51
|
Using CAPTURE to detect spacer acquisition in native CRISPR arrays. Nat Protoc 2019; 14:976-990. [PMID: 30742049 DOI: 10.1038/s41596-018-0123-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 12/20/2018] [Indexed: 11/09/2022]
Abstract
CRISPR-Cas systems are able to acquire immunological memories (spacers) from bacteriophages and plasmids in order to survive infection; however, this often occurs at low frequency within a population, which can make it difficult to detect. Here we describe CAPTURE (CRISPR adaptation PCR technique using reamplification and electrophoresis), a versatile and adaptable protocol to detect spacer-acquisition events by electrophoresis imaging with high-enough sensitivity to identify spacer acquisition in 1 in 105 cells. Our method harnesses two simple PCR steps, separated by automated electrophoresis and extraction of size-selected DNA amplicons, thus allowing the removal of unexpanded arrays from the sample pool and enabling 1,000-times more sensitive detection of new spacers than alternative PCR protocols. CAPTURE is a straightforward method that requires only 1 d to enable the detection of spacer acquisition in all native CRISPR systems and facilitate studies aimed both at unraveling the mechanism of spacer integration and more sensitive tracing of integration events in natural ecosystems.
Collapse
|
52
|
Taylor AJ, Stasiewicz MJ. CRISPR-Based Subtyping Using Whole Genome Sequence Data Does Not Improve Differentiation of Persistent and Sporadic Listeria monocytogenes Strains. J Food Sci 2019; 84:319-326. [PMID: 30620778 DOI: 10.1111/1750-3841.14426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/12/2022]
Abstract
The foodborne pathogen Listeria monocytogenes can persist in food-associated environments for long periods. To identify persistent strains, the subtyping method pulsed-field gel electrophoresis (PFGE) is being replaced by whole genome sequence (WGS)-based subtyping. It was hypothesized that analyzing specific mobile genetic elements, CRISPR (Clustered Regularly Interspaced Short Palindromic Short Repeat) spacer arrays, extracted from WGS data, could differentiate persistent and sporadic isolates within WGS-based clades. To test this hypothesis, 175 L. monocytogenes isolates, previously recovered from retail delis, were analyzed for CRISPR spacers using CRISPRFinder. These isolates represent 23 phylogenetic clades defined by WGS-based single nucleotide polymorphisms and closely related sporadic isolates. In 174/175 (99.4%) of isolates, at least one array with one spacer was identified. Numbers of spacers in a single array ranged from 1 to 28 spacers. Isolates were grouped into 13 spacer patterns (SPs) based on observed variability in the presence or absence of whole spacers. SP variation was consistent with WGS-based clades forming patterns of (i) one SP to one clade, (ii) one SP across many clades, (iii) many SPs within one clade, and (iv) many SPs across many clades. Unfortunately, SPs did not appear to differentiate persistent from sporadic isolates within any WGS-based clade. Overall, these data show that (i) CRISPR arrays are common in WGS data for these food-associated L. monocytogenes and (ii) CRISPR subtyping cannot improve the identification of persistent or sporadic isolates from retail delis. PRACTICAL APPLICATION: CRISPR spacer arrays are present in L. monocytogenes isolates and CRISPR spacer patterns are consistent with previous subtyping methods. These mobile genetic artifacts cannot improve the differentiation between persistent and sporadic L. monocytogenes isolates, used in this study. While CRISPR-based subtyping has been useful for other pathogens, it is not useful in understanding persistence in L. monocytogenes. Thus, the food safety community might be able to use CRISPRs in other areas, but CRISPRs do not seem likely to improve the differentiation of persistence in L. monocytogenes isolates from retail delis.
Collapse
Affiliation(s)
- Alexander J Taylor
- Dept. of Food Science and Human Nutrition, Coll. of Agricultural, Consumer, and Environmental Sciences, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Matthew J Stasiewicz
- Dept. of Food Science and Human Nutrition, Coll. of Agricultural, Consumer, and Environmental Sciences, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| |
Collapse
|
53
|
Triantaphyllopoulos KA, Baltoumas FA, Hamodrakas SJ. Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1). J Comput Aided Mol Des 2018; 33:265-285. [PMID: 30543052 DOI: 10.1007/s10822-018-0179-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/03/2018] [Indexed: 12/22/2022]
Abstract
Natural Resistance-Associated Macrophage Proteins are a family of transmembrane divalent metal ion transporters, with important implications in life of both bacteria and mammals. Among them, the Solute Carrier family 11 member A1 (SLC11A1) has been implicated with susceptibility to infection by Mycobacterium avium subspecies paratuberculosis (MAP), potentially causing Crohn's disease in humans and paratuberculosis (PTB) in ruminants. Our previous research had focused on sequencing the mRNA of the caprine slc11a1 gene and pinpointed polymorphisms that contribute to caprine SLC11A1's susceptibility to infection by MAP in PTB. Despite its importance, little is known on the structural/dynamic features of mammalian SLC11A1 that may influence its function under normal or pathological conditions at the protein level. In this work we studied the structural architecture of SLC11A1 in Capra hircus and Bos taurus through molecular modeling, molecular dynamics simulations in different, functionally relevant configurations, free energy calculations of protein-metal interactions and sequence conservation analysis. The results of this study propose a three dimensional structure for SLC11A1 with conserved sequence and structural features and provide hints for a potential mechanism through which divalent metal ion transport is conducted. Given the importance of SLC11A1 in susceptibility to PTB, this study provides a framework for further studies on the structure and dynamics of SLC11A1 in other organisms, to gain 3D structural insight into the macromolecular arrangements of SLC11A1 but also suggesting a potential mechanism which divalent metal ion transport is conducted.
Collapse
Affiliation(s)
- Kostas A Triantaphyllopoulos
- Department of Animal Breeding and Husbandry, Faculty of Animal Science and Aquaculture, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, 75 Iera Odos St., 11855, Athens, Greece.
| | - Fotis A Baltoumas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Stavros J Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| |
Collapse
|
54
|
Abstract
CRISPR-Cas est un système immunitaire adaptatif utilisé par de nombreux microbes pour se défendre contre l’invasion d’acides nucléiques tels que les génomes viraux et autres éléments génétiques mobiles. Le système microbien utilise son locus CRISPR pour stocker de l’information génétique afin de produire des ARN guides. Ces derniers, de concert avec des endonucléases (Cas), empêchent des invasions futures. Des parties de ce système microbien ont été exploitées pour développer un puissant outil d’édition des génomes dans une panoplie d’organismes. La capacité de CRISPR-Cas9 à couper efficacement et à des endroits très précis de l’ADN pourrait peut-être permettre un jour de guérir certaines maladies génétiques humaines. La malléabilité de cet outil d’édition rend possible une variété d’applications allant de la modulation de l’expression de gènes à des modifications épigénétiques. Les locus CRISPR représentent également une mine d’informations pouvant servir de méthode de typage de souches microbiennes ou encore une façon d’étudier les interactions entre les bactéries et leurs habitats.
Collapse
|
55
|
Kongrueng J, Srinitiwarawong K, Nishibuchi M, Mittraparp-Arthorn P, Vuddhakul V. Characterization and CRISPR-based genotyping of clinical trh-positive Vibrio parahaemolyticus. Gut Pathog 2018; 10:48. [PMID: 30459849 PMCID: PMC6233571 DOI: 10.1186/s13099-018-0275-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/08/2018] [Indexed: 01/15/2023] Open
Abstract
Background Vibrio parahaemolyticus is a causative agent of gastroenteritis. Most of the clinical isolates carry either tdh and/or trh genes which are considered as the major virulence genes of this pathogen. In this study, the clinical isolates of V. parahaemolyticus carrying trh gene (n = 73) obtained from 1886 to 2012 from various countries were investigated for the urease production, haemolytic activity, and biofilm formation. In addition, the potential of clustered regularly interspaced short palindromic repeats (CRISPR)-based genotyping among these isolates was investigated. Results In this study, no significant differences were observed in the urease production between tdh + trh1+ and tdh + trh2+ isolates (p = 0.063) and between the tdh - trh1+ and tdh - trh2+ isolates (p = 0.788). The isolates carrying only the trh gene showed variation in their haemolytic activity. The ratio of urease production and haemolytic activity between the trh1+ and trh2+ isolates and biofilm formation of trh + V. parahaemolyticus isolates were not significantly different. Sixteen of thirty-four tested isolates (47.0%) of trh + V. parahaemolyticus were positive for CRISPR detection. The discriminatory power index (DI) of CRISPR-virulence typing was higher than the DI obtained by CRISPR typing alone. Conclusion The tdh and trh genes were not involved in urease production in the trh + V. parahaemolyticus, and variation of haemolytic activity detected in V. parahaemolyticus carrying only the trh gene might be correlated to the sequence variation within trh1 and trh2 genes. Additionally, biofilm production of V. parahaemolyticus was not associated with harboring of virulence genes. For genotyping, CRISPR sequences combined with virulence genes can be used as genetic markers to differentiate trh + V. parahaemolyticus strains.
