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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.
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Cai R, Wang Z, Wang G, Zhang H, Cheng M, Guo Z, Ji Y, Xi H, Wang X, Xue Y, Ur Rahman S, Sun C, Feng X, Lei L, Tong Y, Han W, Gu J. Biological properties and genomics analysis of vB_KpnS_GH-K3, a Klebsiella phage with a putative depolymerase-like protein. Virus Genes 2019; 55:696-706. [PMID: 31254238 DOI: 10.1007/s11262-019-01681-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/20/2019] [Indexed: 01/21/2023]
Abstract
Bacteriophages have been recently revisited as an alternative biocontrol tool due to the limitations of antibiotic treatment. In this study, we reported on the biological characteristics and genomic information of vB_KpnS_GH-K3 (abbreviated as GH-K3), a Klebsiella phage of the Siphoviridae family, which was previously isolated from a hospital sewage system. One-step growth curve analysis indicated that the burst size of GH-K3 was 291 PFU/cell. GH-K3 maintained a stable titer in a broad range of pH values (6-10) and temperature (up to 50 °C). Based on bioinformatics analysis, GH-K3 comprises of 49,427 bp containing a total of 77 open reading frames (ORFs), which share high degree of nucleotide similarity and close evolutionary relationships with at least 12 other Klebsiella phages. Of note, GH-K3 gp32 was identified as a unique ORF. The major segment of gp32 sequence at the C-terminus (residues 351-907) was found highly variable as determined by its mismatch with the nucleotide and protein sequences available at NCBI database. Furthermore, HHpred analysis indicated that GH-K3 gp32 contains three domains (PDB ID: 5W6S_A, 3GQ8_A and 1BHE_A) similar to depolymerase (depoKP36) of Klebsiella phage KP36 suggestive of a potential depolymerase activity during host receptor-binding in the processes of phage infection. Altogether, the current data revealed a novel putative depolymerase-like protein which is most likely to play an important role in phage-host interaction.
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Affiliation(s)
- Ruopeng Cai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Zijing Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Gang Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Hao Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Mengjun Cheng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Zhimin Guo
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, 130021, People's Republic of China
| | - Yalu Ji
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Hengyu Xi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Xinwu Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Yibing Xue
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Sadeeq Ur Rahman
- College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Changjiang Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Xin Feng
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Liancheng Lei
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 20 Dong-Da Street, Fengtai District, Beijing, 100071, People's Republic of China
| | - Wenyu Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China.,Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, People's Republic of China
| | - Jingmin Gu
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Xi'an Road 5333#, Changchun, 130062, People's Republic of China.
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Dong Y, Zhang F, Wang B, Gao J, Zhang J, Shao Y. Laboratory Evolution Assays and Whole-Genome Sequencing for the Development and Safety Evaluation of Lactobacillus plantarum With Stable Resistance to Gentamicin. Front Microbiol 2019; 10:1235. [PMID: 31231332 PMCID: PMC6558246 DOI: 10.3389/fmicb.2019.01235] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 05/17/2019] [Indexed: 11/13/2022] Open
Abstract
The goal of this work was to use laboratory evolution assays and whole-genome sequencing to develop and test the safety of a probiotic, Lactobacillus plantarum, with high-level of resistance to gentamicin. The evolution of L. plantarum was evaluated under the selective pressure from gentamicin and subsequently when the selective pressure was removed. After 30 days of selective pressure from gentamicin, the minimum inhibitory concentration (MIC) of L. plantarum to gentamicin increased from 4 to 512 μg/mL and remained stable at this level. After removing the selective pressure, the resistance of L. plantarum to gentamicin decreased to 64 μg/mL after 20 days, and remained stable thereafter. Although the MIC declined it was still higher than the cut-off value recommended by EFSA, indicating that the acquisition of gentamicin-resistance was an irreversible process. Using whole-genome sequencing, gene mutations were identified in the strains that had undergone selection pressure from gentamicin as well as in the strains where the selection pressure was subsequently removed. Specifically, four non-synonymous mutations were detected including one single nucleotide polymorphism (SNP), one insertion, and two structural variants (SVs), of which the mutations in genes encoding the drug resistance MFS transporter and transcriptional regulator of AraC family were only detected in the strains under selective pressure from gentamicin. The results indicate that these mutations play an important role in increasing the resistant levels of L. plantarum to gentamicin. The mobility analysis of mutant genes confirmed that they were not located on mobile elements of the genome of highly resistant L. plantarum, indicating that horizontal gene transfer was not possible.
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Affiliation(s)
- Yushan Dong
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Fuxin Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Bini Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Jiayuan Gao
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Jiangtao Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Yuyu Shao
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
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104
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Fang Z, Tan J, Wu S, Li M, Xu C, Xie Z, Zhu H. PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning. Gigascience 2019; 8:giz066. [PMID: 31220250 PMCID: PMC6586199 DOI: 10.1093/gigascience/giz066] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/26/2019] [Accepted: 05/14/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Phages and plasmids are the major components of mobile genetic elements, and fragments from such elements generally co-exist with chromosome-derived fragments in sequenced metagenomic data. However, there is a lack of efficient methods that can simultaneously identify phages and plasmids in metagenomic data, and the existing tools identifying either phages or plasmids have not yet presented satisfactory performance. FINDINGS We present PPR-Meta, a 3-class classifier that allows simultaneous identification of both phage and plasmid fragments from metagenomic assemblies. PPR-Meta consists of several modules for predicting sequences of different lengths. Using deep learning, a novel network architecture, referred to as the Bi-path Convolutional Neural Network, is designed to improve the performance for short fragments. PPR-Meta demonstrates much better performance than currently available similar tools individually for phage or plasmid identification, while testing on both artificial contigs and real metagenomic data. PPR-Meta is freely available via http://cqb.pku.edu.cn/ZhuLab/PPR_Meta or https://github.com/zhenchengfang/PPR-Meta. CONCLUSIONS To the best of our knowledge, PPR-Meta is the first tool that can simultaneously identify phage and plasmid fragments efficiently and reliably. The software is optimized and can be easily run on a local PC by non-computer professionals. We developed PPR-Meta to promote the research on mobile genetic elements and horizontal gene transfer.
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Affiliation(s)
- Zhencheng Fang
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Jie Tan
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Shufang Wu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Mo Li
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Peking University-Tsinghua University - National Institute of Biological Sciences (PTN) joint PhD program, School of Life Sciences, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Congmin Xu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 631 Cherry St, Atlanta, Georgia 30332, GA, USA
| | - Zhongjie Xie
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
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105
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Vivant AL, Boutin C, Prost-Boucle S, Papias S, Ziebal C, Pourcher AM. Fate of two strains of extended-spectrum beta-lactamase producing Escherichia coli in constructed wetland microcosm sediments: survival and change in antibiotic resistance profiles. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2019; 79:1550-1560. [PMID: 31169513 DOI: 10.2166/wst.2019.153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Free water surface constructed wetlands (FWS CW) are efficient technologies to limit the transfer of antibiotic resistant bacteria (ARB) originating from urban effluents into the aquatic environment. However, the decrease in ARB from inflow to outflow through the FWS CW may be explained by their transfer from the water body to the sediment. To investigate the behavior of ARB in the sediment of a FWS CW, we inoculated three microcosms with two strains of extended-spectrum beta-lactamase producing Escherichia coli (ESBL E. coli) belonging to two genotypes. Microcosms were composed of two sediments collected at two locations of an FWS CW from which the strains were isolated. Phragmites were planted in one of the microcosms. The survival curves of the two strains were close regardless of the genotype and the type of sediment. After a rapid decline, both strains were able to survive at low level in the sediments for 50 days. Their fate was not affected by the presence of phragmites. Changes in the bla content and antibiotic resistance of the inoculated strains were observed after three weeks of incubation, indicating that FWS CW sediments are favorable environments for spread of antibiotic resistance genes and for the acquisition of new antibiotic resistance.
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Affiliation(s)
- Anne-Laure Vivant
- Irstea, UR OPAALE, 17 Avenue de Cucillé-CS 64427, F-35044 Rennes, France and Univ Bretagne Loire, CS 54417, 35044 Rennes, France E-mail:
| | - Catherine Boutin
- Irstea, UR REVERSAAL, 5 rue de la Doua, CS 20244, F-69625, Villeurbanne, France
| | | | - Sandrine Papias
- Irstea, UR REVERSAAL, 5 rue de la Doua, CS 20244, F-69625, Villeurbanne, France
| | - Christine Ziebal
- Irstea, UR OPAALE, 17 Avenue de Cucillé-CS 64427, F-35044 Rennes, France and Univ Bretagne Loire, CS 54417, 35044 Rennes, France E-mail:
| | - Anne-Marie Pourcher
- Irstea, UR OPAALE, 17 Avenue de Cucillé-CS 64427, F-35044 Rennes, France and Univ Bretagne Loire, CS 54417, 35044 Rennes, France E-mail:
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106
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Stange C, Sidhu J, Toze S, Tiehm A. Comparative removal of antibiotic resistance genes during chlorination, ozonation, and UV treatment. Int J Hyg Environ Health 2019; 222:541-548. [DOI: 10.1016/j.ijheh.2019.02.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/25/2019] [Accepted: 02/02/2019] [Indexed: 12/31/2022]
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107
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Calero-Cáceres W, Ye M, Balcázar JL. Bacteriophages as Environmental Reservoirs of Antibiotic Resistance. Trends Microbiol 2019; 27:570-577. [PMID: 30905524 DOI: 10.1016/j.tim.2019.02.008] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/07/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023]
Abstract
Although antibiotic resistance represents a significant and growing public health concern, the contribution of bacteriophages (phages) to the mobilization of antibiotic resistance genes (ARGs) in the environment has not been extensively studied. Recent studies, however, suggest that phages play an important role in the acquisition, maintenance, and spread of ARGs than previously expected. This Opinion article offers an update on the contribution of phages to environmental antibiotic resistance. A better understanding of the mechanisms and factors that promote antibiotic resistance may significantly contribute to the implementation of control strategies.
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Affiliation(s)
- William Calero-Cáceres
- UTA-RAM-OneHealth Group, Centro de Investigaciones Agropecuarias, Facultad de Ciencias Agropecuarias, Universidad Técnica de Ambato, Tungurahua, Ecuador
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona 17003, Spain.
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108
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Abia ALK, Alisoltani A, Ubomba-Jaswa E, Dippenaar MA. Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:831-841. [PMID: 30481710 DOI: 10.1016/j.scitotenv.2018.11.302] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 05/20/2023]
Abstract
Recent studies have identified cemeteries as potential environmental reservoirs of multi-drug resistant pathogenic bacteria that could contaminate groundwater sources posing public health threats. However, these findings were based on the identification of culturable bacteria and at times not below burial grounds. Investigation on the bacterial diversity and functional profiles of bacterial communities above and below burial grounds in human cemeteries are few. The current study used high-throughput sequencing techniques to determine the bacterial composition and their associated functional profiles in cemetery soil samples collected at the surface and below burial ground in two South African cemeteries (Maitland Cemetery in Cape Town and Fontein Street Cemetery in Middelburg) to evaluate the potential health threat to surrounding populations through contamination of groundwater. Significant differences were observed between sample depths with the clustering of the surface (0 m) and the 2 m samples into separate groups. Pseudomonas and Corynebacterium were the most abundant genera across all samples. Pseudomonas and Rhodococcus were the dominant genera in the 2 m samples while Prauserella and Staphylococcus were dominant in the surface samples. The 2 m samples showed a lower alpha diversity but recorded higher proportions of human diseases functional classes compared to the surface samples. Human disease functional profiles revealed involvement, in infectious (cholera), neurodegenerative (Alzheimer's disease) cardiovascular (hypertrophic cardiomyopathy) immune system (Systemic lupus erythematosus) metabolic (Type I & II diabetes) diseases and cancer. Antibiotic resistance and antibiotics synthesis signatures were also identified. Thus, cemeteries could be potential sources of microbial and antibiotic pollution in groundwater, especially in areas with shallow water tables such as Maitland. Selection of sites for use as cemeteries should, therefore, require a proper understanding of the hydrogeological characteristics of the selected site. However, further studies are required to trace the actual movement of these pollutants into groundwater resources.
