOI: 10.1016/j.neuro.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/15/2022]
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13
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Dias D, Hipólito D, Figueiredo A, Fonseca C, Caetano T, Mendo S. Unravelling the Diversity and Abundance of the Red Fox (Vulpes vulpes) Faecal Resistome and the Phenotypic Antibiotic Susceptibility of Indicator Bacteria. Animals (Basel) 2022; 12:ani12192572. [PMID: 36230313 PMCID: PMC9558537 DOI: 10.3390/ani12192572] [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: 08/16/2022] [Revised: 09/05/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Antimicrobial resistance was considered one of the major concerns of the twenty-first century by the World Health Organization in 2014. A holistic approach known as “One Health” recognizes the connections and interdependence between the health of people, domestic and wild animals, plants, and the ecosystem. The red fox is the most widespread wild canid in Europe that adapts easily and is distributed in natural environments and urban and peri-urban areas due to its increasing abundance. Foxes are reservoirs and disseminators of antibiotic resistance and zoonotic agents. They interact with watercourses, soils and livestock, and although they have no gastronomic interest, they are a game species, highlighting the potential risk of contamination between them and the hunters. Our main goal was to characterize antibiotic resistance in red foxes. Several clinically relevant antibiotic resistance genes were identified, as well as multidrug-resistant bacteria. Abstract The WHO considers that antimicrobial resistance (AMR) is among the ten greatest global public health risks of the 21st century. The expansion of human populations and anthropogenically related activities, accompanied by the fragmentation of natural habitats, has resulted in increased human–wildlife interaction. Natural ecosystems are therefore subjected to anthropogenic inputs, which affect the resistome of wild animals. Thus, urgent multisectoral action is needed to achieve the Sustainable Development Goals following the One Health approach. The present work falls within the scope of this approach and aims to characterize the AMR of the faecal microbiome of the red fox (Vulpes vulpes), an opportunistic and generalist synanthropic species whose abundance has been increasing in urban and peri-urban areas. A high number of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were screened and quantified using a high-throughput qPCR approach, and the antimicrobial susceptibility of cultivable E. coli and Enterococcus spp. were assessed interpreted with both ECOFFs and clinical breakpoints. The most abundant ARGs detected confer resistance to trimethoprim and tetracyclines, although the first were absent in one of the locations studied. Several ARGs considered to be threats to human health were identified in high relative abundances (blaTEM, ermB, aadA, tetM, tetW, tetL, drfA1 and drfA17), especially in the geographical area with greater anthropogenic influence. Although at a low percentage, resistant and multidrug-resistant (MDR) E. coli and Enterococcus spp. were isolated, including one MDR E. coli showing resistance to 12 antimicrobials from 6 different classes.
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Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Dário Hipólito
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Biology, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Ana Figueiredo
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Bioscience & CEES, University of Oslo, Blindernvn, 31, 0371 Oslo, Norway
| | - Carlos Fonseca
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- ForestWISE—Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: (T.C.); (S.M.)
| | - Sónia Mendo
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: (T.C.); (S.M.)
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14
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Dias D, Fonseca C, Caetano T, Mendo S. Oh, deer! How worried should we be about the diversity and abundance of the faecal resistome of red deer? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153831. [PMID: 35151727 DOI: 10.1016/j.scitotenv.2022.153831] [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: 12/08/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The emergence of antimicrobial resistance (AMR) is a global threat to public health. Antimicrobials are used in animal production and human medicine, which contribute to the circulation of antibiotic resistance genes (ARGs) in the environment. Wildlife can be reservoirs of pathogens and resistant bacteria. Furthermore, anthropogenic pressure can influence their resistome. This work aimed to study the AMR of the faecal microbiome of red deer, one of the most important game species in Europe. To this end, a high-throughput qPCR approach was employed to screen a high number of ARGs and the antimicrobial susceptibility of indicator bacteria was determined. Several genes that confer resistance to different classes of antibiotics were identified, with the most abundant being tetracycline ARGs. Other genes were also present that are considered current and future threats to human health, and some of these were relatively abundant. Multidrug-resistant E. coli and Enterococcus spp. were isolated, although the overall level of antibiotic resistance was low. These results highlight the pressing need to know the origin and transmission of AMR in wildlife. Thus, and considering the One Health concept, studies such as this one shows the need for surveillance programs to prevent the spread of drug-resistant strains and ARGs.
