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Yeh HY, Cox NA, Hinton A, Berrang ME. Detection and Distribution of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in Campylobacter jejuni Isolates from Chicken Livers. J Food Prot 2024; 87:100250. [PMID: 38382707 DOI: 10.1016/j.jfp.2024.100250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Campylobacter jejuni is the leading foodborne bacterial pathogen that causes human gastroenteritis worldwide linked to the consumption of undercooked broiler livers. Application of bacteriophages during poultry production has been used as an alternative approach to reduce contamination of poultry meat by Campylobacter. To make this approach effective, understanding the presence of the bacteriophage sequences in the CRISPR spacers in C. jejuni is critical as they may confer bacterial resistance to bacteriophage treatment. Therefore, in this study, we explored the distribution of the CRISPR arrays from 178 C. jejuni isolated from chicken livers between January and July 2018. Genomic DNA of C. jejuni isolates was extracted, and CRISPR type 1 sequences were amplified by PCR. Amplicons were purified and sequenced by the Sanger dideoxy sequencing method. Direct repeats (DRs) and spacers of CRISPR sequences were identified using the CRISPRFinder program. Further, spacer sequences were submitted to the CRISPRTarget to identify potential homology to bacteriophage types. Even though CRISPR-Cas is reportedly not an active system in Campylobacter, a total of 155 (87%) C. jejuni isolates were found to harbor CRISPR sequences; one type of DR was identified in all 155 isolates. The CRISPR loci lengths ranged from 97 to 431 nucleotides. The numbers of spacers ranged from one to six. A total of 371 spacer sequences were identified in the 155 isolates that could be grouped into 51 distinctive individual sequences. Further comparison of these 51 spacer sequences with those in databases showed that most spacer sequences were homologous to Campylobacter bacteriophage DA10. The results of our study provide important information relative to the development of an effective bacteriophage treatment to mitigate Campylobacter during poultry production.
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Affiliation(s)
- Hung-Yueh Yeh
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA.
| | - Nelson A Cox
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
| | - Arthur Hinton
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
| | - Mark E Berrang
- U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA 30605-2720, USA
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2
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Ohadi E, Azarnezhad A, Lotfollahi L, Asadollahi P, Kaviar VH, Razavi S, Sadeghi Kalani B. Evaluation of Genetic Content of the CRISPR Locus in Listeria monocytogenes Isolated From Clinical, Food, Seafood and Animal Samples in Iran. Curr Microbiol 2023; 80:388. [PMID: 37878078 DOI: 10.1007/s00284-023-03508-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 11/14/2022] [Indexed: 10/26/2023]
Abstract
CRISPR arrays, which are organized to fight against non-self DNA elements, have shown sequence diversity that could be useful in evolution and typing studies. In this study, 55 samples of L. monocytogenes isolated from different sources were evaluated for CRISPR sequence polymorphism. The CRISPR loci were identified using CRISPR databases. A single PCR assay was designed to amplify the target CRISPRs using an appropriate universal primer. Sequencing results were analyzed using CRISPR databases and BLASTn, and the CRISPR locus was present in all the strains. Three hundred repeats including 55 terminal repeats were identified. Four types of consensuses direct repeat (DR) with different lengths and sequences were characterized. Sixty repeat variants were observed which possessed different polymorphisms. Two hundred and fifty spacers were identified from which 35 consensus sequences were determined, indicating the high polymorphism of the CRISPR spacers. The identified spacers showed similarities to listeria phage sequences, other bacterial phage sequences, plasmid sequences and bacterial sequences. In order to control the bacterial outbreaks, a robust and precise system of subtyping is required. High levels of polymorphism in the CRISPR loci in this study might be related to the origin and time of the samples' isolation. However, it is essential to assess, on a case-by-case basis, the characteristics of any given CRISPR locus before its use as an epidemiological marker. In conclusion, the results of this study showed that the use of sequence content of CRISPR area could provide new and valuable information on the evolution and typing of the L. monocytogenes bacterium.
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Affiliation(s)
- Elnaz Ohadi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Hemmat Highway, Tehran, Iran
| | - Asaad Azarnezhad
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Lida Lotfollahi
- Department of Microbiology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Parisa Asadollahi
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Vahab Hasan Kaviar
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Shabnam Razavi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Hemmat Highway, Tehran, Iran.
