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Cui Y, Qu X. CRISPR-Cas systems of lactic acid bacteria and applications in food science. Biotechnol Adv 2024; 71:108323. [PMID: 38346597 DOI: 10.1016/j.biotechadv.2024.108323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/29/2023] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
CRISPR-Cas (Clustered regularly interspaced short palindromic repeats-CRISPR associated proteins) systems are widely distributed in lactic acid bacteria (LAB), contributing to their RNA-mediated adaptive defense immunity. The CRISPR-Cas-based genetic tools have exhibited powerful capability. It has been highly utilized in different organisms, accelerating the development of life science. The review summarized the components, adaptive immunity mechanisms, and classification of CRISPR-Cas systems; analyzed the distribution and characteristics of CRISPR-Cas system in LAB. The review focuses on the development of CRISPR-Cas-based genetic tools in LAB for providing latest development and future trend. The diverse and broad applications of CRISPR-Cas systems in food/probiotic industry are introduced. LAB harbor a plenty of CRISPR-Cas systems, which contribute to generate safer and more robust strains with increased resistance against bacteriophage and prevent the dissemination of plasmids carrying antibiotic-resistance markers. Furthermore, the CRISPR-Cas system from LAB could be used to exploit novel, flexible, programmable genome editing tools of native host and other organisms, resolving the limitation of genetic operation of some LAB species, increasing the important biological functions of probiotics, improving the adaptation of probiotics in complex environments, and inhibiting the growth of foodborne pathogens. The development of the genetic tools based on CRISPR-Cas system in LAB, especially the endogenous CRISPR-Cas system, will open new avenues for precise regulation, rational design, and flexible application of LAB.
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Affiliation(s)
- Yanhua Cui
- Department of Food Nutrition and Health, School of Medicine and Health, Harbin Institute of Technology, Harbin 150001, China.
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
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2
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Kushwaha SK, Kumar AA, Gupta H, Marathe SA. The Phylogenetic Study of the CRISPR-Cas System in Enterobacteriaceae. Curr Microbiol 2023; 80:196. [PMID: 37118221 DOI: 10.1007/s00284-023-03298-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/07/2023] [Indexed: 04/30/2023]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) system is a bacterial and archaeal adaptive immune system undergoing rapid multifaceted evolution. This evolution plausibly occurs due to the genetic exchanges of complete loci or individual entities. Here, we systematically investigate the evolutionary framework of the CRISPR-Cas system in six Enterobacteriaceae species and its evolutionary association with housekeeping genes as determined by the gyrB phenogram. The strains show high variability in the cas3 gene and the CRISPR1 locus among the closely related Enterobacteriaceae species, hinting at a series of genetic exchanges. The CRISPR leader is conserved, especially toward the distal end, and could be a core region of the leader. The spacers are conserved within the strains of most species, while some strains show unique sets of spacers. However, inter-species spacer conservation was rarely observed. For a considerable proportion of these spacers, protospacer sources were not detected. These results advance our understanding of the dynamics of the CRISPR-Cas system; however, the biological functions are yet to be characterised.
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Affiliation(s)
- Simran Krishnakant Kushwaha
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Aryahi A Kumar
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Hardik Gupta
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Faculty Division-III, Birla Institute of Technology & Science, 3277-B, Pilani Campus, Pilani, Rajasthan, 333031, India.
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3
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Das A, Doss K, Mandal J. CRISPR-cas heterogeneity and plasmid incompatibility types in relation to virulence determinants of Shigella. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Virulence factors (VFs) are the most potent weapon in the molecular armoury of
Shigella
. In bacteria, the mobile genetic elements (MGEs) are contributors to the evolution of different types of clustered regularly interspaced short palindromic repeats-CRISPR associated genes (CRISPR-cas) variants and plasmid incompatibility types. The present study explored the virulence potential of
Shigella
in relation to the CRISPR-cas pattern and incompatibility types among the isolates.