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Affiliation(s)
- Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa.
| | - Arghavan Alisoltani
- Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, South Africa.
| | - Eunice Ubomba-Jaswa
- Water Research Commission, Private Bag X03 Gezina, Pretoria 0031, South Africa; Department of Biotechnology, University of Johannesburg, Doornfontein, Johannesburg 2094, South Africa.
| | - Matthys Alois Dippenaar
- Engineering Geology and Hydrogeology, Department of Geology, University of Pretoria, Pretoria 0028, South Africa.
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109
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Impact of Wuyiencin Application on the Soil Microbial Community and Fate of Typical Antibiotic Resistance Genes. Sci Rep 2019; 9:4016. [PMID: 30850695 PMCID: PMC6408571 DOI: 10.1038/s41598-019-40389-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/11/2019] [Indexed: 11/08/2022] Open
Abstract
Antibiotic resistance genes (ARGs) have raised numerous concerns in recent years as emerging environmental contaminants. At present, research on environmental contamination by antibiotics focuses on medical, animal husbandry, and aquaculture fields, with few studies on environmental contamination by agricultural antibiotics in the field of plant protection. Wuyiencin is a low toxicity, high efficiency, and broad-spectrum agricultural antibiotic. It has been widely used in agricultural production and it effectively controls crop fungal diseases. In the present study, pot experiments with four soil treatments (A, B, C and D) were set up in a greenhouse to investigate the effect of the application of wuyiencin on the fate of typical ARGs and microbial community. Eight typical ARGs were detected by real-time PCR and the microbial communities were analyzed using high-throughput sequencing. The results showed that wuyiencin neither significantly influenced ARG abundance and absolute gene copy numbers, nor significantly varied microbial community among treatments. Since it only was short-term results, and the detection number of ARGs was limited, whether wuyiencin is safe or not to ecological environment when using for long-term will need further deep research.
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110
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Calero-Cáceres W, Balcázar JL. Antibiotic resistance genes in bacteriophages from diverse marine habitats. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:452-455. [PMID: 30447583 DOI: 10.1016/j.scitotenv.2018.11.166] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/18/2018] [Accepted: 11/11/2018] [Indexed: 06/09/2023]
Abstract
Although antibiotic resistance represents a significant and growing threat to human and environmental health worldwide, the contribution of bacteriophages (phages) to the acquisition and spread of antibiotic resistance genes (ARGs) in the environment has not been extensively explored. In this study, a comprehensive analysis of several viromes from diverse marine habitats was performed to investigate whether or not phages carry ARGs. The analysis provides strong evidence that phages from marine habitats are potential reservoirs of ARGs. In fact, genes conferring resistance to aminocoumarin, bacitracin and multidrug resistance (particularly the mexB gene) were found in all analyzed marine viromes. Given this, the role of phages as reservoirs of ARGs should not be underestimated considering their global distribution.
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Affiliation(s)
- William Calero-Cáceres
- UTA-RAM-OneHealth Group, Centro de Investigaciones Agropecuarias, Facultad de Ciencias Agropecuarias, Universidad Técnica de Ambato, Tungurahua, Ecuador
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), University of Girona, Girona, Spain.
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111
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Liang W, Tang Y, Li G, Shen P, Tian Y, Jiang H, Jiang X, Lu Y. KlcA HS genes are ubiquitous in clinical, bla KPC-2-positive, Klebsiella pneumoniae isolates. INFECTION GENETICS AND EVOLUTION 2019; 70:84-89. [PMID: 30807842 DOI: 10.1016/j.meegid.2019.02.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 01/28/2023]
Abstract
Carbapenemase-producing Klebsiella pneumoniae has emerged and spread widely throughout the world. The mechanisms involved remain unclear. To provide insight, five plasmids were obtained from carbapenemase-producing K. pneumoniae clinical isolates. The five sequences were acquired, aligned and analyzed. In addition to the blaKPC-2 gene, which encodes beta lactamase, essentially all the plasmids contained a putative anti-restriction protein-encoding gene, KlcAHS. The KlcAHS gene was found in 98.2% of the blaKPC-2-positive, imipenem-resistant K. pneumoniae clinical isolates and in <1% of the blaKPC-2-negative control group. A searched of the GenBank database indicated that KlcAHS was mainly submitted by Chinese investigators beginning in 2010. Seventeen different KlcA amino acid sequences were found in the database using the restricting words: KlcA and Klebsiella pneumoniae. These sequences were used to generate a phylogenetic tree via MEGA6 software, revealing a distant evolutionary relationship between KlcAHS and other KlcAs. The secondary structure of KlcAHS, predicted with PROMALS3D software, exhibited highly conserved α-helices and β-strands. KlcAHS expressed anti-restriction activity in vivo. In summary, KlcAHS genes are ubiquitous in blaKPC-2-positive Klebsiella pneumoniae clinical isolates collected at Huashan Hospital, China. The KlcAHS protein possesses a secondary structure similar to that exhibited by anti-restriction proteins and displays anti-restriction activity. As such, KlcAHS is a probable factor in the accelerated spread of blaKPC-2 and carbapenem-resistance among clinical, K. pneumoniae isolates.
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Affiliation(s)
- Wei Liang
- Department of Laboratory Medicine, the Second People's Hospital of Lianyungang City, Jiangsu Province, China
| | - Yu Tang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gang Li
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pinghua Shen
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yueru Tian
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haoqin Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaofei Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Yuan Lu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
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112
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Huang H, Zeng S, Dong X, Li D, Zhang Y, He M, Du P. Diverse and abundant antibiotics and antibiotic resistance genes in an urban water system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 231:494-503. [PMID: 30388647 DOI: 10.1016/j.jenvman.2018.10.051] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/16/2018] [Accepted: 10/14/2018] [Indexed: 06/08/2023]
Abstract
The widespread use of antibiotics has resulted in pollution associated with antibiotics and antibiotic resistance genes (ARGs) in urban water systems, threatening the public health and the ecological security. In this study, the patterns of the diversity and abundance of the antibiotics and ARGs in a typical city (Kunming, China) were analyzed by monitoring their presence in the tap water, the land block sewage discharge units, the sewage pipes, the influent of WWTP, the effluent of WWTP, and the urban river channel. The results showed that although the average concentration of total antibiotics in tap water was 10 ng/L, the concentrations reached hundreds or even thousands of ng/L in all the other sections, indicating antibiotics entering water system through human or pets discharge. The relative abundances of ARG copies to 16S rRNA gene copies in the effluent of WWTP, the urban river channel which was the downstream of WWTP were higher than those of the sewage pipes, increasing risk of ARG transfer after treatment by WWTP. In general, the relative abundance of ARGs in spring was higher than that in winter. There was no significant correlation between antibiotics concentrations and their corresponding ARGs, except for a correlation between tetracyclines and tet-resistance genes. Due to the existence of transposases, the urban water system is exposed to a widespread risk of horizontal transfer of ARGs.
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Affiliation(s)
- Haiwei Huang
- School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Siyu Zeng
- School of Environment, Tsinghua University, Beijing, 100084, PR China; State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, PR China
| | - Xin Dong
- School of Environment, Tsinghua University, Beijing, 100084, PR China; State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, PR China.
| | - Dan Li
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China.
| | - Ye Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, 200433, PR China
| | - Miao He
- School of Environment, Tsinghua University, Beijing, 100084, PR China; State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, PR China
| | - Pengfei Du
- School of Environment, Tsinghua University, Beijing, 100084, PR China; State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, PR China
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113
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Megaphages infect Prevotella and variants are widespread in gut microbiomes. Nat Microbiol 2019; 4:693-700. [PMID: 30692672 PMCID: PMC6784885 DOI: 10.1038/s41564-018-0338-9] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/05/2018] [Indexed: 02/06/2023]
Abstract
Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.
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114
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Comparative analysis and characterization of Enterobacteria phage SSL-2009a and 'HK578likevirus' bacteriophages. Virus Res 2019; 259:77-84. [PMID: 30395896 DOI: 10.1016/j.virusres.2018.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/03/2018] [Accepted: 10/23/2018] [Indexed: 12/15/2022]
Abstract
Enterobacteria phage SSL-2009a is a virulent bacteriophage with strong and abroad lytic ability against lots of engineering E. coli strains. In this study, we re-sequenced its whole genome and made a detail analysis on its genomic and proteomic characteristics according to the updated genomic sequence. The genome of SSL-2009a is a circular double-stranded DNA of 44,899 base pairs in length, with a 54.67% G + C content. A total of 67 open reading frames were predicted as protein coding sequences, 24 of which encode products highly homologous to known phage proteins. There are 10 promoters and 22 terminators identified in the genome of SSL-2009a, but no tRNA is found. SSL-2009a belongs to the 'HK578likevirus' genus of Siphoviridae. Comparative analyses indicated that other twelve phages share high homology with SSL-2009a at nucleotide and amino acid levels and also should be clustered into the same genus. In-depth analysis was performed to reveal the genomic, proteomic, and morphological features of these 'HK578likevirus' phages, which may promote our understanding of Enterobacteria phage SSL-2009a and the 'HK578likevirus' genus, even the biodiversity and evolution of bacteriophages.
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115
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Zhao H, Chen W, Xu X, Zhou X, Shi C. Transmissible ST3-IncHI2 Plasmids Are Predominant Carriers of Diverse Complex IS 26-Class 1 Integron Arrangements in Multidrug-Resistant Salmonella. Front Microbiol 2018; 9:2492. [PMID: 30405560 PMCID: PMC6206278 DOI: 10.3389/fmicb.2018.02492] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/28/2018] [Indexed: 12/14/2022] Open
Abstract
Diverse mobile genetic elements (MGEs) including plasmids, insertion sequences, and integrons play an important role in the occurrence and spread of multidrug resistance (MDR) in bacteria. It was found in previous studies that IS26 and class 1 integrons integrated on plasmids to speed the dissemination of antibiotic-resistance genes in Salmonella. It is aimed to figure out the patterns of specific genetic arrangements between IS26 and class 1 integrons located in plasmids in MDR Salmonella in this study. A total of 74 plasmid-harboring Salmonella isolates were screened for the presence of IS26 by PCR amplification, and 39 were IS26-positive. Among them, 37 isolates were resistant to at least one antibiotic. The thirty-seven antibiotic-resistant isolates were further involved in PCR detection of class 1 integrons and variable regions, and all were positive for class 1 integrons. Six IS26-class 1 integron arrangements with IS26 inserted into the upstream or downstream of class 1 integrons were characterized. Eight combinations of these IS26-class 1 integron arrangements were identified among 31 antibiotic-resistant isolates. Multidrug-resistance plasmids of the IncHI2 incompatibility group were dominant, which all belonged to ST3 by plasmid double locus sequence typing. These 21 IncHI2-positive isolates harbored six complex IS26-class 1 integron arrangement patterns. Conjugation assays and Southern blot hybridizations confirmed that conjugative multidrug-resistance IncHI2 plasmids harbored the different complex IS26-class 1 integron arrangements. The conjugation frequency of IncHI2 plasmids transferring alone was 10−5-10−6, reflecting that different complex IS26-class 1 integron arrangement patterns didn't significantly affect conjugation frequency (P > 0.05). These data suggested that class 1 integrons represent the hot spot for IS26 insertion, forming diverse MDR loci. And ST3-IncHI2 was the major plasmid lineage contributing to the horizontal transfer of composite IS26-class 1 integron MDR elements in Salmonella.
