1
|
Liu W, Xu C, Li T, Ren Z, Hao S, Chen Z, Huang X, Wen X. Temporal Dynamics and Contribution of Phage Community to the Prevalence of Antibiotic Resistance Genes in a Full-Scale Sludge Anaerobic Digestion Plant. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6296-6304. [PMID: 38556999 DOI: 10.1021/acs.est.4c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Anaerobic digestion (AD) is an important biological resource recovery process, where microorganisms play key roles for material transformation. There has been some knowledge about the prokaryotic community and antibiotic resistance genes (ARGs) in AD, but there has been very limited knowledge of phages. In this study, samples from a full-scale AD plant were collected over 13 months, sequenced, and analyzed for viral and prokaryotic metagenomes. Totally, 3015 viral operational taxonomic units (vOTUs) were detected, mostly assigned to Caudoviricetes. The phage community had faster temporal variation than the prokaryotic community. Warm seasons harbored a higher abundance of both temperate phages and broad host-range phages. Seven ARGs of 6 subtypes were carried by 20 vOTUs, a representative ermT gene was synthesized and expressed, and the resistance activity in the host was examined, confirming the real activity of virus-carried ARGs in the AD process. Some of the ARGs were horizontally transferred between the phage and prokaryotic genomes. However, phage infection was not found to contribute to ARG transfer. This study provided an insight into the ecological patterns of the phage community, confirmed the antibiotic resistance activity of virus-carried ARGs, evaluated the contribution of phages on the ARG prevalence, and laid the foundation for the control strategies of the community and antibiotic resistance in the AD process.
Collapse
Affiliation(s)
- Wei Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Chenyang Xu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tianle Li
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhengran Ren
- Research and Development Center, Beijing Drainage Group Co. Ltd., Beijing 100080, China
| | - Shan Hao
- Research and Development Center, Beijing Drainage Group Co. Ltd., Beijing 100080, China
| | - Zhan Chen
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Xia Huang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Xianghua Wen
- School of Environment, Tsinghua University, Beijing 100084, China
| |
Collapse
|
2
|
Tang Y, Zhou M, Yang C, Liu R, Du H, Ma M. Advances in isolated phages that affect Ralstonia solanacearum and their application in the biocontrol of bacterial wilt in plants. Lett Appl Microbiol 2024; 77:ovae037. [PMID: 38573829 DOI: 10.1093/lambio/ovae037] [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: 01/25/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/06/2024]
Abstract
Bacterial wilt is a widespread and devastating disease that impacts the production of numerous crucial crops worldwide. The main causative agent of the disease is Ralstonia solanacearum. Due to the pathogen's broad host range and prolonged survival in the soil, it is challenging to control the disease with conventional strategies. Therefore, it is of great importance to develop effective alternative disease control strategies. In recent years, phage therapy has emerged as an environmentally friendly and sustainable biocontrol alternative, demonstrating significant potential in controlling this severe disease. This paper summarized basic information about isolated phages that infect R. solanacearum, and presented some examples of their application in the biocontrol of bacterial wilt. The risks of phage application and future prospect in this area were also discussed. Overall, R. solanacearum phages have been isolated from various regions and environments worldwide. These phages belong mainly to the Inoviridae, Autographiviridae, Peduoviridae, and Cystoviridae families, with some being unclassified. Studies on the application of these phages have demonstrated their ability to reduce pathogenicity of R. solanacearum through direct lysis or indirect alteration of the pathogen's physiological properties. These findings suggested bacteriophage is a promising tool for biocontrol of bacterial wilt in plants.
Collapse
Affiliation(s)
- You Tang
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Moxi Zhou
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Chuyun Yang
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Rong Liu
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Hongyi Du
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| | - Ming Ma
- Chongqing Key Laboratory of Scientific Utilization of Tobacco Resources, China Tobacco Chongqing Industrial Co Ltd, Nan'an, Chongqing 400060, China
| |
Collapse
|
3
|
Domingues CPF, Rebelo JS, Dionisio F, Nogueira T. Multi-Drug Resistance in Bacterial Genomes-A Comprehensive Bioinformatic Analysis. Int J Mol Sci 2023; 24:11438. [PMID: 37511196 PMCID: PMC10380340 DOI: 10.3390/ijms241411438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance is presently one of the greatest threats to public health. The excessive and indiscriminate use of antibiotics imposes a continuous selective pressure that triggers the emergence of multi-drug resistance. We performed a large-scale analysis of closed bacterial genomes to identify multi-drug resistance considering the ResFinder antimicrobial classes. We found that more than 95% of the genomes harbor genes associated with resistance to disinfectants, glycopeptides, macrolides, and tetracyclines. On average, each genome encodes resistance to more than nine different classes of antimicrobial drugs. We found higher-than-expected co-occurrences of resistance genes in both plasmids and chromosomes for several classes of antibiotic resistance, including classes categorized as critical according to the World Health Organization (WHO). As a result of antibiotic-resistant priority pathogens, higher-than-expected co-occurrences appear in plasmids, increasing the potential for resistance dissemination. For the first time, co-occurrences of antibiotic resistance have been investigated for priority pathogens as defined by the WHO. For critically important pathogens, co-occurrences appear in plasmids, not in chromosomes, suggesting that the resistances may be epidemic and probably recent. These results hint at the need for new approaches to treating infections caused by critically important bacteria.
Collapse
Affiliation(s)
- Célia P F Domingues
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
| | - João S Rebelo
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Francisco Dionisio
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Teresa Nogueira
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
| |
Collapse
|
4
|
Pilati GVT, Cadamuro RD, Filho VB, Dahmer M, Elois MA, Savi BP, Salles GBC, Muniz EC, Fongaro G. Bacteriophage-Associated Antimicrobial Resistance Genes in Avian Pathogenic Escherichia coli Isolated from Brazilian Poultry. Viruses 2023; 15:1485. [PMID: 37515172 PMCID: PMC10386125 DOI: 10.3390/v15071485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Colibacillosis is a disease caused by Escherichia coli and remains a major concern in poultry production, as it leads to significant economic losses due to carcass condemnation and clinical symptoms. The development of antimicrobial resistance is a growing problem of worldwide concern. Lysogenic bacteriophages are effective vectors for acquiring and disseminating antibiotic resistance genes (ARGs). The aim of this study was to investigate the complete genome of Escherichia coli isolates from the femurs of Brazilian broiler chickens in order to investigate the presence of antimicrobial resistance genes associated with bacteriophages. Samples were collected between August and November 2021 from broiler batches from six Brazilian states. Through whole genome sequencing (WGS), data obtained were analyzed for the presence of antimicrobial resistance genes. Antimicrobial resistance genes against the aminoglycosides class were detected in 79.36% of the isolates; 74.6% had predicted sulfonamides resistance genes, 63.49% had predicted resistance genes against β-lactams, and 49.2% of the isolates had at least one of the tetracycline resistance genes. Among the detected genes, 27 have been described in previous studies and associated with bacteriophages. The findings of this study highlight the role of bacteriophages in the dissemination of ARGs in the poultry industry.
Collapse
Affiliation(s)
- Giulia Von Tönnemann Pilati
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Rafael Dorighello Cadamuro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Vilmar Benetti Filho
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Mariane Dahmer
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Mariana Alves Elois
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Beatriz Pereira Savi
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Gleidson Biasi Carvalho Salles
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
- Zoetis Industry of Veterinary Products LTDA, São Paulo 04709-111, Brazil
| | | | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| |
Collapse
|
5
|
Antibiotic resistance genes, mobile elements, virulence genes, and phages in cultivated ESBL-producing Escherichia coli of poultry origin in Kwara State, North Central Nigeria. Int J Food Microbiol 2023; 389:110086. [PMID: 36738714 DOI: 10.1016/j.ijfoodmicro.2023.110086] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 01/22/2023]
Abstract
The paucity of information on the genomic diversity of drug-resistant bacteria in most food-producing animals, including poultry in Nigeria, has led to poor hazard characterization and the lack of critical control points to safeguard public health. Hence, this study used whole genome sequencing (WGS) to assess the presence and the diversity of antibiotic resistance genes, mobile genetic elements, virulence genes, and phages in Extended Spectrum Beta Lactamase producing Escherichia coli (ESBL - E. coli) isolates obtained from poultry via the EURL guideline of 2017 in Ilorin, Nigeria. The prevalence of ESBL - E. coli in poultry was 10.5 % (n = 37/354). The phenotypic antibiotic susceptibility testing showed that all the ESBL- E. coli isolates were multi-drug resistant (MDR). The in-silico analysis of the WGS raw-read data from 11 purposively selected isolates showed that the isolates had a wide array of ARGs that conferred resistance to beta-lactam antibiotics, and 8 other classes of antibiotics (fluoroquinolones, foliate pathway antagonists, aminoglycoside, phenicol, tetracycline, epoxide, macrolides, and rifamycin). All the ARGs were in the bacterial chromosome except in two isolates where plasmid-mediated quinolone resistance (PMQR) was detected. Two isolates carried the gyrAp.S83L mutation which confers resistance to certain fluoroquinolones. The mobilome consisted of several Col-plasmids and the predominant IncF plasmids belonged to the IncF64:A-:B27 sequence type. The virulome consisted of genes that function as adhesins, iron acquisition genes, toxins, and protectins. Intact phages were found in 8 of the 11 isolates and the phageome consisted of representatives of four families of viruses: Myoviridae (62.5 %, n = 5/8), Siphoviridae (37.5 %, n = 3/8), Inoviridae (12.5 %, n = 1), and Podoviridae (12.5 %, n = 1/8). ESBL - E. coli isolates harboured 1-5 intact phages and no ARGs were identified on any of the phages. Although five of the isolates belonged to phylogroup A, the isolates were diverse as they belonged to different serotype and sequence types. Our findings demonstrate the high genomic diversity of ESBL - E. coli of poultry origin in Ilorin, Nigeria. These diverse isolates harbor clinically relevant ARGs, mobile elements, virulence genes, and phages that may have detrimental zoonotic potentials on human health.