Hypothesis/Gap Statement. The profile of the CRISPR-cas systems among clinical isolates of
Shigella
in India has not been reported earlier. Limited knowledge is available on the pattern of plasmid incompatibility groups among clinical isolates
Shigella
. The bias is always towards studying the genetic elements associated with AMR, but the present study highlights CRISPR-cas and incompatibility types among
Shigella
in association with virulence.
Aim. We aimed to investigate the distribution of virulence factors, CRISPR-cas pattern followed by plasmid incompatibility types among
Shigella
isolates.
Methodology. Between 2012–2017, a total of 187 isolates of
Shigella
were included in the study. The virulence genes' distribution was carried out. CRISPR-cas profiling followed by analysis of the repeats and spacers was carried out. PCR-based replicon typing was used to determine the incompatibility types. The interplay was statistically determined using STATA.
Results. The distribution of virulence genes showed varied pattern with ipaH present in all the isolates followed by ompA (93.6 %), virF (66.8 %), ial and sen (60.4 %), set1A (39.6 %) and set1B (39 %). CRISPR 1, CRISPR 3 and Cas6-Cas5 region were dominantly conserved. Twenty-two types of spacers were identified. The CRISPR3 repeat appeared to have a highly conserved sequence. CRISPR2 being the least common CRISPR type showed a strong association with an array of virulence genes (ial-set1A-set1B-virF) while CRISPR1 being the most dominant showed the least association with virulence genes (sen-virF). The dominant plasmids were found to be belonging to the inc FII group. The incompatibility groups FII, IncIγ, U, FIIS, FIIK, K, A/C, I1alpha was found to be associated with a greater number of virulence genes.
Conclusion. The isolates showed increasing diversity in their gene content that contributes to increasing heterogeneity among the isolates, which is a known virulence strategy among pathogens.
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Affiliation(s)
- Ankita Das
- Department of Microbiology, Jawaharlal Nehru Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India
| | - Kamali Doss
- Jawaharlal Nehru Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India
| | - Jharna Mandal
- Department of Microbiology, Jawaharlal Nehru Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India
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4
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Wang L, Wang L, Liu Y, Wang Z, Chen Q, Liu Z, Hu J. Characterization of type I-F CRISPR-Cas system in Laribacter hongkongensis isolates from animals, the environment and diarrhea patients. Int J Food Microbiol 2021; 346:109153. [PMID: 33744818 DOI: 10.1016/j.ijfoodmicro.2021.109153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
Laribacter hongkongensis is a foodborne organism that is associated with gastroenteritis and diarrhea in humans. Here we describe the structural characteristics and potential function of CRISPR systems to obtain insight into the genotypic diversity of L. hongkongensis. Specifically, we analyzed the genomic content of six L. hongkongensis genomes and identified two CRISPR loci (CRISPR1 and CRISPR2) belonging to the I-F subtype of CRISPR systems. CRISPR1 was flanked on one side by cas genes and a 170 bp-long putative leader sequence, while CRISPR2 arrays located further and processed by the same cas genes. Then a combination of PCR and sequencing was used to determine the prevalence and distribution of the two CRISPR arrays in 112 L. hongkongensis strains isolated from patients, animals, and water reservoirs. In total, the CRISPR1-Cas system of complete subtype I-F was detected in 91.5% (108/118) of the isolates, whereas CRISPR2 locus existed in 72.0% (85/118). Ten strains only possessed part of the cas genes of subtype I-F and four of them with CRISPR2 array. The two loci contained highly conserved and identical direct repeat sequences which were stable in their RNA secondary structure. Additionally, 2564 total spacers including 980 unique spacers arranged in 59 alleles were identified. Homology analysis showed only 1.8% (18/980) of the spacers matched with plasmid or phage. CRISPR polymorphism present in human isolates and frog isolates was more closely related and more extensive than that of fish isolates based on spacer polymorphism. The elucidation of the structural characteristics of the CRISPR-Cas system may be helpful for further studying the specific mechanism of adaptive immunity and other biological functions mediated by CRISPR in L. hongkongensis. The conservation of CRISPR loci and hypervariable repeat-spacer arrays imply the potential for molecular typing of L. hongkongensis.