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Affiliation(s)
- Hang Zhao
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenyao Chen
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - Xiujuan Zhou
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Chunlei Shi
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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116
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Lerminiaux NA, Cameron ADS. Horizontal transfer of antibiotic resistance genes in clinical environments. Can J Microbiol 2018; 65:34-44. [PMID: 30248271 DOI: 10.1139/cjm-2018-0275] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A global medical crisis is unfolding as antibiotics lose effectiveness against a growing number of bacterial pathogens. Horizontal gene transfer (HGT) contributes significantly to the rapid spread of resistance, yet the transmission dynamics of genes that confer antibiotic resistance are poorly understood. Multiple mechanisms of HGT liberate genes from normal vertical inheritance. Conjugation by plasmids, transduction by bacteriophages, and natural transformation by extracellular DNA each allow genetic material to jump between strains and species. Thus, HGT adds an important dimension to infectious disease whereby an antibiotic resistance gene (ARG) can be the agent of an outbreak by transferring resistance to multiple unrelated pathogens. Here, we review the small number of cases where HGT has been detected in clinical environments. We discuss differences and synergies between the spread of plasmid-borne and chromosomal ARGs, with a special consideration of the difficulties of detecting transduction and transformation by routine genetic diagnostics. We highlight how 11 of the top 12 priority antibiotic-resistant pathogens are known or predicted to be naturally transformable, raising the possibility that this mechanism of HGT makes significant contributions to the spread of ARGs. HGT drives the evolution of untreatable "superbugs" by concentrating ARGs together in the same cell, thus HGT must be included in strategies to prevent the emergence of resistant organisms in hospitals and other clinical settings.
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Affiliation(s)
| | - Andrew D S Cameron
- a Department of Biology, University of Regina, Regina, SK S4S 0A2, Canada.,b Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada
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117
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Begum J, Mir NA, Dev K, Khan IA. Dynamics of antibiotic resistance with special reference to Shiga toxin-producing Escherichia coli infections. J Appl Microbiol 2018; 125:1228-1237. [PMID: 29957827 DOI: 10.1111/jam.14034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/21/2018] [Accepted: 06/26/2018] [Indexed: 11/26/2022]
Abstract
The discovery of antibiotics was paralleled by the evolution of antibiotic resistance which is probably the best example of contemporary evolution in action. The selection pressure, imposed by indiscriminate use of antibiotics, has changed the scale, mode and tempo of antibiotic resistance evolution. The presence of multidrug resistance, wide range of adaptability features and the infectivity make antibiotic resistance of Shiga toxin-producing Escherichia coli (STEC) more dangerous. The characterization, prevalence and the virulence factors of STEC have been profusely reported, whereas, the antibiotic resistance has been largely ignored because the antibiotic use in STEC infections is controversial. Thus, the current review has focussed on the source, evolution, persistence, mechanism, dissemination and control of antibiotic resistance viz-a-viz the STEC infections. The resistance development occurs by the inactivation of antibiotics, regulating the membrane permeability, modification of natural antibiotic targets or the use of efflux pumps against antibiotics. And, the dissemination of resistance genes occurs vertically by DNA replication and horizontally by conjugation, transduction and transformation. The prevention of development and dissemination of antibiotic resistance needs international public health bodies to rationalize the antibiotic use, prevent the flux of antibiotics into the environment, develop the rapid diagnostics tests, undertake proper surveillance of antibiotic resistance, promote the research on antibiotic resistance prevention, promote the research and development of novel alternative antibiotics, and encourage the widespread social awareness campaigns against the inappropriate antibiotic usage.
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Affiliation(s)
- J Begum
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, GBPUAT, Panthnagar, Udham Singh Nagar, Uttarakhand, India
| | - N A Mir
- ICAR- Central Avian Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - K Dev
- ICAR- Central Avian Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - I A Khan
- ICAR- Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
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118
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Rands CM, Starikova EV, Brüssow H, Kriventseva EV, Govorun VM, Zdobnov EM. ACI‐1 beta‐lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages. Environ Microbiol 2018; 20:2288-2300. [DOI: 10.1111/1462-2920.14276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Chris M. Rands
- Department of Genetic Medicine and DevelopmentUniversity of Geneva Medical School and Swiss Institute of Bioinformatics Geneva Switzerland
| | - Elizaveta V. Starikova
- Department of Molecular Biology and GeneticsFederal Research and Clinical Center of Physical‐Chemical Medicine Moscow, Russian Federation
| | - Harald Brüssow
- KU Leuven, Department of BiosystemsLaboratory of Gene Technology Leuven Belgium
| | - Evgenia V. Kriventseva
- Department of Genetic Medicine and DevelopmentUniversity of Geneva Medical School and Swiss Institute of Bioinformatics Geneva Switzerland
| | - Vadim M. Govorun
- Department of Molecular Biology and GeneticsFederal Research and Clinical Center of Physical‐Chemical Medicine Moscow, Russian Federation
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and DevelopmentUniversity of Geneva Medical School and Swiss Institute of Bioinformatics Geneva Switzerland
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119
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Tirumalai MR, Stepanov VG, Wünsche A, Montazari S, Gonzalez RO, Venkateswaran K, Fox GE. Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates. BMC Microbiol 2018; 18:57. [PMID: 29884123 PMCID: PMC5994023 DOI: 10.1186/s12866-018-1191-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022] Open
Abstract
Background Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis. Results The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. Conclusions It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group. Electronic supplementary material The online version of this article (10.1186/s12866-018-1191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Madhan R Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Andrea Wünsche
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Racquel O Gonzalez
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Kasturi Venkateswaran
- Biotechnology & Planetary Protection Group, NASA Jet Propulsion Laboratories, California Institute of Technology, Pasadena, CA, 91109, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.
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120
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Nunes MS, Garzon LR, Rampelotto RF, Tizotti MK, Martini R, Locatelli A, Barbosa M, Hörner M, Hörner R. Synthesis, characterization and biological activity of a gold(I) triazenide complex against chronic myeloid leukemia cells and biofilm producing microorganisms. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902017000400191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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121
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Reusing Treated Wastewater: Consideration of the Safety Aspects Associated with Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes. WATER 2018. [DOI: 10.3390/w10030244] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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122
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Flórez AB, Mayo B. Antibiotic Resistance-Susceptibility Profiles of Streptococcus thermophilus Isolated from Raw Milk and Genome Analysis of the Genetic Basis of Acquired Resistances. Front Microbiol 2017; 8:2608. [PMID: 29312272 PMCID: PMC5744436 DOI: 10.3389/fmicb.2017.02608] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/14/2017] [Indexed: 12/26/2022] Open
Abstract
The food chain is thought to play an important role in the transmission of antibiotic resistances from commensal and beneficial bacteria to pathogens. Streptococcus thermophilus is a lactic acid bacterium of major importance as a starter for the dairy industry. This study reports the minimum inhibitory concentration (MIC) of 16 representative antimicrobial agents to 41 isolates of S. thermophilus derived from raw milk. Strains showing resistance to tetracycline (seven), erythromycin and clindamycin (two), and streptomycin and neomycin (one) were found. PCR amplification identified tet(S) in all the tetracycline-resistant strains, and ermB in the two erythromycin/clindamycin-resistant strains. Hybridisation experiments suggested each resistance gene to be located in the chromosome with a similar genetic organization. Five antibiotic-resistant strains -two resistant to tetracycline (St-2 and St-9), two resistant to erythromycin/clindamycin (St-5 and St-6), and one resistant to streptomycin/neomycin (St-10)- were subjected to genome sequencing and analysis. The tet(S) gene was identified in small contigs of 3.2 and 3.7 kbp in St-2 and St-9, respectively, flanked by truncated copies of insertion sequence (IS) elements. Similarly, ermB in St-6 and St-5 was found in contigs of 1.6 and 28.1 kbp, respectively. Sequence analysis and comparison of the largest contig showed it to contain three segments (21.9, 3.7, and 1.4 kbp long) highly homologous to non-collinear sequences of pRE25 from Enterococcus faecalis. These segments contained the ermB gene, a transference module with an origin of transfer (oriT) plus 15 open reading frames encoding proteins involved in conjugation, and modules for plasmid replication and segregation. Homologous stretches were separated by short, IS-related sequences, resembling the genetic organization of the integrative and conjugative elements (ICEs) found in Streptococcus species. No gene known to provide aminoglycoside resistance was seen in St-10. Four strain-specific amino acid substitutions in the RsmG methyltransferase were scored in this strain; these might be associated to its streptomycin/neomycin resistance. Under yogurt manufacturing and storage conditions, no transfer of either tet(S) or ermB from S. thermophilus to L. delbrueckii was detected. The present results contribute toward characterisation of the antibiotic resistance profiles in S. thermophilus, provide evidence for the genetic basis of acquired resistances and deepen on their transference capability.
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Affiliation(s)
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (CSIC), Paseo Río Linares s/n, Asturias, Spain
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123
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Rodríguez-Rubio L, Jofre J, Muniesa M. Is Genetic Mobilization Considered When Using Bacteriophages in Antimicrobial Therapy? Antibiotics (Basel) 2017; 6:antibiotics6040032. [PMID: 29206153 PMCID: PMC5745475 DOI: 10.3390/antibiotics6040032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/15/2017] [Accepted: 12/04/2017] [Indexed: 01/19/2023] Open
Abstract
The emergence of multi-drug resistant bacteria has undermined our capacity to control bacterial infectious diseases. Measures needed to tackle this problem include controlling the spread of antibiotic resistance, designing new antibiotics, and encouraging the use of alternative therapies. Phage therapy seems to be a feasible alternative to antibiotics, although there are still some concerns and legal issues to overcome before it can be implemented on a large scale. Here we highlight some of those concerns, especially those related to the ability of bacteriophages to transport bacterial DNA and, in particular, antibiotic resistance genes.
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Affiliation(s)
- Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Joan Jofre
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Av. Diagonal 643, 08028 Barcelona, Spain.
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124
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Wu D, Dolfing J, Xie B. Bacterial perspectives on the dissemination of antibiotic resistance genes in domestic wastewater bio-treatment systems: beneficiary to victim. Appl Microbiol Biotechnol 2017; 102:597-604. [DOI: 10.1007/s00253-017-8665-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/16/2017] [Accepted: 11/17/2017] [Indexed: 11/24/2022]
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125
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Carding SR, Davis N, Hoyles L. Review article: the human intestinal virome in health and disease. Aliment Pharmacol Ther 2017; 46:800-815. [PMID: 28869283 PMCID: PMC5656937 DOI: 10.1111/apt.14280] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 04/07/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The human virome consists of animal-cell viruses causing transient infections, bacteriophage (phage) predators of bacteria and archaea, endogenous retroviruses and viruses causing persistent and latent infections. High-throughput, inexpensive, sensitive sequencing methods and metagenomics now make it possible to study the contribution dsDNA, ssDNA and RNA virus-like particles make to the human virome, and in particular the intestinal virome. AIM To review and evaluate the pioneering studies that have attempted to characterise the human virome and generated an increased interest in understanding how the intestinal virome might contribute to maintaining health, and the pathogenesis of chronic diseases. METHODS Relevant virome-related articles were selected for review following extensive language- and date-unrestricted, electronic searches of the literature. RESULTS The human intestinal virome is personalised and stable, and dominated by phages. It develops soon after birth in parallel with prokaryotic communities of the microbiota, becoming established during the first few years of life. By infecting specific populations of bacteria, phages can alter microbiota structure by killing host cells or altering their phenotype, enabling phages to contribute to maintaining intestinal homeostasis or microbial imbalance (dysbiosis), and the development of chronic infectious and autoimmune diseases including HIV infection and Crohn's disease, respectively. CONCLUSIONS Our understanding of the intestinal virome is fragmented and requires standardised methods for virus isolation and sequencing to provide a more complete picture of the virome, which is key to explaining the basis of virome-disease associations, and how enteric viruses can contribute to disease aetiologies and be rationalised as targets for interventions.