Collapse
Affiliation(s)
- Jetnapang Kongrueng
- 1Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| | - Kanchana Srinitiwarawong
- 1Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| | | | | | - Varaporn Vuddhakul
- 1Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| |
Collapse
|
56
|
Tymensen L, Zaheer R, Cook SR, Amoako KK, Goji N, Read R, Booker CW, Hannon SJ, Neumann N, McAllister TA. Clonal expansion of environmentally-adapted Escherichia coli contributes to propagation of antibiotic resistance genes in beef cattle feedlots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:657-664. [PMID: 29758422 DOI: 10.1016/j.scitotenv.2018.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 06/08/2023]
Abstract
Livestock wastewater lagoons represent important environmental reservoirs of antibiotic resistance genes (ARGs), although factors contributing to their proliferation within these reservoirs remain poorly understood. Here, we characterized Escherichia coli from feedlot cattle feces and associated wastewater lagoons using CRISPR1 subtyping, and demonstrated that while generic E. coli were genetically diverse, populations were dominated by several 'feedlot-adapted' CRISPR types (CTs) that were widely distributed throughout the feedlot. Moreover, E. coli bearing beta-lactamase genes, which confer reduced susceptibility to third-generation cephalosporin's, predominantly belonged to these feedlot-adapted CTs. Remarkably, the genomic region containing the CRISPR1 allele was more frequently subject to genetic exchange among wastewater isolates compared to fecal isolates, implicating this region in environmental adaptation. This allele is proximal to the mutS-rpoS-nlpD region, which is involved in regulating recombination barriers and adaptive stress responses. There were no loss-of-function mutS or rpoS mutations or beneficial accessory genes present within the mutS-rpoS-nlpD region that would account for increased environmental fitness among feedlot-adapted isolates. However, comparative sequence analysis revealed that protein sequences within this region were conserved among most feedlot-adapted CTs, but not transient fecal CTs, and did not reflect phylogenetic relatedness, implying that adaptation to wastewater environments may be associated with genetic variation related to stress resistance. Collectively, our findings suggest adaptation of E. coli to feedlot environments may contribute to propagation of ARGs in wastewater lagoons.
Collapse
Affiliation(s)
- Lisa Tymensen
- Alberta Agriculture and Forestry, Irrigation and Farm Water Branch, Lethbridge, Alberta T1J 4V6, Canada.
| | - Rahat Zaheer
- Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
| | - Shaun R Cook
- Alberta Agriculture and Forestry, Irrigation and Farm Water Branch, Lethbridge, Alberta T1J 4V6, Canada
| | - Kingsley K Amoako
- Canadian Food Inspection Agency, National Center for Animal Disease, Lethbridge, Alberta, Canada
| | - Noriko Goji
- Canadian Food Inspection Agency, National Center for Animal Disease, Lethbridge, Alberta, Canada
| | - Ron Read
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Alberta T1Y 6J4, Canada
| | - Calvin W Booker
- Feedlot Health Management Services, Ltd., Okotoks, Alberta T1S 2A2, Canada
| | - Sherry J Hannon
- Feedlot Health Management Services, Ltd., Okotoks, Alberta T1S 2A2, Canada
| | - Norman Neumann
- School of Public Health, University of Alberta, 3-300 Edmonton Clinic Health Authority, 11405-87 Ave, Edmonton, Alberta T6G 1C9, Canada
| | - Tim A McAllister
- Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
| |
Collapse
|
57
|
Perinatal Streptococcus agalactiae Epidemiology and Surveillance Targets. Clin Microbiol Rev 2018; 31:31/4/e00049-18. [PMID: 30111577 DOI: 10.1128/cmr.00049-18] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus agalactiae, or group B streptococcus (GBS), is a major neonatal pathogen. Recent data have elucidated the global prevalence of maternal and neonatal colonization, but gaps still remain in the epidemiology of this species. A number of phenotypic and genotypic classifications can be used to identify the diversity of GBS strains, and some are more discriminatory than others. This review explores the main schemes used for GBS epidemiology and further details the targets for epidemiological surveillance. Current screening practices across the world provide a unique opportunity to gain detailed information on maternal colonizing strains and neonatal disease-causing strains, which is vital for monitoring and therapeutics, if sufficient detail can be extracted. Deciphering which isolates are circulating within specific populations and recording targets within invasive strains are crucial steps in monitoring the implementation of therapeutics, such as vaccines, as well as developing novel therapies against prevalent GBS strains. Having a detailed understanding of global GBS epidemiology will prove invaluable for understanding the pathogenesis of this organism and equipping future prevention strategies for success.
Collapse
|
58
|
Zhao X, Yu Z, Xu Z. Study the Features of 57 Confirmed CRISPR Loci in 38 Strains of Staphylococcus aureus. Front Microbiol 2018; 9:1591. [PMID: 30093886 PMCID: PMC6070637 DOI: 10.3389/fmicb.2018.01591] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/26/2018] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus is a foodborne pathogen that causes food contamination and food poisoning, which poses great harm to health, agriculture and other hosts. Clustered regularly interspaced short palindromic repeats (CRISPR) are a recently discovered bacterial immune system that resists foreign genes such as phage DNA. This system inhibits the transfer of specific movable genetic elements that match the CRISPR spacer sequences, thereby preventing the spread of drug-resistant genes between pathogens. In this study, 57 CRISPR loci were screened from 38 strains of S. aureus based on the CRISPR database, and bioinformatics tools were used to investigate the structural features and potential functions of S. aureus CRISPR loci. The results showed that most strains contained only one CRISPR locus, a few strains contained multiple loci with sparsely distributed sites. These loci mainly included highly conserved direct repeat sequences and highly variable spacer sequences, as well as polymorphic cas genes. In addition, the analysis of secondary structure of direct repeat RNA showed that all sites can form stable RNA secondary structure. The results of constructing phylogenetic tree based on spacer sequence showed that some strains contained a high degree of phylogenetic relationship, while the differences among other strains in evolutionary processes were quite obvious. Of the 57 CRISPR loci identified, only the cas gene was found near the 4 CRISPR loci.
Collapse
Affiliation(s)
- Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Key Laboratory for Hubei Novel Reactor & Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Zhixue Yu
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Key Laboratory for Hubei Novel Reactor & Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Zhenbo Xu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| |
Collapse
|
59
|
Wei W, Zhang S, Fleming J, Chen Y, Li Z, Fan S, Liu Y, Wang W, Wang T, Liu Y, Ren B, Wang M, Jiao J, Chen Y, Zhou Y, Zhou Y, Gu S, Zhang X, Wan L, Chen T, Zhou L, Chen Y, Zhang XE, Li C, Zhang H, Bi L. Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features. FASEB J 2018; 33:1496-1509. [PMID: 29979631 DOI: 10.1096/fj.201800557rr] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems are prokaryotic adaptive immune systems against invading nucleic acids. CRISPR locus variability has been exploited in evolutionary and epidemiological studies of Mycobacterium tuberculosis, the causative agent of tuberculosis, for over 20 yr, yet the biological function of this type III-A system is largely unexplored. Here, using cell biology and biochemical, mutagenic, and RNA-seq approaches, we show it is active in invader defense and has features atypical of type III-A systems: mature CRISPR RNA (crRNA) in its crRNA-CRISPR/Cas protein complex are of uniform length (∼71 nt) and appear not to be subject to 3'-end processing after Cas6 cleavage of repeat RNA 8 nt from its 3' end. crRNAs generated resemble mature crRNA in type I systems, having both 5' (8 nt) and 3' (28 nt) repeat tags. Cas6 cleavage of repeat RNA is ion dependent, and accurate cleavage depends on the presence of a 3' hairpin in the repeat RNA and the sequence of its stem base nucleotides. This study unveils further diversity among CRISPR/Cas systems and provides insight into the crRNA recognition mechanism in M. tuberculosis, providing a foundation for investigating the potential of a type III-A-based genome editing system.-Wei, W., Zhang, S., Fleming, J., Chen, Y., Li, Z., Fan, S., Liu, Y., Wang, W., Wang, T., Liu, Y., Ren, B., Wang, M., Jiao, J., Chen, Y., Zhou, Y., Zhou, Y., Gu, S., Zhang, X., Wan, L., Chen, T., Zhou, L., Chen, Y., Zhang, X.-E., Li, C., Zhang, H., Bi, L. Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features.
Collapse
Affiliation(s)
- Wenjing Wei
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shuai Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Joy Fleming
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Ying Chen
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zihui Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Shanghua Fan
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yi Liu
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Wei Wang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Ting Wang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Liu
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Baiguang Ren
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ming Wang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianjian Jiao
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Chen
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhou
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Yafeng Zhou
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Shoujin Gu
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, China
| | - Xiaoli Zhang
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Li Wan
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tao Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China; and
| | - Lin Zhou
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China; and
| | - Yong Chen
- School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Xian-En Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Chuanyou Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongtai Zhang
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lijun Bi
- Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,School of Stomatology and Medicine, Foshan University, Foshan, China.,Guangdong Province Key Laboratory of Tuberculosis Systems Biology and Translational Medicine, Foshan, China
| |
Collapse
|
60
|
Ricke SC, Kim SA, Shi Z, Park SH. Molecular-based identification and detection of Salmonella in food production systems: current perspectives. J Appl Microbiol 2018; 125:313-327. [PMID: 29675864 DOI: 10.1111/jam.13888] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 12/25/2022]
Abstract
Salmonella remains a prominent cause of foodborne illnesses and can originate from a wide range of food products. Given the continued presence of pathogenic Salmonella in food production systems, there is a consistent need to improve identification and detection methods that can identify this pathogen at all stages in food systems. Methods for subtyping have evolved over the years, and the introduction of whole genome sequencing and advancements in PCR technologies have greatly improved the resolution for differentiating strains within a particular serovar. This, in turn, has led to the continued improvement in Salmonella detection technologies for utilization in food production systems. In this review, the focus will be on recent advancements in these technologies, as well as potential issues associated with the application of these tools in food production. In addition, the recent and emerging research developments on Salmonella detection and identification methodologies and their potential application in food production systems will be discussed.
