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Long J, Xu Y, Ou L, Yang H, Xi Y, Chen S, Duan G. Polymorphism of Type I-F CRISPR/Cas system in Escherichia coli of phylogenetic group B2 and its application in genotyping. INFECTION GENETICS AND EVOLUTION 2019; 74:103916. [PMID: 31195154 DOI: 10.1016/j.meegid.2019.103916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/22/2019] [Accepted: 06/07/2019] [Indexed: 12/26/2022]
Abstract
E. coli of phylogenetic group B2 is responsible for many extraintestinal infections, posing a great threat to health. The relatively polymorphic nature of CRISPR in phylogenetically related E. coli strains makes them potential markers for bacterial typing and evolutionary studies. In the current work, we investigated the occurrence and diversity of CRISPR/Cas system and explored its potential for genotyping. Type I-F CRISPR/Cas systems were found in 413 of 1190 strains of E. coli and exhibited the clustering within certain CCs and STs. And CRISPR spacer contents correlated well with MLST types. The divergence analysis of CRISPR showed stronger discriminatory power than MLST, and CRISPR polymorphism was instrumental for differentiating highly closely related strains. The timeline of spacer acquisition and deletion provided important information for inferring the evolution model between distinct serotypes. Identical spacer sequences were shared by strains with the same H-antigen type but not strains with the same O-antigen type. The homology between spacers and antibiotic-resistant plasmids demonstrated the role of Type I-F system in limiting the acquisition of antimicrobial resistance. Collectively, our data presents the dynamic nature of Type I-F CRISPR in E. coli of phylogenetic group B2 and provides new insights into the application of CRISPR-based typing in the species.
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Affiliation(s)
- Jinzhao Long
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yake Xu
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China; School Hospital, Henan University of Science and Technology, Luoyang, Henan, China
| | - Liuyang Ou
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuanlin Xi
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Shuaiyin Chen
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
| | - Guangcai Duan
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China; Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan, China.
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52
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Hoikkala V, Almeida GMF, Laanto E, Sundberg LR. Aquaculture as a source of empirical evidence for coevolution between CRISPR-Cas and phage. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180100. [PMID: 30905289 PMCID: PMC6452259 DOI: 10.1098/rstb.2018.0100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2018] [Indexed: 12/20/2022] Open
Abstract
So far, studies on the bacterial immune system CRISPR-Cas and its ecological and evolutionary effects have been largely limited to laboratory conditions. While providing crucial information on the constituents of CRISPR-Cas, such studies may overlook fundamental components that affect bacterial immunity in natural habitats. Translating laboratory-derived predictions to nature is not a trivial task, owing partly to the instability of natural communities and difficulties in repeated sampling. To this end, we review how aquaculture, the farming of fishes and other aquatic species, may provide suitable semi-natural laboratories for examining the role of CRISPR-Cas in phage/bacterium coevolution. Existing data from disease surveillance conducted in aquaculture, coupled with growing interest towards phage therapy, may have already resulted in large collections of bacterium and phage isolates. These data, combined with premeditated efforts, can provide empirical evidence on phage-bacterium dynamics such as the bacteriophage adherence to mucus hypothesis, phage life cycles and their relationship with CRISPR-Cas and other immune defences. Typing of CRISPR spacer content in pathogenic bacteria can also provide practical information on diversity and origin of isolates during outbreaks. In addition to providing information of CRISPR functionality and phage-bacterium dynamics, aquaculture systems can significantly impact perspectives on design of phage-based disease treatment at the current era of increasing antibiotic resistance. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
| | | | | | - Lotta-Riina Sundberg
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, PO Box 35, 40014 Jyvaskyla, Finland
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53
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Yang L, Zhang X, Liu Y, Li H, Qiu S, Li P, Song H. CSESA: an R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR. BMC Bioinformatics 2019; 20:215. [PMID: 31029079 PMCID: PMC6486994 DOI: 10.1186/s12859-019-2806-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/10/2019] [Indexed: 12/29/2022] Open
Abstract
Background Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Immunological serotyping is the most commonly used typing method to characterize S. enterica isolates, but is time-consuming and requires expensive reagents. Here, we developed an R package CSESA (CRISPR-based Salmonella enterica Serotype Analyzer) to predict the serotype based on the CRISPR loci of S. enterica. Results CSESA has implemented the CRISPR typing method CLSPT and extended its coverage on diverse S. enterica serotypes. This package takes CRISPR sequences or the genome sequences as input and provides users with the predicted serotypes. CSESA has shown excellent performance with currently available sequences of S. enterica. Conclusions CSESA is a convenient and useful tool for the prediction of S. enterica serotypes. The application of CSESA package can improve the efficiency of serotyping for S. enterica and reduce the burden of manpower resources. CSESA is freely available from CRAN at https://cran.r-project.org/web/packages/CSESA/.
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Affiliation(s)
- Lang Yang
- Academy of Military Medical Sciences, Beijing, China.,Center for Disease Control and Prevention of PLA, Beijing, China
| | - Xia Zhang
- School of electronics engineering and computer science, Peking University, Beijing, China
| | - Yuqi Liu
- Academy of Military Medical Sciences, Beijing, China.,Center for Disease Control and Prevention of PLA, Beijing, China
| | - Hao Li
- Academy of Military Medical Sciences, Beijing, China
| | - Shaofu Qiu
- Center for Disease Control and Prevention of PLA, Beijing, China
| | - Peng Li
- Center for Disease Control and Prevention of PLA, Beijing, China.
| | - Hongbin Song
- Center for Disease Control and Prevention of PLA, Beijing, China.
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54
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Fei X, Yin K, Yin C, Hu Y, Li J, Zhou Z, Tian Y, Geng S, Chen X, Pan Z, Li Q, Jiao X. Analyses of prevalence and molecular typing reveal the spread of antimicrobial-resistant Salmonella infection across two breeder chicken farms. Poult Sci 2019; 97:4374-4383. [PMID: 30016482 DOI: 10.3382/ps/pey305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 06/21/2018] [Indexed: 01/22/2023] Open
Abstract
In this study, Salmonella prevalence and antimicrobial resistance were evaluated at various production stages in 2 geographically separated breeder farms (referred to as G and F). Day-old chicks for the breeder flock at farm F were purchased from farm G. A total of 219 Salmonella isolates, all identified as Salmonella enterica subsp. enterica serovar Enteritidis, were recovered from 1,430 samples (sick chicken carcasses and/or dead embryos). The isolation rates at breeder farms G and F were 10.53% (56/532) and 18.15% (163/898), respectively. Resistance to 4-6 antimicrobial agents was the most frequent phenotype during the laying stage at both farms, suggesting that chicks are exposed to higher risk of antimicrobial-resistant Salmonella infection during this stage of the breeding process. Using clustered regularly interspaced short palindromic repeat (CRISPR) typing, 5 CRISPR patterns were identified, out of which one pattern was shared by the 2 farms. In addition, pulsed-field gel electrophoresis (PFGE) typing result indicated that 2 clusters (PF-1 and PF-2) were shared among the 2 breeder farms, suggesting that strains were transmitted from breeder farm G to farm F via the trade of day-old chicks. Our findings suggested that the trade of day-old breeder chicks could be one of the potential Salmonella transmission routes, and antibiotics should be administered with caution during the laying stage.
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Affiliation(s)
- Xiao Fei
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Kequan Yin
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Chao Yin
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Yachen Hu
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Jingwen Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Zihao Zhou
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Yuqi Tian
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Shizhong Geng
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Xiang Chen
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, 225009, China
| | - Zhiming Pan
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, 225009, China
| | - Qiuchun Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, 225009, China
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, 225009, China
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55
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García-Zea JA, de la Herrán R, Robles Rodríguez F, Navajas-Pérez R, Ruiz Rejón C. Detection and variability analyses of CRISPR-like loci in the H. pylori genome. PeerJ 2019; 7:e6221. [PMID: 30648020 PMCID: PMC6330956 DOI: 10.7717/peerj.6221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR-like loci have been recently identified. In this work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure. We confirm the presence of a locus that was previously described in the VlpC gene in al lgenomes, and we characterize new CRISPR-like loci in other genomic locations. By studying the variability and gene location of these loci, the evolution and the possible roles of these sequences are discussed. Additionally, the usefulness of this type of sequences as a phylogenetic marker has been demonstrated, associating the different strains by geographical area.
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Affiliation(s)
| | - Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | | | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Carmelo Ruiz Rejón
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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56
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Wahl A, Battesti A, Ansaldi M. Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host? Mol Microbiol 2018; 111:303-316. [PMID: 30466179 PMCID: PMC7380047 DOI: 10.1111/mmi.14167] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2018] [Indexed: 12/11/2022]
Abstract
Thanks to the exponentially increasing number of publicly available bacterial genome sequences, one can now estimate the important contribution of integrated viral sequences to the diversity of bacterial genomes. Indeed, temperate bacteriophages are able to stably integrate the genome of their host through site‐specific recombination and transmit vertically to the host siblings. Lysogenic conversion has been long acknowledged to provide additional functions to the host, and particularly to bacterial pathogen genomes where prophages contribute important virulence factors. This review aims particularly at highlighting the current knowledge and questions about lysogeny in Salmonella genomes where functional prophages are abundant, and where genetic interactions between host and prophages are of particular importance for human health considerations.