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Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Carlos Fonseca
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
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15
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Smoglica C, Angelucci S, Farooq M, Antonucci A, Marsilio F, Di Francesco CE. Microbial community and antimicrobial resistance in fecal samples from wild and domestic ruminants in Maiella National Park, Italy. One Health 2022; 15:100403. [PMID: 35647256 PMCID: PMC9136667 DOI: 10.1016/j.onehlt.2022.100403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 01/04/2023] Open
Abstract
This study aimed to provide new insights about antimicrobial resistance genes abundance and microbial communities of wild and domestic ruminants in wildlife-livestock interface. In total, 88 fecal samples were recovered from Apennine chamois, red deer, goat, cattle and sheep, and were collected in pools. The populations under study were selected based on ecological data useful to define sympatric and non-sympatric populations. Samples were screened for commonly used in farms under study or critically important antimicrobial resistance genes (aadA2, TetA, TetB, TetK, TetM, mcr-1). The microbial community composition was found to be different based on the species and land use of animals under study. Indeed, it was mostly characterized by phyla Firmicutes in bovine, Bacteroidota in chamois and Proteobacteria in red deer. Additionally, positive correlations between antibiotic resistance genes and microbial taxa (e.g., Tet genes correlated with Firmicutes and Patescibacteria) were described. Of the antimicrobials investigated, the abundance of mcr-1 gene suggests the importance of monitoring the wildlife in order to detect the emerging resistance genes contamination in environment. This study provides new data that highlight the importance of multidisciplinary and uncultured study in order to describe the spreading of antimicrobial resistance and related contamination in the environment. Multidisciplinary approach including ecological data, real time PCRs and 16S rRNA analysis Microbial communities composition of rare species as Apennine chamois Evaluation of antibiotic resistance genes abundance in feces of wild and domestic ruminants Detection of mcr-1 resistance gene relevant for Public Health
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16
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Homeier-Bachmann T, Schütz AK, Dreyer S, Glanz J, Schaufler K, Conraths FJ. Genomic Analysis of ESBL-Producing E. coli in Wildlife from North-Eastern Germany. Antibiotics (Basel) 2022; 11:antibiotics11020123. [PMID: 35203726 PMCID: PMC8868512 DOI: 10.3390/antibiotics11020123] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial resistance (AMR) is a serious global health threat and extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales are a major contributor. This study aimed to gain a deeper insight into the AMR burden of wild animals. In total, 1595 fecal samples were collected by two systematic searches in Mecklenburg-Western Pomerania, north-east Germany. Samples were screened for ESBL-carrying Escherichia (E.) coli and isolates found were further analyzed using antimicrobial susceptibility testing and whole-genome sequencing. We found an estimated prevalence of 1.2% ESBL-producing E. coli in wild boar and 1.1% in wild ruminants. CTX-M-1 was the most abundant CTX-M type. We also examined fecal samples from wild boar and wild ruminants using shotgun metagenomics to gain insight into the resistome in wild animals. The latter revealed significantly lower normalized counts for AMR genes in wildlife samples compared to farm animals. The AMR gene levels were lower in wild ruminants than in wild boar. In conclusion, our study revealed a low prevalence of ESBL-producing E. coli and a low overall AMR gene burden in wild boar and wild ruminants, probably due to the secluded location of the search area.
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Affiliation(s)
- Timo Homeier-Bachmann
- Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald–Insel Riems, Germany; (A.K.S.); (J.G.); (F.J.C.)
- Correspondence: ; Tel.: +49-38351-71505
| | - Anne K. Schütz
- Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald–Insel Riems, Germany; (A.K.S.); (J.G.); (F.J.C.)
| | - Sylvia Dreyer
- Friedrich-Loeffler-Institut, Institute of International Animal Health/One Health, 17493 Greifswald–Insel Riems, Germany;
| | - Julien Glanz
- Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald–Insel Riems, Germany; (A.K.S.); (J.G.); (F.J.C.)
- Wildlife Research Unit, Agricultural Centre Baden-Württemberg, 88326 Aulendorf, Germany
| | - Katharina Schaufler
- Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany;
- Institute of Infection Medicine, Christian-Albrecht University and University Medical Center Schleswig-Holstein, 24118 Kiel, Germany
| | - Franz J. Conraths
- Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald–Insel Riems, Germany; (A.K.S.); (J.G.); (F.J.C.)