Collapse
Affiliation(s)
- S C Ricke
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - S A Kim
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - Z Shi
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| | - S H Park
- Department of Food Science, Center for Food Safety, University of Arkansas, Fayetteville, AR, USA
| |
Collapse
|
61
|
Beauruelle C, Pastuszka A, Mereghetti L, Lanotte P. Group B Streptococcus Vaginal Carriage in Pregnant Women as Deciphered by Clustered Regularly Interspaced Short Palindromic Repeat Analysis. J Clin Microbiol 2018; 56:e01949-17. [PMID: 29618502 PMCID: PMC5971545 DOI: 10.1128/jcm.01949-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/28/2018] [Indexed: 11/20/2022] Open
Abstract
We evaluated the diversity of group B Streptococcus (GBS) vaginal carriage populations in pregnant women. For this purpose, we studied each isolate present in a primary culture of a vaginal swab using a new approach based on clustered regularly interspaced short palindromic repeats (CRISPR) locus analysis. To evaluate the CRISPR array composition rapidly, a restriction fragment length polymorphism (RFLP) analysis was performed. For each different pattern observed, the CRISPR array was sequenced and capsular typing and multilocus sequence typing (MLST) were performed. A total of 970 isolates from 10 women were analyzed by CRISPR-RFLP. Each woman carrying GBS isolates presented one to five specific "personal" patterns. Five women showed similar isolates with specific and unique restriction patterns, suggesting the carriage of a single GBS clone. Different patterns were observed among isolates from the other five women. For three of these, CRISPR locus sequencing highlighted low levels of internal modifications in the locus backbone, whereas there were high levels of modifications for the last two women, suggesting the carriage of two different clones. These two clones were closely related, having the same ancestral spacer(s), the same capsular type and, in one case, the same ST, but showed different antibiotic resistance patterns in pairs. Eight of 10 women were colonized by a single GBS clone, while two of them were colonized by two strains, leading to a risk of selection of more-virulent and/or more-resistant clones during antibiotic prophylaxis. This CRISPR analysis made it possible to separate isolates belonging to a single capsular type and sequence type, highlighting the greater discriminating power of this approach.
Collapse
Affiliation(s)
- Clemence Beauruelle
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- CHRU de Tours, Service de Bactériologie-Virologie, Tours, France
| | - Adeline Pastuszka
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- CHRU de Tours, Service de Bactériologie-Virologie, Tours, France
| | - Laurent Mereghetti
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- CHRU de Tours, Service de Bactériologie-Virologie, Tours, France
| | - Philippe Lanotte
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- CHRU de Tours, Service de Bactériologie-Virologie, Tours, France
| |
Collapse
|
62
|
The prevalence and load of Salmonella, and key risk points of Salmonella contamination in a swine slaughterhouse in Jiangsu province, China. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.12.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
63
|
Karimi Z, Ahmadi A, Najafi A, Ranjbar R. Bacterial CRISPR Regions: General Features and their Potential for Epidemiological Molecular Typing Studies. Open Microbiol J 2018; 12:59-70. [PMID: 29755603 PMCID: PMC5925864 DOI: 10.2174/1874285801812010059] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/08/2018] [Accepted: 04/09/2018] [Indexed: 02/08/2023] Open
Abstract
Introduction CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci as novel and applicable regions in prokaryotic genomes have gained great attraction in the post genomics era. Methods These unique regions are diverse in number and sequence composition in different pathogenic bacteria and thereby can be a suitable candidate for molecular epidemiology and genotyping studies. Results:Furthermore, the arrayed structure of CRISPR loci (several unique repeats spaced with the variable sequence) and associated cas genes act as an active prokaryotic immune system against viral replication and conjugative elements. This property can be used as a tool for RNA editing in bioengineering studies. Conclusion The aim of this review was to survey some details about the history, nature, and potential applications of CRISPR arrays in both genetic engineering and bacterial genotyping studies.
Collapse
Affiliation(s)
- Zahra Karimi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| |
Collapse
|
64
|
Abstract
The number of human salmonellosis within the European Union tended to increase since 2013. One of the reasons might be Salmonella Enteritidis rising in laying hens flocks by around 17% in 2015 vs 2014 and by 57% in 2016 vs 2015. The most important sources of food-borne Salmonella outbreaks are still eggs and egg products as well as ready-to-eat foods having a long shelf life. Specific actions are suggested to restart decreasing the number of human salmonellosis: (1) revision of sampling schemes to solve pathogen under detection in both animals and foods; (2) integration of microbiological criteria with fit for purpose performance objectives and food safety objectives; and (3) improvement of epidemiological investigations of human, food, and animal isolates by using whole-genome sequencing in order to effectively track salmonellosis and verify which prevention measures are most effective.
Collapse
|
65
|
Uppada V, Gokara M, Rasineni GK. Diagnosis and therapy with CRISPR advanced CRISPR based tools for point of care diagnostics and early therapies. Gene 2018; 656:22-29. [PMID: 29496558 DOI: 10.1016/j.gene.2018.02.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/14/2018] [Accepted: 02/24/2018] [Indexed: 12/26/2022]
Abstract
Molecular diagnostics is of critical importance to public health worldwide. It facilitates not only detection and characterization of diseases, but also monitors drug responses, assists in the identification of genetic modifiers and disease susceptibility. Based upon DNA variation, a wide range of molecular-based tests are available to assess/diagnose diseases. The CRISPR-Cas9 system has recently emerged as a versatile tool for biological and medical research. In this system, a single guide RNA (sgRNA) directs the endonuclease Cas9 to a targeted DNA sequence for site-specific manipulation. As designing CRISPR-guided nucleases can be done easily and relatively fast, the CRISPR/Cas9 system has evolved as widely used DNA editing tool. This technique led to a large number of gene editing studies in variety of organisms. CRISPR/Cas9-mediated diagnosis and therapy has picked up pace due to specificity and accuracy of CRISPR. The aim is not only to identify specific pathogens, especially virus but also to repair disease-causing alleles by changing the DNA sequence at the exact location on the chromosome. At present, PCR-based molecular diagnostic testing predominates; however, alternative technologies aimed at reducing genome complexity without PCR are anticipated to gain momentum in the coming years. Furthermore, development of integrated chip devices should allow point-of-care testing and facilitate genetic readouts from single cells and molecules. Together with molecular based therapy CRISPR based diagnostic testing will be a revolution in modern health care settings. In this review, we emphasize on current developing diagnostic techniques based upon CRISPR Cas approach along with short insights on its therapeutic usage.
Collapse
Affiliation(s)
- Vanita Uppada
- Department of Animal Biology, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Mahesh Gokara
- Department of Biochemistry, University of Hyderabad, Hyderabad 500046, Telangana, India
| | | |
Collapse
|
66
|
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.
Collapse
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
| |
Collapse
|
67
|
Donohoue PD, Barrangou R, May AP. Advances in Industrial Biotechnology Using CRISPR-Cas Systems. Trends Biotechnol 2018; 36:134-146. [PMID: 28778606 DOI: 10.1016/j.tibtech.2017.07.007] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 12/14/2022]
Abstract
The term 'clustered regularly interspaced short palindromic repeats' (CRISPR) has recently become synonymous with the genome-editing revolution. The RNA-guided endonuclease CRISPR-associated protein 9 (Cas9), in particular, has attracted attention for its promise in basic research and gene editing-based therapeutics. CRISPR-Cas systems are efficient and easily programmable nucleic acid-targeting tools, with uses reaching beyond research and therapeutic development into the precision breeding of plants and animals and the engineering of industrial microbes. CRISPR-Cas systems have potential for many microbial engineering applications, including bacterial strain typing, immunization of cultures, autoimmunity or self-targeted cell killing, and the engineering or control of metabolic pathways for improved biochemical synthesis. In this review, we explore the fundamental characteristics of CRISPR-Cas systems and highlight how these features can be used in industrial settings.
Collapse
Affiliation(s)
- Paul D Donohoue
- Caribou Biosciences, Inc., 2929 7th St., Suite 105, Berkeley, CA 94710, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Andrew P May
- Caribou Biosciences, Inc., 2929 7th St., Suite 105, Berkeley, CA 94710, USA; Current address: Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA.
| |
Collapse
|
68
|
Comparison of advanced whole genome sequence-based methods to distinguish strains of Salmonella enterica serovar Heidelberg involved in foodborne outbreaks in Québec. Food Microbiol 2018. [PMID: 29526232 DOI: 10.1016/j.fm.2018.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. This serovar ranks second and third among serovars that cause human infections in Québec and Canada, respectively, and has been associated with severe infections. Traditional typing methods such as PFGE do not display adequate discrimination required to resolve outbreak investigations due to the low level of genetic diversity of isolates belonging to this serovar. This study evaluates the ability of four whole genome sequence (WGS)-based typing methods to differentiate among 145 S. Heidelberg strains involved in four distinct outbreak events and sporadic cases of salmonellosis that occurred in Québec between 2007 and 2016. Isolates from all outbreaks were indistinguishable by PFGE. The core genome single nucleotide variant (SNV), core genome multilocus sequence typing (MLST) and whole genome MLST approaches were highly discriminatory and separated outbreak strains into four distinct phylogenetic clusters that were concordant with the epidemiological data. The clustered regularly interspaced short palindromic repeats (CRISPR) typing method was less discriminatory. However, CRISPR typing may be used as a secondary method to differentiate isolates of S. Heidelberg that are genetically similar but epidemiologically unrelated to outbreak events. WGS-based typing methods provide a highly discriminatory alternative to PFGE for the laboratory investigation of foodborne outbreaks.
Collapse
|
69
|
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.
Collapse
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
| |
Collapse
|
70
|
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.