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Affiliation(s)
- Astrid Wahl
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Aurélia Battesti
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, UMR7283, Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
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57
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Chakraborty S, von Mentzer A, Begum YA, Manzur M, Hasan M, Ghosh AN, Hossain MA, Camilli A, Qadri F. Phenotypic and genomic analyses of bacteriophages targeting environmental and clinical CS3-expressing enterotoxigenic Escherichia coli (ETEC) strains. PLoS One 2018; 13:e0209357. [PMID: 30571788 PMCID: PMC6301781 DOI: 10.1371/journal.pone.0209357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/04/2018] [Indexed: 01/21/2023] Open
Abstract
Diarrhea due to infection of enterotoxigenic Escherichia coli (ETEC) is of great concern in several low and middle-income countries. ETEC infection is considered to be the most common cause of diarrhea in Bangladesh and is mainly spread through contaminated water and food. ETEC pathogenesis is mediated by the expression of enterotoxins and colonization factors (CFs) that target the intestinal mucosa. ETEC can survive for extended time periods in water, where they are likely to be attacked by bacteriophages. Antibiotic resistance is common amongst enteric pathogens and therefore is the use of bacteriophages (phage) as a therapeutic tool an interesting approach. This study was designed to identify novel phages that specifically target ETEC virulence factors. In total, 48 phages and 195 ETEC isolates were collected from water sources and stool samples. Amongst the identified ETEC specific phages, an enterobacteria phage T7, designated as IMM-002, showed a significant specificity towards colonization factor CS3-expressing ETEC isolates. Antibody-blocking and phage-neutralization assays revealed that CS3 is used as a host receptor for the IMM-002 phage. The bacterial CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated) defence mechanism can invoke immunity against phages. Genomic analyses coupled with plaque assay experiments indicate that the ETEC CRISPR-Cas system is involved in the resistance against the CS3-specific phage (IMM-002) and the previously identified CS7-specific phage (IMM-001). As environmental water serves as a reservoir for ETEC, it is important to search for new antimicrobial agents such as phages in environmental water as well as the human gut. A better understanding of how the interplay between ETEC-specific phages and ETEC isolates affects the ETEC diversity, both in environmental ecosystems and within the host, is important for the development of new treatments for ETEC infections.
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Affiliation(s)
- Sajib Chakraborty
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
- icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Mohakhali, Dhaka, Bangladesh
| | - Astrid von Mentzer
- Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Yasmin Ara Begum
- icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Mohakhali, Dhaka, Bangladesh
| | - Mehnaz Manzur
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Mahmudul Hasan
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Amar N Ghosh
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - M Anwar Hossain
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, and Howard Hughes Medical Institute, Tufts University School of Medicine, Boston, MA, United States of America
| | - Firdausi Qadri
- icddr,b (International Centre for Diarrhoeal Disease Research, Bangladesh), Mohakhali, Dhaka, Bangladesh
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58
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Weissman JL, Fagan WF, Johnson PLF. Selective Maintenance of Multiple CRISPR Arrays Across Prokaryotes. CRISPR J 2018; 1:405-413. [PMID: 31021246 DOI: 10.1089/crispr.2018.0034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Prokaryotes are under nearly constant attack by viral pathogens. To protect against this threat of infection, bacteria and archaea have evolved a wide array of defense mechanisms, singly and in combination. While immune diversity in a single organism likely reduces the chance of pathogen evolutionary escape, it remains puzzling why many prokaryotes also have multiple, seemingly redundant, copies of the same type of immune system. Here, we focus on the highly flexible CRISPR adaptive immune system, which is present in multiple copies in a surprising 28% of the prokaryotic genomes in RefSeq. We use a comparative genomics approach looking across all prokaryotes to demonstrate that on average, organisms are under selection to maintain more than one CRISPR array. Given this surprising conclusion, we consider several hypotheses concerning the source of selection and include a theoretical analysis of the possibility that a trade-off between memory span and learning speed could select for both "long-term memory" and "short-term memory" CRISPR arrays.
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Affiliation(s)
- Jake L Weissman
- Department of Biology, University of Maryland College Park , College Park, Maryland
| | - William F Fagan
- Department of Biology, University of Maryland College Park , College Park, Maryland
| | - Philip L F Johnson
- Department of Biology, University of Maryland College Park , College Park, Maryland
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59
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Thompson CP, Doak AN, Amirani N, Schroeder EA, Wright J, Kariyawasam S, Lamendella R, Shariat NW. High-Resolution Identification of Multiple Salmonella Serovars in a Single Sample by Using CRISPR-SeroSeq. Appl Environ Microbiol 2018; 84:e01859-18. [PMID: 30170999 PMCID: PMC6193385 DOI: 10.1128/aem.01859-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 08/21/2018] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica is represented by >2,600 serovars that can differ in routes of transmission, host colonization, and in resistance to antimicrobials. S. enterica is the leading bacterial cause of foodborne illness in the United States, with well-established detection methodology. Current surveillance protocols rely on the characterization of a few colonies to represent an entire sample; thus, minority serovars remain undetected. Salmonella contains two CRISPR loci, CRISPR1 and CRISPR2, and the spacer contents of these can be considered serovar specific. We exploited this property to develop an amplicon-based and multiplexed sequencing approach, CRISPR-SeroSeq (serotyping by sequencing of the CRISPR loci), to identify multiple serovars present in a single sample. Using mixed genomic DNA from two Salmonella serovars, we were able to confidently detect a serovar that constituted 0.01% of the sample. Poultry is a major reservoir of Salmonella spp., including serovars that are frequently associated with human illness, as well as those that are not. Numerous studies have examined the prevalence and diversity of Salmonella spp. in poultry, though these studies were limited to culture-based approaches and therefore only identified abundant serovars. CRISPR-SeroSeq was used to investigate samples from broiler houses and a processing facility. Ninety-one percent of samples harbored multiple serovars, and there was one sample in which four different serovars were detected. In another sample, reads for the minority serovar comprised 0.003% of the total number of Salmonella spacer reads. The most abundant serovars identified were Salmonella enterica serovars Montevideo, Kentucky, Enteritidis, and Typhimurium. CRISPR-SeroSeq also differentiated between multiple strains of some serovars. This high resolution of serovar populations has the potential to be utilized as a powerful tool in the surveillance of Salmonella species.IMPORTANCESalmonella enterica is the leading bacterial cause of foodborne illness in the United States and is represented by over 2,600 distinct serovars. Some of these serovars are pathogenic in humans, while others are not. Current surveillance for this pathogen is limited by the detection of only the most abundant serovars, due to the culture-based approaches that are used. Thus, pathogenic serovars that are present in a minority remain undetected. By exploiting serovar-specific differences in the CRISPR arrays of Salmonella spp., we have developed a high-throughput sequencing tool to be able to identify multiple serovars in a single sample and tested this in multiple poultry samples. This novel approach allows differences in the dynamics of individual Salmonella serovars to be measured and can have a significant impact on understanding the ecology of this pathogen with respect to zoonotic risk and public health.
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Affiliation(s)
- Cameron P Thompson
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Alexandra N Doak
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
- Department of Computer Science, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Naufa Amirani
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Erin A Schroeder
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
| | - Justin Wright
- Wright Labs, Juniata Center for Entrepreneurial Leadership, Huntingdon, Pennsylvania, USA
| | - Subhashinie Kariyawasam
- Department of Veterinary Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Regina Lamendella
- Wright Labs, Juniata Center for Entrepreneurial Leadership, Huntingdon, Pennsylvania, USA
- Biology Department, Juniata College, Huntingdon, Pennsylvania, USA
| | - Nikki W Shariat
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania, USA
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60
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Medina-Aparicio L, Dávila S, Rebollar-Flores JE, Calva E, Hernández-Lucas I. The CRISPR-Cas system in Enterobacteriaceae. Pathog Dis 2018; 76:4794941. [PMID: 29325038 DOI: 10.1093/femspd/fty002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/08/2018] [Indexed: 12/20/2022] Open
Abstract
In nature, microorganisms are constantly exposed to multiple viral infections and thus have developed many strategies to survive phage attack and invasion by foreign DNA. One of such strategies is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) bacterial immunological system. This defense mechanism is widespread in prokaryotes including several families such as Enterobacteriaceae. Much knowledge about the CRISPR-Cas system has been generated, including its biological functions, transcriptional regulation, distribution, utility as a molecular marker and as a tool for specific genome editing. This review focuses on these aspects and describes the state of the art of the CRISPR-Cas system in the Enterobacteriaceae bacterial family.
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Affiliation(s)
- Liliana Medina-Aparicio
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Sonia Dávila
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Av. Universidad No. 1001, Cuernavaca, Morelos 62209, México
| | - Javier E Rebollar-Flores
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Edmundo Calva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
| | - Ismael Hernández-Lucas
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos 62210, México
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61
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Genetics of CRISPR arrays in Salmonella Typhimurium 14028 associated with foreign DNA decay. Genes Genomics 2018; 40:865-872. [PMID: 30047111 DOI: 10.1007/s13258-018-0700-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/18/2018] [Indexed: 10/17/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) are a genetic locus of prokaryotes and contain highly conserved direct repeats, spacers, and CRISPR-associated genes. Spacers in CRISPRs are known as adaptive immune markers and reveal what types of phage or foreign DNA have been introduced in the past. The primary objective of this study was to analyze spacer sequences in CRISPR arrays of 15 Salmonella enterica subspecies and to determine if Salmonella CRISPRs are indeed involved in resistance to foreign DNAs. Using a bioinformatics algorithm, the CRISPR arrays of 15 subspecies of S. enterica were predicted. The transformation efficiencies of the wild-type and mutant strains lacking a space were determined using the plasmid harboring the same sequences with the space. Analysis of the CRISPR arrays indicated that S. Typhimurium encoded three possible CRISPR regions in the genome. Notably, 48 or 55 spacers were predicted in the genomes of S. Typhimurium 14028 and LT2 strains, respectively, and 39 were precisely identical. To confirm this prediction, the predicted CRISPR regions of S. Typhimurium 14028 were sequenced using the specific primers. Interestingly, a homology search of individual spacers found that the 2nd spacer of CRISPR 2 was nearly identical to a partial genome region of phage FSL SP-016. The mutant strain showed two to threefold increased transformation efficiency compared to that of the wild-type strain. These results demonstrate that the spacer sequence is dependent on genetic relations, especially for adaptive immunity against phage or foreign DNAs.