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Affiliation(s)
- S. R. Carding
- Norwich Medical SchoolUniversity of East AngliaNorwichUK,The Gut Health and Food Safety Research ProgrammeThe Quadram InstituteNorwich Research ParkNorwichUK
| | - N. Davis
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - L. Hoyles
- Department of Surgery and CancerImperial College LondonLondonUK
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126
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Li R, Xie M, Lv J, Wai-Chi Chan E, Chen S. Complete genetic analysis of plasmids carrying mcr-1 and other resistance genes in an Escherichia coli isolate of animal origin. J Antimicrob Chemother 2017; 72:696-699. [PMID: 27999050 DOI: 10.1093/jac/dkw509] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/27/2016] [Indexed: 11/13/2022] Open
Abstract
Objectives To investigate the genetic features of three plasmids recovered from an MCR-1 and ESBL-producing Escherichia coli strain, HYEC7, and characterize the transmission mechanism of mcr-1 . Methods The genetic profiles of three plasmids were determined by PCR, S1-PFGE, Southern hybridization and WGS analysis. The ability of the mcr-1 -bearing plasmid to undergo conjugation was also assessed. The mcr-1 -bearing transposon Tn 6330 was characterized by PCR and DNA sequencing. Results Complete sequences of three plasmids were obtained. A non-conjugative phage P7-like plasmid, pHYEC7- mcr1 , was found to harbour the mcr-1 -bearing transposon Tn 6330 , which could be excised from the plasmid by generating a circular intermediate harbouring mcr-1 and the IS Apl1 element. The insertion of the circular intermediate into another plasmid, pHYEC7-IncHI2, could form pHNSHP45-2, the original IncHI2-type mcr-1 -carrying plasmid that was reported. The third plasmid, pHYEC7-110, harboured two replicons, IncX1 and IncFIB, and comprised multiple antimicrobial resistance mobile elements, some of which were shared by pHYEC7-IncHI2. Conclusions The Tn 6330 element located in the phage-like plasmid pHYEC7- mcr1 could be excised from the plasmid and formed a circular intermediate that could be integrated into plasmids containing the IS Apl1 element. This phenomenon indicated that Tn 6330 is a key element responsible for widespread dissemination of mcr-1 among various types of plasmids and bacterial chromosomes. The dissemination rate of such an element may be further enhanced upon translocation into phage-like vectors, which may also be transmitted via transduction events.
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Affiliation(s)
- Ruichao Li
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China.,The State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
| | - Miaomiao Xie
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China
| | - Jingzhang Lv
- Division of Food Inspection and Supervision, Shenzhen Entry-Exit Inspection and Quarantine Bureau of the People's Republic of China, Shenzhen, P. R. China
| | - Edward Wai-Chi Chan
- The State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
| | - Sheng Chen
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China.,The State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR
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127
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Lang AS, Westbye AB, Beatty JT. The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange. Annu Rev Virol 2017; 4:87-104. [DOI: 10.1146/annurev-virology-101416-041624] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, A1B 3X9, Canada
| | - Alexander B. Westbye
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - J. Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
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128
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Valero-Rello A, López-Sanz M, Quevedo-Olmos A, Sorokin A, Ayora S. Molecular Mechanisms That Contribute to Horizontal Transfer of Plasmids by the Bacteriophage SPP1. Front Microbiol 2017; 8:1816. [PMID: 29018417 PMCID: PMC5615212 DOI: 10.3389/fmicb.2017.01816] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/06/2017] [Indexed: 01/02/2023] Open
Abstract
Natural transformation and viral-mediated transduction are the main avenues of horizontal gene transfer in Firmicutes. Bacillus subtilis SPP1 is a generalized transducing bacteriophage. Using this lytic phage as a model, we have analyzed how viral replication and recombination systems contribute to the transfer of plasmid-borne antibiotic resistances. Phage SPP1 DNA replication relies on essential phage-encoded replisome organizer (G38P), helicase loader (G39P), hexameric replicative helicase (G40P), recombinase (G35P) and in less extent on the partially dispensable 5′→3′ exonuclease (G34.1P), the single-stranded DNA binding protein (G36P) and the Holliday junction resolvase (G44P). Correspondingly, the accumulation of linear concatemeric plasmid DNA, and the formation of transducing particles were blocked in the absence of G35P, G38P, G39P, and G40P, greatly reduced in the G34.1P, G36P mutants, and slightly reduced in G44P mutants. In contrast, establishment of injected linear plasmid DNA in the recipient host was independent of viral-encoded functions. DNA homology between SPP1 and the plasmid, rather than a viral packaging signal, enhanced the accumulation of packagable plasmid DNA. The transfer efficiency was also dependent on plasmid copy number, and rolling-circle plasmids were encapsidated at higher frequencies than theta-type replicating plasmids.
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Affiliation(s)
- Ana Valero-Rello
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain.,Micalis Institute, INRA, AgroParisTech, Universite Paris-SaclayJouy-en-Josas, France
| | - María López-Sanz
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Alvaro Quevedo-Olmos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Alexei Sorokin
- Micalis Institute, INRA, AgroParisTech, Universite Paris-SaclayJouy-en-Josas, France
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones CientíficasMadrid, Spain
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129
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Vélez DC, Rodríguez V, García NV. Phenotypic and Genotypic Antibiotic Resistance of Salmonella from Chicken Carcasses Marketed at Ibague, Colombia. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2017. [DOI: 10.1590/1806-9061-2016-0405] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
| | - V Rodríguez
- University of Tolima, Colombia; University of Tolima, Colombia
| | - N Verjan García
- University of Tolima, Colombia; University of Tolima, Colombia
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130
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Yılmaz Ç, Özcengiz G. Antibiotics: Pharmacokinetics, toxicity, resistance and multidrug efflux pumps. Biochem Pharmacol 2017; 133:43-62. [DOI: 10.1016/j.bcp.2016.10.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/14/2016] [Indexed: 02/03/2023]
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131
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Flórez AB, Vázquez L, Mayo B. A Functional Metagenomic Analysis of Tetracycline Resistance in Cheese Bacteria. Front Microbiol 2017; 8:907. [PMID: 28596758 PMCID: PMC5442184 DOI: 10.3389/fmicb.2017.00907] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/04/2017] [Indexed: 11/13/2022] Open
Abstract
Metagenomic techniques have been successfully used to monitor antibiotic resistance genes in environmental, animal and human ecosystems. However, despite the claim that the food chain plays a key role in the spread of antibiotic resistance, metagenomic analysis has scarcely been used to investigate food systems. The present work reports a functional metagenomic analysis of the prevalence and evolution of tetracycline resistance determinants in a raw-milk, blue-veined cheese during manufacturing and ripening. For this, the same cheese batch was sampled and analyzed on days 3 and 60 of manufacture. Samples were diluted and grown in the presence of tetracycline on plate count milk agar (PCMA) (non-selective) and de Man Rogosa and Sharpe (MRS) agar (selective for lactic acid bacteria, LAB). DNA from the cultured bacteria was then isolated and used to construct four fosmid libraries, named after the medium and sampling time: PCMA-3D, PCMA-60D, MRS-3D, and MRS-60D. Clones in the libraries were subjected to restriction enzyme analysis, PCR amplification, and sequencing. Among the 300 fosmid clones analyzed, 268 different EcoRI restriction profiles were encountered. Sequence homology of their extremes clustered the clones into 47 groups. Representative clones of all groups were then screened for the presence of tetracycline resistance genes by PCR, targeting well-recognized genes coding for ribosomal protection proteins and efflux pumps. A single tetracycline resistance gene was detected in each of the clones, with four such resistance genes identified in total: tet(A), tet(L), tet(M), and tet(S). tet(A) was the only gene identified in the PCMA-3D library, and tet(L) the only one identified in the PCMA-60D and MRS-60D libraries. tet(M) and tet(S) were both detected in the MRS-3D library and in similar numbers. Six representative clones of the libraries were sequenced and analyzed. Long segments of all clones but one showed extensive homology to plasmids from Gram-positive and Gram-negative bacteria. tet(A) was found within a sequence showing strong similarity to plasmids pMAK2 and pO26-Vir from Salmonella enterica and Escherichia coli, respectively. All other genes were embedded in, or near to, sequences homologous to those of LAB species. These findings strongly suggest an evolution of tetracycline resistance gene types during cheese ripening, which might reflect the succession of the microbial populations. The location of the tetracycline resistance genes in plasmids, surrounded or directly flanked by open reading frames encoding transposases, invertases or mobilization proteins, suggests they might have a strong capacity for transference. Raw-milk cheeses should therefore be considered reservoirs of tetracycline resistance genes that might be horizontally transferred.
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Affiliation(s)
- Ana B Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, IPLA - CSICAsturias, Spain
| | - Lucía Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, IPLA - CSICAsturias, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas, IPLA - CSICAsturias, Spain
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132
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Touchon M, Moura de Sousa JA, Rocha EP. Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer. Curr Opin Microbiol 2017; 38:66-73. [PMID: 28527384 DOI: 10.1016/j.mib.2017.04.010] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 01/21/2023]
Abstract
Bacteriophages and archaeal viruses contribute, through lysogenic conversion or transduction, to the horizontal transfer of genetic material between microbial genomes. Recent genomics, metagenomics, and single cell studies have shown that lysogenic conversion is widespread and provides hosts with adaptive traits often associated with biotic interactions. The quantification of the evolutionary impact of transduction has lagged behind and requires further theoretical and experimental work. Nevertheless, recent studies suggested that generalized transduction plays a role in the transfer of antibiotic resistance genes and in the acquisition of novel genes during intra-specific bacterial competition. The characteristics of transduction and lysogenic conversion complement those of other mechanisms of transfer, and could play a key role in the spread of adaptive genes between communities.
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Affiliation(s)
- Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris, 75015, France; CNRS, UMR3525, 25-28 rue Dr. Roux, Paris, 75015, France
| | - Jorge A Moura de Sousa
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris, 75015, France; CNRS, UMR3525, 25-28 rue Dr. Roux, Paris, 75015, France
| | - Eduardo Pc Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris, 75015, France; CNRS, UMR3525, 25-28 rue Dr. Roux, Paris, 75015, France.