Collapse
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.
| |
Collapse
|
71
|
Bangpanwimon K, Sottisuporn J, Mittraparp-Arthorn P, Ueaphatthanaphanich W, Rattanasupar A, Pourcel C, Vuddhakul V. CRISPR-like sequences in Helicobacter pylori and application in genotyping. Gut Pathog 2017; 9:65. [PMID: 29177012 PMCID: PMC5693588 DOI: 10.1186/s13099-017-0215-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/06/2017] [Indexed: 02/07/2023] Open
Abstract
Background Many bacteria and archaea possess a defense system called clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins (CRISPR-Cas system) against invaders such as phages or plasmids. This system has not been demonstrated in Helicobacter pylori. The numbers of spacer in CRISPR array differ among bacterial strains and can be used as a genetic marker for bacterial typing. Results A total of 36 H. pylori isolates were collected from patients in three hospitals located in the central (PBH) and southern (SKH) regions of Thailand. It is of interest that CRISPR-like sequences of this bacterium were detected in vlpC encoded for VacA-like protein C. Virulence genes were investigated and the most pathogenic genotype (cagA vacA s1m1) was detected in 17 out of 29 (58.6%) isolates from PBH and 5 out of 7 (71.4%) from SKH. vapD gene was identified in each one isolate from PBH and SKH. CRISPR-like sequences and virulence genes of 20 isolates of H. pylori obtained in this study were analyzed and CRISPR-virulence typing was constructed and compared to profiles obtained by the random amplification of polymorphic DNA (RAPD) technique. The discriminatory power (DI) of CRISPR-virulence typing was not different from RAPD typing. Conclusion CRISPR-virulence typing in H. pylori is easy and reliable for epidemiology and can be used for inter-laboratory interpretation. Electronic supplementary material The online version of this article (10.1186/s13099-017-0215-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Khotchawan Bangpanwimon
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| | - Jaksin Sottisuporn
- NKC Institute of Gastroenterology and Hepatology, Songklanagarind Hospital, Faculty of Medicine, Prince of Songkla University, Hat Yai, Thailand
| | | | | | - Attapon Rattanasupar
- KC Center of Gastroenterology and Hepatology, Hat Yai Hospital, Hat Yai, Thailand
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Varaporn Vuddhakul
- Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
| |
Collapse
|
72
|
Mohammed M. Phage typing or CRISPR typing for epidemiological surveillance of Salmonella Typhimurium? BMC Res Notes 2017; 10:578. [PMID: 29115982 PMCID: PMC5678594 DOI: 10.1186/s13104-017-2878-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/26/2017] [Indexed: 11/12/2022] Open
Abstract
Objective Salmonella Typhimurium is the most dominant Salmonella serovar around the world. It is associated with foodborne gastroenteritis outbreaks but has recently been associated with invasive illness and deaths. Characterization of S. Typhimurium is therefore very crucial for epidemiological surveillance. Phage typing has been used for decades for subtyping of S. Typhimurium to determine the epidemiological relation among isolates. Recent studies however have suggested that high throughput clustered regular interspaced short palindromic repeats (CRISPR) typing has the potential to replace phage typing. This study aimed to determine the efficacy of high-throughput CRISPR typing over conventional phage typing in epidemiological surveillance and outbreak investigation of S. Typhimurium. Results In silico analysis of whole genome sequences (WGS) of well-documented phage types of S. Typhimurium reveals the presence of different CRISPR type among strains belong to the same phage type. Furthermore, different phage types of S. Typhimurium share identical CRISPR type. Interestingly, identical spacers were detected among outbreak and non-outbreak associated DT8 strains of S. Typhimurium. Therefore, CRISPR typing is not useful for the epidemiological surveillance and outbreak investigation of S. Typhimurium and phage typing, until it is replaced by WGS, is still the gold standard method for epidemiological surveillance of S. Typhimurium. Electronic supplementary material The online version of this article (10.1186/s13104-017-2878-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Manal Mohammed
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK.
| |
Collapse
|
73
|
Zhang Y, Kitajima M, Whittle AJ, Liu WT. Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems. Front Microbiol 2017; 8:2036. [PMID: 29097994 PMCID: PMC5654357 DOI: 10.3389/fmicb.2017.02036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/05/2017] [Indexed: 11/22/2022] Open
Abstract
The occurrence of pathogenic bacteria in drinking water distribution systems (DWDSs) is a major health concern, and our current understanding is mostly related to pathogenic species such as Legionella pneumophila and Mycobacterium avium but not to bacterial species closely related to them. In this study, genomic-based approaches were used to characterize pathogen-related species in relation to their abundance, diversity, potential pathogenicity, genetic exchange, and distribution across an urban drinking water system. Nine draft genomes recovered from 10 metagenomes were identified as Legionella (4 draft genomes), Mycobacterium (3 draft genomes), Parachlamydia (1 draft genome), and Leptospira (1 draft genome). The pathogenicity potential of these genomes was examined by the presence/absence of virulence machinery, including genes belonging to Type III, IV, and VII secretion systems and their effectors. Several virulence factors known to pathogenic species were detected with these retrieved draft genomes except the Leptospira-related genome. Identical clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) genetic signatures were observed in two draft genomes recovered at different stages of the studied system, suggesting that the spacers in CRISPR-Cas could potentially be used as a biomarker in the monitoring of Legionella related strains at an evolutionary scale of several years across different drinking water production and distribution systems. Overall, metagenomics approach was an effective and complementary tool of culturing techniques to gain insights into the pathogenic characteristics and the CRISPR-Cas signatures of pathogen-related species in DWDSs.
Collapse
Affiliation(s)
- Ya Zhang
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Andrew J Whittle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| |
Collapse
|
74
|
Tomida J, Morita Y, Shibayama K, Kikuchi K, Sawa T, Akaike T, Kawamura Y. Diversity and microevolution of CRISPR loci in Helicobacter cinaedi. PLoS One 2017; 12:e0186241. [PMID: 29028814 PMCID: PMC5640232 DOI: 10.1371/journal.pone.0186241] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/27/2017] [Indexed: 12/30/2022] Open
Abstract
Helicobacter cinaedi is associated with nosocomial infections. The CRISPR-Cas system provides adaptive immunity against foreign genetic elements. We investigated the CRISPR-Cas system in H. cinaedi to assess the potential of the CRISPR-based microevolution of H. cinaedi strains. A genotyping method based on CRISPR spacer organization was carried out using 42 H. cinaedi strains. The results of sequence analysis showed that the H. cinaedi strains used in this study had two CRISPR loci (CRISPR1 and CRISPR2). The lengths of the consensus direct repeat sequences in CRISPR1 and CRISPR2 were both 36 bp-long, and 224 spacers were found in the 42 H. cinaedi strains. Analysis of the organization and sequence similarity of the spacers of the H. cinaedi strains showed that CRISPR arrays could be divided into 7 different genotypes. Each genotype had a different ancestral spacer, and spacer acquisition/deletion events occurred while isolates were spreading. Spacer polymorphisms of conserved arrays across the strains were instrumental for differentiating closely-related strains collected from the same hospital. MLST had little variability, while the CRISPR sequences showed remarkable diversity. Our data revealed the structural features of H. cinaedi CRISPR loci for the first time. CRISPR sequences constitute a valuable basis for genotyping, provide insights into the divergence and relatedness between closely-related strains, and reflect the microevolutionary process of H. cinaedi.
Collapse
Affiliation(s)
- Junko Tomida
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
- * E-mail:
| | - Yuji Morita
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken Kikuchi
- Department of Infectious Diseases, Tokyo Women’s Medical University, Tokyo, Japan
| | - Tomohiro Sawa
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takaaki Akaike
- Department of Environmental Health Sciences and Molecular Toxicology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshiaki Kawamura
- Department of Microbiology, School of Pharmacy, Aichi Gakuin University, Nagoya, Japan
| |
Collapse
|
75
|
Beauruelle C, Pastuszka A, Horvath P, Perrotin F, Mereghetti L, Lanotte P. CRISPR: A Useful Genetic Feature to Follow Vaginal Carriage of Group B Streptococcus. Front Microbiol 2017; 8:1981. [PMID: 29075246 PMCID: PMC5641575 DOI: 10.3389/fmicb.2017.01981] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/25/2017] [Indexed: 11/16/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and Cas (CRISPR-associated proteins) play a critical role in adaptive immunity against mobile genetic elements, especially phages, through their ability to acquire novel spacer sequences. Polarized spacer acquisition results in spacer polymorphism and temporal organization of CRISPR loci, making them attractive epidemiological markers. Group B Streptococcus (GBS), a genital commensal for 10 to 30% of healthy women and a major neonatal pathogen, possesses a ubiquitous and functional CRISPR1 locus. Our aim was to assess the CRISPR1 locus as an epidemiological marker to follow vaginal carriage of GBS in women. This study also allowed us to observe the evolution of the CRISPR1 locus in response to probable phage infection occurring in vivo. We followed carriage of GBS among 100 women over an 11-year period, with a median duration of approximately 2 years. The CRISPR1 locus was highly conserved over time. The isolates that show the same CRISPR1 genotype were collected from 83% of women. There was an agreement between CRISPR genotyping and other typing methods [MLVA (multilocus variable number of tandem repeat Analysis) and MLST (multilocus sequence typing)] for 94% of the cases. The CRISPR1 locus of the isolates from 18 women showed modifications, four of which acquired polarized spacer, highlighting the in vivo functionality of the system. The novel spacer of one isolate had sequence similarity with phage, suggesting that phage infection occurred during carriage. These findings improve our understanding of CRISPR-Cas evolution in GBS and provide a glimpse of host-phage dynamics in vivo.
Collapse
Affiliation(s)
- Clémence Beauruelle
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France.,INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France.,Service de Bactériologie-Virologie, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Adeline Pastuszka
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France.,INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France.,Service de Bactériologie-Virologie, Centre Hospitalier Universitaire de Tours, Tours, France
| | | | - Franck Perrotin
- Inserm U930, Université François Rabelais de Tours, Tours, France.,Département d'Obstétrique de Gynécologie et de Médecine Fœtale, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Laurent Mereghetti
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France.,INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France.,Service de Bactériologie-Virologie, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Philippe Lanotte
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France.,INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France.,Service de Bactériologie-Virologie, Centre Hospitalier Universitaire de Tours, Tours, France
| |
Collapse
|
76
|
Ogrodzki P, Forsythe SJ. DNA-Sequence Based Typing of the Cronobacter Genus Using MLST, CRISPR- cas Array and Capsular Profiling. Front Microbiol 2017; 8:1875. [PMID: 29033918 PMCID: PMC5626840 DOI: 10.3389/fmicb.2017.01875] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/13/2017] [Indexed: 11/13/2022] Open
Abstract
The Cronobacter genus is composed of seven species, within which a number of pathovars have been described. The most notable infections by Cronobacter spp. are of infants through the consumption of contaminated infant formula. The description of the genus has greatly improved in recent years through DNA sequencing techniques, and this has led to a robust means of identification. However some species are highly clonal and this limits the ability to discriminate between unrelated strains by some methods of genotyping. This article updates the application of three genotyping methods across the Cronobacter genus. The three genotyping methods were multilocus sequence typing (MLST), capsular profiling of the K-antigen and colanic acid (CA) biosynthesis regions, and CRISPR-cas array profiling. A total of 1654 MLST profiled and 286 whole genome sequenced strains, available by open access at the PubMLST Cronobacter database, were used this analysis. The predominance of C. sakazakii and C. malonaticus in clinical infections was confirmed. The majority of clinical strains being in the C. sakazakii clonal complexes (CC) 1 and 4, sequence types (ST) 8 and 12 and C. malonaticus ST7. The capsular profile K2:CA2, previously proposed as being strongly associated with C. sakazakii and C. malonaticus isolates from severe neonatal infections, was also found in C. turicensis, C. dublinensis and C. universalis. The majority of CRISPR-cas types across the genus was the I-E (Ecoli) type. Some strains of C. dublinensis and C. muytjensii encoded the I-F (Ypseudo) type, and others lacked the cas gene loci. The significance of the expanding profiling will be of benefit to researchers as well as governmental and industrial risk assessors.