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Behrooz Sadeghi Kalani
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran.
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran.
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3
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Detection and identification of Lactobacillus acidophilus species and its commercial probiotic strains using CRISPR loci-based amplicon analysis. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Wang X, Zhuo Q, Hong Y, Wu Y, Gu Q, Yuan D, Dong Q, Shao J. Correlation between Multilocus Sequence Typing and Antibiotic Resistance, Virulence Potential of Campylobacter jejuni Isolates from Poultry Meat. Foods 2022; 11:foods11121768. [PMID: 35741967 PMCID: PMC9222796 DOI: 10.3390/foods11121768] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/30/2022] [Accepted: 06/11/2022] [Indexed: 12/10/2022] Open
Abstract
Campylobacter jejuni is a major foodborne pathogen and can be transmitted to human beings via the consumption of poultry products. This study aimed to determine antibiotic resistance and virulence potential of one hundred C. jejuni isolates from poultry meat and to explore the correlation between them and the multilocus sequence types (MLST). A total of 29 STs and 13 CCs were identified by MLST, of which 8 STs were first identified. The dominant ST was ST583 (21%), followed by ST42 (15%), ST61 (12%), and ST2276 (10%). Eighty-eight isolates showed resistance to at least one antibiotic. The resistance rate to fluoroquinolones was the highest (81%), followed by tetracycline (59%), whereas all the isolates were susceptible to erythromycin and telithromycin. Multi-antibiotic resistance was detected in 18 C. jejuni isolates. Great variability in the adhesion and invasion ability to Caco-2 cells was observed for the 100 isolates, with adhesion rates varying between 0.02% and 28.48%, and invasion rates varied from 0 to 6.26%. A correlation between STs and antibiotic resistance or virulence was observed. The ST61 isolates were significantly sensitive to CIP, while the TET resistance was significantly associated with ST354 and ST6175 complex. ST11326 showed substantially higher resistance to gentamicin and higher adhesion and invasion abilities to Caco-2 cells. The results helped improve our understanding of the potential hazard of different genotypes C. jejuni and provided critical information for the risk assessment of campylobacteriosis infection.
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Affiliation(s)
- Xiang Wang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China; (X.W.); (Q.Z.); (Y.H.); (Q.D.)
| | - Qiyun Zhuo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China; (X.W.); (Q.Z.); (Y.H.); (Q.D.)
| | - Yi Hong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China; (X.W.); (Q.Z.); (Y.H.); (Q.D.)
| | - Yufan Wu
- Centre of Analysis and Test, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
- Technology Center of Zhangjiagang Customs, Suzhou 215600, China; (Q.G.); (D.Y.)
- Correspondence: (Y.W.); (J.S.); Tel.: +86-21-64252849 (Y.W.); +86-512-56302785 (J.S.)
| | - Qiang Gu
- Technology Center of Zhangjiagang Customs, Suzhou 215600, China; (Q.G.); (D.Y.)
| | - Dawei Yuan
- Technology Center of Zhangjiagang Customs, Suzhou 215600, China; (Q.G.); (D.Y.)
| | - Qingli Dong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China; (X.W.); (Q.Z.); (Y.H.); (Q.D.)
| | - Jingdong Shao
- Technology Center of Zhangjiagang Customs, Suzhou 215600, China; (Q.G.); (D.Y.)
- Correspondence: (Y.W.); (J.S.); Tel.: +86-21-64252849 (Y.W.); +86-512-56302785 (J.S.)