Collapse
|
6
|
Salmonella Prophages, Their Propagation, Host Specificity and Antimicrobial Resistance Gene Transduction. Antibiotics (Basel) 2023; 12:antibiotics12030595. [PMID: 36978463 PMCID: PMC10045043 DOI: 10.3390/antibiotics12030595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Salmonella enterica subsp. enterica is a zoonotic bacterial pathogen that causes foodborne outbreaks in humans. Lytic bacteriophages to control Salmonella in food production are already being used in scientific studies and some are commercially available. However, phage application is still controversial. In addition to virulent phages, which are used in phage therapy and lyse the bacterial host, lysogenic phages coexist in the environment and can reside as prophages in the bacterial host. Therefore, information about Salmonella prophages is essential to understand successful phage therapy. In 100 Salmonella food isolates of the serovars Enteritidis and Typhimurium, we propagated prophages by oxidative stress. In isolates of the serovars Typhimurium and Enteritidis, 80% and 8% prophages could be activated, respectively. In the phage lysates from the serovar Typhimurium, the following antibiotic resistance genes or gene fragments were detected by PCR: sul1, sul2, blaTEM, strA and cmlA; however, no tetA,B,C, blaOXA, blaCMY, aadA1, dfr1,2 or cat were detected. In contrast, no resistance genes were amplified in the phage lysates of the serovar Enteritidis. None of the phage lysates was able to transduce phenotypic resistance to WT 14028s. Most of the prophage lysates isolated were able to infect the various Salmonella serovars tested. The high abundance of prophages in the genome of the serovar Typhimurium may counteract phage therapy through phage resistance and the development of hybrid phages.
Collapse
|
7
|
Mak PHW, Rehman MA, Kiarie EG, Topp E, Diarra MS. Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: a review. J Anim Sci Biotechnol 2022; 13:148. [PMID: 36514172 DOI: 10.1186/s40104-022-00786-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/18/2022] [Indexed: 12/15/2022] Open
Abstract
Economic losses and market constraints caused by bacterial diseases such as colibacillosis due to avian pathogenic Escherichia coli and necrotic enteritis due to Clostridium perfringens remain major problems for poultry producers, despite substantial efforts in prevention and control. Antibiotics have been used not only for the treatment and prevention of such diseases, but also for growth promotion. Consequently, these practices have been linked to the selection and spread of antimicrobial resistant bacteria which constitute a significant global threat to humans, animals, and the environment. To break down the antimicrobial resistance (AMR), poultry producers are restricting the antimicrobial use (AMU) while adopting the antibiotic-free (ABF) and organic production practices to satisfy consumers' demands. However, it is not well understood how ABF and organic poultry production practices influence AMR profiles in the poultry gut microbiome. Various Gram-negative (Salmonella enterica serovars, Campylobacter jejuni/coli, E. coli) and Gram-positive (Enterococcus spp., Staphylococcus spp. and C. perfringens) bacteria harboring multiple AMR determinants have been reported in poultry including organically- and ABF-raised chickens. In this review, we discussed major poultry production systems (conventional, ABF and organic) and their impacts on AMR in some potential pathogenic Gram-negative and Gram-positive bacteria which could allow identifying issues and opportunities to develop efficient and safe production practices in controlling pathogens.
Collapse
Affiliation(s)
- Philip H W Mak
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Guelph, ON, Canada.,Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Muhammad Attiq Rehman
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Guelph, ON, Canada
| | - Elijah G Kiarie
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Edward Topp
- London Research and Development Center, AAFC, London, ON, Canada
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Guelph, ON, Canada.
| |
Collapse
|
8
|
Ramamurthy T, Ghosh A, Chowdhury G, Mukhopadhyay AK, Dutta S, Miyoshi SI. Deciphering the genetic network and programmed regulation of antimicrobial resistance in bacterial pathogens. Front Cell Infect Microbiol 2022; 12:952491. [PMID: 36506027 PMCID: PMC9727169 DOI: 10.3389/fcimb.2022.952491] [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: 05/25/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is an important global health problem affecting humans, animals, and the environment. AMR is considered as one of the major components in the "global one health". Misuse/overuse of antibiotics in any one of the segments can impact the integrity of the others. In the presence of antibiotic selective pressure, bacteria tend to develop several defense mechanisms, which include structural changes of the bacterial outer membrane, enzymatic processes, gene upregulation, mutations, adaptive resistance, and biofilm formation. Several components of mobile genetic elements (MGEs) play an important role in the dissemination of AMR. Each one of these components has a specific function that lasts long, irrespective of any antibiotic pressure. Integrative and conjugative elements (ICEs), insertion sequence elements (ISs), and transposons carry the antimicrobial resistance genes (ARGs) on different genetic backbones. Successful transfer of ARGs depends on the class of plasmids, regulons, ISs proximity, and type of recombination systems. Additionally, phage-bacterial networks play a major role in the transmission of ARGs, especially in bacteria from the environment and foods of animal origin. Several other functional attributes of bacteria also get successfully modified to acquire ARGs. These include efflux pumps, toxin-antitoxin systems, regulatory small RNAs, guanosine pentaphosphate signaling, quorum sensing, two-component system, and clustered regularly interspaced short palindromic repeats (CRISPR) systems. The metabolic and virulence state of bacteria is also associated with a range of genetic and phenotypic resistance mechanisms. In spite of the availability of a considerable information on AMR, the network associations between selection pressures and several of the components mentioned above are poorly understood. Understanding how a pathogen resists and regulates the ARGs in response to antimicrobials can help in controlling the development of resistance. Here, we provide an overview of the importance of genetic network and regulation of AMR in bacterial pathogens.
Collapse
Affiliation(s)
- Thandavarayan Ramamurthy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Thandavarayan Ramamurthy,
| | - Amit Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Asish K. Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-inchi Miyoshi
- Collaborative Research Centre of Okayama University for Infectious Diseases at ICMR- National Institute of Cholera and Enteric Diseases, Kolkata, India,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| |
Collapse
|
9
|
Tang X, Fan C, Zeng G, Zhong L, Li C, Ren X, Song B, Liu X. Phage-host interactions: The neglected part of biological wastewater treatment. WATER RESEARCH 2022; 226:119183. [PMID: 36244146 DOI: 10.1016/j.watres.2022.119183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/29/2022] [Accepted: 09/29/2022] [Indexed: 05/25/2023]
Abstract
In wastewater treatment plants (WWTPs), the stable operation of biological wastewater treatment is strongly dependent on the stability of associated microbiota. Bacteriophages (phages), viruses that specifically infect bacteria and archaea, are highly abundant and diverse in WWTPs. Although phages do not have known metabolic functions for themselves, they can shape functional microbiota via various phage-host interactions to impact biological wastewater treatment. However, the developments of phage-host interaction in WWTPs and their impact on biological wastewater treatment are overlooked. Here, we review the current knowledge regarding the phage-host interactions in biological wastewater treatment, mainly focusing on the characteristics of different phage populations, the phage-driven changes in functional microbiota, and the potential driving factors of phage-host interactions. We also discuss the efforts required further to understand and manipulate the phage-host interactions in biological wastewater treatment. Overall, this review advocates more attention to the phage dynamics in WWTPs.
Collapse
Affiliation(s)
- Xiang Tang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Changzheng Fan
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China.
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Linrui Zhong
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Chao Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China; Nova Skantek (Hunan) Environ Energy Co., Ltd., Changsha 410100, P.R. China
| | - Xiaoya Ren
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| | - Xigui Liu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, P.R. China
| |
Collapse
|
10
|
Antimicrobial Resistance Trends of Escherichia coli Isolates: A Three-Year Prospective Study of Poultry Production in Spain. Antibiotics (Basel) 2022; 11:antibiotics11081064. [PMID: 36009933 PMCID: PMC9404938 DOI: 10.3390/antibiotics11081064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
Antimicrobial resistance (AMR) poses a major threat to health worldwide. Poultry products are one of the main threats, due to the transmission of antimicrobial resistance genes throughout the food chain. Escherichia coli is the main cause of mortality in the poultry industry, mainly mitigated with antibiotics, but due to the high genetic strain variability, recurrent outbreaks of multidrug resistant E. coli take place. The major challenge to tackling AMR is understanding the burden of resistance. For this reason, one of the main strategies is monitoring AMR by phenotypic characterisation. Our study aimed to monitor the resistance of E. coli strains isolated from the poultry sector over a period of three years (2019–2021) to provide information on the resistance magnitude and trends. Promising results have been found concerning the low frequency of resistance to cephalosporins, polymyxin, and fluoroquinolones. However, levels of resistance found to antimicrobials such as erythromycin (100%), tylosin (98%), or penicillin (97%) suggest the need to continue working on the limitation of use of antimicrobials in poultry to achieve the demise of MDR.
Collapse
|
11
|
Zhang Y, Guo Y, Qiu T, Gao M, Wang X. Bacteriophages: Underestimated vehicles of antibiotic resistance genes in the soil. Front Microbiol 2022; 13:936267. [PMID: 35992716 PMCID: PMC9386270 DOI: 10.3389/fmicb.2022.936267] [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: 05/05/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteriophages (phages), the most abundant biological entities on Earth, have a significant effect on the composition and dynamics of microbial communities, biogeochemical cycles of global ecosystems, and bacterial evolution. A variety of antibiotic resistance genes (ARGs) have been identified in phage genomes in different soil samples. Phages can mediate the transfer of ARGs between bacteria via transduction. Recent studies have suggested that anthropogenic activities promote phage-mediated horizontal gene transfer events. Therefore, the role of phages in the dissemination of ARGs, which are a potential threat to human health, may be underestimated. However, the contribution of phages to the transfer of ARGs is still poorly understood. Considering the growing and wide concerns of antibiotic resistance, phages should be considered a research focus in the mobile resistome. This review aimed to provide an overview of phages as vehicles of ARGs in soil. Here, we summarized the current knowledge on the diversity and abundance of ARGs in soilborne phages and analyzed the contribution of phages to the horizontal transfer of ARGs. Finally, research deficiencies and future perspectives were discussed. This study provides a reference for preventing and controlling ARG pollution in agricultural systems.
Collapse
|
12
|
Salmonella spp. Response to Lytic Bacteriophage and Lactic Acid on Marinated and Tenderized Raw Pork Loins. Foods 2022; 11:foods11060879. [PMID: 35327301 PMCID: PMC8951642 DOI: 10.3390/foods11060879] [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: 02/24/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial food poisoning cases due to Salmonella have been linked with a variety of pork products. This study evaluated the effects of a Salmonella-specific lytic bacteriophage and lactic acid (LA) on Salmonella Enteritidis, Salmonella Montevideo, and Salmonella Heidelberg growth on raw pork loins. Pork loins were cut into approximately 4 cm thick slices. Pork slices were randomly assigned to five treatment groups (control, DI water, LA 2.5%, phage 5%, and LA 2.5% + phage 5%) with six slices per group per replication. Pork loins were inoculated with 106 CFU/mL of Salmonella spp. and stored at 4 °C for 30 min. After 1 h of treatment application and marination, phage 5% significantly (p < 0.05) reduced the surface bacterial population by 2.30 logs when compared with the control group. Moreover, the combined treatment of LA 2.5% + phage 5% significantly (p < 0.05) reduced the surface bacterial population by more than 2.36 logs after 1 h of marination. In the post-tenderization surface samples, the combination of both phage and LA showed a significant reduction (p < 0.05) when compared with the control group. However, the treatments had no effect (p > 0.05) when analyzing the translocation of pathogens on pork loins.