Collapse
Affiliation(s)
- Pauline Ogrodzki
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | | |
Collapse
|
77
|
How a Genetically Stable Extremophile Evolves: Modes of Genome Diversification in the Archaeon Sulfolobus acidocaldarius. J Bacteriol 2017. [PMID: 28630130 DOI: 10.1128/jb.00177-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In order to analyze in molecular terms how Sulfolobus genomes diverge, damage-induced mutations and natural polymorphisms (PMs) were identified in laboratory constructs and wild-type isolates, respectively, of Sulfolobus acidocaldarius Among wild-type isolates drawn from one local population, pairwise nucleotide divergence averaged 4 × 10-6, which is about 0.15% of the corresponding divergence reported for Sulfolobus islandicus The most variable features of wild-type S. acidocaldarius genomes were homopolymer (mononucleotide) tracts and longer tandem repeats, consistent with the spontaneous mutations that occur under laboratory conditions. Natural isolates, however, also revealed large insertions/deletions and inversions, which did not occur in any of the laboratory-manipulated strains. Several of the large insertions/deletions could be attributed to the integration or excision of mobile genetic elements (MGEs), and each MGE represented a distinct system of site-specific recombination. The mode of recombination associated with one MGE, a provirus related to Sulfolobus turreted icosahedral virus, was also seen in certain chromosomal inversions. Artificially induced mutations, non-MGE insertions/deletions, and small PMs exhibited different distributions over the genome, suggesting that large-scale patterning of Sulfolobus genomes begins early in the divergence process. Unlike induced mutations, natural base pair substitutions occurred in clusters, and one cluster exhibited properties expected of nonreciprocal recombination (gene conversion) between dispersed imperfect repeats. Taken together, the results identify simple replication errors, slipped-strand events promoted by tandem repeats, homologous recombination, and rearrangements promoted by MGEs as the primary sources of genetic variation for this extremely acidophilic archaeon in its geothermal environment.IMPORTANCE The optimal growth temperatures of hyperthermophilic archaea accelerate DNA decomposition, which is expected to make DNA repair especially important for their genetic stability, yet these archaea lack certain broadly conserved types of DNA repair proteins. In this study, the genome of the extreme thermoacidophile Sulfolobus acidocaldarius was found to be remarkably stable, accumulating few mutations in many (though not all) laboratory manipulations and in natural populations. Furthermore, all the genetic processes that were inferred to diversify these genomes also operate in mesophilic bacteria and eukaryotes. This suggests that a common set of mechanisms produces most of the genetic variation in all microorganisms, despite the fundamental differences in physiology, DNA repair systems, and genome structure represented in the three domains of life.
Collapse
|
78
|
Emond-Rheault JG, Jeukens J, Freschi L, Kukavica-Ibrulj I, Boyle B, Dupont MJ, Colavecchio A, Barrere V, Cadieux B, Arya G, Bekal S, Berry C, Burnett E, Cavestri C, Chapin TK, Crouse A, Daigle F, Danyluk MD, Delaquis P, Dewar K, Doualla-Bell F, Fliss I, Fong K, Fournier E, Franz E, Garduno R, Gill A, Gruenheid S, Harris L, Huang CB, Huang H, Johnson R, Joly Y, Kerhoas M, Kong N, Lapointe G, Larivière L, Loignon S, Malo D, Moineau S, Mottawea W, Mukhopadhyay K, Nadon C, Nash J, Ngueng Feze I, Ogunremi D, Perets A, Pilar AV, Reimer AR, Robertson J, Rohde J, Sanderson KE, Song L, Stephan R, Tamber S, Thomassin P, Tremblay D, Usongo V, Vincent C, Wang S, Weadge JT, Wiedmann M, Wijnands L, Wilson ED, Wittum T, Yoshida C, Youfsi K, Zhu L, Weimer BC, Goodridge L, Levesque RC. A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis. Front Microbiol 2017. [PMID: 28626454 PMCID: PMC5454079 DOI: 10.3389/fmicb.2017.00996] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.
Collapse
Affiliation(s)
| | - Julie Jeukens
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Luca Freschi
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Irena Kukavica-Ibrulj
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Brian Boyle
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | - Marie-Josée Dupont
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| | | | | | | | - Gitanjali Arya
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Sadjia Bekal
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Chrystal Berry
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | | | - Travis K Chapin
- Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
| | | | - France Daigle
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| | - Michelle D Danyluk
- Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
| | | | - Ken Dewar
- McGill University, MontréalQC, Canada.,Génome Québec Innovation Center, MontréalQC, Canada
| | | | | | - Karen Fong
- Food Safety Engineering, Faculty of Land and Food Systems, University of British Columbia, VancouverBC, Canada
| | - Eric Fournier
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Eelco Franz
- National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | | | - Alexander Gill
- Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
| | | | - Linda Harris
- UC Davis Food Science and Technology, DavisCA, United States
| | - Carol B Huang
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | - Roger Johnson
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Yann Joly
- McGill University, MontréalQC, Canada
| | - Maud Kerhoas
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, MontréalQC, Canada
| | - Nguyet Kong
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | | | | | | | | | - Walid Mottawea
- McGill University, MontréalQC, Canada.,Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura UniversityMansoura, Egypt
| | | | - Céline Nadon
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - John Nash
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | | | - Ann Perets
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | | | - Aleisha R Reimer
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - James Robertson
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - John Rohde
- Department of Microbiology and Immunology, Dalhousie University, HalifaxNS, Canada
| | | | | | - Roger Stephan
- Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, OttawaON, Canada
| | | | | | - Valentine Usongo
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Caroline Vincent
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Siyun Wang
- Food Safety Engineering, Faculty of Land and Food Systems, University of British Columbia, VancouverBC, Canada
| | - Joel T Weadge
- Biological and Chemical Sciences, Wilfrid Laurier University, WaterlooON, Canada
| | - Martin Wiedmann
- Department of Food Science, Cornell University, IthacaNY, United States
| | - Lucas Wijnands
- National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | - Emily D Wilson
- Biological and Chemical Sciences, Wilfrid Laurier University, WaterlooON, Canada
| | - Thomas Wittum
- College of Veterinary Medicine, The Ohio State University, ColumbusOH, United States
| | - Catherine Yoshida
- National Microbiology Laboratory, Public Health Agency of Canada, OttawaON, Canada
| | - Khadija Youfsi
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-BellevueQC, Canada
| | - Lei Zhu
- McGill University, MontréalQC, Canada
| | - Bart C Weimer
- UC Davis School of Veterinary Medicine, DavisCA, United States
| | | | - Roger C Levesque
- Institute for Integrative and Systems Biology, Université Laval, Québec CityQC, Canada
| |
Collapse
|
79
|
Feng P, Delannoy S, Lacher DW, Bosilevac JM, Fach P. Characterization and Virulence Potential of Serogroup O113 Shiga Toxin-Producing Escherichia coli Strains Isolated from Beef and Cattle in the United States. J Food Prot 2017; 80:383-391. [PMID: 28199145 DOI: 10.4315/0362-028x.jfp-16-325] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) of serotype O113:H21 have caused severe diseases but are unusual in that they do not produce the intimin protein required for adherence to intestinal epithelial cells. Strains of serogroup O113 are one of the most common STEC found in ground beef and beef products in the United States, but their virulence potential is unknown. We used a microarray to characterize 65 O113 strains isolated in the United States from ground beef, beef trim, cattle feces, and fresh spinach. Most were O113:H21 strains, but there were also nine strains of O113:H4 serotype. Although strains within the same serotype had similar profiles for the genes that were tested on the array, the profiles were distinct between the two serotypes, and the strains belonged to different clonal groups. Analysis by clustered regularly interspaced short palindromic repeat analysis showed that O113:H4 strains are conserved genetically, but the O113:H21 strains showed considerable polymorphism and genetic diversity. In comparison to the O113:H21 strains from Australia that were implicated in severe disease, the U.S. isolates showed similar genetic profiles to the known pathogens from Australia, suggesting that these may also have the potential to cause infections.
Collapse
Affiliation(s)
- Peter Feng
- Division of Microbiology, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, Maryland 20740, USA
| | - Sabine Delannoy
- French Agency for Food, Environmental and Occupational Health and Safety, 27-31 Avenue du General Leclerc, 94701 Maisons-Alfort, France
| | - David W Lacher
- Division of Molecular Biology, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708, USA
| | - Joseph M Bosilevac
- U.S. Meat Animal Research Center, Agricultural Research Service, U.S. Department of Agriculture, P.O. Box 166, State Spur 18D, Clay Center, Nebraska 68933, USA
| | - Patrick Fach
- French Agency for Food, Environmental and Occupational Health and Safety, 27-31 Avenue du General Leclerc, 94701 Maisons-Alfort, France
| |
Collapse
|
80
|
Zheng H, Hu Y, Li Q, Tao J, Cai Y, Wang Y, Li J, Zhou Z, Pan Z, Jiao X. Subtyping Salmonella enterica serovar Derby with multilocus sequence typing (MLST) and clustered regularly interspaced short palindromic repeats (CRISPRs). Food Control 2017. [DOI: 10.1016/j.foodcont.2016.08.051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
81
|
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.