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Rauch HE, Vosik D, Kariyawasam S, M'ikanatha N, Shariat NW. Prevalence of Group I Salmonella Kentucky in domestic food animals from Pennsylvania and overlap with human clinical CRISPR sequence types. Zoonoses Public Health 2018; 65:831-837. [PMID: 30014599 DOI: 10.1111/zph.12506] [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: 04/25/2018] [Revised: 06/21/2018] [Accepted: 06/21/2018] [Indexed: 01/29/2023]
Abstract
Although infrequently associated with illness in humans, Salmonella enterica, subsp. enterica serovar Kentucky is the most common non-clinical, non-human serovar reported in the United States, being largely found in poultry and poultry products, as well as being associated with cattle. This serovar is polyphyletic and can be separated into two groups, Group I and II, based on CRISPR-typing analysis. In Salmonella Kentucky isolates from human clinical samples in Pennsylvania, both lineages are equally represented. The goal of this study was to determine whether both groups were also represented in domestic food animals in Pennsylvania. We analysed the CRISPR arrays from 67 Salmonella Kentucky isolates used PCR and sequencing of CRISPR arrays or analysis of whole genome sequences to analyse the CRISPR arrays and Across a collection of 67 Salmonella Kentucky isolates that includes those collected from farms, veterinary clinical samples as well as isolates from retail meats, we show that Group I Salmonella Kentucky are the exclusive lineage present. We reveal that the specific subtype of over a quarter of these animal isolates are also found to be responsible for causing human salmonellosis in the same region over the same time period.
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Affiliation(s)
- Hallie E Rauch
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania
| | - Dorothy Vosik
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania
| | - Subhashinie Kariyawasam
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, Pennsylvania
| | - Nkuchia M'ikanatha
- Division of Infectious Disease Epidemiology, Pennsylvania Department of Health, Harrisburg, Pennsylvania.,Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nikki W Shariat
- Department of Biology, Gettysburg College, Gettysburg, Pennsylvania
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63
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Noll LW, Chall R, Shridhar PB, Liu X, Bai J, Delannoy S, Fach P, Nagaraja TG. Validation and Application of a Real-Time PCR Assay Based on the CRISPR Array for Serotype-Specific Detection and Quantification of Enterohemorrhagic Escherichia coli O157:H7 in Cattle Feces †. J Food Prot 2018; 81:1157-1164. [PMID: 29939793 DOI: 10.4315/0362-028x.jfp-18-049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Several real-time quantitative PCR (qPCR) assays have been developed for detection and quantification of Escherichia coli O157:H7 in complex matrices by targeting genes for serogroup-specific O-antigen ( rfbEO157), H7 antigen, and one or more major virulence factors (Shiga toxin and intimin). A major limitation of such assays is that coamplification of H7 and virulence genes in a sample does not signal association of those genes with the O157 serogroup. Clusters of regularly interspaced short palindromic repeats (CRISPR) polymorphisms are highly correlated with certain enterohemorrhagic E. coli (EHEC) serotypes, including O157:H7, and the presence of genes for Shiga toxin ( stx1 and stx2) and intimin ( eae). Our objectives were to develop and validate a qPCR assay targeting the CRISPR array for the detection and quantification of EHEC O157:H7 in cattle feces and to evaluate the applicability of the assay for detection of and comparison with a four-plex qPCR assay targeting rfbEO157, stx1, stx2, and eae genes and a culture method. Detection limits of the CRISPRO157:H7 qPCR assay for cattle feces spiked with pure cultures were 2.1 × 103 and 2.3 × 100 CFU/g before and after enrichment, respectively. Detection of E. coli O157 in feedlot cattle fecal samples ( n = 576) was compared among the CRISPRO157:H7 qPCR assay, culture method, and four-plex qPCR assay. The CRISPRO157:H7 qPCR detected 42.2% of the samples (243 of 576 samples) as positive for E. coli O157:H7, compared with 30.4% (175 samples) by the culture method. Nearly all samples (97.2%; 560 samples) were positive for rfbEO157 by the four-plex PCR, but 21.8% (122 of 560 samples) were negative for the stx and/or eae genes, making it unlikely that EHEC O157:H7 was present in these samples. Cohen's kappa statistic indicated a fair and poor agreement beyond that due to chance between the CRISPR assay and the culture method and four-plex assay, respectively. This novel qPCR assay can detect the EHEC O157:H7 serotype in cattle feces by targeting CRISPR polymorphisms.
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Affiliation(s)
- Lance W Noll
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Rachel Chall
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Pragathi B Shridhar
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Xuming Liu
- 2 Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Jianfa Bai
- 2 Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - Sabine Delannoy
- 3 Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - Patrick Fach
- 3 Agency for Food, Environmental and Occupational Health and Safety (ANSES), Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - T G Nagaraja
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
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64
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Kimura S, Uehara M, Morimoto D, Yamanaka M, Sako Y, Yoshida T. Incomplete Selective Sweeps of Microcystis Population Detected by the Leader-End CRISPR Fragment Analysis in a Natural Pond. Front Microbiol 2018; 9:425. [PMID: 29568293 PMCID: PMC5852275 DOI: 10.3389/fmicb.2018.00425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/22/2018] [Indexed: 11/13/2022] Open
Abstract
The freshwater cyanobacterium Microcystis aeruginosa frequently forms toxic massive blooms and exists in an arms race with its infectious phages in aquatic natural environments, and as a result, has evolved extremely diverse and elaborate antiviral defense systems, including the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated genes (Cas) system. Here, to assess Microcystis population dynamics associated with exogenous mobile genetic elements such as phages and plasmids, we examined the temporal variation in CRISPR genotypes (CTs) by analyzing spacer sequences detected in a natural pond between June and October 2013 when a cyanobacterial bloom occurred. A total of 463,954 high-quality leader-end CRISPR sequences were obtained and the sequences containing spacers were classified into 31 previously reported CTs and 68 new CTs based on the shared order of the leader-end spacers. CT19 was the most dominant genotype (32%) among the 16 most common CTs, followed by CT52 (14%) and CT58 (9%). Spacer repertoires of CT19 showed mainly two different types; CT19origin, which was identical to the CT19 spacer repertoire of previously isolated strains, and CT19new+, which contained a new spacer at the leader-end of the CRISPR region of CT19origin, which were present in almost equal abundance, accounting for up to 99.94% of CT19 sequences. Surprisingly, we observed the spacer repertoires of the second to tenth spacers of CT19origin at the most leader-end of proto-genotype sequences of CT19origin. These were observed during the sampling in this study and our previous study at the same ecosystem in 2010 and 2011, suggesting these CTs persisted from 2011 to 2013 in spite of phage pressure. The leader-end variants were observed in other CT genotypes. These findings indicated an incomplete selective sweep of Microcystis populations. We explained the phenomenon as follow; the abundance of Microcystis varied seasonally and drastically, resulting that Microcystis populations experience a bottleneck once a year, and thereby founder effects following a bottleneck mean that older CTs have an equal chance of increasing in prevalence as the CTs generated following acquisition of newer spacers.
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Affiliation(s)
- Shigeko Kimura
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan.,School of Environmental Science, The University of Shiga Prefecture, Hikone, Japan
| | - Mika Uehara
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Daichi Morimoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Momoko Yamanaka
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiko Sako
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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65
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Vosik D, Tewari D, Dettinger L, M'ikanatha NM, Shariat NW. CRISPR Typing and Antibiotic Resistance Correlates with Polyphyletic Distribution in Human Isolates of Salmonella Kentucky. Foodborne Pathog Dis 2018; 15:101-108. [PMID: 29394097 DOI: 10.1089/fpd.2017.2298] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although infrequently associated with reported salmonellosis in humans, Salmonella enterica, subsp. enterica serovar Kentucky (ser. Kentucky) is the most common nonclinical, nonhuman serovar reported in the United States. The goal of this study was to use Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-multi-virulence-locus sequence typing (MVLST) to subtype a collection of human clinical isolates of ser. Kentucky submitted to the Pennsylvania Department of Health and to determine the extent of antibiotic resistance in these strains. This analysis highlighted the polyphyletic nature of ser. Kentucky, and separated our isolates into two groups, Group I and Group II, which were equally represented in our collection. Furthermore, antimicrobial susceptibility testing on all isolates using a National Antimicrobial Resistance Monitoring System (NARMS) panel of antibiotics demonstrated that resistance profiles could be divided into two groups. Group I isolates were resistant to cephems and penicillins, whereas Group II isolates were resistant to quinolones, gentamicin, and sulfisoxazole. Collectively, 50% of isolates were resistant to three or more classes of antibiotics and 30% were resistant to five or more classes. The correlation of antibiotic resistance with the two different lineages may reflect adaptation within two distinct reservoirs of ser. Kentucky, with differential exposure to antimicrobials.
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Affiliation(s)
- Dorothy Vosik
- 1 Department of Biology, Gettysburg College , Gettysburg, Pennsylvania
| | - Deepanker Tewari
- 2 Pennsylvania Veterinary Laboratory , Pennsylvania Department of Agriculture, Harrisburg, Pennsylvania
| | - Lisa Dettinger
- 3 Bureau of Laboratories , Pennsylvania Department of Health, Exton, Pennsylvania
| | - Nkuchia M M'ikanatha
- 4 Division of Infectious Disease Epidemiology , Pennsylvania Department of Health, Harrisburg, Pennsylvania.,5 Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania
| | - Nikki W Shariat
- 1 Department of Biology, Gettysburg College , Gettysburg, Pennsylvania
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66
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Ferrari RG, Panzenhagen PHN, Conte-Junior CA. Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking. Front Microbiol 2017; 8:2587. [PMID: 29312260 PMCID: PMC5744012 DOI: 10.3389/fmicb.2017.02587] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/12/2017] [Indexed: 11/13/2022] Open
Abstract
Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST) has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models). Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.