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van Vliet AHM, Charity OJ, Reuter M. A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare? Microb Genom 2021; 7. [PMID: 34766904 PMCID: PMC8743540 DOI: 10.1099/mgen.0.000729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Microbial genomes are highly adaptable, with mobile genetic elements (MGEs) such as integrative conjugative elements (ICEs) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanisms such as CRISPR-Cas systems, which limit invading MGEs by sequence-specific targeting. Here we report the distribution of the pVir, pTet and PCC42 plasmids and a new 70–129 kb ICE (CampyICE1) in the foodborne bacterial pathogens Campylobacter jejuni and Campylobacter coli. CampyICE1 contains a degenerated Type II-C CRISPR system consisting of a sole Cas9 protein, which is distinct from the previously described Cas9 proteins from C. jejuni and C. coli. CampyICE1 is conserved in structure and gene order, containing blocks of genes predicted to be involved in recombination, regulation and conjugation. CampyICE1 was detected in 134/5829 (2.3 %) C. jejuni genomes and 92/1347 (6.8 %) C. coli genomes. Similar ICEs were detected in a number of non-jejuni/coli Campylobacter species, although these lacked a CRISPR-Cas system. CampyICE1 carries three separate short CRISPR spacer arrays containing a combination of 108 unique spacers and 16 spacer-variant families. A total of 69 spacers and 10 spacer-variant families (63.7 %) were predicted to target Campylobacter plasmids. The presence of a functional CampyICE1 Cas9 protein and matching anti-plasmid spacers was associated with the absence of the pVir, pTet and pCC42 plasmids (188/214 genomes, 87.9 %), suggesting that the CampyICE1-encoded CRISPR-Cas has contributed to the exclusion of competing plasmids. In conclusion, the characteristics of the CRISPR-Cas9 system on CampyICE1 suggests a history of plasmid warfare in Campylobacter.
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Affiliation(s)
- Arnoud H M van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Oliver J Charity
- Quadram Institute Bioscience, Microbes in the Food Chain programme, Norwich, UK
| | - Mark Reuter
- Quadram Institute Bioscience, Microbes in the Food Chain programme, Norwich, UK
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Le Gratiet T, Le Marechal C, Devaere M, Chemaly M, Woudstra C. Exploration of the Diversity of Clustered Regularly Interspaced Short Palindromic Repeats-Cas Systems in Clostridium novyi sensu lato. Front Microbiol 2021; 12:711413. [PMID: 34589070 PMCID: PMC8473940 DOI: 10.3389/fmicb.2021.711413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Classified as the genospecies Clostridium novyi sensu lato and distributed into four lineages (I-IV), Clostridium botulinum (group III), Clostridium novyi, and Clostridium haemolyticum are clostridial pathogens that cause animal diseases. Clostridium novyi sensu lato contains a large mobilome consisting of plasmids and circular bacteriophages. Here, we explored clustered regularly interspaced short palindromic repeats (CRISPR) arrays and their associated proteins (Cas) to shed light on the link between evolution of CRISPR-Cas systems and the plasmid and phage composition in a study of 58 Clostridium novyi sensu lato genomes. In 55 of these genomes, types I-B (complete or partial), I-D, II-C, III-B, III-D, or V-U CRISPR-Cas systems were detected in chromosomes as well as in mobile genetic elements (MGEs). Type I-B predominated (67.2%) and was the only CRISPR type detected in the Ia, III, and IV genomic lineages. Putative type V-U CRISPR Cas14a genes were detected in two different cases: next to partial type-IB CRISPR loci on the phage encoding the botulinum neurotoxin (BoNT) in lineage Ia and in 12 lineage II genomes, as part of a putative integrative element related to a phage-inducible chromosomal island (PICI). In the putative PICI, Cas14a was associated with CRISPR arrays and restriction modification (RM) systems as part of an accessory locus. This is the first time a PICI containing such locus has been detected in C. botulinum. Mobilome composition and dynamics were also investigated based on the contents of the CRISPR arrays and the study of spacers. A large proportion of identified protospacers (20.2%) originated from Clostridium novyi sensu lato (p1_Cst, p4_BKT015925, p6_Cst, CWou-2020a, p1_BKT015925, and p2_BKT015925), confirming active exchanges within this genospecies and the key importance of specific MGEs in Clostridium novyi sensu lato.