Collapse
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
| |
Collapse
|
82
|
Calleros L, Betancor L, Iraola G, Méndez A, Morsella C, Paolicchi F, Silveyra S, Velilla A, Pérez R. Assessing the intra-species genetic variability in the clonal pathogen Campylobacter fetus: CRISPRs are highly polymorphic DNA markers. J Microbiol Methods 2016; 132:86-94. [PMID: 27867047 DOI: 10.1016/j.mimet.2016.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/15/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022]
Abstract
Campylobacter fetus is a Gram-negative, microaerophilic bacterium that infects animals and humans. The subspecies Campylobacter fetus subsp. fetus (Cff) affects a broad range of vertebrate hosts and induces abortion in cows and sheep. Campylobacter fetus subsp. venerealis (Cfv) is restricted to cattle and causes the endemic disease bovine genital campylobacteriosis, which triggers reproductive problems and is responsible for major economic losses. Campylobacter fetus subsp. testudinum (Cft) has been isolated mostly from apparently healthy reptiles belonging to different species but also from ill snakes and humans. Genotypic differentiation of Cff and Cfv is difficult, and epidemiological information is scarce because there are few methods to study the genetic diversity of the strains. We analyze the efficacy of MLST, ribosomal sequences (23S gene and internal spacer region), and CRISPRs to assess the genetic variability of C. fetus in bovine and human isolates. Sequences retrieved from complete genomes were included in the analysis for comparative purposes. MLST and ribosomal sequences had scarce or null variability, while the CRISPR-cas system structure and the sequence of CRISPR1 locus showed remarkable diversity. None of the sequences here analyzed provided evidence of a genetic differentiation of Cff and Cfv in bovine isolates. Comparison of bovine and human isolates with Cft strains showed a striking divergence. Inter-host differences raise the possibility of determining the original host of human infections using CRISPR sequences. CRISPRs are the most variable sequences analyzed in C. fetus so far, and constitute excellent representatives of a dynamic fraction of the genome. CRISPR typing is a promising tool to characterize isolates and to track the source and transmission route of C. fetus infections.
Collapse
Affiliation(s)
- Lucía Calleros
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| | - Laura Betancor
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Dr. Alfredo Navarro 3051, 11600 Montevideo, Uruguay.
| | - Gregorio Iraola
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay; Unidad de Bioinformática, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay.
| | - Alejandra Méndez
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Ruta 226 km. 76.5, Balcarce 7620, Argentina.
| | - Claudia Morsella
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Ruta 226 km. 76.5, Balcarce 7620, Argentina.
| | - Fernando Paolicchi
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Ruta 226 km. 76.5, Balcarce 7620, Argentina.
| | - Silvia Silveyra
- División de Laboratorios Veterinarios, Ministerio de Ganadería Agricultura y Pesca, Ruta 8 Brig. Gral. J. A. Lavalleja Km. 17.500, Montevideo, 12000, Uruguay.
| | - Alejandra Velilla
- Laboratorio de Bacteriología, Unidad Integrada INTA-Universidad Nacional de Mar del Plata, Ruta 226 km. 76.5, Balcarce 7620, Argentina.
| | - Ruben Pérez
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| |
Collapse
|
83
|
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.
Collapse
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
| |
Collapse
|
84
|
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;
| |
Collapse
|
85
|
Andersen JM, Shoup M, Robinson C, Britton R, Olsen KEP, Barrangou R. CRISPR Diversity and Microevolution in Clostridium difficile. Genome Biol Evol 2016; 8:2841-55. [PMID: 27576538 PMCID: PMC5630864 DOI: 10.1093/gbe/evw203] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2016] [Indexed: 12/20/2022] Open
Abstract
Virulent strains of Clostridium difficile have become a global health problem associated with morbidity and mortality. Traditional typing methods do not provide ideal resolution to track outbreak strains, ascertain genetic diversity between isolates, or monitor the phylogeny of this species on a global basis. Here, we investigate the occurrence and diversity of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) in C. difficile to assess the potential of CRISPR-based phylogeny and high-resolution genotyping. A single Type-IB CRISPR-Cas system was identified in 217 analyzed genomes with cas gene clusters present at conserved chromosomal locations, suggesting vertical evolution of the system, assessing a total of 1,865 CRISPR arrays. The CRISPR arrays, markedly enriched (8.5 arrays/genome) compared with other species, occur both at conserved and variable locations across strains, and thus provide a basis for typing based on locus occurrence and spacer polymorphism. Clustering of strains by array composition correlated with sequence type (ST) analysis. Spacer content and polymorphism within conserved CRISPR arrays revealed phylogenetic relationship across clades and within ST. Spacer polymorphisms of conserved arrays were instrumental for differentiating closely related strains, e.g., ST1/RT027/B1 strains and pathogenicity locus encoding ST3/RT001 strains. CRISPR spacers showed sequence similarity to phage sequences, which is consistent with the native role of CRISPR-Cas as adaptive immune systems in bacteria. Overall, CRISPR-Cas sequences constitute a valuable basis for genotyping of C. difficile isolates, provide insights into the micro-evolutionary events that occur between closely related strains, and reflect the evolutionary trajectory of these genomes.
Collapse
Affiliation(s)
- Joakim M Andersen
- Department of Food, Processing and Nutritional Sciences, North Carolina State University, NC
| | - Madelyn Shoup
- Department of Microbiology and Molecular Genetics, Michigan State University, MI
| | - Cathy Robinson
- Department of Microbiology and Molecular Genetics, Michigan State University, MI
| | - Robert Britton
- Department of Molecular Virology and Microbiology, Center for Metagenomics and Microbiome Research, Baylor College of Medicine, TX
| | - Katharina E P Olsen
- Microbial Competence Centre, Novo Nordisk, Bagsværd, Denmark (Former Employment: Department of Microbiology & Infection Control, Statens Serum Institut, Copenhagen, Denmark)
| | - Rodolphe Barrangou
- Department of Food, Processing and Nutritional Sciences, North Carolina State University, NC
| |
Collapse
|
86
|
Wu F, Xu X, Xie J, Yi S, Wang J, Yang X, Yang C, Liang B, Ma Q, Li H, Song H, Qiu S. Molecular Characterization of Salmonella enterica Serovar Aberdeen Negative for H2S Production in China. PLoS One 2016; 11:e0161352. [PMID: 27552230 PMCID: PMC4994947 DOI: 10.1371/journal.pone.0161352] [Citation(s) in RCA: 8] [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: 05/30/2016] [Accepted: 08/03/2016] [Indexed: 12/31/2022] Open
Abstract
Salmonella enterica infections continue to be a significant burden on public health worldwide. The ability of S. enterica to produce hydrogen sulfide (H2S) is an important phenotypic characteristic used to screen and identify Salmonella with selective medium; however, H2S-negative Salmonella have recently emerged. In this study, the H2S phenotype of Salmonella isolates was confirmed, and the selected isolates were subjected to antimicrobial susceptibility testing and molecular identification by multilocus sequence typing, pulsed-field gel electrophoresis, and clustered regularly interspaced short palindromic repeat (CRISPR) analysis. The phs genetic operon was also analyzed. A total of 160 S. enterica serovar Aberdeen isolates were detected between 2005 and 2013 in China. Of them, seven non-H2S-producing isolates were detected. Notably, four samples yielded four pairs of isolates with different H2S phenotypes, simultaneously. The data demonstrated that H2S-negative isolates were genetically closely related to H2S-positive isolates. Three new spacers (Abe1, Abe2, and Abe3) were identified in CRISPR locus 1 in four pairs of isolates with different H2S phenotypes from the same samples. Sequence analysis revealed a new nonsense mutation at position 208 in the phsA gene of all non-H2S-producing isolates. Additionally, we describe a new screening procedure to avoid H2S-negative Salmonella, which would normally be overlooked during laboratory and hospital screening. The prevalence of this pathogen may be underestimated; therefore, it is important to focus on improving surveillance of this organism to control its spread.
Collapse
Affiliation(s)
- Fuli Wu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Xuebin Xu
- Shanghai Municipal Centre for Disease Control and Prevention, Shanghai, 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
| | - Xiaoxia Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Chaojie Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Beibei Liang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Qiuxia Ma
- 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
| | - Hongbin Song
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
- * E-mail: (SQ); (HS)
| | - Shaofu Qiu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
- * E-mail: (SQ); (HS)
| |
Collapse
|
87
|
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.
Collapse
|
88
|
Fratamico PM, DebRoy C, Liu Y, Needleman DS, Baranzoni GM, Feng P. Advances in Molecular Serotyping and Subtyping of Escherichia coli. Front Microbiol 2016; 7:644. [PMID: 27199968 PMCID: PMC4853403 DOI: 10.3389/fmicb.2016.00644] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/18/2016] [Indexed: 01/25/2023] Open
Abstract
Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing E. coli have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for E. coli, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of E. coli is replacing established subtyping methods such as pulsed-field gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. A variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers.
Collapse
Affiliation(s)
- Pina M. Fratamico
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Chitrita DebRoy
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University ParkPA, USA
| | - Yanhong Liu
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - David S. Needleman
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Gian Marco Baranzoni
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Peter Feng
- Division of Microbiology, U.S. Food and Drug Administration, College ParkMD, USA
| |
Collapse
|
89
|
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.
Collapse
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
| |
Collapse
|
90
|
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.