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Affiliation(s)
- Rafaela G. Ferrari
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil
- Food Science Program, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro H. N. Panzenhagen
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil
- Food Science Program, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos A. Conte-Junior
- Molecular and Analytical Laboratory Center, Department of Food Technology, Faculty of Veterinary, Universidade Federal Fluminense, Niterói, Brazil
- Food Science Program, Chemistry Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- National Institute of Health Quality Control, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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67
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Li Q, Wang X, Yin K, Hu Y, Xu H, Xie X, Xu L, Fei X, Chen X, Jiao X. Genetic analysis and CRISPR typing of Salmonella enterica serovar Enteritidis from different sources revealed potential transmission from poultry and pig to human. Int J Food Microbiol 2017; 266:119-125. [PMID: 29212058 DOI: 10.1016/j.ijfoodmicro.2017.11.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/21/2017] [Accepted: 11/26/2017] [Indexed: 10/18/2022]
Abstract
Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the most prevalent serotypes in Salmonella isolated from poultry and the most commonly reported cause of human salmonellosis. In this study, we aimed to assess the genetic diversity of 329 S. Enteritidis strains isolated from different sources from 2009 to 2016 in China. Clustered regularly interspaced short palindromic repeat (CRISPR) typing was used to characterize these 262 chicken clinical isolates, 38 human isolates, 18 pig isolates, six duck isolates, three goose isolates and two isolates of unknown source. A total of 18 Enteritidis CRISPR types (ECTs) were identified, with ECT2, ECT8 and ECT4 as the top three ECTs. CRISPR typing identified ECT2 as the most prevalent ECT, which accounted for 41% of S. Enteritidis strains from all the sources except duck. ECT9 and ECT13 were identified in both pig and human isolates and revealed potential transmission from pig to human. A cluster analysis distributed 18 ECTs, including the top three ECTs, into four lineages with LI as the predominant lineage. Forty-eight out of 329 isolates were subjected to whole genome sequence typing, which divided them into four clusters, with Cluster I as the predominant cluster. Cluster I included 92% (34/37) of strains located in LI identified from the CRISPR typing, confirming the good correspondence between both typing methods. In addition, the CRISPR typing also revealed the close relationship between ECTs and isolated areas, confirming that CRISPR spacers might be obtained by bacteria from the unique phage or plasmid pools in the environment. However, further analysis is needed to determine the function of CRISPR-Cas systems in Salmonella and the relationship between spacers and the environment.
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Affiliation(s)
- Qiuchun Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China.
| | - Xin Wang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China
| | - Kequan Yin
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China
| | - Yachen Hu
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China
| | - Haiyan Xu
- Nantong Center for Disease Control and Prevention, China
| | - Xiaolei Xie
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China
| | - Lijuan Xu
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China
| | - Xiao Fei
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China
| | - Xiang Chen
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, China; Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China.
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68
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Hullahalli K, Rodrigues M, Palmer KL. Exploiting CRISPR-Cas to manipulate Enterococcus faecalis populations. eLife 2017; 6:e26664. [PMID: 28644125 PMCID: PMC5491264 DOI: 10.7554/elife.26664] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/15/2017] [Indexed: 12/21/2022] Open
Abstract
CRISPR-Cas provides a barrier to horizontal gene transfer in prokaryotes. It was previously observed that functional CRISPR-Cas systems are absent from multidrug-resistant (MDR) Enterococcus faecalis, which only possess an orphan CRISPR locus, termed CRISPR2, lacking cas genes. Here, we investigate how the interplay between CRISPR-Cas genome defense and antibiotic selection for mobile genetic elements shapes in vitro E. faecalis populations. We demonstrate that CRISPR2 can be reactivated for genome defense in MDR strains. Interestingly, we observe that E. faecalis transiently maintains CRISPR targets despite active CRISPR-Cas systems. Subsequently, if selection for the CRISPR target is present, toxic CRISPR spacers are lost over time, while in the absence of selection, CRISPR targets are lost over time. We find that forced maintenance of CRISPR targets induces a fitness cost that can be exploited to alter heterogeneous E. faecalis populations.
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Affiliation(s)
- Karthik Hullahalli
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, United States
| | - Marinelle Rodrigues
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, United States
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, United States
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69
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Gholizadeh P, Aghazadeh M, Asgharzadeh M, Kafil HS. Suppressing the CRISPR/Cas adaptive immune system in bacterial infections. Eur J Clin Microbiol Infect Dis 2017; 36:2043-2051. [PMID: 28601970 DOI: 10.1007/s10096-017-3036-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 05/31/2017] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) coupled with CRISPR-associated (Cas) proteins (CRISPR/Cas) are the adaptive immune system of eubacteria and archaebacteria. This system provides protection of bacteria against invading foreign DNA, such as transposons, bacteriophages and plasmids. Three-stage processes in this system for immunity against foreign DNAs are defined as adaptation, expression and interference. Recent studies suggested a correlation between the interfering of the CRISPR/Cas locus, acquisition of antibiotic resistance and pathogenicity island. In this review article, we demonstrate and discuss the CRISPR/Cas system's roles in interference with acquisition of antibiotic resistance and pathogenicity island in some eubacteria. Totally, these systems function as the adaptive immune system of bacteria against invading foreign DNA, blocking the acquisition of antibiotic resistance and virulence factor, detecting serotypes, indirect effects of CRISPR self-targeting, associating with physiological functions, associating with infections in humans at the transmission stage, interfering with natural transformation, a tool for genome editing in genome engineering, monitoring foodborne pathogens etc. These results showed that the CRISPR/Cas system might prevent the emergence of virulence both in vitro and in vivo. Moreover, this system was shown to be a strong selective pressure for the acquisition of antibiotic resistance and virulence factor in bacterial pathogens.
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Affiliation(s)
- P Gholizadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - M Aghazadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - M Asgharzadeh
- Infectious and Tropical Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - H S Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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70
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Aydin S, Personne Y, Newire E, Laverick R, Russell O, Roberts AP, Enne VI. Presence of Type I-F CRISPR/Cas systems is associated with antimicrobial susceptibility in Escherichia coli. J Antimicrob Chemother 2017; 72:2213-2218. [DOI: 10.1093/jac/dkx137] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/11/2017] [Indexed: 01/19/2023] Open
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71
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Militello KT, Lazatin JC. Discovery of Escherichia coli CRISPR sequences in an undergraduate laboratory. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 45:262-269. [PMID: 27677251 DOI: 10.1002/bmb.21025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/01/2016] [Indexed: 06/06/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) represent a novel type of adaptive immune system found in eubacteria and archaebacteria. CRISPRs have recently generated a lot of attention due to their unique ability to catalog foreign nucleic acids, their ability to destroy foreign nucleic acids in a mechanism that shares some similarity to RNA interference, and the ability to utilize reconstituted CRISPR systems for genome editing in numerous organisms. In order to introduce CRISPR biology into an undergraduate upper-level laboratory, a five-week set of exercises was designed to allow students to examine the CRISPR status of uncharacterized Escherichia coli strains and to allow the discovery of new repeats and spacers. Students started the project by isolating genomic DNA from E. coli and amplifying the iap CRISPR locus using the polymerase chain reaction (PCR). The PCR products were analyzed by Sanger DNA sequencing, and the sequences were examined for the presence of CRISPR repeat sequences. The regions between the repeats, the spacers, were extracted and analyzed with BLASTN searches. Overall, CRISPR loci were sequenced from several previously uncharacterized E. coli strains and one E. coli K-12 strain. Sanger DNA sequencing resulted in the discovery of 36 spacer sequences and their corresponding surrounding repeat sequences. Five of the spacers were homologous to foreign (non-E. coli) DNA. Assessment of the laboratory indicates that improvements were made in the ability of students to answer questions relating to the structure and function of CRISPRs. Future directions of the laboratory are presented and discussed. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):262-269, 2017.
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Affiliation(s)
- Kevin T Militello
- Biology Department, State University of New York at Geneseo, Geneseo, New York, 14454
| | - Justine C Lazatin
- Biology Department, State University of New York at Geneseo, Geneseo, New York, 14454
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72
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Why new antibiotics are not obviously useful now. Int J Antimicrob Agents 2017; 49:549-553. [DOI: 10.1016/j.ijantimicag.2016.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/08/2016] [Accepted: 11/12/2016] [Indexed: 01/22/2023]
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73
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Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains. mSphere 2017; 2:mSphere00390-16. [PMID: 28405633 PMCID: PMC5381267 DOI: 10.1128/msphere.00390-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/12/2017] [Indexed: 12/26/2022] Open
Abstract
Antibiotic resistance in bacterial pathogens is a major public health concern. This work was motivated by the observation that only a small proportion of ST95 isolates, a major pandemic lineage of extraintestinal pathogenic E. coli, have acquired antibiotic resistance, in contrast to many other pandemic lineages. Understanding bacterial genetic factors that may prevent acquisition of resistance could contribute to the development of new biological, medical, or public health strategies to reduce antibiotic-resistant infections. Extraintestinal pathogenic Escherichia coli (ExPEC) strains belonging to multilocus sequence type 95 (ST95) are globally distributed and a common cause of infections in humans and domestic fowl. ST95 isolates generally show a lower prevalence of acquired antimicrobial resistance than other pandemic ExPEC lineages. We took a genomic approach to identify factors that may underlie reduced resistance. We fully assembled genomes for four ST95 isolates representing the four major fimH-based lineages within ST95 and also analyzed draft-level genomes from another 82 ST95 isolates, largely from the western United States. The fully assembled genomes of antibiotic-resistant isolates carried resistance genes exclusively on large (>90-kb) IncFIB/IncFII plasmids. These replicons were common in the draft genomes as well, particularly in antibiotic-resistant isolates, but we also observed multiple instances of a smaller (8.3-kb) ampicillin resistance plasmid that had been previously identified in Salmonella enterica. Among ST95 isolates, pansusceptibility to antibiotics was significantly associated with the fimH6 lineage and the presence of homologs of the previously identified 114-kb IncFIB/IncFII plasmid pUTI89, both of which were also associated with reduced carriage of other plasmids. Potential mechanistic explanations for lineage- and plasmid-specific effects on the prevalence of antibiotic resistance within the ST95 group are discussed. IMPORTANCE Antibiotic resistance in bacterial pathogens is a major public health concern. This work was motivated by the observation that only a small proportion of ST95 isolates, a major pandemic lineage of extraintestinal pathogenic E. coli, have acquired antibiotic resistance, in contrast to many other pandemic lineages. Understanding bacterial genetic factors that may prevent acquisition of resistance could contribute to the development of new biological, medical, or public health strategies to reduce antibiotic-resistant infections.