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Affiliation(s)
- Thibault Le Gratiet
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
- UFR of Life Sciences and Environment, University of Rennes, Rennes, France
| | - Caroline Le Marechal
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Marie Devaere
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Marianne Chemaly
- Hygiene and Quality of Poultry and Pig Products Unit, ANSES, French Agency for Food, Environmental and Occupational Health Safety, Ploufragan, France
| | - Cédric Woudstra
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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7
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Yeh HY, Awad A, Rothrock MJ. Detection of Campylobacter jejuni diversity by clustered regularly interspaced short palindromic repeats (CRISPR) from an animal farm. Vet Med Sci 2021; 7:2381-2388. [PMID: 34510794 PMCID: PMC8604122 DOI: 10.1002/vms3.622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background Campylobacter jejuni is the leading bacterial pathogen that causes foodborne illness worldwide. Because of genetic diversity and sophisticated growth requirements of C. jejuni, several genotyping methods have been investigated to classify this bacterium during the outbreaks. One of such method is to use clustered regularly interspaced short palindromic repeats (CRISPR). Objectives The goal of this study was to explore the diversity of C. jejuni isolates with CRISPR from an animal farm. Methods Seventy‐seven C. jejuni isolates from an animal farm were used in this study. The day‐old broilers were reared with other poultry and farm animals, including layer hens, guinea hens, dairy goats and sheep. A small swine herd was also present on an adjacent, but separate plot of land. Isolation and identification of C. jejuni were performed according to the standard procedures. The CRISPR type 1 was PCR amplified from genomic DNA, and the amplicons were sequenced by the Sanger dideoxy method. The direct repeats (DRs) and spacers of the CRISPR sequences were identified using the CRISPRFinder. Results The CRISPR sequences were detected in all 77 isolates. One type of DRs was identified in these 77 isolates. The lengths of the CRISPR locus ranged from 100 to 560 nucleotides, whereas the number of spacers ranged from one to eight. The distributions of the numbers of CRISPR spacers from different sources seemed to be random. Overall, 17 out of 77 (22%) C. jejuni isolates had two and five spacers, whereas 14 out of 77 (18%) isolates had three spaces in their genomes. By further analysis of spacer sequences, a total of 266 spacer sequences were identified in 77 C. jejuni isolates. By comparison with known published spacer sequences, we observed that 49 sequences were unique in this study. The CRISPR sequence combination of Nos. 16, 19, 48 and 57 was found among a total of 15 C. jejuni isolates containing various multi‐locus sequence typing (MLST) types (ST‐50, ST‐607, ST‐2231 and ST‐5602). No. 57 spacer sequence was unique from this study, whereas the other three (Nos. 16, 19 and 48) sequences were found in previous reports. Combination of Nos. 5, 9, 15, 30 and 45 was associated with ST‐353. To compare the CRISPR genotyping with other methods, the MLST was selected due to its high discriminatory power to differentiate isolates. Based on calculation of the Simpson's index of diversity, a combination of both methods had higher Simpson's index value than those for CRISPR or MLST, respectively. Conclusions Our results suggest that the MLST from C. jejuni isolates can be discriminated based on the CRISPR unique spacer sequences and the numbers of spacers. In the future, investigation on the CRISPR resolution for C. jejuni identification in outbreaks is needed. A database that integrates both MLST sequences and CRISPR sequences and is searchable is greatly in demand for tracking outbreaks and evolution of this bacterium.
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Affiliation(s)
- Hung-Yueh Yeh
- Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, USA
| | - Amal Awad
- Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, USA.,Bacteriology, Mycology and Immunology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Michael J Rothrock
- Egg Safety and Quality Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, Athens, Georgia, USA
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8
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Perez M, Angers B, Young CR, Juniper SK. Shining light on a deep-sea bacterial symbiont population structure with CRISPR. Microb Genom 2021; 7:000625. [PMID: 34448690 PMCID: PMC8549365 DOI: 10.1099/mgen.0.000625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/07/2021] [Indexed: 01/04/2023] Open
Abstract
Many foundation species in chemosynthesis-based ecosystems rely on environmentally acquired symbiotic bacteria for their survival. Hence, understanding the biogeographic distributions of these symbionts at regional scales is key to understanding patterns of connectivity and predicting resilience of their host populations (and thus whole communities). However, such assessments are challenging because they necessitate measuring bacterial genetic diversity at fine resolutions. For this purpose, the recently discovered clustered regularly interspaced short palindromic repeats (CRISPR) constitutes a promising new genetic marker. These DNA sequences harboured by about half of bacteria hold their viral immune memory, and as such, might allow discrimination of different lineages or strains of otherwise indistinguishable bacteria. In this study, we assessed the potential of CRISPR as a hypervariable phylogenetic marker in the context of a population genetic study of an uncultured bacterial species. We used high-throughput CRISPR-based typing along with multi-locus sequence analysis (MLSA) to characterize the regional population structure of the obligate but environmentally acquired symbiont species Candidatus Endoriftia persephone on the Juan de Fuca Ridge. Mixed symbiont populations of Ca. Endoriftia persephone were sampled across individual Ridgeia piscesae hosts from contrasting habitats in order to determine if environmental conditions rather than barriers to connectivity are more important drivers of symbiont diversity. We showed that CRISPR revealed a much higher symbiont genetic diversity than the other housekeeping genes. Several lines of evidence imply this diversity is indicative of environmental strains. Finally, we found with both CRISPR and gene markers that local symbiont populations are strongly differentiated across sites known to be isolated by deep-sea circulation patterns. This research showed the high power of CRISPR to resolve the genetic structure of uncultured bacterial populations and represents a step towards making keystone microbial species an integral part of conservation policies for upcoming mining operations on the seafloor.