Collapse
|
13
|
In Silico Characterisation of Putative Prophages in Lactobacillaceae Used in Probiotics for Vaginal Health. Microorganisms 2022; 10:microorganisms10020214. [PMID: 35208669 PMCID: PMC8879116 DOI: 10.3390/microorganisms10020214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/15/2021] [Accepted: 12/18/2021] [Indexed: 01/27/2023] Open
Abstract
While live biotherapeutics offer a promising approach to optimizing vaginal microbiota, the presence of functional prophages within introduced Lactobacillaceae strains could impact their safety and efficacy. We evaluated the presence of prophages in 895 publicly available Lactobacillaceae genomes using Phaster, Phigaro, Phispy, Prophet and Virsorter. Prophages were identified according to stringent (detected by ≥4 methods) or lenient criteria (detected by ≥2 methods), both with >80% reciprocal sequence overlap. The stringent approach identified 448 prophages within 359 genomes, with 40.1% genomes harbouring at least one prophage, while the lenient approach identified 1671 prophages within 83.7% of the genomes. To confirm our in silico estimates in vitro, we tested for inducible prophages in 57 vaginally-derived and commercial Lactobacillaceae isolates and found inducible prophages in 61.4% of the isolates. We characterised the in silico predicted prophages based on weighted gene repertoire relatedness and found that most belonged to the Siphoviridae or Myoviridae families. ResFam and eggNOG identified four potential antimicrobial resistance genes within the predicted prophages. Our results suggest that while Lactobacillaceae prophages seldomly carry clinically concerning genes and thus unlikely a pose a direct risk to human vaginal microbiomes, their high prevalence warrants the characterisation of Lactobacillaceae prophages in live biotherapeutics.
Collapse
|
14
|
Happel AU, Balle C, Maust BS, Konstantinus IN, Gill K, Bekker LG, Froissart R, Passmore JA, Karaoz U, Varsani A, Jaspan H. Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents. Viruses 2021; 13:2341. [PMID: 34960611 PMCID: PMC8708031 DOI: 10.3390/v13122341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/18/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022] Open
Abstract
The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.
Collapse
Affiliation(s)
- Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
| | - Christina Balle
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
| | - Brandon S. Maust
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA;
- Department of Pediatrics, University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA
| | - Iyaloo N. Konstantinus
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Namibia Institute of Pathology, Hosea Kutako, Windhoek 10005, Namibia
| | - Katherine Gill
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
| | - Rémy Froissart
- CNRS, IRD, Université Montpellier, UMR 5290, MIVEGEC, 34394 Montpellier, France;
| | - Jo-Ann Passmore
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Desmond Tutu HIV Centre, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (K.G.); (L.-G.B.)
- NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa
- National Health Laboratory Service, Anzio Road, Cape Town 7925, South Africa
| | - Ulas Karaoz
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, 1 Cyclotron Rd., Berkeley, CA 94720, USA;
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ 85281, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa
| | - Heather Jaspan
- Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Cape Town 7925, South Africa; (A.-U.H.); (C.B.); (I.N.K.); (J.-A.P.)
- Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109, USA;
- Department of Pediatrics, University of Washington School of Medicine, 1959 NE Pacific St., Seattle, WA 98195, USA
- Department of Global Health, University of Washington School of Public Health, 1510 San Juan Road NE, Seattle, WA 98195, USA
| |
Collapse
|
15
|
Chen ML, An XL, Liao H, Yang K, Su JQ, Zhu YG. Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:13881-13890. [PMID: 34596377 DOI: 10.1021/acs.est.1c03847] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance is a global health concern. Long-term organic fertilization can influence the antibiotic resistome of agricultural soils, posing potential risks to human health. However, little is known about the contribution of viruses to the dissemination of antibiotic resistance genes (ARGs) in this context. Here, we profiled the viral communities and virus-associated ARGs in a long-term (over 10 years) organic fertilized field by viral metagenomic analysis. A total of 61,520 viral populations (viral operational taxonomic units, vOTUs) were retrieved, of which 21,308 were assigned at the family level. The viral community structures were significantly correlated with the bacterial community structures (P < 0.001) and the dosage of applied sewage sludge (r2 = 0.782). A total of 16 unique ARGs were detected in soil viromes, and the number of virus-associated ARG subtypes was higher in sewage sludge treatments (except for 1 SS) than others. The network analysis showed that the application of the organic fertilizer increased the bacteria-virus interactions, suggesting that the chances of ARG exchange between viruses and their hosts may increase. Overall, our results provide a novel understanding about virus-associated ARGs and factors affecting the profile of viral community in fertilized soil.
Collapse
Affiliation(s)
- Mo-Lian Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hu Liao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Kai Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| |
Collapse
|
16
|
Knezevic P, Petrovic Fabijan A, Gavric D, Pejic J, Doffkay Z, Rakhely G. Phages from Genus Bruynoghevirus and Phage Therapy: Pseudomonas Phage Delta Case. Viruses 2021; 13:1965. [PMID: 34696396 PMCID: PMC8540360 DOI: 10.3390/v13101965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
The applicability and safety of bacteriophage Delta as a potential anti-Pseudomonas aeruginosa agent belonging to genus Bruynoghevirus (family Podoviridae) was characterised. Phage Delta belongs to the species Pseudomonas virus PaP3, which has been described as a temperate, with cos sites at the end of the genome. The phage Delta possesses a genome of 45,970 bp that encodes tRNA for proline (Pro), aspartic acid (Asp) and asparagine (Asn) and does not encode any known protein involved in lysogeny formation or persistence. Analysis showed that phage Delta has 182 bp direct terminal repeats at the end of genome and lysogeny was confirmed, neither upon infection at low nor at high multiplicity of infection (MOI). The turbid plaques that appear on certain host lawns can result from bacteriophage insensitive mutants that occur with higher frequency (10-4). In silico analysis showed that the genome of Delta phage does not encode any known bacterial toxin or virulence factor, determinants of antibiotic resistance and known human allergens. Based on the broad host range and high lytic activity against planktonic and biofilm cells, phage Delta represents a promising candidate for phage therapy.
Collapse
Affiliation(s)
- Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Aleksandra Petrovic Fabijan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Damir Gavric
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Jovana Pejic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, 21 000 Novi Sad, Serbia; (A.P.F.); (D.G.); (J.P.)
| | - Zsolt Doffkay
- Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary; (Z.D.); (G.R.)
| | - Gábor Rakhely
- Department of Biotechnology, University of Szeged, Temesvari krt. 62, H-6726 Szeged, Hungary; (Z.D.); (G.R.)
| |
Collapse
|
17
|
Froissart R, Brives C. Evolutionary biology and development model of medicines: A necessary 'pas de deux' for future successful bacteriophage therapy. J Evol Biol 2021; 34:1855-1866. [PMID: 34288190 DOI: 10.1111/jeb.13904] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/29/2021] [Accepted: 06/15/2021] [Indexed: 12/12/2022]
Abstract
The increase in frequency of multidrug-resistant bacteria worldwide is largely the result of the massive use of antibiotics in the second half of the 20th century. These relatively recent changes in human societies revealed the great evolutionary capacities of bacteria towards drug resistance. In this article, we hypothesize that the success of future antibacterial strategies lies in taking into account both these evolutionary processes and the way human activities influence them. Faced with the increasing prevalence of multidrug-resistant bacteria and the scarcity of new antibacterial chemical molecules, the use of bacteriophages is considered as a complementary and/or alternative therapy. After presenting the evolutionary capacities of bacteriophages and bacteria, we show how the development model currently envisaged (based on the classification of bacteriophages as medicinal products similar to antibacterial chemical molecules) ignores the evolutionary processes inherent in bacteriophage therapy. This categorization imposes to bacteriophage therapy a specific conception of what a treatment and a therapeutic scheme should be as well as its mode of production and prescription. We argue that a new development model is needed that would allow the use of therapeutic bacteriophages fully adapted (after in vitro 'bacteriophage training') to the aetiologic bacteria and/or aimed at rendering bacteria either avirulent or antibiotic-susceptible ('bacteriophage steering'). To not repeat the mistakes made with antibiotics, we must now think about and learn from the ways in which the materialities of microbes (e.g. evolutionary capacities of both bacteriophages and bacteria) are intertwined with those of societies.
Collapse
Affiliation(s)
- Rémy Froissart
- MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
| | | |
Collapse
|
18
|
Fong K, Wong CW, Wang S, Delaquis P. How Broad Is Enough: The Host Range of Bacteriophages and Its Impact on the Agri-Food Sector. PHAGE 2021; 2:83-91. [PMID: 36148040 PMCID: PMC9041489 DOI: 10.1089/phage.2020.0036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Novel bacteriophages (phages) possessing a broad host range are consistently and routinely reported, yet there is presently no consensus on the definition of “broad host range.” As phages are increasingly being used in the development of methods for the detection and biocontrol of human pathogens, it is important to address the limitations associated with the host range. For instance, unanticipated host range breadth may result in the detection of nonpathogenic targets, thereby increasing the false-positive rate. Moreover, a broad host range is generally favored in biocontrol applications despite the risk of undesirable ancillary effects against nontarget species. Here, we discuss the research progress, applications, and implications of broad host range phages with a focus on tailed broad host range phages infecting human pathogens of concern in the Agri-Food sector.