Collapse
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;
| |
Collapse
|
91
|
Clustered Regularly Interspaced Short Palindromic Repeats Are emm Type-Specific in Highly Prevalent Group A Streptococci. PLoS One 2015; 10:e0145223. [PMID: 26710228 PMCID: PMC4692479 DOI: 10.1371/journal.pone.0145223] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 11/30/2015] [Indexed: 12/20/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) are the bacterial adaptive immune system against foreign nucleic acids. Given the variable nature of CRISPR, it could be a good marker for molecular epidemiology. Group A streptococcus is one of the major human pathogens. It has two CRISPR loci, including CRISPR01 and CRISPR02. The aim of this study was to analyze the distribution of CRISPR-associated gene cassettes (cas) and CRISPR arrays in highly prevalent emm types. The cas cassette and CRISPR array in two CRISPR loci were analyzed in a total of 332 strains, including emm1, emm3, emm4, emm12, and emm28 strains. The CRISPR type was defined by the spacer content of each CRISPR array. All strains had at least one cas cassette or CRISPR array. More than 90% of the spacers were found in one emm type, specifically. Comparing the consistency between emm and CRISPR types by Simpson’s index of diversity and the adjusted Wallace coefficient, CRISPR01 type was concordant to emm type, and CRISPR02 showed unidirectional congruence to emm type, suggesting that at least for the majority of isolates causing infection in high income countries, the emm type can be inferred from CRISPR analysis, which can further discriminate isolates sharing the same emm type.
Collapse
|
92
|
Förster H, McGhee GC, Sundin GW, Adaskaveg JE. Characterization of Streptomycin Resistance in Isolates of Erwinia amylovora in California. PHYTOPATHOLOGY 2015; 105:1302-1310. [PMID: 26413887 DOI: 10.1094/phyto-03-15-0078-r] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In surveys from 2006 to 2014, streptomycin resistance in Erwinia amylovora from pear-growing areas in California declined from very high incidence in 2006 and 2007 to very low incidence in 2013 and 2014. The majority of resistant strains were designated as moderately resistant-low (MR-L), and were almost exclusively found in Sacramento County, whereas highly resistant (HR) strains were only recovered in Sutter-Yuba and San Joaquin counties. Resistance of HR strains was associated with a mutation in codon 43 of the chromosomal rpsL gene that results in a change from lysine to arginine, the same mutation that was originally reported for resistant strains from California in the mid-1970s. MR-L strains were found to harbor the strA-strB streptomycin resistance genes on transposon Tn5393a. This transposon lacks insertion sequence IS1133 that provides a promoter for efficient expression of strA-strB, resulting in lower minimum inhibitory concentrations of MR-L strains compared with those from other locations that harbor strA-strB on Tn5393::IS1133. In contrast to previously described plasmid-mediated resistance where Tn5393 is inserted in pEa34, or pEA29, Tn5393a in MR-L strains was located on plasmid pEU30. This plasmid was first described in E. amylovora from the western United States but was not associated with streptomycin resistance determinants previously. We hypothesize that Tn5393a was introduced into an E. amylovora strain carrying pEU30 and transposed into that plasmid. This hypothesis was supported by clustered regularly interspaced short palindromic repeat (CRISPR) sequence analysis that showed that two MR-L strains share the same CRISPR1 pattern as a streptomycin-sensitive strain. With current low resistance levels in California growing regions, streptomycin could be successfully used again, but applications per season should be limited and the antibiotic should be mixed and rotated with different modes of action.
Collapse
Affiliation(s)
- Helga Förster
- First and fourth authors: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; and second and third authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing 48824
| | - Gayle C McGhee
- First and fourth authors: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; and second and third authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing 48824
| | - George W Sundin
- First and fourth authors: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; and second and third authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing 48824
| | - James E Adaskaveg
- First and fourth authors: Department of Plant Pathology and Microbiology, University of California, Riverside 92521; and second and third authors: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing 48824
| |
Collapse
|
93
|
Hullahalli K, Rodrigues M, Schmidt BD, Li X, Bhardwaj P, Palmer KL. Comparative Analysis of the Orphan CRISPR2 Locus in 242 Enterococcus faecalis Strains. PLoS One 2015; 10:e0138890. [PMID: 26398194 PMCID: PMC4580645 DOI: 10.1371/journal.pone.0138890] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/04/2015] [Indexed: 12/18/2022] Open
Abstract
Clustered, Regularly Interspaced Short Palindromic Repeats and their associated Cas proteins (CRISPR-Cas) provide prokaryotes with a mechanism for defense against mobile genetic elements (MGEs). A CRISPR locus is a molecular memory of MGE encounters. It contains an array of short sequences, called spacers, that generally have sequence identity to MGEs. Three different CRISPR loci have been identified among strains of the opportunistic pathogen Enterococcus faecalis. CRISPR1 and CRISPR3 are associated with the cas genes necessary for blocking MGEs, but these loci are present in only a subset of E. faecalis strains. The orphan CRISPR2 lacks cas genes and is ubiquitous in E. faecalis, although its spacer content varies from strain to strain. Because CRISPR2 is a variable locus occurring in all E. faecalis, comparative analysis of CRISPR2 sequences may provide information about the clonality of E. faecalis strains. We examined CRISPR2 sequences from 228 E. faecalis genomes in relationship to subspecies phylogenetic lineages (sequence types; STs) determined by multilocus sequence typing (MLST), and to a genome phylogeny generated for a representative 71 genomes. We found that specific CRISPR2 sequences are associated with specific STs and with specific branches on the genome tree. To explore possible applications of CRISPR2 analysis, we evaluated 14 E. faecalis bloodstream isolates using CRISPR2 analysis and MLST. CRISPR2 analysis identified two groups of clonal strains among the 14 isolates, an assessment that was confirmed by MLST. CRISPR2 analysis was also used to accurately predict the ST of a subset of isolates. We conclude that CRISPR2 analysis, while not a replacement for MLST, is an inexpensive method to assess clonality among E. faecalis isolates, and can be used in conjunction with MLST to identify recombination events occurring between STs.
Collapse
Affiliation(s)
- Karthik Hullahalli
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
| | - Marinelle Rodrigues
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
| | - Brendan D. Schmidt
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
| | - Xiang Li
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
| | - Pooja Bhardwaj
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
| | - Kelli L. Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
- * E-mail:
| |
Collapse
|
94
|
Very KJ, Kirchner MK, Shariat N, Cottrell W, Sandt CH, Dudley EG, Kariyawasam S, Jayarao BM. Prevalence and Spatial Distribution of Salmonella Infections in the Pennsylvania Raccoon (Procyon lotor). Zoonoses Public Health 2015; 63:223-33. [PMID: 26272724 DOI: 10.1111/zph.12222] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 11/30/2022]
Abstract
A study was conducted to determine the prevalence and spatial distribution of Salmonella infection in Pennsylvania raccoons (Procyon lotor), common wildlife mammals known to occupy overlapping habitats with humans and domestic food animals. The Pennsylvania Game Commission provided a total of 371 raccoon intestinal samples from trapped and road-killed raccoons collected between May and November 2011. Salmonella was isolated from the faeces of 56 (15.1%) of 371 raccoons in 35 (54%) of 65 counties across Pennsylvania. The five most frequently isolated serotypes were Newport (28.6%), Enteritidis (19.6%), Typhimurium (10.7%), Braenderup (8.9%) and Bareilly (7.1%). Pulsed-field gel electrophoresis (PFGE) analysis of the Salmonella isolates and subsequent comparison to the Pennsylvania Department of Health human Salmonella PFGE database revealed 16 different pulsetypes in Salmonella isolates recovered from raccoons that were indistinguishable from pulsetypes of Salmonella collected from clinically ill humans during the study period. The pulsetypes of seven raccoon Salmonella isolates matched those of 56 human Salmonella isolates by month and geographical region of sample collection. Results from Clustered Regularly Interspaced Short Palindromic Repeats and Multi-Virulence Locus Sequence Typing (CRISPR-MVLST) analysis corroborated the PFGE and serotyping data. The findings of this study show that several PFGE pulsetypes of Salmonella were shared between humans and raccoons in Pennsylvania, indicating that raccoons and humans might share the same source of Salmonella.
Collapse
Affiliation(s)
- K J Very
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - M K Kirchner
- Department of Food Science, The Pennsylvania State University, University Park, PA, USA
| | - N Shariat
- Department of Food Science, The Pennsylvania State University, University Park, PA, USA
| | - W Cottrell
- Northeast Wildlife Disease Cooperative, Bradford, VT, USA
| | - C H Sandt
- Bureau of Laboratories, Division of Clinical Microbiology, Pennsylvania Department of Health, Exton, PA, USA
| | - E G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, PA, USA
| | - S Kariyawasam
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - B M Jayarao
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
95
|
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]
|
96
|
Kupczok A, Landan G, Dagan T. The Contribution of Genetic Recombination to CRISPR Array Evolution. Genome Biol Evol 2015; 7:1925-39. [PMID: 26085541 PMCID: PMC4524480 DOI: 10.1093/gbe/evv113] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2015] [Indexed: 12/19/2022] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats) is a microbial immune system against foreign DNA. Recognition sequences (spacers) encoded within the CRISPR array mediate the immune reaction in a sequence-specific manner. The known mechanisms for the evolution of CRISPR arrays include spacer acquisition from foreign DNA elements at the time of invasion and array erosion through spacer deletion. Here, we consider the contribution of genetic recombination between homologous CRISPR arrays to the evolution of spacer repertoire. Acquisition of spacers from exogenic arrays via recombination may confer the recipient with immunity against unencountered antagonists. For this purpose, we develop a novel method for the detection of recombination in CRISPR arrays by modeling the spacer order in arrays from multiple strains from the same species. Because the evolutionary signal of spacer recombination may be similar to that of pervasive spacer deletions or independent spacer acquisition, our method entails a robustness analysis of the recombination inference by a statistical comparison to resampled and perturbed data sets. We analyze CRISPR data sets from four bacterial species: two Gammaproteobacteria species harboring CRISPR type I and two Streptococcus species harboring CRISPR type II loci. We find that CRISPR array evolution in Escherichia coli and Streptococcus agalactiae can be explained solely by vertical inheritance and differential spacer deletion. In Pseudomonas aeruginosa, we find an excess of single spacers potentially incorporated into the CRISPR locus during independent acquisition events. In Streptococcus thermophilus, evidence for spacer acquisition by recombination is present in 5 out of 70 strains. Genetic recombination has been proposed to accelerate adaptation by combining beneficial mutations that arose in independent lineages. However, for most species under study, we find that CRISPR evolution is shaped mainly by spacer acquisition and loss rather than recombination. Since the evolution of spacer content is characterized by a rapid turnover, it is likely that recombination is not beneficial for improving phage resistance in the strains under study, or that it cannot be detected in the resolution of intraspecies comparisons.