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Savitskaya E, Lopatina A, Medvedeva S, Kapustin M, Shmakov S, Tikhonov A, Artamonova II, Logacheva M, Severinov K. Dynamics of Escherichia coli type I-E CRISPR spacers over 42 000 years. Mol Ecol 2017; 26:2019-2026. [PMID: 27997045 PMCID: PMC5851898 DOI: 10.1111/mec.13961] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/29/2016] [Accepted: 12/05/2016] [Indexed: 01/14/2023]
Abstract
CRISPR-Cas are nucleic acid-based prokaryotic immune systems. CRISPR arrays accumulate spacers from foreign DNA and provide resistance to mobile genetic elements containing identical or similar sequences. Thus, the set of spacers present in a given bacterium can be regarded as a record of encounters of its ancestors with genetic invaders. Such records should be specific for different lineages and change with time, as earlier acquired spacers get obsolete and are lost. Here, we studied type I-E CRISPR spacers of Escherichia coli from extinct pachyderm. We find that many spacers recovered from intestines of a 42 000-year-old mammoth match spacers of present-day E. coli. Present-day CRISPR arrays can be reconstructed from palaeo sequences, indicating that the order of spacers has also been preserved. The results suggest that E. coli CRISPR arrays were not subject to intensive change through adaptive acquisition during this time.
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Affiliation(s)
- Ekaterina Savitskaya
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Anna Lopatina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sofia Medvedeva
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Sergey Shmakov
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexey Tikhonov
- Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
- Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk, Russia
| | - Irena I. Artamonova
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- A.A. Kharkevich Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | | | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
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CRISPR-based assay for the molecular identification of highly prevalent Salmonella serotypes. Food Microbiol 2017; 71:8-16. [PMID: 29366473 DOI: 10.1016/j.fm.2017.03.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/16/2017] [Accepted: 03/26/2017] [Indexed: 11/22/2022]
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76
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Xie X, Hu Y, Xu Y, Yin K, Li Y, Chen Y, Xia J, Xu L, Liu Z, Geng S, Li Q, Jiao X, Chen X, Pan Z. Genetic analysis of Salmonella enterica serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence. Vet Microbiol 2017; 203:81-87. [PMID: 28619172 DOI: 10.1016/j.vetmic.2017.02.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/20/2017] [Accepted: 02/20/2017] [Indexed: 11/19/2022]
Abstract
Salmonella enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is the cause of pullorum disease, characterized by white diarrhea, which leads to high mortality in poultry. In this study, we aimed to assess the genetic diversity of 655 S. Pullorum strains from 1962 to 2015 in China, Europe, and South America. A sequence typing scheme based on clustered regularly interspaced short palindromic repeats (CRISPR) was used to reveal the genetic relationships among these strains in this study. Overall, a total of 20 Pullorum sequence types (PSTs) of CRISPR were identified in the 655 isolates with PST7 (74%, 486/655) and PST3 (13%, 86/655) to be the most two frequent PSTs belonging to two different lineages, which confirmed the genetic conservation of S. Pullorum strains isolated from six provinces and two direct-controlled municipalities (Beijing and Shanghai) in China. However, the identification of seven new PSTs distributed in strains isolated since 2001 implied that genetic variation continues to develop in S. Pullorum. Interestingly, the whole-genome single-nucleotide polymorphism typing (WGST) of 96 strains out of the 655 isolates divided them into four lineages based on SNP analysis of core genomic sequence and exhibit good correspondence with the CRISPR subtyping method. Notably, 22 out of 26 isolates from Europe and South America were distributed in five distinctive PSTs (with no Chinese strains). Additionally, CRISPR data of spacers and their arrangement exhibit subtle but distinct specificity between different strains, and the dynamic adaptive nature of CRISPR loci provides critical insights into the evolution of S. Pullorum as the bacteria are influenced by their environment.
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Affiliation(s)
- Xiaolei Xie
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yachen Hu
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yaohui Xu
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Henan, China
| | - Kequan Yin
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yang Li
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yun Chen
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jie Xia
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lijuan Xu
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zijian Liu
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Shizhong Geng
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Qiuchun Li
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China.
| | - Xinan Jiao
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China.
| | - Xiang Chen
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zhiming Pan
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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Shen J, Lv L, Wang X, Xiu Z, Chen G. Comparative analysis of CRISPR-Cas systems inKlebsiellagenomes. J Basic Microbiol 2017; 57:325-336. [DOI: 10.1002/jobm.201600589] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 01/15/2017] [Accepted: 01/21/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Juntao Shen
- School of Life Science and Biotechnology; Dalian University of Technology; Dalian PR China
| | - Li Lv
- School of Life Sciences; Tsinghua University; Beijing PR China
| | - Xudong Wang
- School of Life Science and Biotechnology; Dalian University of Technology; Dalian PR China
| | - Zhilong Xiu
- School of Life Science and Biotechnology; Dalian University of Technology; Dalian PR China
| | - Guoqiang Chen
- School of Life Sciences; Tsinghua University; Beijing PR China
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Ren L, Deng LH, Zhang RP, Wang CD, Li DS, Xi LX, Chen ZR, Yang R, Huang J, Zeng YR, Wu HL, Cao SJ, Wu R, Huang Y, Yan QG. Relationship between drug resistance and the clustered, regularly interspaced, short, palindromic repeat-associated protein genes cas1 and cas2 in Shigella from giant panda dung. Medicine (Baltimore) 2017; 96:e5922. [PMID: 28207509 PMCID: PMC5319498 DOI: 10.1097/md.0000000000005922] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/14/2016] [Accepted: 12/17/2016] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND To detect drug resistance in Shigella obtained from the dung of the giant panda, explore the factors leading to drug resistance in Shigella, understand the characteristics of clustered, regularly interspaced, short, palindromic repeats (CRISPR), and assess the relationship between CRISPR and drug resistance. METHODS We collected fresh feces from 27 healthy giant pandas in the Giant Panda Conservation base (Wolong, China). We identified the strains of Shigella in the samples by using nucleotide sequence analysis. Further, the Kirby-Bauer paper method was used to determine drug sensitivity of the Shigella strains. CRISPR-associated protein genes cas1 and cas2 in Shigella were detected by polymerase chain reaction (PCR), and the PCR products were sequenced and compared. RESULTS We isolated and identified 17 strains of Shigella from 27 samples, including 14 strains of Shigella flexneri, 2 strains of Shigella sonnei, and 1 strain of Shigella dysenteriae. Further, drug resistance to cefazolin, imipenem, and amoxicillin-clavulanic acid was identified as a serious problem, as multidrug-resistant strains were detected. Further, cas1 and cas2 showed different degrees of point mutations. CONCLUSION The CRISPR system widely exists in Shigella and shares homology with that in Escherichia coli. The cas1 and cas 2 mutations contribute to the different levels of resistance. Point mutations at sites 3176455, 3176590, and 3176465 in cas1 (a); sites 3176989, 3176992, and 3176995 in cas1 (b); sites 3176156 and 3176236 in cas2 may affect the resistance of bacteria, cause emergence of multidrug resistance, and increase the types of drug resistance.
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Affiliation(s)
- Lu Ren
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lin-Hua Deng
- China Conservation and Research Centre for the Giant Panda, Wolong, China
| | - Ri-Peng Zhang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Cheng-Dong Wang
- China Conservation and Research Centre for the Giant Panda, Wolong, China
| | - De-Sheng Li
- China Conservation and Research Centre for the Giant Panda, Wolong, China
| | - Li-Xin Xi
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhen-rong Chen
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Rui Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jie Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yang-ru Zeng
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hong-Lin Wu
- China Conservation and Research Centre for the Giant Panda, Wolong, China
| | - San-Jie Cao
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Rui Wu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yong Huang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qi-Gui Yan
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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79
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Olm MR, Brown CT, Brooks B, Firek B, Baker R, Burstein D, Soenjoyo K, Thomas BC, Morowitz M, Banfield JF. Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. Genome Res 2017; 27:601-612. [PMID: 28073918 PMCID: PMC5378178 DOI: 10.1101/gr.213256.116] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/09/2017] [Indexed: 12/22/2022]
Abstract
The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99.9%, colonized multiple body sites, yet none were shared between infants. Gut-associated Citrobacter koseri genomes harbored 47 polymorphic sites that we used to define 10 subpopulations, one of which appeared in the gut after 1 wk but did not spread to other body sites. Differential genome coverage was used to measure bacterial population replication rates in situ. In all cases where the same bacterial population was detected in multiple body sites, replication rates were faster in mouth and skin compared to the gut. The ability of identical strains to colonize multiple body sites underscores the habit flexibility of initial colonists, whereas differences in microbial replication rates between body sites suggest differences in host control and/or resource availability. Population genomic analyses revealed microdiversity within bacterial populations, implying initial inoculation by multiple individual cells with distinct genotypes. Overall, however, the overlap of strains across body sites implies that the premature infant microbiome can exhibit very low microbial diversity.
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Affiliation(s)
- Matthew R Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Christopher T Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Brandon Brooks
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Brian Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Robyn Baker
- Division of Newborn Medicine, Children's Hospital of Pittsburgh and Magee-Womens Hospital of UPMC, Pittsburgh, Pennsylvania 15213, USA
| | - David Burstein
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Karina Soenjoyo
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA
| | - Michael Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94709, USA.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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80
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Tikh IB, Samuelson JC. Leveraging modern DNA assembly techniques for rapid, markerless genome modification. Biol Methods Protoc 2016; 1:bpw004. [PMID: 32368618 PMCID: PMC7189271 DOI: 10.1093/biomethods/bpw004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/06/2016] [Accepted: 09/26/2016] [Indexed: 11/14/2022] Open
Abstract
The ability to alter the genomic material of a prokaryotic cell is necessary for experiments designed to define the biology of the organism. In addition, the production of biomolecules may be significantly improved by application of engineered prokaryotic host cells. Furthermore, in the age of synthetic biology, speed and efficiency are key factors when choosing a method for genome alteration. To address these needs, we have developed a method for modification of the Escherichia coli genome named FAST-GE for Fast Assembly-mediated Scarless Targeted Genome Editing. Traditional cloning steps such as plasmid transformation, propagation and isolation were eliminated. Instead, we developed a DNA assembly-based approach for generating scarless strain modifications, which may include point mutations, deletions and gene replacements, within 48 h after the receipt of polymerase chain reaction primers. The protocol uses established, but optimized, genome modification components such as I-SceI endonuclease to improve recombination efficiency and SacB as a counter-selection mechanism. All DNA-encoded components are assembled into a single allele-exchange vector named pDEL. We were able to rapidly modify the genomes of both E. coli B and K-12 strains with high efficiency. In principle, the method may be applied to other prokaryotic organisms capable of circular dsDNA uptake and homologous recombination.