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133
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Liang W, Xie Y, Xiong W, Tang Y, Li G, Jiang X, Lu Y. Anti-Restriction Protein, KlcA HS, Promotes Dissemination of Carbapenem Resistance. Front Cell Infect Microbiol 2017; 7:150. [PMID: 28512626 PMCID: PMC5411435 DOI: 10.3389/fcimb.2017.00150] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/11/2017] [Indexed: 11/13/2022] Open
Abstract
Carbapenemase-producing Klebsiella pneumoniae (KPC) has emerged and spread throughout the world. A retrospective analysis was performed on carbapenem-resistant K. pneumoniae isolated at our teaching hospital during the period 2009–2010, when the initial outbreak occurred. To determine the mechanism(s) that underlies the increased infectivity exhibited by KPC, Multilocus Sequence Typing (MLST) was conducted. A series of plasmids was also extracted, sequenced and analyzed. Concurrently, the complete sequences of blaKPC−2-harboring plasmids deposited in GenBank were summarized and aligned. The blaKPC−2 and KlcAHS genes in the carbapenem-resistant K. pneumoniae isolates were examined. E. coli strains, carrying different Type I Restriction and Modification (RM) systems, were selected to study the interaction between RM systems, anti-RM systems and horizontal gene transfer (HGT). The ST11 clone predominated among 102 carbapenem-resistant K. pneumoniae isolates, all harbored the blaKPC−2 gene; 98% contained the KlcAHS gene. KlcAHS was one of the core genes in the backbone region of most blaKPC−2 carrying plasmids. Type I RM systems in the host bacteria reduced the rate of pHS10842 plasmid transformation by 30- to 40-fold. Presence of the anti-restriction protein, KlcAHS, on the other hand, increased transformation efficiency by 3- to 6-fold. These results indicate that RM systems can significantly restrict HGT. In contrast, KlcAHS can disrupt the RM systems and promote HGT by transformation. These findings suggest that the anti-restriction protein, KlcAHS, represents a novel mechanism that facilitates the increased transfer of blaKPC-2 and KlcAHS-carrying plasmids among K. pneumoniae strains.
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Affiliation(s)
- Wei Liang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan UniversityShanghai, China
| | - Yingzhou Xie
- State Key Laboratory for Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong UniversityShanghai, China
| | - Wei Xiong
- State Key Laboratory for Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong UniversityShanghai, China
| | - Yu Tang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan UniversityShanghai, China
| | - Gang Li
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan UniversityShanghai, China
| | - Xiaofei Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan UniversityShanghai, China
| | - Yuan Lu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan UniversityShanghai, China
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134
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Calero-Cáceres W, Méndez J, Martín-Díaz J, Muniesa M. The occurrence of antibiotic resistance genes in a Mediterranean river and their persistence in the riverbed sediment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 223:384-394. [PMID: 28126386 DOI: 10.1016/j.envpol.2017.01.035] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/13/2017] [Accepted: 01/15/2017] [Indexed: 05/25/2023]
Abstract
The spread of antibiotic resistance genes (ARGs) in the environment is a serious concern. Bacterial ARGs can spread via different mobile genetic elements as phage particles, which thereby emerge as novel vectors for environmental dissemination. To assess how climate events, such as heavy rains or water scarcity, could affect the spread of ARGs, it is necessary to know their prevalence and abundance in aquatic environments as well as the potential reservoirs from which they could become mobile. This study evaluates the occurrence of ARGs in the water and sediment of a Mediterranean river. Six clinically relevant ARGs (blaTEM, blaCTX-M, qnrA, qnrS, mecA and sul1) were quantified by qPCR in the bacterial and phage fractions of 69 water and 70 sediment samples from the River Llobregat (NE Spain), collected during both dry and rainy periods. blaTEM and sul1 were the most prevalent and abundant ARGs; the others were more variable. Significant seasonal differences in ARG prevalences and abundances were observed. Since ARGs were detected in the sediment, the persistence of the most abundant ARGs naturally occurring in that sediment (blaTEM and sul1) was evaluated under three conditions. No ARG inactivation occurred in fresh sediment over 14 days; while the ARGs declined by less than 2 log10 units over 35 days in semi-dry and dry sediment. The occurrence of ARGs in water and sediment is influenced by seasonal conditions and they can be mobilized by bacteria and phage particles. In sediment, ARGs persist for long periods and hence sediment can be a natural reservoir of ARGs, from where they can spread and cause the emergence of new resistant strains.
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Affiliation(s)
- William Calero-Cáceres
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - Javier Méndez
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - Julia Martín-Díaz
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, Annex, Floor 0, E-08028 Barcelona, Spain.
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135
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Huang H, Zheng X, Chen Y, Liu H, Wan R, Su Y. Alkaline fermentation of waste sludge causes a significant reduction of antibiotic resistance genes in anaerobic reactors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 580:380-387. [PMID: 28011019 DOI: 10.1016/j.scitotenv.2016.11.186] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 06/06/2023]
Abstract
Alkaline fermentation has been reported to be an effective method to recover valuable products from waste sludge. However, to date, the potential effect of alkaline pH on the fate of antibiotic resistance genes (ARGs) during anaerobic fermentation of sludge has never been documented. In this study, the target ARGs in sludge was observed to be removed effectively and stably when sludge was anaerobically fermented at pH10. Compared with the control (without pH adjustment), the abundances of target ARGs at pH10 were reduced by 0.87 (sulI), 1.36 (sulII), 0.42 (tet(O)), 1.11 (tet(Q)), 0.79 (tet(C)) and 1.04 (tet(X)) log units. Further investigations revealed that alkaline fermentation shifted the community structures of potential ARGs hosts. Moreover, alkaline fermentation remarkably decreased the quantities and the ARGs-possessing ability of genetic vectors (plasmid DNA, extracellular DNA and phage DNA), which might limit the transfer of ARGs via conjugation, transformation and transduction. These results suggest that the shifted compositions of gene hosts and restricted gene transfer potential might be the critical reasons for the attenuation of ARGs at pH10.
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Affiliation(s)
- Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xiong Zheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
| | - Hui Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Rui Wan
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinglong Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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136
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Abstract
Bacteriophages infect an estimated 1023 to 1025 bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub "superspreaders," releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation. Two novel Escherichia coli phage superspreaders, SUSP1 and SUSP2, liberated four evolutionarily distinct plasmids with equal efficiency, including two close relatives of prominent antibiotic resistance vectors in natural environments. SUSP2 also mediated the extensive lateral transfer of antibiotic resistance in unbiased communities of soil bacteria from Maryland and Wyoming. Furthermore, the addition of SUSP2 to cocultures of kanamycin-resistant E. coli and kanamycin-sensitive Bacillus sp. bacteria resulted in roughly 1,000-fold more kanamycin-resistant Bacillus sp. bacteria than arose in phage-free controls. Unlike many other lytic phages, neither SUSP1 nor SUSP2 encodes homologs to known hydrolytic endonucleases, suggesting a simple potential mechanism underlying the superspreading phenotype. Consistent with this model, the deletion of endonuclease IV and the nucleoid-disrupting protein ndd from coliphage T4, a phage known to extensively degrade chromosomal DNA, significantly increased its ability to promote plasmid transformation. Taken together, our results suggest that phage superspreaders may play key roles in microbial evolution and ecology but should be avoided in phage therapy and other medical applications. IMPORTANCE Bacteriophages (phages), viruses that infect bacteria, are the planet's most numerous biological entities and kill vast numbers of bacteria in natural environments. Many of these bacteria carry plasmids, extrachromosomal DNA elements that frequently encode antibiotic resistance. However, it is largely unknown whether plasmids are destroyed during phage infection or released intact upon phage lysis, whereupon their encoded resistance could be acquired and manifested by other bacteria (transformation). Because phages are being developed to combat antibiotic-resistant bacteria and because transformation is a principal form of horizontal gene transfer, this question has important implications for biomedicine and microbial evolution alike. Here we report the isolation and characterization of two novel Escherichia coli phages, dubbed "superspreaders," that promote extensive plasmid transformation and efficiently disperse antibiotic resistance genes. Our work suggests that phage superspreaders are not suitable for use in medicine but may help drive bacterial evolution in natural environments.
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137
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Roberts L. From isolate to answer: how whole genome sequencing is helping us rapidly characterise nosocomial bacterial outbreaks. MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The occurrence of highly resistant bacterial pathogens has risen in recent years, causing immense strain on the healthcare industry. Hospital-acquired infections are arguably of most concern, as bacterial outbreaks in clinical settings provide an ideal environment for proliferation among vulnerable populations. Understanding these outbreaks beyond what can be determined with traditional clinical diagnostics and implementing these new techniques routinely in the hospital environment has now become a major focus. This brief review will discuss the three main whole genome sequence techniques available today, and how they are being used to further discriminate bacterial outbreaks in nosocomial settings.
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138
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Lekunberri I, Subirats J, Borrego CM, Balcázar JL. Exploring the contribution of bacteriophages to antibiotic resistance. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 220:981-984. [PMID: 27890586 DOI: 10.1016/j.envpol.2016.11.059] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 05/04/2023]
Abstract
Bacteriophages (phages) are the most abundant and diverse biological entities in our planet. They infect susceptible bacterial hosts into which they either multiply or persist. In the latter case, phages can confer new functions to their hosts as a result of gene transfer, thus contributing to their adaptation (short-term) and evolution (long-term). In this regard, the role of phages on the dissemination of antibiotic resistance genes (ARGs) among bacterial hosts in natural environments has not yet been clearly resolved. Here, we carry out a comprehensive analysis of thirty-three viromes from different habitats to investigate whether phages harbor ARGs. Our results demonstrate that while human-associated viromes do not or rarely carry ARGs, viromes from non-human sources (e.g. pig feces, raw sewage, and freshwater and marine environments) contain a large reservoir of ARGs, thus pointing out that phages could play a part on the spread of antibiotic resistance. Given this, the role of phages should not be underestimated and it should be considered when designing strategies to tackle the global crisis of antibiotic resistance.
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Affiliation(s)
- Itziar Lekunberri
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
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139
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Martínez JL, Coque TM, Lanza VF, de la Cruz F, Baquero F. Genomic and metagenomic technologies to explore the antibiotic resistance mobilome. Ann N Y Acad Sci 2016; 1388:26-41. [PMID: 27861983 DOI: 10.1111/nyas.13282] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance is a relevant problem for human health that requires global approaches to establish a deep understanding of the processes of acquisition, stabilization, and spread of resistance among human bacterial pathogens. Since natural (nonclinical) ecosystems are reservoirs of resistance genes, a health-integrated study of the epidemiology of antibiotic resistance requires the exploration of such ecosystems with the aim of determining the role they may play in the selection, evolution, and spread of antibiotic resistance genes, involving the so-called resistance mobilome. High-throughput sequencing techniques allow an unprecedented opportunity to describe the genetic composition of a given microbiome without the need to subculture the organisms present inside. However, bioinformatic methods for analyzing this bulk of data, mainly with respect to binning each resistance gene with the organism hosting it, are still in their infancy. Here, we discuss how current genomic methodologies can serve to analyze the resistance mobilome and its linkage with different bacterial genomes and metagenomes. In addition, we describe the drawbacks of current methodologies for analyzing the resistance mobilome, mainly in cases of complex microbiotas, and discuss the possibility of implementing novel tools to improve our current metagenomic toolbox.
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Affiliation(s)
- José L Martínez
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Madrid, Spain
| | - Teresa M Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
| | - Val F Lanza
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Cantabria, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain.,CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
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140
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Singer AC, Shaw H, Rhodes V, Hart A. Review of Antimicrobial Resistance in the Environment and Its Relevance to Environmental Regulators. Front Microbiol 2016; 7:1728. [PMID: 27847505 PMCID: PMC5088501 DOI: 10.3389/fmicb.2016.01728] [Citation(s) in RCA: 391] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/17/2016] [Indexed: 01/25/2023] Open
Abstract
The environment is increasingly being recognized for the role it might play in the global spread of clinically relevant antibiotic resistance. Environmental regulators monitor and control many of the pathways responsible for the release of resistance-driving chemicals into the environment (e.g., antimicrobials, metals, and biocides). Hence, environmental regulators should be contributing significantly to the development of global and national antimicrobial resistance (AMR) action plans. It is argued that the lack of environment-facing mitigation actions included in existing AMR action plans is likely a function of our poor fundamental understanding of many of the key issues. Here, we aim to present the problem with AMR in the environment through the lens of an environmental regulator, using the Environment Agency (England’s regulator) as an example from which parallels can be drawn globally. The issues that are pertinent to environmental regulators are drawn out to answer: What are the drivers and pathways of AMR? How do these relate to the normal work, powers and duties of environmental regulators? What are the knowledge gaps that hinder the delivery of environmental protection from AMR? We offer several thought experiments for how different mitigation strategies might proceed. We conclude that: (1) AMR Action Plans do not tackle all the potentially relevant pathways and drivers of AMR in the environment; and (2) AMR Action Plans are deficient partly because the science to inform policy is lacking and this needs to be addressed.