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Affiliation(s)
- Ling Wang
- Department of Nosocomial Infection Administration, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Li Wang
- Office, Luohu district Center for Disease Control and Prevention, Shenzhen 518000, China
| | - Youzhao Liu
- Department of AIDS Prevention and Control, Guangdong Center for Disease Control and Prevention, Guangzhou 510300, China
| | - Zhiyun Wang
- Department of Immunization Programmes, Baiyun district Center for Disease Control and Prevention, Guangzhou 510540, China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Zhihua Liu
- Department of Infectious Disease, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
| | - Jing Hu
- Department of Nosocomial Infection Administration, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
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Chon C, Chon G, Matsui Y, Zeng H, Lai ZC, Liu A. Efficient multiplexed genome engineering with a polycistronic tRNA and CRISPR guide-RNA reveals an important role of detonator in reproduction of Drosophila melanogaster. PLoS One 2021; 16:e0245454. [PMID: 33444382 PMCID: PMC7808601 DOI: 10.1371/journal.pone.0245454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 01/03/2021] [Indexed: 11/18/2022] Open
Abstract
Genome association studies in human and genetic studies in mouse implicated members of the transmembrane protein 132 (TMEM132) family in multiple conditions including panic disorder, hearing loss, limb and kidney malformation. However, the presence of five TMEM132 paralogs in mammalian genomes makes it extremely challenging to reveal the full requirement for these proteins in vivo. In contrast, there is only one TMEM132 homolog, detonator (dtn), in the genome of fruit fly Drosophila melanogaster, enabling straightforward research into its in vivo function. In the current study, we generate multiple loss-of-function dtn mutant fly strains through a polycistronic tRNA-gRNA approach, and show that most embryos lacking both maternal and paternal dtn fail to hatch into larvae, indicating an essential role of dtn in Drosophila reproduction.
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Affiliation(s)
- Cristin Chon
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
| | - Grace Chon
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
| | - Yurika Matsui
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
| | - Huiqing Zeng
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
| | - Zhi-Chun Lai
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
| | - Aimin Liu
- Department of Biology, Eberly College of Science, Centers for Cellular Dynamics and Cellular and Molecular Investigation of Neurological Diseases, Huck Institutes of Life Sciences, The Pennsylvania State University, State College, PA, United States of America
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6
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Tanmoy AM, Saha C, Sajib MSI, Saha S, Komurian-Pradel F, van Belkum A, Louwen R, Saha SK, Endtz HP. CRISPR-Cas Diversity in Clinical Salmonella enterica Serovar Typhi Isolates from South Asian Countries. Genes (Basel) 2020; 11:E1365. [PMID: 33218076 PMCID: PMC7698835 DOI: 10.3390/genes11111365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), is a global health concern and its treatment is problematic due to the rise in antimicrobial resistance (AMR). Rapid detection of patients infected with AMR positive S. Typhi is, therefore, crucial to prevent further spreading. Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated genes (CRISPR-Cas), is an adaptive immune system that initially was used for typing purposes. Later, it was discovered to play a role in defense against phages and plasmids, including ones that carry AMR genes, and, at present, it is being explored for its usage in diagnostics. Despite the availability of whole-genome sequences (WGS), very few studied the CRISPR-Cas system of S. Typhi, let alone in typing purposes or relation to AMR. In the present study, we analyzed the CRISPR-Cas system of S. Typhi using WGS data of 1059 isolates obtained from Bangladesh, India, Nepal, and Pakistan in combination with demographic data and AMR status. Our results reveal that the S. Typhi CRISPR loci can be classified into two groups: A (evidence level >2) and B (evidence level ≤2), in which we identified a total of 47 unique spacers and 15 unique direct repeats. Further analysis of the identified spacers and repeats demonstrated specific patterns that harbored significant associations with genotype, demographic characteristics, and AMR status, thus raising the possibility of their usage as biomarkers. Potential spacer targets were identified and, interestingly, the phage-targeting spacers belonged to the group-A and plasmid-targeting spacers to the group-B CRISPR loci. Further analyses of the spacer targets led to the identification of an S. Typhi protospacer adjacent motif (PAM) sequence, TTTCA/T. New cas-genes known as DinG, DEDDh, and WYL were also discovered in the S. Typhi genome. However, a specific variant of the WYL gene was only identified in the extensively drug-resistant (XDR) lineage from Pakistan and ciprofloxacin-resistant lineage from Bangladesh. From this work, we conclude that there are strong correlations between variations identified in the S. Typhi CRISPR-Cas system and endemic AMR positive S. Typhi isolates.