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Affiliation(s)
- Ilya B Tikh
- Protein Expression and Modification Division, New England BioLabs, Inc., Ipswich, MA, 01938-2723, USA
| | - James C Samuelson
- Protein Expression and Modification Division, New England BioLabs, Inc., Ipswich, MA, 01938-2723, USA
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81
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Almeida F, Medeiros MIC, Rodrigues DDP, Allard MW, Falcão JP. Molecular characterization of Salmonella Typhimurium isolated in Brazil by CRISPR-MVLST. J Microbiol Methods 2016; 133:55-61. [PMID: 28034696 DOI: 10.1016/j.mimet.2016.12.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 11/17/2022]
Abstract
CRISPR-multi-locus virulence sequence typing (CRISPR-MVLST) was performed to type 92 S. Typhimurium strains isolated from humans and food sources between 1983 and 2013 in Brazil and assess the suitability of this methodology comparing it with PFGE already used for subtyping the same strains. Among the 92 S. Typhimurium strains studied, we identified 25 CRISPR1 alleles, 27 CRISPR2 alleles, 2 fimH alleles and 3 sseL alleles showing that the genetic variability is much higher in the CRISPRs loci than in the virulence genes. The CRISPR-MVLST analysis provided similar results to the PFGE previously published used to type the same set of strains, demonstrating that CRISPR-MVLST is a very efficient approach for subtyping S. Typhimurium serovar and can be used to complement and validate results obtained by the PFGE methodology.
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Affiliation(s)
- Fernanda Almeida
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Av. do Café s/n°, Ribeirão Preto, SP, Brazil
| | | | - Dália Dos Prazeres Rodrigues
- Laboratório de Enterobactérias, FIOCRUZ/Fundação Instituto Oswaldo Cruz, Avenida Brasil, 4365, Pavilhão Rocha Lima, 3°andar, Manguinhos, 21040-360 Rio de Janeiro, RJ, Brazil
| | - Marc W Allard
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Av. do Café s/n°, Ribeirão Preto, SP, Brazil.
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82
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Buerger P, Wood-Charlson EM, Weynberg KD, Willis BL, van Oppen MJH. CRISPR-Cas Defense System and Potential Prophages in Cyanobacteria Associated with the Coral Black Band Disease. Front Microbiol 2016; 7:2077. [PMID: 28066391 PMCID: PMC5177637 DOI: 10.3389/fmicb.2016.02077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 12/08/2016] [Indexed: 12/01/2022] Open
Abstract
Understanding how pathogens maintain their virulence is critical to developing tools to mitigate disease in animal populations. We sequenced and assembled the first draft genome of Roseofilum reptotaenium AO1, the dominant cyanobacterium underlying pathogenicity of the virulent coral black band disease (BBD), and analyzed parts of the BBD-associated Geitlerinema sp. BBD_1991 genome in silico. Both cyanobacteria are equipped with an adaptive, heritable clustered regularly interspaced short palindromic repeats (CRISPR)-Cas defense system type I-D and have potential virulence genes located within several prophage regions. The defense system helps to prevent infection by viruses and mobile genetic elements via identification of short fingerprints of the intruding DNA, which are stored as templates in the bacterial genome, in so-called "CRISPRs." Analysis of CRISPR target sequences (protospacers) revealed an unusually high number of self-targeting spacers in R. reptotaenium AO1 and extraordinary long CRIPSR arrays of up to 260 spacers in Geitlerinema sp. BBD_1991. The self-targeting spacers are unlikely to be a form of autoimmunity; instead these target an incomplete lysogenic bacteriophage. Lysogenic virus induction experiments with mitomycin C and UV light did not reveal an actively replicating virus population in R. reptotaenium AO1 cultures, suggesting that phage functionality is compromised or excision could be blocked by the CRISPR-Cas system. Potential prophages were identified in three regions of R. reptotaenium AO1 and five regions of Geitlerinema sp. BBD_1991, containing putative BBD relevant virulence genes, such as an NAD-dependent epimerase/dehydratase (a homolog in terms of functionality to the third and fourth most expressed gene in BBD), lysozyme/metalloendopeptidases and other lipopolysaccharide modification genes. To date, viruses have not been considered to be a component of the BBD consortium or a contributor to the virulence of R. reptotaenium AO1 and Geitlerinema sp. BBD_1991. We suggest that the presence of virulence genes in potential prophage regions, and the CRISPR-Cas defense systems are evidence of an arms race between the respective cyanobacteria and their bacteriophage predators. The presence of such a defense system likely reduces the number of successful bacteriophage infections and mortality in the cyanobacteria, facilitating the progress of BBD.
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Affiliation(s)
- Patrick Buerger
- Australian Institute of Marine Science (AIMS), TownsvilleQLD, Australia
- Australian Institute of Marine Science, James Cook University (AIMS@JCU), TownsvilleQLD, Australia
- College of Science and Engineering, James Cook University (JCU), TownsvilleQLD, Australia
| | - Elisha M. Wood-Charlson
- Center for Microbial Oceanography: Research and Education, University of Hawaii, HonoluluHI, USA
| | - Karen D. Weynberg
- Australian Institute of Marine Science (AIMS), TownsvilleQLD, Australia
| | - Bette L. Willis
- College of Science and Engineering, James Cook University (JCU), TownsvilleQLD, Australia
- Australian Research Council (ARC) Centre of Excellence for Coral Reef Studies, College of Science and Engineering, TownsvilleQLD, Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science (AIMS), TownsvilleQLD, Australia
- School of BioSciences, University of Melbourne, MelbourneVIC, Australia
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Sváb D, Bálint B, Maróti G, Tóth I. Cytolethal distending toxin producing Escherichia coli O157:H43 strain T22 represents a novel evolutionary lineage within the O157 serogroup. INFECTION GENETICS AND EVOLUTION 2016; 46:110-117. [DOI: 10.1016/j.meegid.2016.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/14/2016] [Accepted: 11/03/2016] [Indexed: 12/15/2022]
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84
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Touchon M, Bernheim A, Rocha EP. Genetic and life-history traits associated with the distribution of prophages in bacteria. THE ISME JOURNAL 2016; 10:2744-2754. [PMID: 27015004 PMCID: PMC5113838 DOI: 10.1038/ismej.2016.47] [Citation(s) in RCA: 211] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 02/17/2016] [Accepted: 02/24/2016] [Indexed: 01/07/2023]
Abstract
Nearly half of the sequenced bacteria are lysogens and many of their prophages encode adaptive traits. Yet, the variables driving prophage distribution remain undetermined. We identified 2246 prophages in complete bacterial genomes to study the genetic and life-history traits associated with lysogeny. While optimal growth temperatures and average cell volumes were not associated with lysogeny, prophages were more frequent in pathogens and in bacteria with small minimal doubling times. Their frequency also increased with genome size, but only for genomes smaller than 6 Mb. The number of spacers in CRISPR-Cas systems and the frequency of type III systems were anticorrelated with prophage frequency, but lysogens were more likely to encode type I and type II systems. The minimal doubling time was the trait most correlated with lysogeny, followed by genome size and pathogenicity. We propose that bacteria with highly variable growth rates often encounter lower opportunity costs for lysogeny relative to lysis. These results contribute to explain the paucity of temperate phages in certain bacterial clades and of bacterial lysogens in certain environments. They suggest that genetic and life-history traits affect the contributions of temperate phages to bacterial genomes.
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Affiliation(s)
- Marie Touchon
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France
- CNRS, UMR3525, Paris, France
| | - Aude Bernheim
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France
- CNRS, UMR3525, Paris, France
| | - Eduardo Pc Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France
- CNRS, UMR3525, Paris, France
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85
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Westra ER, Dowling AJ, Broniewski JM, van Houte S. Evolution and Ecology of CRISPR. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032428] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Edze R. Westra
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Andrea J. Dowling
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Jenny M. Broniewski
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Stineke van Houte
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
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86
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van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev 2016; 80:745-63. [PMID: 27412881 PMCID: PMC4981670 DOI: 10.1128/mmbr.00011-16] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.
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Affiliation(s)
- Stineke van Houte
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Angus Buckling
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Edze R Westra
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
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87
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Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis. Sci Rep 2016; 6:30379. [PMID: 27461509 PMCID: PMC4961963 DOI: 10.1038/srep30379] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/04/2016] [Indexed: 02/01/2023] Open
Abstract
Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology.
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88
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Zhang J, Cao G, Xu X, Allard M, Li P, Brown E, Yang X, Pan H, Meng J. Evolution and Diversity of Listeria monocytogenes from Clinical and Food Samples in Shanghai, China. Front Microbiol 2016; 7:1138. [PMID: 27499751 PMCID: PMC4956650 DOI: 10.3389/fmicb.2016.01138] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/07/2016] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes is a significant foodborne pathogen causing severe systemic infections in humans with high mortality rates. The objectives of this work were to establish a phylogenetic framework of L. monocytogenes from China and to investigate sequence diversity among different serotypes. We selected 17 L. monocytogenes strains recovered from patients and foods in China representing serotypes 1/2a, 1/2b, and 1/2c. Draft genome sequences were determined using Illumina MiSeq technique and associated protocols. Open reading frames were assigned using prokaryotic genome annotation pipeline by NCBI. Twenty-four published genomes were included for comparative genomic and phylogenetic analysis. More than 154,000 single nucleotide polymorphisms (SNPs) were identified from multiple genome alignment and used to reconstruct maximum likelihood phylogenetic tree. The 41 genomes were differentiated into lineages I and II, which consisted of 4 and 11 subgroups, respectively. A clinical strain from China (SHL009) contained significant SNP differences compared to the rest genomes, whereas clinical strain SHL001 shared most recent common ancestor with strain SHL017 from food. Moreover, clinical strains SHL004 and SHL015 clustered together with two strains (08-5578 and 08-5923) recovered from an outbreak in Canada. Partial sequences of a plasmid found in the Canadian strain were also present in SHL004. We investigated the presence of various genes and gene clusters associated with virulence and subgroup-specific genes, including internalins, L. monocytogenes pathogenicity islands (LIPIs), L. monocytogenes genomic islands (LGIs), stress survival islet 1 (SSI-1), and clustered regularly interspaced short palindromic repeats (CRISPR)/cas system. A novel genomic island, denoted as LGI-2 was identified. Comparative sequence analysis revealed differences among the L. monocytogenes strains related to virulence, survival abilities, and attributes against foreign genetic elements. L. monocytogenes from China were genetically diverse. Strains from clinical specimens and food related closely suggesting foodborne transmission of human listeriosis.