Collapse
Affiliation(s)
- Anne Kupczok
- Institute of General Microbiology, Christian-Albrechts-University Kiel, Germany
| | - Giddy Landan
- Institute of General Microbiology, Christian-Albrechts-University Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Christian-Albrechts-University Kiel, Germany
| |
Collapse
|
97
|
Lier C, Baticle E, Horvath P, Haguenoer E, Valentin AS, Glaser P, Mereghetti L, Lanotte P. Analysis of the type II-A CRISPR-Cas system of Streptococcus agalactiae reveals distinctive features according to genetic lineages. Front Genet 2015; 6:214. [PMID: 26124774 PMCID: PMC4466440 DOI: 10.3389/fgene.2015.00214] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/01/2015] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) are found in 90% of archaea and about 40% of bacteria. In this original system, CRISPR arrays comprise short, almost unique sequences called spacers that are interspersed with conserved palindromic repeats. These systems play a role in adaptive immunity and participate to fight non-self DNA such as integrative and conjugative elements, plasmids, and phages. In Streptococcus agalactiae, a bacterium implicated in colonization and infections in humans since the 1960s, two CRISPR-Cas systems have been described. A type II-A system, characterized by proteins Cas9, Cas1, Cas2, and Csn2, is ubiquitous, and a type I–C system, with the Cas8c signature protein, is present in about 20% of the isolates. Unlike type I–C, which appears to be non-functional, type II-A appears fully functional. Here we studied type II-A CRISPR-cas loci from 126 human isolates of S. agalactiae belonging to different clonal complexes that represent the diversity of the species and that have been implicated in colonization or infection. The CRISPR-cas locus was analyzed both at spacer and repeat levels. Major distinctive features were identified according to the phylogenetic lineages previously defined by multilocus sequence typing, especially for the sequence type (ST) 17, which is considered hypervirulent. Among other idiosyncrasies, ST-17 shows a significantly lower number of spacers in comparison with other lineages. This characteristic could reflect the peculiar virulence or colonization specificities of this lineage.
Collapse
Affiliation(s)
- Clément Lier
- UMR1282 Infectiologie et Santé Publique, Bactéries et Risque Materno-Foetal, Université de Tours, Tours France ; INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly France ; Service de Bactériologie-Virologie, Hôpital Bretonneau - Centre Hospitalier Régional et Universitaire de Tours, Tours France
| | - Elodie Baticle
- Service de Bactériologie-Virologie, Hôpital Bretonneau - Centre Hospitalier Régional et Universitaire de Tours, Tours France
| | | | - Eve Haguenoer
- UMR1282 Infectiologie et Santé Publique, Bactéries et Risque Materno-Foetal, Université de Tours, Tours France ; INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly France
| | - Anne-Sophie Valentin
- UMR1282 Infectiologie et Santé Publique, Bactéries et Risque Materno-Foetal, Université de Tours, Tours France ; INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly France ; Service de Bactériologie-Virologie, Hôpital Bretonneau - Centre Hospitalier Régional et Universitaire de Tours, Tours France
| | - Philippe Glaser
- Unité de Biologie des Bactéries Pathogènes à Gram Positif, Institut Pasteur, Paris France ; CNRS UMR 3525, Paris France
| | - Laurent Mereghetti
- UMR1282 Infectiologie et Santé Publique, Bactéries et Risque Materno-Foetal, Université de Tours, Tours France ; INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly France ; Service de Bactériologie-Virologie, Hôpital Bretonneau - Centre Hospitalier Régional et Universitaire de Tours, Tours France
| | - Philippe Lanotte
- UMR1282 Infectiologie et Santé Publique, Bactéries et Risque Materno-Foetal, Université de Tours, Tours France ; INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly France ; Service de Bactériologie-Virologie, Hôpital Bretonneau - Centre Hospitalier Régional et Universitaire de Tours, Tours France
| |
Collapse
|
98
|
Koskela KA, Mattinen L, Kalin-Mänttäri L, Vergnaud G, Gorgé O, Nikkari S, Skurnik M. Generation of a CRISPR database forYersinia pseudotuberculosiscomplex and role of CRISPR-based immunity in conjugation. Environ Microbiol 2015; 17:4306-21. [DOI: 10.1111/1462-2920.12816] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 02/11/2015] [Indexed: 12/26/2022]
Affiliation(s)
- Katja A. Koskela
- Research and Development Department; Centre for Military Medicine; Helsinki Finland
| | - Laura Mattinen
- Department of Bacteriology and Immunology; Haartman Institute and Research Programs Unit; Immunobiology; University of Helsinki; PO Box 21, 00014 Helsinki Finland
| | - Laura Kalin-Mänttäri
- Research and Development Department; Centre for Military Medicine; Helsinki Finland
- Department of Bacteriology and Immunology; Haartman Institute and Research Programs Unit; Immunobiology; University of Helsinki; PO Box 21, 00014 Helsinki Finland
| | - Gilles Vergnaud
- Univ Paris-Sud; Institut de Génétique et Microbiologie; UMR8621; Orsay France
- CNRS; Orsay France
- ENSTA ParisTech; Palaiseau France
| | - Olivier Gorgé
- Univ Paris-Sud; Institut de Génétique et Microbiologie; UMR8621; Orsay France
- CNRS; Orsay France
- DGA/MNRBC; Vert le Petit France
| | - Simo Nikkari
- Research and Development Department; Centre for Military Medicine; Helsinki Finland
| | - Mikael Skurnik
- Department of Bacteriology and Immunology; Haartman Institute and Research Programs Unit; Immunobiology; University of Helsinki; PO Box 21, 00014 Helsinki Finland
- Helsinki University Central Hospital Laboratory Diagnostics; Helsinki Finland
| |
Collapse
|
99
|
Karah N, Samuelsen Ø, Zarrilli R, Sahl JW, Wai SN, Uhlin BE. CRISPR-cas subtype I-Fb in Acinetobacter baumannii: evolution and utilization for strain subtyping. PLoS One 2015; 10:e0118205. [PMID: 25706932 PMCID: PMC4338279 DOI: 10.1371/journal.pone.0118205] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/09/2015] [Indexed: 12/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) are polymorphic elements found in the genome of some or all strains of particular bacterial species, providing them with a system of acquired immunity against invading bacteriophages and plasmids. Two CRISPR-Cas systems have been identified in Acinetobacter baumannii, an opportunistic pathogen with a remarkable capacity for clonal dissemination. In this study, we investigated the mode of evolution and diversity of spacers of the CRISPR-cas subtype I-Fb locus in a global collection of 76 isolates of A. baumannii obtained from 14 countries and 4 continents. The locus has basically evolved from a common ancestor following two main lineages and several pathways of vertical descent. However, this vertical passage has been interrupted by occasional events of horizontal transfer of the whole locus between distinct isolates. The isolates were assigned into 40 CRISPR-based sequence types (CST). CST1 and CST23-24 comprised 18 and 9 isolates, representing two main sub-clones of international clones CC1 and CC25, respectively. Epidemiological data showed that some of the CST1 isolates were acquired or imported from Iraq, where it has probably been endemic for more than one decade and occasionally been able to spread to USA, Canada, and Europe. CST23-24 has shown a remarkable ability to cause national outbreaks of infections in Sweden, Argentina, UAE, and USA. The three isolates of CST19 were independently imported from Thailand to Sweden and Norway, raising a concern about the prevalence of CST19 in Thailand. Our study highlights the dynamic nature of the CRISPR-cas subtype I-Fb locus in A. baumannii, and demonstrates the possibility of using a CRISPR-based approach for subtyping a significant part of the global population of A. baumannii.
Collapse
Affiliation(s)
- Nabil Karah
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- * E-mail:
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples “Federico II”, Naples, Italy
- CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Jason W. Sahl
- Department of Pathogen Genomics, Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Sun Nyunt Wai
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Bernt Eric Uhlin
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| |
Collapse
|
100
|
Bull CT, Koike ST. Practical benefits of knowing the enemy: modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant-pathogenic bacteria. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:157-80. [PMID: 26002289 DOI: 10.1146/annurev-phyto-080614-120122] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Knowing the identity of bacterial plant pathogens is essential to strategic and sustainable disease management in agricultural systems. This knowledge is critical for growers, diagnosticians, extension agents, and others dealing with crops. However, such identifications are linked to bacterial taxonomy, a complicated and changing discipline that depends on methods and information that are often not used by those who are diagnosing field problems. Modern molecular tools for fingerprinting and sequencing allow for pathogen identification in the absence of distinguishing or conveniently tested phenotypic characteristics. These methods are also useful in studying the etiology and epidemiology of phytopathogenic bacteria from epidemics, as was done in numerous studies conducted in California's Salinas Valley. Multilocus and whole-genome sequence analyses are becoming the cornerstones of studies of microbial diversity and bacterial taxonomy. Whole-genome sequence analysis needs to become adequately accessible, automated, and affordable in order to be used routinely for identification and epidemiology. The power of molecular tools in accurately identifying bacterial pathogenesis is therefore of value to the farmer, diagnostician, phytobacteriologist, and taxonomist.
Collapse
Affiliation(s)
- Carolee T Bull
- United States Department of Agriculture, Agricultural Research Service, Salinas, California 93905;
| | | |
Collapse
|