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Yeh HY, Awad A. Genotyping of Campylobacter jejuni Isolates from Poultry by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR). Curr Microbiol 2020; 77:1647-1652. [PMID: 32279188 DOI: 10.1007/s00284-020-01965-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/24/2020] [Indexed: 01/22/2023]
Abstract
Campylobacter jejuni is the leading bacterial foodborne pathogen that causes human acute gastrointestinal illness worldwide. Due to its genetic diversity, fastidious growth and sophisticated biochemical requirements, classification of Campylobacter by traditional techniques is problematic. Several molecular typing methods have been explored in this bacterium. One such method is to use clustered regularly interspaced short palindromic repeats (CRISPR). These CRISPRs consist of a direct repeat interspaced with nonrepetitive spacer sequences. In this study, we applied this genotyping method to explore the genetic diversity of C. jejuni isolated from poultry sources. Ninety-nine C. jejuni isolates from poultry environments in four different US states were used. Genomic DNA of the isolates were extracted from cultures using a commercial kit. PCR primers and conditions for CRISPR type 1 amplification were described previously. The amplicons were purified and sequenced by the Sanger dideoxy sequencing method. The direct repeats (DR) and spacers of the CRISPR sequences were identified using the CRISPRFinder. The results show there were 21% isolates no detectable, 30% isolates questionable, and 49% isolates confirmed CRISPR, respectively. The lengths of CRISPR range from 100 to 695 nucleotides. One type of DR was found in CRISPR of these isolates. The number of spacers in CRISPR ranges from 1 to 10 with various sequences. A total of 55 distinctive spacer sequences were identified in 78 isolates. Among them, 33 sequences were found unique in this study. In addition, the CRISPR genotyping had higher the Simpson's index of diversity value than that from flaA nucleotide typing. The results of our study show the CRISPR genotyping on C. jejuni may be complementary to the other genotyping methods.
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Affiliation(s)
- Hung-Yueh Yeh
- Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA, 30605-2720, USA.