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Affiliation(s)
- Jianmin Zhang
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Guojie Cao
- Department of Nutrition and Food Science and Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park College Park, MD, USA
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention Shanghai, China
| | - Marc Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration College Park, MD, USA
| | - Peng Li
- Institute of Disease Control and Prevention, Academy of Military Medical Science Beijing, China
| | - Eric Brown
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration College Park, MD, USA
| | - Xiaowei Yang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Haijian Pan
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Jianghong Meng
- Department of Nutrition and Food Science and Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park College Park, MD, USA
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89
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Anti-cas spacers in orphan CRISPR4 arrays prevent uptake of active CRISPR-Cas I-F systems. Nat Microbiol 2016; 1:16081. [PMID: 27573106 DOI: 10.1038/nmicrobiol.2016.81] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/28/2016] [Indexed: 11/09/2022]
Abstract
Archaea and bacteria harbour clustered regularly interspaced short palindromic repeats (CRISPR) loci. These arrays encode RNA molecules (crRNA), each containing a sequence of a single repeat-intervening spacer. The crRNAs guide CRISPR-associated (Cas) proteins to cleave nucleic acids complementary to the crRNA spacer, thus interfering with targeted foreign elements. Notably, pre-existing spacers may trigger the acquisition of new spacers from the target molecule by means of a primed adaptation mechanism. Here, we show that naturally occurring orphan CRISPR arrays that contain spacers matching sequences of the cognate (absent) cas genes are able to elicit both primed adaptation and direct interference against genetic elements carrying those genes. Our findings show the existence of an anti-cas mechanism that prevents the transfer of a fully equipped CRISPR-Cas system. Hence, they suggest that CRISPR immunity may be undesired by particular prokaryotes, potentially because they could limit possibilities for gaining favourable sequences by lateral transfer.
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90
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Delannoy S, Beutin L, Fach P. Improved traceability of Shiga-toxin-producing Escherichia coli using CRISPRs for detection and typing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:8163-8174. [PMID: 26449676 DOI: 10.1007/s11356-015-5446-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/16/2015] [Indexed: 06/05/2023]
Abstract
Among strains of Shiga-toxin-producing Escherichia coli (STEC), seven serogroups (O26, O45, O103, O111, O121, O145, and O157) are frequently associated with severe clinical illness in humans. The development of methods for their reliable detection from complex samples such as food has been challenging thus far, and is currently based on the PCR detection of the major virulence genes stx1, stx2, and eae, and O-serogroup-specific genes. However, this approach lacks resolution. Moreover, new STEC serotypes are continuously emerging worldwide. For example, in May 2011, strains belonging to the hitherto rarely detected STEC serotype O104:H4 were identified as causative agents of one of the world's largest outbreak of disease with a high incidence of hemorrhagic colitis and hemolytic uremic syndrome in the infected patients. Discriminant typing of pathogens is crucial for epidemiological surveillance and investigations of outbreaks, and especially for tracking and tracing in case of accidental and deliberate contamination of food and water samples. Clustered regularly interspaced short palindromic repeats (CRISPRs) are composed of short, highly conserved DNA repeats separated by unique sequences of similar length. This distinctive sequence signature of CRISPRs can be used for strain typing in several bacterial species including STEC. This review discusses how CRISPRs have recently been used for STEC identification and typing.
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Affiliation(s)
- Sabine Delannoy
- ANSES, Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France.
| | - Lothar Beutin
- Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Patrick Fach
- ANSES, Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
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91
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Vale PF, Lafforgue G, Gatchitch F, Gardan R, Moineau S, Gandon S. Costs of CRISPR-Cas-mediated resistance in Streptococcus thermophilus. Proc Biol Sci 2016. [PMID: 26224708 DOI: 10.1098/rspb.2015.1270] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas is a form of adaptive sequence-specific immunity in microbes. This system offers unique opportunities for the study of coevolution between bacteria and their viral pathogens, bacteriophages. A full understanding of the coevolutionary dynamics of CRISPR-Cas requires knowing the magnitude of the cost of resisting infection. Here, using the gram-positive bacterium Streptococcus thermophilus and its associated virulent phage 2972, a well-established model system harbouring at least two type II functional CRISPR-Cas systems, we obtained different fitness measures based on growth assays in isolation or in pairwise competition. We measured the fitness cost associated with different components of this adaptive immune system: the cost of Cas protein expression, the constitutive cost of increasing immune memory through additional spacers, and the conditional costs of immunity during phage exposure. We found that Cas protein expression is particularly costly, as Cas-deficient mutants achieved higher competitive abilities than the wild-type strain with functional Cas proteins. Increasing immune memory by acquiring up to four phage-derived spacers was not associated with fitness costs. In addition, the activation of the CRISPR-Cas system during phage exposure induces significant but small fitness costs. Together these results suggest that the costs of the CRISPR-Cas system arise mainly due to the maintenance of the defence system. We discuss the implications of these results for the evolution of CRISPR-Cas-mediated immunity.
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Affiliation(s)
- Pedro F Vale
- Centre for Immunity, Infection, and Evolution, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, UK
| | - Guillaume Lafforgue
- CEFE UMR 5175, CNRS-Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, 1919, route de Mende 34293 Montpellier Cedex 5, France
| | - Francois Gatchitch
- CEFE UMR 5175, CNRS-Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, 1919, route de Mende 34293 Montpellier Cedex 5, France
| | | | - Sylvain Moineau
- GREB and Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Québec, Canada G1V 0A6 Département de biochimie, de microbiologie et de bio-informatique and PROTEO, Faculté des sciences et de génie, Université Laval, Québec, Canada G1V 0A6
| | - Sylvain Gandon
- CEFE UMR 5175, CNRS-Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, 1919, route de Mende 34293 Montpellier Cedex 5, France
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92
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Lopatina A, Medvedeva S, Shmakov S, Logacheva MD, Krylenkov V, Severinov K. Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow. Front Microbiol 2016; 7:398. [PMID: 27064693 PMCID: PMC4814470 DOI: 10.3389/fmicb.2016.00398] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/14/2016] [Indexed: 11/23/2022] Open
Abstract
The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.
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Affiliation(s)
- Anna Lopatina
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia; Department of Molecular Genetics of Microorganisms, Institute of Gene Biology, Russian Academy of SciencesMoscow, Russia; Research Complex of "Nanobiotechnology", Saint-Petersburg State Polytechnical UniversitySaint-Petersburg, Russia
| | - Sofia Medvedeva
- Department of Molecular Genetics of Microorganisms, Institute of Gene Biology, Russian Academy of SciencesMoscow, Russia; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and TechnologySkolkovo, Russia
| | - Sergey Shmakov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology Skolkovo, Russia
| | - Maria D Logacheva
- Belozersky Institute of Physico-Chemical Biology, Moscow State University Moscow, Russia
| | - Vjacheslav Krylenkov
- Department of Botany, Saint-Petersburg State University Saint-Petersburg, Russia
| | - Konstantin Severinov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia; Research Complex of "Nanobiotechnology", Saint-Petersburg State Polytechnical UniversitySaint-Petersburg, Russia; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and TechnologySkolkovo, Russia
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93
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Wang P, Zhang B, Duan G, Wang Y, Hong L, Wang L, Guo X, Xi Y, Yang H. Bioinformatics analyses of Shigella CRISPR structure and spacer classification. World J Microbiol Biotechnol 2016; 32:38. [PMID: 26867599 DOI: 10.1007/s11274-015-2002-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 12/16/2015] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) are inheritable genetic elements of a variety of archaea and bacteria and indicative of the bacterial ecological adaptation, conferring acquired immunity against invading foreign nucleic acids. Shigella is an important pathogen for anthroponosis. This study aimed to analyze the features of Shigella CRISPR structure and classify the spacers through bioinformatics approach. Among 107 Shigella, 434 CRISPR structure loci were identified with two to seven loci in different strains. CRISPR-Q1, CRISPR-Q4 and CRISPR-Q5 were widely distributed in Shigella strains. Comparison of the first and last repeats of CRISPR1, CRISPR2 and CRISPR3 revealed several base variants and different stem-loop structures. A total of 259 cas genes were found among these 107 Shigella strains. The cas gene deletions were discovered in 88 strains. However, there is one strain that does not contain cas gene. Intact clusters of cas genes were found in 19 strains. From comprehensive analysis of sequence signature and BLAST and CRISPRTarget score, the 708 spacers were classified into three subtypes: Type I, Type II and Type III. Of them, Type I spacer referred to those linked with one gene segment, Type II spacer linked with two or more different gene segments, and Type III spacer undefined. This study examined the diversity of CRISPR/cas system in Shigella strains, demonstrated the main features of CRISPR structure and spacer classification, which provided critical information for elucidation of the mechanisms of spacer formation and exploration of the role the spacers play in the function of the CRISPR/cas system.