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17
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Dias D, Fonseca C, Mendo S, Caetano T. A closer look on the variety and abundance of the faecal resistome of wild boar. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118406. [PMID: 34710519 DOI: 10.1016/j.envpol.2021.118406] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/19/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Antimicrobial resistance (AMR) is a serious problem for public and animal health, and also for the environment. Monitoring and reporting the occurrence of AMR determinants and bacteria with the potential to disseminate is a priority for health surveillance programs around the world and critical to the One Health concept. Wildlife is a reservoir of AMR, and human activities can strongly influence their resistome. The main goal of this work was to study the resistome of wild boar faecal microbiome, one of the most important game species in Europe using metagenomic and culturing approaches. The most abundant genes identified by the high-throughput qPCR array encode mobile genetic elements, including integrons, which can promote the dissemination of AMR determinants. A diverse set of genes (n = 62) conferring resistance to several classes of antibiotics (ARGs), some of them included in the WHO list of critically important antimicrobials were also detected. The most abundant ARGs confer resistance to tetracyclines and aminoglycosides. The phenotypic resistance of E. coli and Enterococcus spp. were also investigated, and together supported the metagenomic results. As the wild boar is an omnivorous animal, it can be a disseminator of AMR bacteria and ARGs to livestock, humans, and the environment. This study supports that wild boar can be a key sentinel species in ecosystems surveillance and should be included in National Action Plans to fight AMR, adopting a One Health approach.
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Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Carlos Fonseca
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801, Vila Real, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
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18
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Yang D, Heederik DJJ, Scherpenisse P, Van Gompel L, Luiken REC, Wadepohl K, Skarżyńska M, Van Heijnsbergen E, Wouters IM, Greve GD, Jongerius-Gortemaker BGM, Tersteeg-Zijderveld M, Portengen L, Juraschek K, Fischer J, Zając M, Wasyl D, Wagenaar JA, Mevius DJ, Smit LAM, Schmitt H. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1883-1893. [PMID: 35466367 PMCID: PMC9244224 DOI: 10.1093/jac/dkac133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Abstract
Background Real-time quantitative PCR (qPCR) is an affordable method to quantify antimicrobial resistance gene (ARG) targets, allowing comparisons of ARG abundance along animal production chains. Objectives We present a comparison of ARG abundance across various animal species, production environments and humans in Europe. AMR variation sources were quantified. The correlation of ARG abundance between qPCR data and previously published metagenomic data was assessed. Methods A cross-sectional study was conducted in nine European countries, comprising 9572 samples. qPCR was used to quantify abundance of ARGs [aph(3′)-III, erm(B), sul2, tet(W)] and 16S rRNA. Variance component analysis was conducted to explore AMR variation sources. Spearman’s rank correlation of ARG abundance values was evaluated between pooled qPCR data and earlier published pooled metagenomic data. Results ARG abundance varied strongly among animal species, environments and humans. This variation was dominated by between-farm variation (pigs) or within-farm variation (broilers, veal calves and turkeys). A decrease in ARG abundance along pig and broiler production chains (‘farm to fork’) was observed. ARG abundance was higher in farmers than in slaughterhouse workers, and lowest in control subjects. ARG abundance showed a high correlation (Spearman’s ρ > 0.7) between qPCR data and metagenomic data of pooled samples. Conclusions qPCR analysis is a valuable tool to assess ARG abundance in a large collection of livestock-associated samples. The between-country and between-farm variation of ARG abundance could partially be explained by antimicrobial use and farm biosecurity levels. ARG abundance in human faeces was related to livestock antimicrobial resistance exposure.