Collapse
Affiliation(s)
- Karen Fong
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, Canada
- Address correspondence to: Karen Fong, PhD, Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Postal Box 5000, Summerland BC V0H1Z0, Canada
| | - Catherine W.Y. Wong
- Food, Nutrition and Health, University of British Columbia, Vancouver, Canada
| | - Siyun Wang
- Food, Nutrition and Health, University of British Columbia, Vancouver, Canada
| | - Pascal Delaquis
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, Canada
| |
Collapse
|
19
|
Rodríguez-Rubio L, Haarmann N, Schwidder M, Muniesa M, Schmidt H. Bacteriophages of Shiga Toxin-Producing Escherichia coli and Their Contribution to Pathogenicity. Pathogens 2021; 10:404. [PMID: 33805526 PMCID: PMC8065619 DOI: 10.3390/pathogens10040404] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
Shiga toxins (Stx) of Shiga toxin-producing Escherichia coli (STEC) are generally encoded in the genome of lambdoid bacteriophages, which spend the most time of their life cycle integrated as prophages in specific sites of the bacterial chromosome. Upon spontaneous induction or induction by chemical or physical stimuli, the stx genes are co-transcribed together with the late phase genes of the prophages. After being assembled in the cytoplasm, and after host cell lysis, mature bacteriophage particles are released into the environment, together with Stx. As members of the group of lambdoid phages, Stx phages share many genetic features with the archetypical temperate phage Lambda, but are heterogeneous in their DNA sequences due to frequent recombination events. In addition to Stx phages, the genome of pathogenic STEC bacteria may contain numerous prophages, which are either cryptic or functional. These prophages may carry foreign genes, some of them related to virulence, besides those necessary for the phage life cycle. Since the production of one or more Stx is considered the major pathogenicity factor of STEC, we aim to highlight the new insights on the contribution of Stx phages and other STEC phages to pathogenicity.
Collapse
Affiliation(s)
- Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (L.R.-R.); (M.M.)
| | - Nadja Haarmann
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| | - Maike Schwidder
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (L.R.-R.); (M.M.)
| | - Herbert Schmidt
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| |
Collapse
|
20
|
Freeland G, Hettiarachchy N, Atungulu GG, Apple J, Mukherjee S. Strategies to Combat Antimicrobial Resistance from Farm to Table. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.1893744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Gabriella Freeland
- Department of Family and Consumer Sciences, Canastota Central School District, Canastota, New York, USA
| | - Navam Hettiarachchy
- Department of Food Science, University of Arkansas, Fayetteville, Arkansas, USA
| | | | - Jason Apple
- Department of Animal Science, University of Arkansas, Fayetteville, Arkansas, USA
| | - Soma Mukherjee
- Department of Food Science, University of Arkansas, Fayetteville, Arkansas, USA
| |
Collapse
|
21
|
Vasilevskaya ER, Fedulova LV, Chernukha IM, Kotenkova EA, Fokina AI. Effects of tissue-specific biomolecules on piglets after-weaning period. Vet World 2021; 14:168-175. [PMID: 33642801 PMCID: PMC7896913 DOI: 10.14202/vetworld.2021.168-175] [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: 09/04/2020] [Accepted: 12/01/2020] [Indexed: 01/14/2023] Open
Abstract
Background and Aim Now-a-days antibiotics are the main tool for correcting the pathological conditions of pigs; unfortunately, antibiotics are a potential threat to the environment, as they lead to the spread of antibiotic-resistant infections. This study aimed to study the immunomodulatory encapsulated biomolecules on piglets in the post-weaning period. Materials and Methods An immunomodulator based on biomolecules obtained from animal raw materials included in alginate capsules to improve absorption has been developed. The study presents the results of a study on 25 weaned piglets (25-30 days old) which received biomolecules at a dose of 200 mg/piglet for 14 days, followed by 400 mg/piglet from days 15 to 28. Blood was taken from animals for analysis (biochemical, hematological, cytometric, and enzyme immunoassay) and the integral index of blood serum antimicrobial activity was determined. Results Experimental animals, whose initial weight was 1.6 times less than that of the control animals, were able to bridge this gap and, on the 28th day, there were no differences in weight. Stimulation of the production of cytokines interleukin (IL)-2 and IL-4 was observed and the antimicrobial resistance of blood serum to Escherichia coli also increased. A positive effect on the metabolism of piglets was noted, which helped them adapt to a change in diet (from colostrum to solid food). Conclusion The results show that the immunomodulation at the dose of 150 mg/kg body weight has a great potential for improving weaned pigs.
Collapse
|
22
|
Chaturvedi P, Shukla P, Giri BS, Chowdhary P, Chandra R, Gupta P, Pandey A. Prevalence and hazardous impact of pharmaceutical and personal care products and antibiotics in environment: A review on emerging contaminants. ENVIRONMENTAL RESEARCH 2021; 194:110664. [PMID: 33400949 DOI: 10.1016/j.envres.2020.110664] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/02/2020] [Accepted: 12/20/2020] [Indexed: 05/24/2023]
Abstract
Antibiotic resistance is a global health emergency linked to unrestrained use of pharmaceutical and personal care products (PPCPs) as prophylactic agent and therapeutic purposes across various industries. Occurrence of pharmaceuticals are identified in ground water, surface water, soils, and wastewater treatment plants (WWTPs) in ng/L to μg/L concentration range. The prevalence of organic compounds including antimicrobial agents, hormones, antibiotics, preservatives, disinfectants, synthetic musks etc. in environment have posed serious health concerns. The aim of this review is to elucidate the major sources accountable for emergence of antibiotic resistance. For this purpose, variety of introductory sources and fate of PPCPs in aquatic environment including human and veterinary wastes, aquaculture and agriculture related wastes, and other anthropogenic activities have been discussed. Furthermore, genetic and enzymatic factors responsible for transfer and appearance of antibiotic resistance genes are presented. Ecotoxicity of PPCPs has been studied in environment in order to present risk imposed to human and ecological health. As per published literature reports, the removal of antibiotics and related traces being difficult, couples the possibility of emergence of antibiotic resistance and hence sustainability in global water resources. Therefore, research on environmental behavior and control strategies should be conducted along with assessing their chronic toxicity to identify potential human and ecological risks.
Collapse
Affiliation(s)
- Preeti Chaturvedi
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, M.G. Marg, Lucknow, 226001, Uttar Pradesh, India; Department of Biotechnology, National Institute of Technology-Raipur, G.E. Road, Raipur, 492010, Chhattisgarh, India.
| | - Parul Shukla
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, M.G. Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Balendu Shekher Giri
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, M.G. Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Pankaj Chowdhary
- Aquatic Toxicology Laboratory, Environmental Toxicology Group, Council of Scientific and Industrial Research-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, M.G. Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Ram Chandra
- Department of Microbiology, Babasaheb Bhimrao Ambedkar University (A Central University), Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226 025, India
| | - Pratima Gupta
- Department of Biotechnology, National Institute of Technology-Raipur, G.E. Road, Raipur, 492010, Chhattisgarh, India.
| | - Ashok Pandey
- Centre for Innovation and Transnational Research, CSIR-Indian Institute of Toxicology Research, Lucknow, 226 001, Uttar Pradesh, India
| |
Collapse
|
23
|
Hassan AY, Lin JT, Ricker N, Anany H. The Age of Phage: Friend or Foe in the New Dawn of Therapeutic and Biocontrol Applications? Pharmaceuticals (Basel) 2021; 14:199. [PMID: 33670836 PMCID: PMC7997343 DOI: 10.3390/ph14030199] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023] Open
Abstract
Extended overuse and misuse of antibiotics and other antibacterial agents has resulted in an antimicrobial resistance crisis. Bacteriophages, viruses that infect bacteria, have emerged as a legitimate alternative antibacterial agent with a wide scope of applications which continue to be discovered and refined. However, the potential of some bacteriophages to aid in the acquisition, maintenance, and dissemination of negatively associated bacterial genes, including resistance and virulence genes, through transduction is of concern and requires deeper understanding in order to be properly addressed. In particular, their ability to interact with mobile genetic elements such as plasmids, genomic islands, and integrative conjugative elements (ICEs) enables bacteriophages to contribute greatly to bacterial evolution. Nonetheless, bacteriophages have the potential to be used as therapeutic and biocontrol agents within medical, agricultural, and food processing settings, against bacteria in both planktonic and biofilm environments. Additionally, bacteriophages have been deployed in developing rapid, sensitive, and specific biosensors for various bacterial targets. Intriguingly, their bioengineering capabilities show great promise in improving their adaptability and effectiveness as biocontrol and detection tools. This review aims to provide a balanced perspective on bacteriophages by outlining advantages, challenges, and future steps needed in order to boost their therapeutic and biocontrol potential, while also providing insight on their potential role in contributing to bacterial evolution and survival.
Collapse
Affiliation(s)
- Ahmad Y. Hassan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada;
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Janet T. Lin
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Nicole Ricker
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Hany Anany
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada;
- Department of Food Science, Ontario Agricultural College, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
24
|
Talavera-González JM, Talavera-Rojas M, Soriano-Vargas E, Vázquez-Navarrete J, Salgado-Miranda C. In vitro transduction of antimicrobial resistance genes into Escherichia coli isolates from backyard poultry in Mexico. Can J Microbiol 2021; 67:415-425. [PMID: 33395360 DOI: 10.1139/cjm-2020-0280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The transmission of multidrug-resistant pathogens and antimicrobial resistance genes is an emerging problem involving multiple factors (humans, domestic animals, wildlife). The aim of this study was to investigate the presence of Escherichia coli isolates with different antimicrobial resistance genes from backyard poultry and to demonstrate the in vitro transduction phenomenon of these genes between phages from migratory wild birds and poultry E. coli isolates. We collected 197 E. coli isolates from chickens, turkeys, and ducks in backyard production units (northern region of the State of Mexico). Isolates were resistant to ampicillin (80.7%), tetracycline (64.4%), carbenicillin (56.3%), and nalidixic acid and trimethoprim-sulfamethoxazole (both, 26.9%). Moreover, the genes blaTEM (56.3%), tetB (20.8%), tetA (19.2%), sulI (7.6%), sulII (10.1%), qnrA (9.6%), and qnrB (5.5%) were found. In vitro transduction using phages from migratory wild birds sampled in the wetland Chimaliapan (State of Mexico) was successfully achieved. It was possible to transduce qnrA, tetB, blaTEM, and sulII genes to E. coli isolates from poultry. This is the first report that describes the transduction of antimicrobial resistance genes from phages of migratory wild birds to poultry and suggests the possible transmission in backyard production units.