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Affiliation(s)
- Arif Mohammad Tanmoy
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands; (A.M.T.); (C.S.); (H.P.E.)
- Child Health Research Foundation, 23/2 SEL Huq Skypark, Block-B, Khilji Rd, Dhaka 1207, Bangladesh; (M.S.I.S.); (S.S.); (S.K.S.)
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, 69365 Lyon, France;
| | - Chinmoy Saha
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands; (A.M.T.); (C.S.); (H.P.E.)
| | - Mohammad Saiful Islam Sajib
- Child Health Research Foundation, 23/2 SEL Huq Skypark, Block-B, Khilji Rd, Dhaka 1207, Bangladesh; (M.S.I.S.); (S.S.); (S.K.S.)
| | - Senjuti Saha
- Child Health Research Foundation, 23/2 SEL Huq Skypark, Block-B, Khilji Rd, Dhaka 1207, Bangladesh; (M.S.I.S.); (S.S.); (S.K.S.)
| | - Florence Komurian-Pradel
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, 69365 Lyon, France;
| | - Alex van Belkum
- Data Analytics Unit, bioMérieux, 3, Route de Port Michaud, 38390 La Balme Les Grottes, France;
| | - Rogier Louwen
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands; (A.M.T.); (C.S.); (H.P.E.)
| | - Samir Kumar Saha
- Child Health Research Foundation, 23/2 SEL Huq Skypark, Block-B, Khilji Rd, Dhaka 1207, Bangladesh; (M.S.I.S.); (S.S.); (S.K.S.)
- Bangladesh Institute of Child Health, Dhaka Shishu Hospital, Dhaka 1207, Bangladesh
| | - Hubert P. Endtz
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands; (A.M.T.); (C.S.); (H.P.E.)
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, 69365 Lyon, France;
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7
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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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8
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Chen Y, Hammer EE, Richards VP. Phylogenetic signature of lateral exchange of genes for antibiotic production and resistance among bacteria highlights a pattern of global transmission of pathogens between humans and livestock. Mol Phylogenet Evol 2018; 125:255-264. [DOI: 10.1016/j.ympev.2018.03.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 01/08/2023]
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9
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Seecharran T, Kalin-Manttari L, Koskela K, Nikkari S, Dickins B, Corander J, Skurnik M, McNally A. Phylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis. Microb Genom 2017; 3:e000133. [PMID: 29177091 PMCID: PMC5695210 DOI: 10.1099/mgen.0.000133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/21/2017] [Indexed: 01/02/2023] Open
Abstract
Yersinia pseudotuberculosis is a Gram-negative intestinal pathogen of humans and has been responsible for several nationwide gastrointestinal outbreaks. Large-scale population genomic studies have been performed on the other human pathogenic species of the genus Yersinia, Yersinia pestis and Yersinia enterocolitica allowing a high-resolution understanding of the ecology, evolution and dissemination of these pathogens. However, to date no purpose-designed large-scale global population genomic analysis of Y. pseudotuberculosis has been performed. Here we present analyses of the genomes of 134 strains of Y. pseudotuberculosis isolated from around the world, from multiple ecosystems since the 1960s. Our data display a phylogeographic split within the population, with an Asian ancestry and subsequent dispersal of successful clonal lineages into Europe and the rest of the world. These lineages can be differentiated by CRISPR cluster arrays, and we show that the lineages are limited with respect to inter-lineage genetic exchange. This restriction of genetic exchange maintains the discrete lineage structure in the population despite co-existence of lineages for thousands of years in multiple countries. Our data highlights how CRISPR can be informative of the evolutionary trajectory of bacterial lineages, and merits further study across bacteria.