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Affiliation(s)
| | - Helen Shaw
- Department for Environment, Food and Rural Affairs London, UK
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141
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Parmar KM, Hathi ZJ, Dafale NA. Control of Multidrug-Resistant Gene Flow in the Environment Through Bacteriophage Intervention. Appl Biochem Biotechnol 2016; 181:1007-1029. [PMID: 27723009 DOI: 10.1007/s12010-016-2265-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/23/2016] [Indexed: 02/06/2023]
Abstract
The spread of multidrug-resistant (MDR) bacteria is an emerging threat to the environment and public wellness. Inappropriate use and indiscriminate release of antibiotics in the environment through un-metabolized form create a scenario for the emergence of virulent pathogens and MDR bugs in the surroundings. Mechanisms underlying the spread of resistance include horizontal and vertical gene transfers causing the transmittance of MDR genes packed in different host, which pass across different food webs. Several controlling agents have been used for combating pathogens; however, the use of lytic bacteriophages proves to be one of the most eco-friendly due to their specificity, killing only target bacteria without damaging the indigenous beneficial flora of the habitat. Phages are part of the natural microflora present in different environmental niches and are remarkably stable in the environment. Diverse range of phage products, such as phage enzymes, phage peptides having antimicrobial properties, and phage cocktails also have been used to eradicate pathogens along with whole phages. Recently, the ability of phages to control pathogens has extended from the different areas of medicine, agriculture, aquaculture, food industry, and into the environment. To avoid the arrival of pre-antibiotic epoch, phage intervention proves to be a potential option to eradicate harmful pathogens generated by the MDR gene flow which are uneasy to cure by conventional treatments.
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Affiliation(s)
- Krupa M Parmar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Zubeen J Hathi
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India.
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142
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Fercher C, Probst I, Kohler V, Goessweiner-Mohr N, Arends K, Grohmann E, Zangger K, Meyer NH, Keller W. VirB8-like protein TraH is crucial for DNA transfer in Enterococcus faecalis. Sci Rep 2016; 6:24643. [PMID: 27103580 PMCID: PMC4840375 DOI: 10.1038/srep24643] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/04/2016] [Indexed: 12/02/2022] Open
Abstract
Untreatable bacterial infections caused by a perpetual increase of antibiotic resistant strains represent a serious threat to human healthcare in the 21(st) century. Conjugative DNA transfer is the most important mechanism for antibiotic resistance and virulence gene dissemination among bacteria and is mediated by a protein complex, known as type IV secretion system (T4SS). The core of the T4SS is a multiprotein complex that spans the bacterial envelope as a channel for macromolecular secretion. We report the NMR structure and functional characterization of the transfer protein TraH encoded by the conjugative Gram-positive broad-host range plasmid pIP501. The structure exhibits a striking similarity to VirB8 proteins of Gram-negative secretion systems where they play an essential role in the scaffold of the secretion machinery. Considering TraM as the first VirB8-like protein discovered in pIP501, TraH represents the second protein affiliated with this family in the respective transfer operon. A markerless traH deletion in pIP501 resulted in a total loss of transfer in Enterococcus faecalis as compared with the pIP501 wild type (wt) plasmid, demonstrating that TraH is essential for pIP501 mediated conjugation. Moreover, oligomerization state and topology of TraH in the native membrane were determined providing insights in molecular organization of a Gram-positive T4SS.
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Affiliation(s)
- Christian Fercher
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Austria
| | - Ines Probst
- Division of Infectious Diseases, University Medical Center Freiburg, Germany
- Faculty of Biology, Microbiology, Albert-Ludwigs-University Freiburg, Germany
| | - Verena Kohler
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Austria
| | - Nikolaus Goessweiner-Mohr
- Center for Structural System Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Elisabeth Grohmann
- Division of Infectious Diseases, University Medical Center Freiburg, Germany
- Beuth University of Applied Sciences, Berlin, Germany
| | - Klaus Zangger
- Institute of Chemistry, University of Graz, Graz, Austria
| | - N. Helge Meyer
- Department of General and Visceral Surgery, University of Oldenburg, Germany
| | - Walter Keller
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Austria
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143
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Carraro N, Libante V, Morel C, Charron-Bourgoin F, Leblond P, Guédon G. Plasmid-like replication of a minimal streptococcal integrative and conjugative element. MICROBIOLOGY-SGM 2016; 162:622-632. [PMID: 26825653 DOI: 10.1099/mic.0.000219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements encoding their own excision from a replicon of their bacterial host, transfer by conjugation to a recipient bacterium and reintegration for maintenance. The conjugation, recombination and regulation modules of ICEs of the ICESt3 family are grouped together in a region called the ICE 'core region'. In addition to this core region, elements belonging to this family carry a highly variable region including cargo genes that could be involved in bacterial adaptation or in the maintenance of the element. Although ICEs are a major class of mobile elements through bacterial genomes, the functionality of an element encoding only its excision, transfer, integration and regulation has never been demonstrated experimentally. We engineered MiniICESt3, an artificial ICE derived from ICESt3, devoid of its cargo genes and thus only harbouring the core region. The functionality of this minimal element was assessed. MiniICESt3 was found to be able to excise at a rate of 3.1 %, transfer with a frequency of 1.0 × 10- 5 transconjugants per donor cell and stably maintain by site-specific integration into the 3' end of the fda gene, the same as ICESt3. Furthermore, MiniICESt3 was found in ∼10 copies per chromosome, this multicopy state likely contributing to its stability for >100 generations even in the absence of selection. Therefore, although ICEs were primarily assumed to only replicate along with the chromosome, our results uncovered extrachromosomal rolling-circle replicating plasmid-like forms of MiniICESt3.
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Affiliation(s)
- Nicolas Carraro
- INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Virginie Libante
- INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Catherine Morel
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Florence Charron-Bourgoin
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Pierre Leblond
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
| | - Gérard Guédon
- Université de Lorraine, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France.,INRA, DynAMic, UMR1128, Vandoeuvre-lès-Nancy, France
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144
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von Wintersdorff CJH, Penders J, van Niekerk JM, Mills ND, Majumder S, van Alphen LB, Savelkoul PHM, Wolffs PFG. Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer. Front Microbiol 2016; 7:173. [PMID: 26925045 PMCID: PMC4759269 DOI: 10.3389/fmicb.2016.00173] [Citation(s) in RCA: 757] [Impact Index Per Article: 94.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
The emergence and spread of antibiotic resistance among pathogenic bacteria has been a rising problem for public health in recent decades. It is becoming increasingly recognized that not only antibiotic resistance genes (ARGs) encountered in clinical pathogens are of relevance, but rather, all pathogenic, commensal as well as environmental bacteria—and also mobile genetic elements and bacteriophages—form a reservoir of ARGs (the resistome) from which pathogenic bacteria can acquire resistance via horizontal gene transfer (HGT). HGT has caused antibiotic resistance to spread from commensal and environmental species to pathogenic ones, as has been shown for some clinically important ARGs. Of the three canonical mechanisms of HGT, conjugation is thought to have the greatest influence on the dissemination of ARGs. While transformation and transduction are deemed less important, recent discoveries suggest their role may be larger than previously thought. Understanding the extent of the resistome and how its mobilization to pathogenic bacteria takes place is essential for efforts to control the dissemination of these genes. Here, we will discuss the concept of the resistome, provide examples of HGT of clinically relevant ARGs and present an overview of the current knowledge of the contributions the various HGT mechanisms make to the spread of antibiotic resistance.
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Affiliation(s)
- Christian J H von Wintersdorff
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+ Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands
| | - Julius M van Niekerk
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Nathan D Mills
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Snehali Majumder
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Lieke B van Alphen
- Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+ Maastricht, Netherlands
| | - Paul H M Savelkoul
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology and Infection Control, VU University Medical CenterAmsterdam, Netherlands
| | - Petra F G Wolffs
- Department of Medical Microbiology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+Maastricht, Netherlands; Department of Medical Microbiology, Caphri School for Public Health and Primary Care, Maastricht University Medical Center+Maastricht, Netherlands
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145
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Hammerl JA, Göllner C, Al Dahouk S, Nöckler K, Reetz J, Hertwig S. Analysis of the First Temperate Broad Host Range Brucellaphage (BiPBO1) Isolated from B. inopinata. Front Microbiol 2016; 7:24. [PMID: 26858702 PMCID: PMC4729917 DOI: 10.3389/fmicb.2016.00024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022] Open
Abstract
Brucella species are important human and animal pathogens. Though, only little is known about mobile genetic elements of these highly pathogenic bacteria. To date, neither plasmids nor temperate phages have been described in brucellae. We analyzed genomic sequences of various reference and type strains and identified a number of putative prophages residing within the Brucella chromosomes. By induction, phage BiPBO1 was isolated from Brucella inopinata. BiPBO1 is a siphovirus that infects several Brucella species including Brucella abortus and Brucella melitensis. Integration of the phage genome occurs adjacent to a tRNA gene in chromosome 1 (chr 1). The bacterial (attB) and phage (attP) attachment sites comprise an identical sequence of 46 bp. This sequence exists in many Brucella and Ochrobactrum species. The BiPBO1 genome is composed of a 46,877 bp double-stranded DNA. Eighty-seven putative gene products were determined, of which 32 could be functionally assigned. Strongest similarities were found to a temperate phage residing in the chromosome of Ochrobactrum anthropi ATCC 49188 and to prophages identified in several families belonging to the order rhizobiales. The data suggest that horizontal gene transfer may occur between Brucella and Ochrobactrum and underpin the close relationship of these environmental and pathogenic bacteria.