Collapse
Affiliation(s)
- Juan Martín Talavera-González
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca, Estado de México 50200, México
| | - Martín Talavera-Rojas
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca, Estado de México 50200, México
| | - Edgardo Soriano-Vargas
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca, Estado de México 50200, México
| | - Jesús Vázquez-Navarrete
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Carretera México-Toluca Km. 15.5, Ciudad de México, México
| | - Celene Salgado-Miranda
- Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México, Carretera Toluca-Atlacomulco, Km 15.5, Toluca, Estado de México 50200, México
| |
Collapse
|
25
|
Pan Y, Fang Y, Feng Y, Lyu N, Chen L, Li J, Xu X, Zhu B, Hu Y. Discovery of mcr-3.1 gene carried by a prophage located in a conjugative IncA/C2 plasmid from a Salmonella Choleraesuis clinical isolate. J Infect 2020; 82:414-451. [PMID: 33007341 DOI: 10.1016/j.jinf.2020.09.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Yuanlong Pan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Yuan Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Na Lyu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Luping Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Xuebin Xu
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China; Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| |
Collapse
|
26
|
Antimicrobial Resistance in Escherichia coli and Resistance Genes in Coliphages from a Small Animal Clinic and in a Patient Dog with Chronic Urinary Tract Infection. Antibiotics (Basel) 2020; 9:antibiotics9100652. [PMID: 33003333 PMCID: PMC7600197 DOI: 10.3390/antibiotics9100652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance is on the rise in certain pathogens that infect pets and their owners. This has raised concerns about the use of antibiotics and the transfer of resistance elements in small animal clinics. We sampled a surgery unit, diagnostic rooms after disinfection, and a dog with chronic urinary tract infection (UTI), in a small animal clinic in Austria, and isolated/characterized phages and Escherichia (E.) coli for antimicrobial resistance, resistance genes and transduction ability. Neither the coliphages nor E. coli were isolated in the 20 samples of the surgery units and diagnostic rooms. From the urinary tract of the dog, we recovered 57 E. coli isolates and 60 coliphages. All of the E. coli isolates were determined as resistant against nalidixic acid, 47 against ampicillin, 34 against sulfonamides, and 33 against streptomycin. No isolate held resistance against tetracycline, trimethoprim, kanamycin, or chloramphenicol. Among the 60 phages, 29 tested positive for one or more resistance gene(s) by PCR, but none was able to transduce it to a laboratory strain or to an E. coli isolated from samples. Nevertheless, six phages out of 60 were able to transduce ampicillin resistance (bla gene) after being grown on a puc19 harboring E. coli strain.
Collapse
|
27
|
Blanco-Picazo P, Roscales G, Toribio-Avedillo D, Gómez-Gómez C, Avila C, Ballesté E, Muniesa M, Rodríguez-Rubio L. Antibiotic Resistance Genes in Phage Particles from Antarctic and Mediterranean Seawater Ecosystems. Microorganisms 2020; 8:microorganisms8091293. [PMID: 32847015 PMCID: PMC7565065 DOI: 10.3390/microorganisms8091293] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 01/17/2023] Open
Abstract
Anthropogenic activities are a key factor in the development of antibiotic resistance in bacteria, a growing problem worldwide. Nevertheless, antibiotics and resistances were being generated by bacterial communities long before their discovery by humankind, and might occur in areas without human influence. Bacteriophages are known to play a relevant role in the dissemination of antibiotic resistance genes (ARGs) in aquatic environments. In this study, five ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, sul1 and tetW) were monitored in phage particles isolated from seawater of two different locations: (i) the Mediterranean coast, subjected to high anthropogenic pressure, and (ii) the Antarctic coast, where the anthropogenic impact is low. Although found in lower quantities, ARG-containing phage particles were more prevalent among the Antarctic than the Mediterranean seawater samples and Antarctic bacterial communities were confirmed as their source. In the Mediterranean area, ARG-containing phages from anthropogenic fecal pollution might allow ARG transmission through the food chain. ARGs were detected in phage particles isolated from fish (Mediterranean, Atlantic, farmed, and frozen), the most abundant being β-lactamases. Some of these particles were infectious in cultures of the fecal bacteria Escherichia coli. By serving as ARG reservoirs in marine environments, including those with low human activity, such as the Antarctic, phages could contribute to ARG transmission between bacterial communities.
Collapse
Affiliation(s)
- Pedro Blanco-Picazo
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
| | - Gabriel Roscales
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
| | - Daniel Toribio-Avedillo
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
| | - Clara Gómez-Gómez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
| | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences (BEECA), Faculty of Biology, and Biodiversity Research Institute (IrBIO), University of Barcelona, Diagonal 643, 08028 Barcelona, Spain;
| | - Elisenda Ballesté
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
- Correspondence: (M.M.); (L.R.-R.)
| | - Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, 08028 Barcelona, Spain; (P.B.-P.); (G.R.); (D.T.-A.); (C.G.-G.); (E.B.)
- Correspondence: (M.M.); (L.R.-R.)
| |
Collapse
|
28
|
Woegerbauer M, Bellanger X, Merlin C. Cell-Free DNA: An Underestimated Source of Antibiotic Resistance Gene Dissemination at the Interface Between Human Activities and Downstream Environments in the Context of Wastewater Reuse. Front Microbiol 2020; 11:671. [PMID: 32390973 PMCID: PMC7192050 DOI: 10.3389/fmicb.2020.00671] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/24/2020] [Indexed: 12/31/2022] Open
Abstract
The dissemination of antimicrobial resistance (AMR) is one of the biggest challenges faced by mankind in the public health domains. It is currently favored by a lack of confinement between waste disposal and food production in the environmental compartment. To date, much effort has been devoted into the elucidation and control of cell-associated propagation of AMR. However, substantial knowledge gaps remain on the contribution of cell-free DNA to promote horizontal transfers of resistance genes in wastewater and downstream environments. Cell free DNA, which covers free extracellular DNA (exDNA) as well as DNA encapsulated in vesicles or bacteriophages, can persist after disinfection and promote gene transfer in the absence of physical and temporal contact between a donor and recipient bacteria. The increasing water scarcity associated to climatic change requires developing innovative wastewater reuse practices and, concomitantly, a robust evaluation of AMR occurrence by implementing treatment technologies able to exert a stringent control on AMR propagation in downstream environments exposed to treated or non-treated wastewater. This necessarily implies understanding the fate of ARGs on various forms of cell-free DNA, especially during treatment processes that are permissive to their formation. We propose that comprehensive approaches, investigating both the occurrence of ARGs and their compartmentalization in different forms of cellular or cell-free associated DNA should be established for each treatment technology. This should then allow selecting and tuning technologies for their capacity to limit the propagation of ARGs in any of their forms.
Collapse
Affiliation(s)
- Markus Woegerbauer
- Department for Integrative Risk Assessment, Division for Risk Assessment, Data and Statistics, AGES – Austrian Agency for Health and Food Safety, Vienna, Austria
| | | | | |
Collapse
|
29
|
Balcázar JL. Implications of bacteriophages on the acquisition and spread of antibiotic resistance in the environment. Int Microbiol 2020; 23:475-479. [PMID: 32002743 DOI: 10.1007/s10123-020-00121-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 12/30/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022]
Abstract
Although bacteriophages (or simply phages) are the most abundant biological entities and have the potential to transfer genetic material between bacterial hosts, their contribution to the acquisition and spread of antibiotic resistance genes in the environment has not been extensively studied. The environment is continually exposed to a wide variety of pollutants from anthropogenic sources, which may promote horizontal gene transfer events, including those mediated by phages. Considering the significant and growing concern of antibiotic resistance, phages should be taken into consideration during the implementation of mitigation measures. This review is focused on the emergence and spread of antibiotic resistance in the environment, with a special emphasis on the role of phages.
Collapse
Affiliation(s)
- José Luis Balcázar
- Catalan Institute for Water Research (ICRA), 17003, Girona, Spain.
- University of Girona, 17004, Girona, Spain.
| |
Collapse
|
30
|
Yang Y, Xie X, Tang M, Liu J, Tuo H, Gu J, Tang Y, Lei C, Wang H, Zhang A. Exploring the profile of antimicrobial resistance genes harboring by bacteriophage in chicken feces. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 700:134446. [PMID: 31648121 DOI: 10.1016/j.scitotenv.2019.134446] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/08/2019] [Accepted: 09/12/2019] [Indexed: 05/04/2023]
Abstract
Bacteriophage may play an important role in antimicrobial resistance genes (ARGs) transmission. However, the contribution of bacteriophage to the spread of ARGs in environment, especially in poultry farm environment, is rarely known. In this study, the prevalence of ARGs in bacteriophage DNA was investigated in chicken feces from 30 different poultry farms in China. Then the abundance of the aac(6')-Ib-cr, blaCTX-M, ermB, floR, mcr-1, sul1, tetM and intI1 genes was determined by qPCR in bacteriophage and compared with certain representative plasmid DNA samples. The results showed that 12 ARGs (aac(6')-Ib-cr, aph(3')-IIIa, blaCTX-M, ermB, ermF, floR, mcr-1, qnrS, sul1, sul2, vanA, tetM genes) and class 1 integron gene intI1 were detected in bacteriophage DNA fraction. The sul1, tetM and aac(6')-Ib-cr genes were most prevalent with high detection rates of 77%, 61% and 55%, respectively. To our best knowledge, this study firstly reported the presence of the mcr-1 gene in bacteriophage DNA derived from farms environments. We found that the gene copy (GC) numbers of the aac(6')-Ib-cr, ermB and sul1 genes were as high as 5.47, 5.22 and 5.54 log10 GC/g, respectively. Both the prevalence and abundance of ARGs in broiler fecal wastes were also generally higher than in laying hens. In addition, although the GC numbers of the aac(6')-Ib-cr, floR and tetM genes in plasmid DNA was higher than that in phage DNA fraction by 4.68, 3.59 and 3.9 orders of magnitude, respectively, the absolute abundances of the blaCTX-M and mcr-1 genes in phage DNA were close to or even higher than that in plasmid DNA at farm SIL2, SIL4 and SIB1. As potential vessels for ARGs, bacteriophage could not be ignored due to their unique extracellular persistence in environments. Overall, this is the first comprehensive survey about bacteriophage carried ARGs from farms in different regions in China.