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Affiliation(s)
| | - Dick J J Heederik
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Peter Scherpenisse
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Liese Van Gompel
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Roosmarijn E C Luiken
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Katharina Wadepohl
- Außenstelle für Epidemiologie, Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - Eri Van Heijnsbergen
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Inge M Wouters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Gerdit D Greve
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Monique Tersteeg-Zijderveld
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Lützen Portengen
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Katharina Juraschek
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Magdalena Zając
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Pulawy, Poland
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Dik J Mevius
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
- Department of Bacteriology and Epidemiology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Lidwien A M Smit
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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19
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Impact of Antibiotic Therapies on Resistance Genes Dynamic and Composition of the Animal Gut Microbiota. Animals (Basel) 2021; 11:ani11113280. [PMID: 34828011 PMCID: PMC8614244 DOI: 10.3390/ani11113280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotics are major disruptors of the gastrointestinal microbiota, depleting bacterial species beneficial for the host health and favoring the emergence of potential pathogens. Furthermore, the intestine is a reactor of antibiotic resistance emergence, and the presence of antibiotics exacerbates the selection of resistant bacteria that can disseminate in the environment and propagate to further hosts. We reviewed studies analyzing the effect of antibiotics on the intestinal microbiota and antibiotic resistance conducted on animals, focusing on the main food-producing and companion animals. Irrespective of antibiotic classes and animal hosts, therapeutic dosage decreased species diversity and richness favoring the bloom of potential enteropathogens and the selection of antibiotic resistance. These negative effects of antibiotic therapies seem ineluctable but often were mitigated when an antibiotic was administered by parenteral route. Sub-therapeutic dosages caused the augmentation of taxa involved in sugar metabolism, suggesting a link with weight gain. This result should not be interpreted positively, considering that parallel information on antibiotic resistance selection was rarely reported and selection of antibiotic resistance is known to occur also at low antibiotic concentration. However, studies on the effect of antibiotics as growth promoters put the basis for understanding the gut microbiota composition and function in this situation. This knowledge could inspire alternative strategies to antibiotics, such as probiotics, for improving animal performance. This review encompasses the analysis of the main animal hosts and all antibiotic classes, and highlights the future challenges and gaps of knowledge that should be filled. Further studies are necessary for elucidating pharmacodynamics in animals in order to improve therapy duration, antibiotic dosages, and administration routes for mitigating negative effects of antibiotic therapies. Furthermore, this review highlights that studies on aminoglycosides are almost inexistent, and they should be increased, considering that aminoglycosides are the first most commonly used antibiotic family in companion animals. Harmonization of experimental procedures is necessary in this research field. In fact, current studies are based on different experimental set-up varying for antibiotic dosage, regimen, administration, and downstream microbiota analysis. In the future, shotgun metagenomics coupled with long-reads sequencing should become a standard experimental approach enabling to gather comprehensive knowledge on GIM in terms of composition and taxonomic functions, and of ARGs. Decorticating GIM in animals will unveil revolutionary strategies for medication and improvement of animals' health status, with positive consequences on global health.
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20
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McCubbin KD, Anholt RM, de Jong E, Ida JA, Nóbrega DB, Kastelic JP, Conly JM, Götte M, McAllister TA, Orsel K, Lewis I, Jackson L, Plastow G, Wieden HJ, McCoy K, Leslie M, Robinson JL, Hardcastle L, Hollis A, Ashbolt NJ, Checkley S, Tyrrell GJ, Buret AG, Rennert-May E, Goddard E, Otto SJG, Barkema HW. Knowledge Gaps in the Understanding of Antimicrobial Resistance in Canada. Front Public Health 2021; 9:726484. [PMID: 34778169 PMCID: PMC8582488 DOI: 10.3389/fpubh.2021.726484] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/16/2021] [Indexed: 01/21/2023] Open
Abstract
Current limitations in the understanding and control of antimicrobial resistance (AMR) in Canada are described through a comprehensive review focusing on: (1) treatment optimization; (2) surveillance of antimicrobial use and AMR; and (3) prevention of transmission of AMR. Without addressing gaps in identified areas, sustained progress in AMR mitigation is unlikely. Expert opinions and perspectives contributed to prioritizing identified gaps. Using Canada as an example, this review emphasizes the importance and necessity of a One Health approach for understanding and mitigating AMR. Specifically, antimicrobial use in human, animal, crop, and environmental sectors cannot be regarded as independent; therefore, a One Health approach is needed in AMR research and understanding, current surveillance efforts, and policy. Discussions regarding addressing described knowledge gaps are separated into four categories: (1) further research; (2) increased capacity/resources; (3) increased prescriber/end-user knowledge; and (4) policy development/enforcement. This review highlights the research and increased capacity and resources to generate new knowledge and implement recommendations needed to address all identified gaps, including economic, social, and environmental considerations. More prescriber/end-user knowledge and policy development/enforcement are needed, but must be informed by realistic recommendations, with input from all relevant stakeholders. For most knowledge gaps, important next steps are uncertain. In conclusion, identified knowledge gaps underlined the need for AMR policy decisions to be considered in a One Health framework, while highlighting critical needs to achieve realistic and meaningful progress.