| | - Amal Awad
- Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, United States Department of Agriculture, 950 College Station Road, Athens, GA, 30605-2720, USA.,Bacteriology, Mycology and Immunology Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
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10
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Blankenship HM, Mosci RE, Phan Q, Fontana J, Rudrik JT, Manning SD. Genetic Diversity of Non-O157 Shiga Toxin-Producing Escherichia coli Recovered From Patients in Michigan and Connecticut. Front Microbiol 2020; 11:529. [PMID: 32300338 PMCID: PMC7145412 DOI: 10.3389/fmicb.2020.00529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are important foodborne pathogens and non-O157 serotypes have been gradually increasing in frequency. The non-O157 STEC population is diverse and is often characterized using serotyping and/or multilocus sequence typing (MLST). Although spacers within clustered regularly interspaced repeat (CRISPR) regions were shown to comprise horizontally acquired DNA elements, this region does not actively acquire spacers in STEC. Hence, it is useful for further characterizing non-O157 STEC and examining relationships between strains. Our study goal was to evaluate the genetic relatedness of 41 clinical non-O157 isolates identified in Michigan between 2001 and 2005 while comparing to 114 isolates from Connecticut during an overlapping time period. Whole genome sequencing (WGS) was performed, and sequences were extracted for serotyping, MLST and CRISPR analysis. Phylogenetic analysis of MLST and CRISPR data was performed using the Neighbor joining and unweighted pair group method with arithmetic mean (UPGMA) algorithms, respectively. In all, 29 serogroups were identified; eight were unique to Michigan and 13 to Connecticut. “Big-six” serogroup frequencies were similar by state (Michigan: 73.2%, Connecticut: 81.6%), though STEC O121 was not found in Michigan. The distribution of sequence types (STs) and CRISPR profiles was also similar across states. Interestingly, big-six serogroups such as O103 and O26, grouped into different STs located on distinct branches of the phylogeny, further confirming that serotyping alone is not adequate for evaluating strain relatedness. Comparatively, the CRISPR analysis identified 361 unique spacers that grouped into 80 different CRISPR profiles. CRISPR spacers 231 and 317 were isolated from 79.2% (n = 118) and 59.1% (n = 88) of strains, respectively, regardless of serogroup and ST. Spacer profiles clustered according to the MLST analysis, though some discrepancies were noted. Indeed, use of both MLST and CRISPR typing enhanced the discriminatory power when compared to the use of each tool separately. These data highlight the genetic diversity of clinical STEC from different locations and show that CRISPR profiling can be used alongside MLST to discriminate related strains. Use of targeted sequencing approaches are particularly helpful for sites without WGS capabilities and can help define which strains require additional characterization using more discriminatory methods.
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Affiliation(s)
- Heather M Blankenship
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Rebekah E Mosci
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Quyen Phan
- Connecticut Department of Public Health, Hartford, CT, United States
| | - John Fontana
- Connecticut Department of Public Health, Hartford, CT, United States
| | - James T Rudrik
- Bureau of Laboratories, Michigan Department of Health and Human Services, Lansing, MI, United States
| | - Shannon D Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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11
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Gomes CN, Frazão MR, Passaglia J, Duque SS, Medeiros MIC, Falcão JP. Molecular Epidemiology and Resistance Profile of Campylobacter jejuni and Campylobacter coli Strains Isolated from Different Sources in Brazil. Microb Drug Resist 2019; 26:1516-1525. [PMID: 31794692 DOI: 10.1089/mdr.2019.0266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aims: The objectives of this study were to genotype a total of 48 Campylobacter jejuni and 39 Campylobacter coli strains isolated in Brazil from 1995 to 2016 by multilocus sequence typing (MLST) and to determine their resistance profile. The presence or points of mutation in the related resistance genes was verified. Results: By MLST, C. jejuni strains were typed into 36 STs and C. coli strains were typed into 27 STs. A total of 70.8% of C. jejuni and 35.9% of C. coli were resistant to at least one antimicrobial tested. The tet(O) gene was detected in 43.7% C. jejuni and in 12.8% C. coli. The ermB gene was not detected and one C. jejuni presented the mutation in the 23S rRNA gene. Besides, 58.3% C. jejuni presented the substitution T86I in the quinolone resistance-determining region of gyrA and 15.4% C. coli presented the substitution T38I. The cmeB gene was detected in 97.9% C. jejuni and in 97.4% C. coli. Conclusion: The presence of C. jejuni and C. coli resistant to some antimicrobial agents of clinical use is of public health concern. The presence of STs shared between Brazilian strains and isolates of different countries is of concern since it might suggest a possible spread of these shared types.