Collapse
Affiliation(s)
- Yanxian Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China; Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xianjun Xie
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Mengjun Tang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Jiangsu 225009, China
| | - Jinxin Liu
- Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, CA 95616, USA
| | - Hongmei Tuo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Ju Gu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Yizhi Tang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Changwei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Hongning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China
| | - Anyun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610010, China.
| |
Collapse
|
31
|
Mohan Raj JR, Vittal R, Shivakumaraswamy SK, Deekshit VK, Chakraborty A, Karunasagar I. Presence & mobility of antimicrobial resistance in Gram-negative bacteria from environmental samples in coastal Karnataka, India. Indian J Med Res 2019; 149:290-294. [PMID: 31219097 PMCID: PMC6563727 DOI: 10.4103/ijmr.ijmr_2088_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
To understand antimicrobial resistance (AMR) patterns and mechanisms of horizontal gene transfer in human-associated environments is essential to AMR surveillance. Gram-negative bacteria (1122 isolates) from food-animal environments were characterized for antimicrobial susceptibility and AMR genes. Seventy five per cent of the isolates (837 of 1122) were resistant to at least one of the antibiotics tested. Resistance to more than three groups of antimicrobials (multidrug resistance) was observed in 43 isolates with most often encountered (12 of 43) resistance to β-lactams, tetracycline, quinolones and nitrofurantoin. The profile of frequently reported plasmid-mediated resistance gene in these isolates was determined. The mobility of these elements as plasmids or phages was examined. The blaCTX-M gene was present in the plasmid of 61 per cent and packed in induced phage fractions in 72 per cent of the isolates and blaTEM in 69 per cent phage fractions compared to 15 per cent presence in the plasmid.
Collapse
Affiliation(s)
- Juliet Roshini Mohan Raj
- Division of Infectious Diseases, Nitte University Centre for Science Education & Research, Mangaluru, India
| | - Rajeshwari Vittal
- Division of Infectious Diseases, Nitte University Centre for Science Education & Research, Mangaluru, India
| | | | - Vijaya Kumar Deekshit
- Division of Infectious Diseases, Nitte University Centre for Science Education & Research, Mangaluru, India
| | - Anirban Chakraborty
- Division of Infectious Diseases, Nitte University Centre for Science Education & Research, Mangaluru, India
| | | |
Collapse
|
32
|
Tawakol MM, Nabil NM, Samy A. Evaluation of bacteriophage efficacy in reducing the impact of single and mixed infections with Escherichia coli and infectious bronchitis in chickens. Infect Ecol Epidemiol 2019; 9:1686822. [PMID: 31839902 PMCID: PMC6896464 DOI: 10.1080/20008686.2019.1686822] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/23/2019] [Indexed: 12/23/2022] Open
Abstract
Infectious bronchitis virus (IBV) represents a major threat to poultry production worldwide particularly when complicated with bacterial infection. In the present study samples were collected from forty broiler farms with respiratory manifestations to characterize IBV and E. coli. Bacteriophages were isolated and enriched from sampled farms to study its efficacy to control single and mixed infections with E. coli and IBV in vivo. Twelve out of forty farms were positive for IBV. Phylogenetic analysis of partial spike protein revealed that all positive cases clustered within the GI-23 genotype. Eight out of forty farms were positive for E. coli serogroups O26, O78, O86, O114, O119, with O125 found on three farms. Bacteriophage treatment delayed the onset and reduced the severity of clinical signs, and prevented the mortality associated with single and mixed infection with IBV and E. coli. Furthermore, in mixed infections, bacteriophage treatment significantly reduced E. coli as well as IBV shedding. Groups treated with bacteriophages showed a significant reduction of E. coli shedding that gradually decreased over time, in contrast to higher and gradually increasing shedding without bacteriophage treatment. In conclusion, bacteriophage treatment significantly reduced the pathogenicity and shedding of IBVand E. coli in mixed infections.
Collapse
Affiliation(s)
- Maram M. Tawakol
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza, Egypt
| | - Nehal M. Nabil
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza, Egypt
| | - Ahmed Samy
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza, Egypt
| |
Collapse
|
33
|
Affiliation(s)
- Juliet Roshini Mohan Raj
- Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, India
| | - Indrani Karunasagar
- Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, India
| |
Collapse
|
34
|
Pacífico C, Hilbert M, Sofka D, Dinhopl N, Pap IJ, Aspöck C, Carriço JA, Hilbert F. Natural Occurrence of Escherichia coli-Infecting Bacteriophages in Clinical Samples. Front Microbiol 2019; 10:2484. [PMID: 31736918 PMCID: PMC6834657 DOI: 10.3389/fmicb.2019.02484] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
The interaction between bacteriophages, bacteria and the human host as a tripartite system has recently captured attention. The taxonomic diversity of bacteriophages, as a natural parasite of bacteria, still remains obscure in human body biomes, representing a so-called “viral dark matter.” Here, we isolated and characterized coliphages from blood, urine and tracheal aspirates samples collected at a tertiary care hospital in Austria. Phages were more often isolated from blood, followed by urine and tracheal aspirates. Phylogenetic analysis and genome comparisons allowed the identification of phages belonging to the Tunavirinae subfamily, and to the Peduovirus and Tequintavirus genera. Tunavirinae phages cluster together and are found in samples from 14 patients, suggesting their prevalence across a variety of human samples. When compared with other phage genomes, the highest similarity level was at 87.69% average nucleotide identity (ANI), which suggests that these are in fact a newly isolated phage species. Tequintavirus phages share a 95.90% with phage 3_29, challenging the ANI threshold currently accepted to differentiate phage species. The isolated phages appear to be virulent, with the exception of the Peduovirus members, which are integrative and seem to reside as prophages in bacterial genomes.
Collapse
Affiliation(s)
- Cátia Pacífico
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Miriam Hilbert
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Karl Landsteiner University of Health Sciences, Krems, Austria
| | - Dmitrij Sofka
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Nora Dinhopl
- Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria
| | - Ildiko-Julia Pap
- Institute of Hygiene and Microbiology, University Hospital St. Pölten, St. Pölten, Austria
| | - Christoph Aspöck
- Karl Landsteiner University of Health Sciences, Krems, Austria.,Institute of Hygiene and Microbiology, University Hospital St. Pölten, St. Pölten, Austria
| | - João André Carriço
- Faculty of Medicine, Instituto de Medicina Molecular, University of Lisbon, Lisbon, Portugal
| | - Friederike Hilbert
- Department of Farm Animals and Veterinary Public Health, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| |
Collapse
|
35
|
Draft Genome Sequence of Escherichia coli DSM 12242, a Highly Efficient Host Strain for the Isolation of Somatic Coliphages. Microbiol Resour Announc 2019; 8:8/38/e00953-19. [PMID: 31537671 PMCID: PMC6753275 DOI: 10.1128/mra.00953-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Here, we report the draft genome sequence and characterization of the commercial strain Escherichia coli DSM 12242 (=ATCC 13706/60 =NZRM 3262) derived from strain C (ATCC 13706), which is suitable for the isolation of coliphages from environmental and clinical samples. Here, we report the draft genome sequence and characterization of the commercial strain Escherichia coli DSM 12242 (=ATCC 13706/60 =NZRM 3262) derived from strain C (ATCC 13706), which is suitable for the isolation of coliphages from environmental and clinical samples.
Collapse
|
36
|
Infectious phage particles packaging antibiotic resistance genes found in meat products and chicken feces. Sci Rep 2019; 9:13281. [PMID: 31527758 PMCID: PMC6746790 DOI: 10.1038/s41598-019-49898-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/29/2019] [Indexed: 11/08/2022] Open
Abstract
Bacteriophages can package part of their host's genetic material, including antibiotic resistance genes (ARGs), contributing to a rapid dissemination of resistances among bacteria. Phage particles containing ARGs were evaluated in meat, pork, beef and chicken minced meat, and ham and mortadella, purchased in local retailer. Ten ARGs (blaTEM, blaCTX-M-1, blaCTX-M-9, blaOXA-48, blaVIM, qnrA, qnrS, mecA, armA and sul1) were analyzed by qPCR in the phage DNA fraction. The genes were quantified, before and after propagation experiments in Escherichia coli, to evaluate the ability of ARG-carrying phage particles to infect and propagate in a bacterial host. According to microbiological parameters, all samples were acceptable for consumption. ARGs were detected in most of the samples after particle propagation indicating that at least part of the isolated phage particles were infectious, being sul1the most abundant ARG in all the matrices followed by β-lactamase genes. ARGs were also found in the phage DNA fraction of thirty-seven archive chicken cecal samples, confirming chicken fecal microbiota as an important ARG reservoir and the plausible origin of the particles found in meat. Phages are vehicles for gene transmission in meat that should not be underestimated as a risk factor in the global crisis of antibiotic resistance.
Collapse
|
37
|
Characterization of Bacteria and Inducible Phages in an Intensive Care Unit. J Clin Med 2019; 8:jcm8091433. [PMID: 31510095 PMCID: PMC6780966 DOI: 10.3390/jcm8091433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/08/2019] [Indexed: 12/29/2022] Open
Abstract
Intensive care units (ICUs) are critical locations for the transmission of pathogenic and opportunistic microorganisms. Bacteria may develop a synergistic relationship with bacteriophages and more effectively resist various stresses, enabling them to persist despite disinfection and antimicrobial treatment. We collected 77 environmental samples from the surroundings of 12 patients with infection/colonizations by Escherichia coli, Staphylococcus aureus or Klebsiella spp. in an ICU in Austria. Surface swabs were tested for lytic phages and bacterial isolates for mitomycin C-inducible prophages. No lytic bacteriophages were detected, but S. aureus was isolated from the surroundings of all patients. About 85% of the colonies isolated from surface samples were resistant to antimicrobials, with 94% of them multidrug resistant. Two inducible temperate bacteriophages—myovirus vB_EcoM_P5 and siphovirus vB_SauS_P9—were recovered from two clinical isolates. Staphylococci phage vB_SauS_P9 lysed S. aureus isolates from the surface swabs collected from the surroundings of three patients. No transductants were obtained on propagation in phage-sensitive antimicrobial-resistant isolates. The two phages were sensitive to 0.25% (v/v) of the disinfectant TPH Protect, which eliminated viable phages after 15 min. Coliphage vB_EcoM_P5 was inactivated at 70 °C and staphylococci phage vB_SauS_P9 at 60 °C after 60 min.