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Affiliation(s)
- Kayley D. McCubbin
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
| | | | - Ellen de Jong
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
| | - Jennifer A. Ida
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Diego B. Nóbrega
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - John P. Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - John M. Conly
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Health Services, Calgary, AB, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Tim A. McAllister
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, AB, Canada
| | - Karin Orsel
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
| | - Ian Lewis
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Leland Jackson
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Hans-Joachim Wieden
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
| | - Kathy McCoy
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Myles Leslie
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- School of Public Policy, University of Calgary, Calgary, AB, Canada
| | - Joan L. Robinson
- Department of Pediatrics, Faculty of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Lorian Hardcastle
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Faculty of Law, University of Calgary, Calgary, AB, Canada
| | - Aidan Hollis
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Department of Economics, Faculty of Arts, University of Calgary, Calgary, AB, Canada
| | - Nicholas J. Ashbolt
- Faculty of Science and Engineering, Southern Cross University, Lismore, NSW, Australia
| | - Sylvia Checkley
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Gregory J. Tyrrell
- Alberta Precision Laboratories, Alberta Health Services, Calgary, AB, Canada
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Calgary, AB, Canada
| | - André G. Buret
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Elissa Rennert-May
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Health Services, Calgary, AB, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ellen Goddard
- Department of Resource Economics and Environmental Sociology, Faculty of Agriculture, Life and Environmental Science, University of Alberta, Edmonton, AB, Canada
| | - Simon J. G. Otto
- HEAT-AMR Research Group, School of Public Health, University of Alberta, Edmonton, AB, Canada
- Thematic Area Lead, Healthy Environments, Centre for Healthy Communities, School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- One Health at UCalgary, University of Calgary, Calgary, AB, Canada
- O'Brien Institute of Public Health, University of Calgary, Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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21
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Antibiotic Resistance: From Pig to Meat. Antibiotics (Basel) 2021; 10:antibiotics10101209. [PMID: 34680790 PMCID: PMC8532907 DOI: 10.3390/antibiotics10101209] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/14/2022] Open
Abstract
Pork meat is in high demand worldwide and this is expected to increase. Pork is often raised in intensive conditions, which is conducive to the spread of infectious diseases. Vaccines, antibiotics, and other biosafety measures help mitigate the impact of infectious diseases. However, bacterial strains resistant to antibiotics are more and more frequently found in pig farms, animals, and the environment. It is now recognized that a holistic perspective is needed to sustainably fight antibiotic resistance, and that an integrated One Health approach is essential. With this in mind, this review tackles antibiotic resistance throughout the pork raising process, including their microbiome; many factors of their environment (agricultural workers, farms, rivers, etc.); and an overview of the impact of antibiotic resistance on pork meat, which is the end product available to consumers. Antibiotic resistance, while a natural process, is a public health concern. If we react, and act, collectively, it is expected to be, at least partially, reversible with judicious antibiotic usage and the development of innovative strategies and tools to foster animal health.
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22
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Genomic evolution of antimicrobial resistance in Escherichia coli. Sci Rep 2021; 11:15108. [PMID: 34301966 PMCID: PMC8302606 DOI: 10.1038/s41598-021-93970-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
The emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.
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23
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Risk Factors for Antimicrobial Resistance in Turkey Farms: A Cross-Sectional Study in Three European Countries. Antibiotics (Basel) 2021; 10:antibiotics10070820. [PMID: 34356741 PMCID: PMC8300668 DOI: 10.3390/antibiotics10070820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
Food-producing animals are an important reservoir and potential source of transmission of antimicrobial resistance (AMR) to humans. However, research on AMR in turkey farms is limited. This study aimed to identify risk factors for AMR in turkey farms in three European countries (Germany, France, and Spain). Between 2014 and 2016, faecal samples, antimicrobial usage (AMU), and biosecurity information were collected from 60 farms. The level of AMR in faecal samples was quantified in three ways: By measuring the abundance of AMR genes through (i) shotgun metagenomics sequencing (n = 60), (ii) quantitative real-time polymerase chain reaction (qPCR) targeting ermB, tetW, sul2, and aph3′-III; (n = 304), and (iii) by identifying the phenotypic prevalence of AMR in Escherichia coli isolates by minimum inhibitory concentrations (MIC) (n = 600). The association between AMU or biosecurity and AMR was explored. Significant positive associations were detected between AMU and both genotypic and phenotypic AMR for specific antimicrobial classes. Beta-lactam and colistin resistance (metagenomics sequencing); ampicillin and ciprofloxacin resistance (MIC) were associated with AMU. However, no robust AMU-AMR association was detected by analyzing qPCR targets. In addition, no evidence was found that lower biosecurity increases AMR abundance. Using multiple complementary AMR detection methods added insights into AMU-AMR associations at turkey farms.