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Affiliation(s)
- Jens A. Hammerl
- Department of Biological Safety, Federal Institute for Risk AssessmentBerlin, Germany
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146
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Sartelli M, Weber DG, Ruppé E, Bassetti M, Wright BJ, Ansaloni L, Catena F, Coccolini F, Abu-Zidan FM, Coimbra R, Moore EE, Moore FA, Maier RV, De Waele JJ, Kirkpatrick AW, Griffiths EA, Eckmann C, Brink AJ, Mazuski JE, May AK, Sawyer RG, Mertz D, Montravers P, Kumar A, Roberts JA, Vincent JL, Watkins RR, Lowman W, Spellberg B, Abbott IJ, Adesunkanmi AK, Al-Dahir S, Al-Hasan MN, Agresta F, Althani AA, Ansari S, Ansumana R, Augustin G, Bala M, Balogh ZJ, Baraket O, Bhangu A, Beltrán MA, Bernhard M, Biffl WL, Boermeester MA, Brecher SM, Cherry-Bukowiec JR, Buyne OR, Cainzos MA, Cairns KA, Camacho-Ortiz A, Chandy SJ, Che Jusoh A, Chichom-Mefire A, Colijn C, Corcione F, Cui Y, Curcio D, Delibegovic S, Demetrashvili Z, De Simone B, Dhingra S, Diaz JJ, Di Carlo I, Dillip A, Di Saverio S, Doyle MP, Dorj G, Dogjani A, Dupont H, Eachempati SR, Enani MA, Egiev VN, Elmangory MM, Ferrada P, Fitchett JR, Fraga GP, Guessennd N, Giamarellou H, Ghnnam W, Gkiokas G, Goldberg SR, Gomes CA, Gomi H, Guzmán-Blanco M, Haque M, Hansen S, Hecker A, Heizmann WR, Herzog T, Hodonou AM, Hong SK, Kafka-Ritsch R, Kaplan LJ, Kapoor G, Karamarkovic A, Kees MG, Kenig J, Kiguba R, Kim PK, Kluger Y, Khokha V, Koike K, Kok KYY, Kong V, Knox MC, Inaba K, Isik A, Iskandar K, Ivatury RR, Labbate M, Labricciosa FM, Laterre PF, Latifi R, Lee JG, Lee YR, Leone M, Leppaniemi A, Li Y, Liang SY, Loho T, Maegele M, Malama S, Marei HE, Martin-Loeches I, Marwah S, Massele A, McFarlane M, Melo RB, Negoi I, Nicolau DP, Nord CE, Ofori-Asenso R, Omari AH, Ordonez CA, Ouadii M, Pereira Júnior GA, Piazza D, Pupelis G, Rawson TM, Rems M, Rizoli S, Rocha C, Sakakhushev B, Sanchez-Garcia M, Sato N, Segovia Lohse HA, Sganga G, Siribumrungwong B, Shelat VG, Soreide K, Soto R, Talving P, Tilsed JV, Timsit JF, Trueba G, Trung NT, Ulrych J, van Goor H, Vereczkei A, Vohra RS, Wani I, Uhl W, Xiao Y, Yuan KC, Zachariah SK, Zahar JR, Zakrison TL, Corcione A, Melotti RM, Viscoli C, Viale P. Antimicrobials: a global alliance for optimizing their rational use in intra-abdominal infections (AGORA). World J Emerg Surg 2016; 11:33. [PMID: 27429642 PMCID: PMC4946132 DOI: 10.1186/s13017-016-0089-y] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/04/2016] [Indexed: 02/08/2023] Open
Abstract
Intra-abdominal infections (IAI) are an important cause of morbidity and are frequently associated with poor prognosis, particularly in high-risk patients. The cornerstones in the management of complicated IAIs are timely effective source control with appropriate antimicrobial therapy. Empiric antimicrobial therapy is important in the management of intra-abdominal infections and must be broad enough to cover all likely organisms because inappropriate initial antimicrobial therapy is associated with poor patient outcomes and the development of bacterial resistance. The overuse of antimicrobials is widely accepted as a major driver of some emerging infections (such as C. difficile), the selection of resistant pathogens in individual patients, and for the continued development of antimicrobial resistance globally. The growing emergence of multi-drug resistant organisms and the limited development of new agents available to counteract them have caused an impending crisis with alarming implications, especially with regards to Gram-negative bacteria. An international task force from 79 different countries has joined this project by sharing a document on the rational use of antimicrobials for patients with IAIs. The project has been termed AGORA (Antimicrobials: A Global Alliance for Optimizing their Rational Use in Intra-Abdominal Infections). The authors hope that AGORA, involving many of the world's leading experts, can actively raise awareness in health workers and can improve prescribing behavior in treating IAIs.
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Affiliation(s)
- Massimo Sartelli
- Department of Surgery, Macerata Hospital, Via Santa Lucia 2, 62100 Macerata, Italy
| | - Dieter G. Weber
- Department of Trauma Surgery, Royal Perth Hospital, Perth, Australia
| | - Etienne Ruppé
- Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Matteo Bassetti
- Infectious Diseases Division, Santa Maria Misericordia University Hospital, Udine, Italy
| | - Brian J. Wright
- Department of Emergency Medicine and Surgery, Stony Brook University School of Medicine, Stony Brook, NY USA
| | - Luca Ansaloni
- General Surgery Department, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Fausto Catena
- Department of General, Maggiore Hospital, Parma, Italy
| | | | - Fikri M. Abu-Zidan
- Department of Surgery, College of Medicine and Health Sciences, UAE University, Al-Ain, United Arab Emirates
| | - Raul Coimbra
- Department of Surgery, UC San Diego Medical Center, San Diego, USA
| | - Ernest E. Moore
- Department of Surgery, University of Colorado, Denver Health Medical Center, Denver, CO USA
| | - Frederick A. Moore
- Department of Surgery, Division of Acute Care Surgery, and Center for Sepsis and Critical Illness Research, University of Florida College of Medicine, Gainesville, FL USA
| | - Ronald V. Maier
- Department of Surgery, University of Washington, Seattle, WA USA
| | - Jan J. De Waele
- Department of Critical Care Medicine, Ghent University Hospital, Ghent, Belgium
| | - Andrew W. Kirkpatrick
- General, Acute Care, and Trauma Surgery, Foothills Medical Centre, Calgary, AB Canada
| | - Ewen A. Griffiths
- General and Upper GI Surgery, Queen Elizabeth Hospital, Birmingham, UK
| | - Christian Eckmann
- Department of General, Visceral, and Thoracic Surgery, Klinikum Peine, Academic Hospital of Medical University Hannover, Peine, Germany
| | - Adrian J. Brink
- Department of Clinical microbiology, Ampath National Laboratory Services, Milpark Hospital, Johannesburg, South Africa
| | - John E. Mazuski
- Department of Surgery, School of Medicine, Washington University in Saint Louis, Missouri, USA
| | - Addison K. May
- Departments of Surgery and Anesthesiology, Division of Trauma and Surgical Critical Care, Vanderbilt University Medical Center, Nashville, TN USA
| | - Rob G. Sawyer
- Department of Surgery, University of Virginia Health System, Charlottesville, VA USA
| | - Dominik Mertz
- Departments of Medicine, Clinical Epidemiology and Biostatistics, and Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada
| | - Philippe Montravers
- Département d’Anesthésie-Réanimation, CHU Bichat Claude-Bernard-HUPNVS, Assistance Publique-Hôpitaux de Paris, University Denis Diderot, Paris, France
| | - Anand Kumar
- Section of Critical Care Medicine and Section of Infectious Diseases, Department of Medicine, Medical Microbiology and Pharmacology/Therapeutics, University of Manitoba, Winnipeg, MB Canada
| | - Jason A. Roberts
- Australia Pharmacy Department, Royal Brisbane and Womens’ Hospital; Burns, Trauma, and Critical Care Research Centre, Australia School of Pharmacy, The University of Queensland, Brisbane, QLD Australia
| | - Jean-Louis Vincent
- Department of Intensive Care, Erasme Hospital, Université libre de Bruxelles, Brussels, Belgium
| | - Richard R. Watkins
- Department of Internal Medicine, Division of Infectious Diseases, Akron General Medical Center, Northeast Ohio Medical University, Akron, OH USA
| | - Warren Lowman
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Brad Spellberg
- Division of Infectious Diseases, Los Angeles County-University of Southern California (USC) Medical Center, Keck School of Medicine at USC, Los Angeles, CA USA
| | - Iain J. Abbott
- Department of Infectious Diseases, Alfred Hospital, Melbourne, VIC Australia
| | | | - Sara Al-Dahir
- Division of Clinical and Administrative Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA USA
| | - Majdi N. Al-Hasan
- Department of Medicine, Division of Infectious Diseases, University of South Carolina School of Medicine, Columbia, SC USA
| | | | | | - Shamshul Ansari
- Department of Microbiology, Chitwan Medical College, and Department of Environmental and Preventive Medicine, Oita University, Oita, Japan
| | - Rashid Ansumana
- Centre for Neglected Tropical Diseases, Liverpool School of Tropical Medicine, University of Liverpool, and Mercy Hospital Research Laboratory, Njala University, Bo, Sierra Leone
| | - Goran Augustin
- Department of Surgery, University Hospital Center, Zagreb, Croatia
| | - Miklosh Bala
- Trauma and Acute Care Surgery Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Zsolt J. Balogh
- Department of Traumatology, John Hunter Hospital and University of Newcastle, Newcastle, NSW Australia
| | | | - Aneel Bhangu
- Academic Department of Surgery, Queen Elizabeth Hospital, Birmingham, UK
| | - Marcelo A. Beltrán
- Department of General Surgery, Hospital San Juan de Dios de La Serena, La Serena, Chile
| | | | - Walter L. Biffl
- Department of Surgery, University of Colorado, Denver, CO USA
| | | | - Stephen M. Brecher
- Department of Pathology and Laboratory Medicine, VA Boston HealthCare System, and Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA USA
| | - Jill R. Cherry-Bukowiec
- Division of Acute Care Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI USA
| | - Otmar R. Buyne
- Department of Surgery, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Miguel A. Cainzos
- Department of Surgery, Hospital Clínico Universitario, Santiago de Compostela, Spain
| | - Kelly A. Cairns
- Pharmacy Department, Alfred Health, Melbourne, VIC Australia
| | - Adrian Camacho-Ortiz
- Hospital Epidemiology and Infectious Diseases, Hospital Universitario Dr Jose Eleuterio Gonzalez, Monterrey, Mexico
| | - Sujith J. Chandy
- Department of Pharmacology, Pushpagiri Institute of Medical Sciences and Research Centre, Thiruvalla, Kerala India
| | - Asri Che Jusoh
- Department of General Surgery, Kuala Krai Hospital, Kuala Krai, Kelantan Malaysia
| | - Alain Chichom-Mefire
- Department of Surgery and Obstetrics/Gynaecology, Regional Hospital, Limbe, Cameroon
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, UK
| | - Francesco Corcione
- Department of Laparoscopic and Robotic Surgery, Colli-Monaldi Hospital, Naples, Italy
| | - Yunfeng Cui
- Department of Surgery, Tianjin Nankai Hospital, Nankai Clinical School of Medicine, Tianjin Medical University, Tianjin, China
| | - Daniel Curcio
- Infectología Institucional SRL, Hospital Municipal Chivilcoy, Buenos Aires, Argentina
| | - Samir Delibegovic
- Department of Surgery, University Clinical Center of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Zaza Demetrashvili
- Department General Surgery, Kipshidze Central University Hospital, Tbilisi, Georgia
| | | | - Sameer Dhingra
- School of Pharmacy, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Eric Williams Medical Sciences Complex, Uriah Butler Highway, Champ Fleurs, Trinidad and Tobago
| | - José J. Diaz
- Division of Acute Care Surgery, Program in Trauma, R Adams Cowley Shock Trauma Center, University of Maryland, Baltimore, MD USA
| | - Isidoro Di Carlo
- Department of Surgical Sciences, Cannizzaro Hospital, University of Catania, Catania, Italy
| | - Angel Dillip
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | | | - Michael P. Doyle
- Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, GA USA
| | - Gereltuya Dorj
- School of Pharmacy and Biomedicine, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Agron Dogjani
- Department of Surgery, University Hospital of Trauma, Tirana, Albania
| | - Hervé Dupont
- Département d’Anesthésie-Réanimation, CHU Amiens-Picardie, and INSERM U1088, Université de Picardie Jules Verne, Amiens, France
| | - Soumitra R. Eachempati
- Department of Surgery, Division of Burn, Critical Care, and Trauma Surgery (K.P.S., S.R.E.), Weill Cornell Medical College/New York-Presbyterian Hospital, New York, USA
| | - Mushira Abdulaziz Enani
- Department of Medicine, Infectious Disease Division, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Valery N. Egiev
- Department of Surgery, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Mutasim M. Elmangory