Collapse
|
38
|
Viruses as key reservoirs of antibiotic resistance genes in the environment. ISME JOURNAL 2019; 13:2856-2867. [PMID: 31358910 DOI: 10.1038/s41396-019-0478-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/03/2019] [Accepted: 06/21/2019] [Indexed: 11/08/2022]
Abstract
Antibiotic resistance is a rapidly growing health care problem globally and causes many illnesses and deaths. Bacteria can acquire antibiotic resistance genes (ARGs) by horizontal transfer mediated by mobile genetic elements, where the role of phages in their dissemination in natural environments has not yet been clearly resolved. From metagenomic studies, we showed that the mean proportion of predicted ARGs found in prophages (0-0.0028%) was lower than those present in the free viruses (0.001-0.1%). Beta-lactamase, from viruses in the swine gut, represented 0.10 % of the predicted genes. Overall, in the environment, the ARG distribution associated with viruses was strongly linked to human activity, and the low dN/dS ratio observed advocated for a negative selection of the ARGs harbored by the viruses. Our network approach showed that viruses were linked to putative pathogens (Enterobacterales and vibrionaceae) and were considered key vehicles in ARG transfer, similar to plasmids. Therefore, these ARGs could then be disseminated at larger temporal and spatial scales than those included in the bacterial genomes, allowing for time-delayed genetic exchanges.
Collapse
|
39
|
Bacanlı M, Başaran N. Importance of antibiotic residues in animal food. Food Chem Toxicol 2019; 125:462-466. [DOI: 10.1016/j.fct.2019.01.033] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/25/2023]
|
40
|
Saha D, Mukherjee R. Ameliorating the antimicrobial resistance crisis: phage therapy. IUBMB Life 2019; 71:781-790. [DOI: 10.1002/iub.2010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/22/2018] [Accepted: 01/05/2019] [Indexed: 01/21/2023]
Affiliation(s)
- Dibya Saha
- Department of Biology; Indian Institute of Science Education and Research; Tirupati India
| | - Raju Mukherjee
- Department of Biology; Indian Institute of Science Education and Research; Tirupati India
| |
Collapse
|
41
|
Leungtongkam U, Thummeepak R, Tasanapak K, Sitthisak S. Acquisition and transfer of antibiotic resistance genes in association with conjugative plasmid or class 1 integrons of Acinetobacter baumannii. PLoS One 2018; 13:e0208468. [PMID: 30521623 PMCID: PMC6283642 DOI: 10.1371/journal.pone.0208468] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/16/2018] [Indexed: 12/30/2022] Open
Abstract
Conjugation is a type of horizontal gene transfer (HGT) that serves as the primary mechanism responsible for accelerating the spread of antibiotic resistance genes in Gram-negative bacteria. The present study aimed to elucidate the mechanisms underlying the conjugation-mediated gene transfer from the extensively drug-resistant Acinetobacter baumannii (XDR-AB) and New Delhi Metallo-beta-lactamase-1-producing Acinetobacter baumannii (NDM-AB) to environmental isolates of Acinetobacter spp. Conjugation experiments demonstrated that resistance to ticarcillin and kanamycin could be transferred from four donors to two sodium azide-resistant A. baumannii strains, namely, NU013R and NU015R. No transconjugants were detected on Mueller-Hinton Agar (MHA) plates containing tetracycline. Plasmids obtained from donors as well as successful transconjugants were characterized by PCR-based replicon typing and S1-nuclease pulsed-field gel electrophoresis (S1-PFGE). Detection of antibiotic resistance genes and integrase genes (int) was performed using PCR. Results revealed that the donor AB364 strain can transfer the blaOXA-23 and blaPER-1 genes to both recipients in association with int1. A 240-kb plasmid was successfully transferred from the donor AB364 to recipients. In addition, the aphA6 and blaPER-1 genes were co-transferred with the int1 gene from the donor strains AB352 and AB405. The transfer of a 220-kb plasmid from the donors to recipient was detected. The GR6 plasmid containing the kanamycin resistance gene (aphA6) was successfully transferred from the donor strain AB140 to both recipient strains. However, the blaNDM-1 and tet(B) genes were not detected in all transconjugants. Our study is the first to demonstrate successful in vitro conjugation, which indicated that XDR-AB contained combination mechanisms of the co-transfer of antimicrobial resistance elements with integron cassettes or with the plasmid group GR6. Thus, conjugation could be responsible for the emergence of new types of antibiotic-resistant strains.
Collapse
Affiliation(s)
- Udomluk Leungtongkam
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Rapee Thummeepak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Kannipa Tasanapak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Sutthirat Sitthisak
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
- Centre of Excellence in Medical Biotechnology, Naresuan University, Phitsanulok, Thailand
- * E-mail:
| |
Collapse
|
42
|
Genomic Sequencing of High-Efficiency Transducing Streptococcal Bacteriophage A25: Consequences of Escape from Lysogeny. J Bacteriol 2018; 200:JB.00358-18. [PMID: 30224437 DOI: 10.1128/jb.00358-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022] Open
Abstract
Lytic bacteriophage A25, which infects Streptococcus pyogenes and several related species, has been used to better understand phage-microbe interactions due to its ability to mediate high-efficiency transduction. Most of these studies, however, are decades old and were conducted prior to the advent of next-generation sequencing and bioinformatics. The aim of our study was to gain a better understanding of the mechanism of high-efficiency transduction through analysis of the A25 genome. We show here that phage A25 is related to a family of genome prophages and became a lytic phage following escape from lysogeny. A lambdoid-like residual lysogeny module consisting of an operator site with two promoters and a cro-like antirepressor gene was identified, but the genes for the cI-like repressor and integrase are missing. Additionally, the genetic organization of the A25 genome was found to be modular in nature and similar to that of many prophages of S. pyogenes as well as from other streptococcal species. A study of A25 homology to all annotated prophages within S. pyogenes revealed near identity within the remnant lysogeny module of the A25 phage genome to the corresponding regions in resident prophages of genome strains MGAS10270 (M2), MGAS315 (M3), MGAS10570 (M4), and STAB902 (M4). Host range studies of MGAS10270, MGAS315, and MGAS10750 demonstrated that these strains were resistant to A25 infection. The resistance mechanism of superinfection immunity was confirmed experimentally through complementation of the operator region and cI-like repressor from prophage MGAS10270.2 into susceptible strains SF370, CEM1Δ4 (SF370ΔSpyCIM1), and ATCC 12204, which rendered all three strains resistant to A25 infection. In silico prediction of packaging through homology analysis of the terminase large subunit from bacteriophages within the known packaging mechanism of Gram-positive bacteria as well as the evidence of terminally redundant and/or circularly permuted sequences suggested that A25 grouped with phages employing the less stringent pac-type packaging mechanisms, which likely explains the characteristic A25 high-efficiency transduction capabilities. Only a few examples of lytic phages appearing following loss of part or all of the lysogeny module have been reported previously, and the genetic mosaicism of A25 suggests that this event may not have been a recent one. However, the discovery that this lytic bacteriophage shares some of the genetic pool of S. pyogenes prophages emphasizes the importance of genetic and biological characterization of bacteriophages when selecting phages for therapeutics or disinfectants, as phage-phage and phage-microbe interactions can be complex, requiring more than just assessment of host range and carriage of toxoid or virulence genes.IMPORTANCE Bacteriophages (bacterial viruses) play an important role in the shaping of bacterial populations as well as the dissemination of bacterial genetic material to new strains, resulting in the spread of virulence factors and antibiotic resistance genes. This study identified the genetic origins of Streptococcus pyogenes phage A25 and uncovered the molecular mechanism employed to promote horizontal transfer of DNA by transduction to new strains of this bacterium as well as identified the basis for its host range.
Collapse
|
43
|
Deblais L, Lorentz B, Scaria J, Nagaraja KV, Nisar M, Lauer D, Voss S, Rajashekara G. Comparative Genomic Studies of Salmonella Heidelberg Isolated From Chicken- and Turkey-Associated Farm Environmental Samples. Front Microbiol 2018; 9:1841. [PMID: 30147682 PMCID: PMC6097345 DOI: 10.3389/fmicb.2018.01841] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/23/2018] [Indexed: 11/13/2022] Open
Abstract
Salmonella is one of the leading causes of human foodborne gastroenteritis in the United States. In addition, Salmonella contributes to morbidity and mortality in livestock. The control of Salmonella is an increasing problematic issue in livestock production due to lack of effective control methods and the constant adaptation of Salmonella to new management practices, which is often related to horizontal acquisition of virulence or antibiotic resistance genes. Salmonella enterica serotype Heidelberg is one of the most commonly isolated serotypes in all poultry production systems in North America. Emergence and persistence of multi-drug resistant Salmonella Heidelberg isolates further impact the poultry production and public health. We hypothesized that distinct poultry production environments affect Salmonella genomic content, and by consequence its survival and virulence abilities. This study compared the genomic composition of S. Heidelberg isolated from environmental samples (19 chicken and 12 turkey isolates) of different breeder farms (16 chicken and 8 turkey farms) in the Midwest, United States. Whole genome comparison of 31 genomes using RAST and SEED identified differences in specific sub-systems in isolates between the chicken- and turkey-associated farm environmental samples. Genes associated with the type IV secretion system (n = 12) and conjugative transfer (n = 3) were absent in turkey farm isolates compared to the chicken ones (p-value < 0.01); Further, turkey farm isolates were enriched in prophage proteins (n = 53; p-value < 0.01). Complementary studies using PHASTER showed that prophages were all Caudovirales phages and were more represented in turkey environmental isolates than the chicken isolates. This study corroborates that isolates from distinct farm environment show differences in S. Heidelberg genome content related to horizontal transfer between bacteria or through viral infections. Complementary microbiome studies of these samples would provide critical insights on sources of these variations. Overall, our findings enhance the understanding of Salmonella genome plasticity and may aid in the development of future effective management practices to control Salmonella.