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Affiliation(s)
- Pengfei Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Bing Zhang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China. .,Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan, People's Republic of China.
| | - Yingfang Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.,Department of Public Health, College of Medical Sciences, Henan University of Science and Technology, Luoyang, 471023, Henan, People's Republic of China
| | - Lijuan Hong
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Linlin Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Xiangjiao Guo
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Yuanlin Xi
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
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94
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Salmonella and Campylobacter : Antimicrobial resistance and bacteriophage control in poultry. Food Microbiol 2016; 53:104-9. [DOI: 10.1016/j.fm.2015.09.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/12/2015] [Accepted: 09/10/2015] [Indexed: 01/21/2023]
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95
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Abstract
Bacteria occur ubiquitously in nature and are broadly relevant throughout the food supply chain, with diverse and variable tolerance levels depending on their origin, biological role, and impact on the quality and safety of the product as well as on the health of the consumer. With increasing knowledge of and accessibility to the microbial composition of our environments, food supply, and host-associated microbiota, our understanding of and appreciation for the ratio of beneficial to undesirable bacteria are rapidly evolving. Therefore, there is a need for tools and technologies that allow definite, accurate, and high-resolution identification and typing of various groups of bacteria that include beneficial microbes such as starter cultures and probiotics, innocuous commensals, and undesirable pathogens and spoilage organisms. During the transition from the current molecular biology-based PFGE (pulsed-field gel electrophoresis) gold standard to the increasingly accessible omics-level whole-genome sequencing (WGS) N-gen standard, high-resolution technologies such as CRISPR-based genotyping constitute practical and powerful alternatives that provide valuable insights into genome microevolution and evolutionary trajectories. Indeed, several studies have shown potential for CRISPR-based typing of industrial starter cultures, health-promoting probiotic strains, animal commensal species, and problematic pathogens. Emerging CRISPR-based typing methods open new avenues for high-resolution typing of a broad range of bacteria and constitute a practical means for rapid tracking of a diversity of food-associated microbes.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695; .,Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Edward G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802;
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96
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Vorontsova D, Datsenko KA, Medvedeva S, Bondy-Denomy J, Savitskaya EE, Pougach K, Logacheva M, Wiedenheft B, Davidson AR, Severinov K, Semenova E. Foreign DNA acquisition by the I-F CRISPR-Cas system requires all components of the interference machinery. Nucleic Acids Res 2015; 43:10848-60. [PMID: 26586803 PMCID: PMC4678832 DOI: 10.1093/nar/gkv1261] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022] Open
Abstract
CRISPR immunity depends on acquisition of fragments of foreign DNA into CRISPR arrays. For type I-E CRISPR–Cas systems two modes of spacer acquisition, naïve and primed adaptation, were described. Naïve adaptation requires just two most conserved Cas1 and Cas2 proteins; it leads to spacer acquisition from both foreign and bacterial DNA and results in multiple spacers incapable of immune response. Primed adaptation requires all Cas proteins and a CRISPR RNA recognizing a partially matching target. It leads to selective acquisition of spacers from DNA molecules recognized by priming CRISPR RNA, with most spacers capable of protecting the host. Here, we studied spacer acquisition by a type I-F CRISPR–Cas system. We observe both naïve and primed adaptation. Both processes require not just Cas1 and Cas2, but also intact Csy complex and CRISPR RNA. Primed adaptation shows a gradient of acquisition efficiency as a function of distance from the priming site and a strand bias that is consistent with existence of single-stranded adaption intermediates. The results provide new insights into the mechanism of spacer acquisition and illustrate surprising mechanistic diversity of related CRISPR–Cas systems.
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Affiliation(s)
- Daria Vorontsova
- Skolkovo Institute of Science and Technology, Skolkovo, Russia Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Kirill A Datsenko
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Sofia Medvedeva
- Skolkovo Institute of Science and Technology, Skolkovo, Russia Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Joseph Bondy-Denomy
- Department of Molecular Genetics and Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ekaterina E Savitskaya
- Skolkovo Institute of Science and Technology, Skolkovo, Russia Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ksenia Pougach
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Alan R Davidson
- Department of Molecular Genetics and Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Skolkovo, Russia Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Semenova
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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97
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Yang C, Li P, Su W, Li H, Liu H, Yang G, Xie J, Yi S, Wang J, Cui X, Wu Z, Wang L, Hao R, Jia L, Qiu S, Song H. Polymorphism of CRISPR shows separated natural groupings of Shigella subtypes and evidence of horizontal transfer of CRISPR. RNA Biol 2015; 12:1109-20. [PMID: 26327282 PMCID: PMC4829275 DOI: 10.1080/15476286.2015.1085150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/30/2015] [Accepted: 08/15/2015] [Indexed: 10/23/2022] Open
Abstract
Clustered, regularly interspaced, short palindromic repeats (CRISPR) act as an adaptive RNA-mediated immune mechanism in bacteria. They can also be used for identification and evolutionary studies based on polymorphisms within the CRISPR locus. We amplified and analyzed 6 CRISPR loci from 237 Shigella strains belonging to the 4 species groups, as well as 13 Escherichia coli strains. The CRISPR-associated (cas) gene sequence arrays of these strains were screened and compared. The CRISPR sequences from Shigella were conserved among subtypes, suggesting that CRISPR may represent a new identification tool for the detection and discrimination of Shigella species. Secondary structure analysis showed a different stem-loop structure at the terminal repeat, suggesting a distinct recognition mechanism in the formation of crRNA. In addition, the presence of "self-target" spacers and polymorphisms within CRISPR in Shigella indicated a selective pressure for inhibition of this system, which has the potential to damage "self DNA." Homology analysis of spacers showed that CRISPR might be involved in the regulation of virulence transmission. Phylogenetic analysis based on CRISPR sequences from Shigella and E. coli indicated that although phenotypic properties maintain convergent evolution, the 4 Shigella species do not represent natural groupings. Surprisingly, comparative analysis of Shigella repeats with other species provided new evidence for CRISPR horizontal transfer. Our results suggested that CRISPR analysis is applicable for the detection of Shigella species and for investigation of evolutionary relationships.
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Affiliation(s)
- Chaojie Yang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Peng Li
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Wenli Su
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Hao Li
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Hongbo Liu
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Guang Yang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Jing Xie
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Shengjie Yi
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Jian Wang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Xianyan Cui
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Zhihao Wu
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Ligui Wang
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Rongzhang Hao
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Leili Jia
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Shaofu Qiu
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
| | - Hongbin Song
- Institute of Disease Control and Prevention; Academy of Military Medical Sciences; Beijing, China
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98
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Liu J, Yan R, Zhong Q, Ngo S, Bangayan NJ, Nguyen L, Lui T, Liu M, Erfe MC, Craft N, Tomida S, Li H. The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin. THE ISME JOURNAL 2015; 9:2078-93. [PMID: 25848871 PMCID: PMC4542041 DOI: 10.1038/ismej.2015.47] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/12/2015] [Accepted: 02/26/2015] [Indexed: 02/08/2023]
Abstract
The viral population, including bacteriophages, is an important component of the human microbiota, yet is poorly understood. We aim to determine whether bacteriophages modulate the composition of the bacterial populations, thus potentially playing a role in health or disease. We investigated the diversity and host interactions of the bacteriophages of Propionibacterium acnes, a major human skin commensal implicated in acne pathogenesis. By sequencing 48 P. acnes phages isolated from acne patients and healthy individuals and by analyzing the P. acnes phage populations in healthy skin metagenomes, we revealed that P. acnes phage populations in the skin microbial community are often dominated by one strain. We also found phage strains shared among both related and unrelated individuals, suggesting that a pool of common phages exists in the human population and that transmission of phages may occur between individuals. To better understand the bacterium-phage interactions in the skin microbiota, we determined the outcomes of 74 genetically defined Propionibacterium strains challenged by 15 sequenced phages. Depending on the Propionibacterium lineage, phage infection can result in lysis, pseudolysogeny, or resistance. In type II P. acnes strains, we found that encoding matching clustered regularly interspaced short palindromic repeat spacers is insufficient to confer phage resistance. Overall, our findings suggest that the prey-predator relationship between bacteria and phages may have a role in modulating the composition of the microbiota. Our study also suggests that the microbiome structure of an individual may be an important factor in the design of phage-based therapy.
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Affiliation(s)
- Jared Liu
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Riceley Yan
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Qiao Zhong
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Laboratory Medicine, Suzhou Municipal Hospital, Suzhou Hospital Affiliated to Nanjing Medical University, Suzhou, China
| | - Sam Ngo
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Nathanael J Bangayan
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Lin Nguyen
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Timothy Lui
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Minghsun Liu
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Marie C Erfe
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - Noah Craft
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Los Angeles, CA, USA
| | - Shuta Tomida
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Huiying Li
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
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99
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Yang S, Liu J, Shao F, Wang P, Duan G, Yang H. Analysis of the features of 45 identified CRISPR loci in 32 Staphylococcus aureus. Biochem Biophys Res Commun 2015; 464:894-900. [PMID: 26188514 DOI: 10.1016/j.bbrc.2015.07.062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/13/2015] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus (S. aureus) is a common pathogen that can cause serious infections, even death. Because of the horizontal gene transfer (HGT) of antibiotic resistance genes, the drug resistant condition is becoming increasingly prevalent. Recently, an adaptive immunity system, named clustered regularly interspaced short palindromic repeats (CRISPR), was discovered and demonstrated to confer a defense against foreign invading elements that may carry the antibiotic resistance genes. In this study, we reveal the features of 45 identified CRISPR loci and the CRISPR associated gene (Cas) in 32 S. aureus strains from CRISPR database. Five spacers of S. aureus 08BA02176 and MSHR1132 were homologous with foreign genetic sequences from phages or plasmids, even containing a spacer sequence identical to part of some phages' genomes containing lukPV gene that encodes the PVL toxin. Many S. aureus strains with the same CRISPR type shared the same MLST type. CRISPR loci that had 3 or more similar protein loci mostly belonged to the same CRISPR type. We came to the conclusion that the CRISPR/Cas of strains 08BA02176 and MSHR1132 were inherited from a common ancestor or recombined from Staphylococcus lugdunensis. CRISPR loci can be mobilized and can transfer among different but closely related species, and the same types of MLST strains exhibit a higher affinity to the same types of CRISPR loci. Bacteriophages may be the predominant challenge facing S. aureus. The CRISPR/Cas structure may limit the transmission of bacterial virulence among S. aureus.
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Affiliation(s)
- Siyu Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jing Liu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Fuye Shao
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Pengfei Wang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
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100
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Diversity of CRISPR loci and virulence genes in pathogenic Escherichia coli isolates from various sources. Int J Food Microbiol 2015; 204:41-6. [DOI: 10.1016/j.ijfoodmicro.2015.03.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 03/15/2015] [Accepted: 03/22/2015] [Indexed: 12/16/2022]
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