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24
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Skarżyńska M, Zaja C M, Bomba A, Bocian Ł, Kozdruń W, Polak M, Wia Cek J, Wasyl D. Antimicrobial Resistance Glides in the Sky-Free-Living Birds as a Reservoir of Resistant Escherichia coli With Zoonotic Potential. Front Microbiol 2021; 12:656223. [PMID: 33897669 PMCID: PMC8062882 DOI: 10.3389/fmicb.2021.656223] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most important global health concerns; therefore, the identification of AMR reservoirs and vectors is essential. Attention should be paid to the recognition of potential hazards associated with wildlife as this field still seems to be incompletely explored. In this context, the role of free-living birds as AMR carriers is noteworthy. Therefore, we applied methods used in AMR monitoring, supplemented by colistin resistance screening, to investigate the AMR status of Escherichia coli from free-living birds coming from natural habitats and rescue centers. Whole-genome sequencing (WGS) of strains enabled to determine resistance mechanisms and investigate their epidemiological relationships and virulence potential. As far as we know, this study is one of the few that applied WGS of that number (n = 71) of strains coming from a wild avian reservoir. The primary concerns arising from our study relate to resistance and its determinants toward antimicrobial classes of the highest priority for the treatment of critical infections in people, e.g., cephalosporins, quinolones, polymyxins, and aminoglycosides, as well as fosfomycin. Among the numerous determinants, bla CTX-M-15, bla CMY-2, bla SHV-12, bla TEM-1B, qnrS1, qnrB19, mcr-1, fosA7, aac(3)-IIa, ant(3")-Ia, and aph(6)-Id and chromosomal gyrA, parC, and parE mutations were identified. Fifty-two sequence types (STs) noted among 71 E. coli included the global lineages ST131, ST10, and ST224 as well as the three novel STs 11104, 11105, and 11194. Numerous virulence factors were noted with the prevailing terC, gad, ompT, iss, traT, lpfA, and sitA. Single E. coli was Shiga toxin-producing. Our study shows that the clonal spread of E. coli lineages of public and animal health relevance is a serious avian-associated hazard.
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Affiliation(s)
- Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Magdalena Zaja C
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Arkadiusz Bomba
- Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
| | - Łukasz Bocian
- Department of Epidemiology and Risk Assessment, National Veterinary Research Institute, Puławy, Poland
| | - Wojciech Kozdruń
- Department of Poultry Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Marcin Polak
- Department of Zoology and Nature Protection, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Jarosław Wia Cek
- Department of Zoology and Nature Protection, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland.,Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
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25
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Bacteria Broadly-Resistant to Last Resort Antibiotics Detected in Commercial Chicken Farms. Microorganisms 2021; 9:microorganisms9010141. [PMID: 33435450 PMCID: PMC7826917 DOI: 10.3390/microorganisms9010141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/27/2022] Open
Abstract
Resistance to last resort antibiotics in bacteria is an emerging threat to human and animal health. It is important to identify the source of these antimicrobial resistant (AMR) bacteria that are resistant to clinically important antibiotics and evaluate their potential transfer among bacteria. The objectives of this study were to (i) detect bacteria resistant to colistin, carbapenems, and β-lactams in commercial poultry farms, (ii) characterize phylogenetic and virulence markers of E. coli isolates to potentiate virulence risk, and (iii) assess potential transfer of AMR from these isolates via conjugation. Ceca contents from laying hens from conventional cage (CC) and cage-free (CF) farms at three maturity stages were randomly sampled and screened for extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, carbapenem-resistant Acinetobacter (CRA), and colistin resistant Escherichia coli (CRE) using CHROMagar™ selective media. We found a wide-spread abundance of CRE in both CC and CF hens across all three maturity stages. Extraintestinal pathogenic Escherichia coli phylogenetic groups B2 and D, as well as plasmidic virulence markers iss and iutA, were widely associated with AMR E. coli isolates. ESBL-producing Enterobacteriaceae were uniquely detected in the early lay period of both CC and CF, while multidrug resistant (MDR) Acinetobacter were found in peak and late lay periods of both CC and CF. CRA was detected in CF hens only. blaCMY
was detected in ESBL-producing E. coli in CC and CF and MDR Acinetobacter spp. in CC. Finally, the blaCMY
was shown to be transferrable via an IncK/B plasmid in CC. The presence of MDR to the last-resort antibiotics that are transferable between bacteria in food-producing animals is alarming and warrants studies to develop strategies for their mitigation in the environment.
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