- Sudan National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan
| | - Paula Ferrada
- Department of Surgery, Virginia Commonwealth University, Richmond, VA USA
| | - Joseph R. Fitchett
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Gustavo P. Fraga
- Division of Trauma Surgery, Department of Surgery, School of Medical Sciences, University of Campinas (Unicamp), Campinas, SP Brazil
| | | | - Helen Giamarellou
- 6th Department of Internal Medicine, Hygeia General Hospital, Athens, Greece
| | - Wagih Ghnnam
- Department of General Surgery, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - George Gkiokas
- 2nd Department of Surgery, Aretaieion University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Carlos Augusto Gomes
- Department of Surgery, Hospital Universitário Terezinha de Jesus, Faculdade de Ciências Médicas e da Saúde de Juiz de Fora, Juiz de Fora, Brazil
| | - Harumi Gomi
- Center for Global Health, Mito Kyodo General Hospital, University of Tsukuba, Mito, Ibaraki Japan
| | - Manuel Guzmán-Blanco
- Hospital Privado Centro Médico de Caracas and Hospital Vargas de Caracas, Caracas, Venezuela
| | - Mainul Haque
- Unit of Pharmacology, Faculty of Medicine and Defense Health, National Defence University of Malaysia, Kuala Lumpur, Malaysia
| | - Sonja Hansen
- Institute of Hygiene, Charité-Universitätsmedizin Berlin, Hindenburgdamm 27, 12203 Berlin, Germany
| | - Andreas Hecker
- Department of General and Thoracic Surgery, University Hospital Giessen, Giessen, Germany
| | | | - Torsten Herzog
- Department of Surgery, St. Josef Hospital, Ruhr University Bochum, Bochum, Germany
| | - Adrien Montcho Hodonou
- Department of Surgery, Faculté de médecine, Université de Parakou, BP 123 Parakou, Bénin
| | - Suk-Kyung Hong
- Division of Trauma and Surgical Critical Care, Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Reinhold Kafka-Ritsch
- Department of Visceral, Transplant and Thoracic Surgery, Innsbruck Medical University, Innsbruck, Austria
| | - Lewis J. Kaplan
- Department of Surgery Philadelphia VA Medical Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Garima Kapoor
- Department of Microbiology, Gandhi Medical College, Bhopal, India
| | | | - Martin G. Kees
- Department of Anesthesiology and Intensive Care, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Jakub Kenig
- 3rd Department of General Surgery, Jagiellonian University Medical College, Krakow, Poland
| | - Ronald Kiguba
- Department of Pharmacology and Therapeutics, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Peter K. Kim
- Department of Surgery, Albert Einstein College of Medicine and Jacobi Medical Center, Bronx, NY USA
| | - Yoram Kluger
- Department of General Surgery, Division of Surgery, Rambam Health Care Campus, Haifa, Israel
| | - Vladimir Khokha
- Department of Emergency Surgery, City Hospital, Mozyr, Belarus
| | - Kaoru Koike
- Department of Primary Care and Emergency Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenneth Y. Y. Kok
- Department of Surgery, The Brunei Cancer Centre, Jerudong Park, Brunei
| | - Victory Kong
- Department of Surgery, Edendale Hospital, Pietermaritzburg, South Africa
| | - Matthew C. Knox
- School of Medicine, Western Sydney University, Campbelltown, NSW Australia
| | - Kenji Inaba
- Division of Acute Care Surgery and Surgical Critical Care, Department of Surgery, Los Angeles County and University of Southern California Medical Center, University of Southern California, Los Angeles, CA USA
| | - Arda Isik
- Department of General Surgery, Erzincan University, Faculty of Medicine, Erzincan, Turkey
| | - Katia Iskandar
- Department of Pharmacy, Lebanese International University, Beirut, Lebanon
| | - Rao R. Ivatury
- Department of Surgery, Virginia Commonwealth University, Richmond, VA USA
| | - Maurizio Labbate
- School of Life Science and The ithree Institute, University of Technology, Sydney, NSW Australia
| | - Francesco M. Labricciosa
- Department of Biomedical Sciences and Public Health, Unit of Hygiene, Preventive Medicine and Public Health, UNIVMP, Ancona, Italy
| | - Pierre-François Laterre
- Department of Critical Care Medicine, Cliniques Universitaires Saint Luc, Université Catholique de Louvain (UCL), Brussels, Belgium
| | - Rifat Latifi
- Department of Surgery, Division of Trauma, University of Arizona, Tucson, AZ USA
| | - Jae Gil Lee
- Department of Surgery, Yonsei University College of Medicine, Seoul, South Korea
| | - Young Ran Lee
- Texas Tech University Health Sciences Center School of Pharmacy, Abilene, TX USA
| | - Marc Leone
- Department of Anaesthesiology and Critical Care, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Aix Marseille Université, Marseille, France
| | - Ari Leppaniemi
- Abdominal Center, University Hospital Meilahti, Helsinki, Finland
| | - Yousheng Li
- Department of Surgery, Inling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Stephen Y. Liang
- Division of Infectious Diseases, Division of Emergency Medicine, Washington University School of Medicine, St. Louis, MO USA
| | - Tonny Loho
- Division of Infectious Diseases, Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
| | - Marc Maegele
- Department for Traumatology and Orthopedic Surgery, Cologne Merheim Medical Center (CMMC), University of Witten/Herdecke (UW/H), Cologne, Germany
| | - Sydney Malama
- Health Research Program, Institute of Economic and Social Research, University of Zambia, Lusaka, Zambia
| | - Hany E. Marei
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Ignacio Martin-Loeches
- Multidisciplinary Intensive Care Research Organization (MICRO), Wellcome Trust-HRB Clinical Research, Department of Clinical Medicine, Trinity Centre for Health Sciences, St James’ University Hospital, Dublin, Ireland
| | - Sanjay Marwah
- Department of Surgery, Post-Graduate Institute of Medical Sciences, Rohtak, India
| | - Amos Massele
- Department of Clinical Pharmacology, School of Medicine, University of Botswana, Gaborone, Botswana
| | - Michael McFarlane
- Department of Surgery, Radiology, University Hospital of the West Indies, Kingston, Jamaica
| | - Renato Bessa Melo
- General Surgery Department, Centro Hospitalar de São João, Porto, Portugal
| | - Ionut Negoi
- Department of Surgery, Emergency Hospital of Bucharest, Bucharest, Romania
| | - David P. Nicolau
- Center of Anti-Infective Research and Development, Hartford, CT USA
| | - Carl Erik Nord
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | | | | | - Carlos A. Ordonez
- Department of Surgery and Critical Care, Universidad del Valle, Fundación Valle del Lili, Cali, Colombia
| | - Mouaqit Ouadii
- Department of Surgery, Hassan II University Hospital, Medical School of Fez, Sidi Mohamed Benabdellah University, Fez, Morocco
| | | | - Diego Piazza
- Division of Surgery, Vittorio Emanuele Hospital, Catania, Italy
| | - Guntars Pupelis
- Department of General and Emergency Surgery, Riga East University Hospital ‘Gailezers’, Riga, Latvia
| | - Timothy Miles Rawson
- National Institute for Health Research, Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Hammersmith Campus, London, UK
| | - Miran Rems
- Department of General Surgery, Jesenice General Hospital, Jesenice, Slovenia
| | - Sandro Rizoli
- Trauma and Acute Care Service, St Michael’s Hospital, University of Toronto, Toronto, Canada
| | | | - Boris Sakakhushev
- General Surgery Department, Medical University, University Hospital St George, Plovdiv, Bulgaria
| | | | - Norio Sato
- Department of Primary Care and Emergency Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Helmut A. Segovia Lohse
- II Cátedra de Clínica Quirúrgica, Hospital de Clínicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Gabriele Sganga
- Department of Surgery, Catholic University of Sacred Heart, Policlinico A Gemelli, Rome, Italy
| | - Boonying Siribumrungwong
- Department of Surgery, Faculty of Medicine, Thammasat University Hospital, Thammasat University, Pathum Thani, Thailand
| | - Vishal G. Shelat
- Department of General Surgery, Tan Tock Seng Hospital, Tan Tock Seng, Singapore
| | - Kjetil Soreide
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Rodolfo Soto
- Department of Emergency Surgery and Critical Care, Centro Medico Imbanaco, Cali, Colombia
| | - Peep Talving
- Department of Surgery, North Estonia Medical Center, Tallinn, Estonia
| | - Jonathan V. Tilsed
- Surgery Health Care Group, Hull and East Yorkshire Hospitals NHS Trust, Hull, UK
| | | | - Gabriel Trueba
- Institute of Microbiology, Biological and Environmental Sciences College, University San Francisco de Quito, Quito, Ecuador
| | - Ngo Tat Trung
- Department of Molecular Biology, Tran Hung Dao Hospital, No 1, Tran Hung Dao Street, Hai Ba Trung Dist, Hanoi, Vietnam
| | - Jan Ulrych
- 1st Department of Surgery - Department of Abdominal, Thoracic Surgery and Traumatology, General University Hospital, Prague, Czech Republic
| | - Harry van Goor
- Department of Surgery, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Andras Vereczkei
- Department of Surgery, Medical School University of Pécs, Pécs, Hungary
| | - Ravinder S. Vohra
- Nottingham Oesophago-Gastric Unit, Nottingham University Hospitals, Nottingham, UK
| | - Imtiaz Wani
- Department of Surgery, Sheri-Kashmir Institute of Medical Sciences, Srinagar, India
| | - Waldemar Uhl
- Department of Surgery, St. Josef Hospital, Ruhr University Bochum, Bochum, Germany
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affilliated Hospital, Zhejiang University, Zhejiang, China
| | - Kuo-Ching Yuan
- Trauma and Emergency Surgery Department, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | | | - Jean-Ralph Zahar
- Infection Control Unit, Angers University, CHU d’Angers, Angers, France
| | - Tanya L. Zakrison
- Division of Trauma and Surgical Critical Care, DeWitt Daughtry Family Department of Surgry, University of Miami, Miami, FL USA
| | - Antonio Corcione
- Anesthesia and Intensive Care Unit, AORN dei Colli Vincenzo Monaldi Hospital, Naples, Italy
| | - Rita M. Melotti
- Anesthesiology and Intensive Care Unit, Sant’Orsola University Hospital, Bologna, Italy
| | - Claudio Viscoli
- Infectious Diseases Unit, University of Genoa (DISSAL) and IRCCS San Martino-IST, Genoa, Italy
| | - Perluigi Viale
- Infectious Diseases Unit, Department of Medical and Surgical Sciences, Sant’ Orsola Hospital, University of Bologna, Bologna, Italy
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Roach DR, Donovan DM. Antimicrobial bacteriophage-derived proteins and therapeutic applications. BACTERIOPHAGE 2015; 5:e1062590. [PMID: 26442196 DOI: 10.1080/21597081.2015.1062590] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/08/2015] [Accepted: 06/11/2015] [Indexed: 02/07/2023]
Abstract
Antibiotics have the remarkable power to control bacterial infections. Unfortunately, widespread use, whether regarded as prudent or not, has favored the emergence and persistence of antibiotic resistant strains of human pathogenic bacteria, resulting in a global health threat. Bacteriophages (phages) are parasites that invade the cells of virtually all known bacteria. Phages reproduce by utilizing the host cell's machinery to replicate viral proteins and genomic material, generally damaging and killing the cell in the process. Thus, phage can be exploited therapeutically as bacteriolytic agents against bacteria. Furthermore, understanding of the molecular processes involved in the viral life cycle, particularly the entry and cell lysis steps, has led to the development of viral proteins as antibacterial agents. Here we review the current preclinical state of using phage-derived endolysins, virion-associated peptidoglycan hydrolases, polysaccharide depolymerases, and holins for the treatment of bacterial infection. The scope of this review is a focus on the viral proteins that have been assessed for protective effects against human pathogenic bacteria in animal models of infection and disease.
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Affiliation(s)
- Dwayne R Roach
- Molecular Biology of the Genes in Extremophiles; Department of Microbiology; Institute Pasteur ; Paris, France
| | - David M Donovan
- Animal Biosciences and Biotechnology Laboratory; NEA; Agricultural Research Service; US Department of Agriculture ; Beltsville, MD USA
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