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Affiliation(s)
- Tristan Seecharran
- 1Nottingham Trent University, 50 Shakespeare St, Nottingham NG1 4FQ, UK
| | | | - Katja Koskela
- 3Centre for Military Medicine, Tykkikentäntie 1, Riihimäki, Finland
| | - Simo Nikkari
- 3Centre for Military Medicine, Tykkikentäntie 1, Riihimäki, Finland
| | - Benjamin Dickins
- 1Nottingham Trent University, 50 Shakespeare St, Nottingham NG1 4FQ, UK
| | | | - Mikael Skurnik
- 2University of Helsinki, Yliopistonkatu 4, 00100 Helsinki, Finland
| | - Alan McNally
- 5Institute of Microbiology and Infection, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
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10
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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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11
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Ogrodzki P, Forsythe SJ. CRISPR-cas loci profiling of Cronobacter sakazakii pathovars. Future Microbiol 2016; 11:1507-1519. [PMID: 27831749 DOI: 10.2217/fmb-2016-0070] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
AIM Cronobacter sakazakii sequence types 1, 4, 8 and 12 are associated with outbreaks of neonatal meningitis and necrotizing enterocolitis infections. However clonality results in strains which are indistinguishable using conventional methods. This study investigated the use of clustered regularly interspaced short palindromic repeats (CRISPR)-cas loci profiling for epidemiological investigations. MATERIALS & METHODS Seventy whole genomes of C. sakazakii strains from four clonal complexes which were widely distributed temporally, geographically and origin of source were profiled. RESULTS & CONCLUSION All strains encoded the same type I-E subtype CRISPR-cas system with a total of 12 different CRISPR spacer arrays. This study demonstrated the greater discriminatory power of CRISPR spacer array profiling compared with multilocus sequence typing, which will be of use in source attribution during Cronobacter outbreak investigations.
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Affiliation(s)
- Pauline Ogrodzki
- Pathogen Research Group, School of Science & Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Stephen James Forsythe
- Pathogen Research Group, School of Science & Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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12
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Dover JA, Burmeister AR, Molineux IJ, Parent KN. Evolved Populations of Shigella flexneri Phage Sf6 Acquire Large Deletions, Altered Genomic Architecture, and Faster Life Cycles. Genome Biol Evol 2016; 8:2827-40. [PMID: 27497318 PMCID: PMC5630979 DOI: 10.1093/gbe/evw177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Genomic architecture is the framework within which genes and regulatory elements evolve and where specific constructs may constrain or potentiate particular adaptations. One such construct is evident in phages that use a headful packaging strategy that results in progeny phage heads packaged with DNA until full rather than encapsidating a simple unit-length genome. Here, we investigate the evolution of the headful packaging phage Sf6 in response to barriers that impede efficient phage adsorption to the host cell. Ten replicate populations evolved faster Sf6 life cycles by parallel mutations found in a phage lysis gene and/or by large, 1.2- to 4.0-kb deletions that remove a mobile genetic IS911 element present in the ancestral phage genome. The fastest life cycles were found in phages that acquired both mutations. No mutations were found in genes encoding phage structural proteins, which were a priori expected from the experimental design that imposed a challenge for phage adsorption by using a Shigella flexneri host lacking receptors preferred by Sf6. We used DNA sequencing, molecular approaches, and physiological experiments on 82 clonal isolates taken from all 10 populations to reveal the genetic basis of the faster Sf6 life cycle. The majority of our isolates acquired deletions in the phage genome. Our results suggest that deletions are adaptive and can influence the duration of the phage life cycle while acting in conjunction with other lysis time-determining point mutations.
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Affiliation(s)
- John A Dover
- Department of Biochemistry and Molecular Biology, Michigan State University
| | - Alita R Burmeister
- Department of Microbiology and Molecular Genetics, Michigan State University
| | - Ian J Molineux
- Department of Molecular Biosciences, University of Texas at Austin
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University
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