Collapse
Affiliation(s)
- Loïc Deblais
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, OARDC, Wooster, OH, United States.,Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH, United States
| | - Benjamin Lorentz
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, OARDC, Wooster, OH, United States
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, United States
| | - Kakambi V Nagaraja
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Muhammad Nisar
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Dale Lauer
- Minnesota Poultry Testing Laboratory, University of Minnesota Veterinary Diagnostic Laboratory, Minnesota Board of Animal Health, Willmar, MN, United States
| | - Shauna Voss
- Minnesota Poultry Testing Laboratory, University of Minnesota Veterinary Diagnostic Laboratory, Minnesota Board of Animal Health, Willmar, MN, United States
| | - Gireesh Rajashekara
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, OARDC, Wooster, OH, United States
| |
Collapse
|
44
|
Wang M, Liu P, Zhou Q, Tao W, Sun Y, Zeng Z. Estimating the contribution of bacteriophage to the dissemination of antibiotic resistance genes in pig feces. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 238:291-298. [PMID: 29573711 DOI: 10.1016/j.envpol.2018.03.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 05/04/2023]
Abstract
The transfer of antibiotic resistance genes (ARGs) in the environment is a threat to both human and animal health. However, the contribution of bacteriophages to the dissemination of resistance genes via transduction is rarely explored. In this study, we screened pig feces from three commercial farms in China for 32 clinically relevant ARG types to assess the presence of the ARG population in bacteria and bacteriophage and further to estimate the contribution of bacteriophages to the dissemination of antibiotic resistance. We found that bacteriophage DNA contained 35.5% of the target ARG types and sul1, blaTEM and ermB were found in 100% of the phage DNA samples. The most abundant genes in the bacterial population were ermB and fexA whereas ermB was the most abundant in bacteriophage. In contrast, floR was the least abundant ARG in both populations. Also, the ratio index of the abundance of ARGs in bacteriophage and bacteria was firstly used in this study as an estimator of bacteriophage ability to transmit ARGs. The ratio for qnrA was the greatest (about 10-1) and differed from the most abundant bacteriophage ARG ermB. In addition, fexA had the lowest ratio value (about 10-6) and not floR. These results illustrate that ARGs abundance and detection rates used alone probably be not suitable for comprehensively judging the contribution of bacteriophage to the dissemination of antibiotic resistance. A more suitable model is the application of three indices; occurrence rate, absolute abundance in bacteriophage and the ratio value as warning and monitoring tools for environmental ARG assessments in bacteriophages.
Collapse
Affiliation(s)
- Mianzhi Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Peng Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Qin Zhou
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Wanyu Tao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Yongxue Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
| | - Zhenling Zeng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
| |
Collapse
|
45
|
Mohan Raj JR, Vittal R, Huilgol P, Bhat U, Karunasagar I. T4-like Escherichia coli phages from the environment carry bla CTX-M. Lett Appl Microbiol 2018; 67:9-14. [PMID: 29675838 DOI: 10.1111/lam.12994] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 03/13/2018] [Accepted: 03/13/2018] [Indexed: 11/30/2022]
Abstract
The resistance determinant blaCTX-M has many variants and has been the most commonly reported gene in clinical isolates of extended spectrum beta-lactamase producing Escherichia coli. Phages have been speculated as potential reservoirs of resistance genes and efficient vehicles for horizontal gene transfer. The objective of the study was to determine the prevalence and characterize bacteriophages that harbour the resistance determinant blaCTX-M . Escherichia coli specific bacteriophages were isolated from 15 samples including soil and water across Mangaluru, India using bacterial hosts that were sensitive to β-lactams. Phenotypic and genotypic characterization based on plaque morphology, host range, restriction fragment length polymorphism (RFLP), presence of blaCTX-M and electron microscopy was performed. Of 36 phages isolated, seven were positive for Group 1 of blaCTX-M . Based on host range and RFLP pattern, the seven phages were classified into four distinct groups, each harbouring a variant of blaCTX-M . Five phages were T4-like Myoviridae by electron microscopy which was further confirmed by polymerase chain reaction (PCR) for T4 specific gp14. Generalized transduction of the CTX-M gene from these phages was also observed. The high prevalence (20%) of this gene blaCTX-M in the phage pool confirms the significant role of Myoviridae members, specifically T4-like phages in the dissemination of this resistance gene. SIGNIFICANCE AND IMPACT OF THE STUDY The CTX-M gene that confers resistance to Beta-lactam class of drugs is widespread and diverse. Understanding mechanisms of antimicrobial resistance transfer is a key to devise methods for controlling it. Few studies indicate that bacteriophages are involved in the transfer of this gene but the type of phages involved and the degree of involvement remains to be explored. Our work has been able to identify the class of phages and the magnitude of involvement in the dissemination of this gene.
Collapse
Affiliation(s)
- J R Mohan Raj
- Nitte University Centre for Science Education and Research, Mangaluru, India
| | - R Vittal
- Nitte University Centre for Science Education and Research, Mangaluru, India
| | - P Huilgol
- National Institute of Technology Karnataka, Surathkal, Mangaluru, India
| | - U Bhat
- National Institute of Technology Karnataka, Surathkal, Mangaluru, India
| | - I Karunasagar
- Nitte University Centre for Science Education and Research, Mangaluru, India
| |
Collapse
|
46
|
Oniciuc EA, Likotrafiti E, Alvarez-Molina A, Prieto M, Santos JA, Alvarez-Ordóñez A. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes (Basel) 2018; 9:E268. [PMID: 29789467 PMCID: PMC5977208 DOI: 10.3390/genes9050268] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.
Collapse
Affiliation(s)
- Elena A Oniciuc
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati 800008, Romania.
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Technology, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki T.K. 57400, Greece.
| | - Adrián Alvarez-Molina
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Miguel Prieto
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| |
Collapse
|
47
|
Zhou W, Liu L, Feng Y, Zong Z. A P7 Phage-Like Plasmid Carrying mcr-1 in an ST15 Klebsiella pneumoniae Clinical Isolate. Front Microbiol 2018; 9:11. [PMID: 29403463 PMCID: PMC5786510 DOI: 10.3389/fmicb.2018.00011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 01/05/2018] [Indexed: 02/05/2023] Open
Abstract
A Klebsiella pneumoniae clinical strain, named SCKP83, was isolated and found to be resistant to colistin thanks to the presence plasmid-borne colistin resistant gene mcr-1. The strain was subjected to whole genome sequencing and conjugation experiments. The subsequent analysis indicated that the strain belongs to ST15 and the capsular type K41. In SCKP83, mcr-1 was carried by a 97.4-kb non-self-transmissible plasmid, a 90.9-kb region of which was predicted as an intact phage. This phage was 47.79% GC content, encoded 105 proteins and contained three tRNAs. mcr-1 was located downstream of two copies of the insertion sequence ISApl1 (one complete and one truncated) and was inserted in the ant1 gene, which encodes a putative antirepressor for antagonizing C1 repression, in this phage. The phage is highly similar to phage P7 (77% coverage and 98% identity) from Escherichia coli. Several similar mcr-1-carrying plasmids have been found in E. coli at various locations in China, suggesting that these phage-like plasmids have circulated in China. The findings in this study suggest that the P7 phage-like plasmids are not restricted to E. coli and may represent new vehicles to mediate the inter-species spread of mcr-1.
Collapse
Affiliation(s)
- Weilong Zhou
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Lu Liu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.,Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China.,Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
48
|
Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria. Proc Natl Acad Sci U S A 2018; 115:567-572. [PMID: 29298913 DOI: 10.1073/pnas.1714658115] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Engineered bacteriophages provide powerful tools for biotechnology, diagnostics, pathogen control, and therapy. However, current techniques for phage editing are experimentally challenging and limited to few phages and host organisms. Viruses that target Gram-positive bacteria are particularly difficult to modify. Here, we present a platform technology that enables rapid, accurate, and selection-free construction of synthetic, tailor-made phages that infect Gram-positive bacteria. To this end, custom-designed, synthetic phage genomes were assembled in vitro from smaller DNA fragments. We show that replicating, cell wall-deficient Listeria monocytogenes L-form bacteria can reboot synthetic phage genomes upon transfection, i.e., produce virus particles from naked, synthetic DNA. Surprisingly, Listeria L-form cells not only support rebooting of native and synthetic Listeria phage genomes but also enable cross-genus reactivation of Bacillus and Staphylococcus phages from their DNA, thereby broadening the approach to phages that infect other important Gram-positive pathogens. We then used this platform to generate virulent phages by targeted modification of temperate phage genomes and demonstrated their superior killing efficacy. These synthetic, virulent phages were further armed by incorporation of enzybiotics into their genomes as a genetic payload, which allowed targeting of phage-resistant bystander cells. In conclusion, this straightforward and robust synthetic biology approach redefines the possibilities for the development of improved and completely new phage applications, including phage therapy.
Collapse
|
49
|
Hilbert M, Csadek I, Auer U, Hilbert F. Antimicrobial Resistance-Transducing Bacteriophages Isolated from Surfaces of Equine Surgery Clinics - A Pilot Study. Eur J Microbiol Immunol (Bp) 2017; 7:296-302. [PMID: 29403658 PMCID: PMC5793699 DOI: 10.1556/1886.2017.00032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/09/2017] [Indexed: 12/26/2022] Open
Abstract
In the past, the horizontal transfer of antimicrobial resistance genes was mainly associated with conjugative plasmids or transposons, whereas transduction by bacteriophages was thought to be a rare event. In order to analyze the likelihood of transduction of antimicrobial resistance in the field of clinical veterinary medicine, we isolated phages from Escherichia coli from a surgery suite of an equine clinic. In a pilot study, the surgery suite of a horse clinic was sampled directly after surgery and subsequently sampled after cleaning and disinfection following a sampling plan based on hygiene, surgery, and anesthesia. In total, 31 surface sampling sites were defined and sampled. At 24 of these 31 surface sampling sites, coliphages were isolated. At 12 sites, coliphages were found after cleaning and disinfection. Randomly selected phages were tested for their ability of antimicrobial resistance transduction. Ten of 31 phages were detected to transfer antimicrobial resistance. These phages most often transduced resistance to streptomycin, encoded by the addA1 gene (n = 9), followed by resistance to chloramphenicol by cmlA (n = 3) and ampicillin (n = 1). This is, to the best of our knowledge, the first report on antimicrobial resistance-transferring bacteriophages that have been isolated at equine veterinary clinics.
Collapse
Affiliation(s)
- Miriam Hilbert
- Institute of Meat Hygiene, Meat Technology and Food Science, University of Veterinary Medicine, Vienna, Austria
| | - Isabella Csadek
- Institute of Meat Hygiene, Meat Technology and Food Science, University of Veterinary Medicine, Vienna, Austria
| | - Ulrike Auer
- Clinic of Anaesthesiology and Perioperative Intensive Care, University of Veterinary Medicine Vienna, Austria
| | - Friederike Hilbert
- Institute of Meat Hygiene, Meat Technology and Food Science, University of Veterinary Medicine, Vienna, Austria
| |
Collapse
|
50
|
Phages in urban wastewater have the potential to disseminate antibiotic resistance. Int J Antimicrob Agents 2017; 50:678-683. [DOI: 10.1016/j.ijantimicag.2017.08.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/01/2017] [Accepted: 08/05/2017] [Indexed: 11/22/2022]
|