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Affiliation(s)
- Carolina N Gomes
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Miliane R Frazão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Jaqueline Passaglia
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Sheila S Duque
- Fundação Oswaldo Cruz-FIOCRUZ, Instituto Oswaldo Cruz-IOC, Pavilhão Rocha Lima, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Juliana P Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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12
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Verma R, Sahu R, Singh DD, Egbo TE. A CRISPR/Cas9 based polymeric nanoparticles to treat/inhibit microbial infections. Semin Cell Dev Biol 2019; 96:44-52. [PMID: 30986568 DOI: 10.1016/j.semcdb.2019.04.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/11/2019] [Indexed: 12/17/2022]
Abstract
The latest breakthrough towards the adequate and decisive methods of gene editing tools provided by CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR Associated System), has been repurposed into a tool for genetically engineering eukaryotic cells and now considered as the major innovation in gene-related disorders. Nanotechnology has provided an alternate way to overcome the conventional problems where methods to deliver therapeutic agents have failed. The use of nanotechnology has the potential to safe-side the CRISPR/Cas9 components delivery by using customized polymeric nanoparticles for safety and efficacy. The pairing of two (CRISPR/Cas9 and nanotechnology) has the potential for opening new avenues in therapeutic use. In this review, we will discuss the most recent advances in developing nanoparticle-based CRISPR/Cas9 gene editing cargo delivery with a focus on several polymeric nanoparticles including fabrication proposals to combat microbial infections.
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Affiliation(s)
- Richa Verma
- Center for Nanobiotechnology Research, Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Rajnish Sahu
- Center for Nanobiotechnology Research, Department of Biological Sciences, Alabama State University, Montgomery, AL, 36104, USA
| | - Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University, Jaipur, Rajasthan, 303002, India
| | - Timothy E Egbo
- Department of Biological Sciences, College of Science Technology Engineering and Mathematics, Alabama State University, Montgomery, AL, 36104, USA.
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13
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Hidalgo-Cantabrana C, Goh YJ, Barrangou R. Characterization and Repurposing of Type I and Type II CRISPR-Cas Systems in Bacteria. J Mol Biol 2019; 431:21-33. [PMID: 30261168 DOI: 10.1016/j.jmb.2018.09.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 12/20/2022]
Abstract
CRISPR-Cas systems constitute the adaptive immune system of bacteria and archaea, as a sequence-specific nucleic acid targeting defense mechanism. The sequence-specific recognition and cleavage of Cas effector complexes has been harnessed to developed CRISPR-based technologies and drive the genome editing revolution underway, due to their efficacy, efficiency, and ease of implementation in a broad range of organisms. CRISPR-based technologies offer a wide variety of opportunities in genome remodeling and transcriptional regulation, opening new avenues for therapeutic and biotechnological applications. To repurpose CRISPR-Cas systems for these applications, the various elements of the system need to be first identified and functionally characterized in their native host. Bioinformatic tools are first used to identify putative CRISPR arrays and their associated genes, followed by a comprehensive characterization of the CRISPR-Cas system, encompassing predictions for guide and target sequences. Subsequently, interference assays and transcriptomic analyses should be performed to probe the functionality of the CRISPR-Cas system. Once an endogenous CRISPR-Cas system is characterized as functional, they can be readily repurposed by delivering an engineered synthetic CRISPR array or a small RNA guide for targeted gene manipulation. Alternatively, developing a plasmid-based system for heterologous expression of the necessary CRISPR components can enable exploitation in other organisms. Altogether, there is a wide diversity of native CRISPR-Cas systems in many bacteria and most archaea that await functional characterization and repurposing for genome editing applications in prokaryotes.
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Affiliation(s)
- Claudio Hidalgo-Cantabrana
- Department of Food, Processing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Yong Jun Goh
- Department of Food, Processing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Rodolphe Barrangou
- Department of Food, Processing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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14
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Hidalgo-Cantabrana C, Crawley AB, Sanchez B, Barrangou R. Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum. Front Microbiol 2017; 8:1851. [PMID: 29033911 PMCID: PMC5626976 DOI: 10.3389/fmicb.2017.01851] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022] Open
Abstract
Diverse CRISPR-Cas systems provide adaptive immunity in many bacteria and most archaea, via a DNA-encoded, RNA-mediated, nucleic-acid targeting mechanism. Over time, CRISPR loci expand via iterative uptake of invasive DNA sequences into the CRISPR array during the adaptation process. These genetic vaccination cards thus provide insights into the exposure of strains to phages and plasmids in space and time, revealing the historical predatory exposure of a strain. These genetic loci thus constitute a unique basis for genotyping of strains, with potential of resolution at the strain-level. Here, we investigate the occurrence and diversity of CRISPR-Cas systems in the genomes of various Bifidobacterium longum strains across three sub-species. Specifically, we analyzed the genomic content of 66 genomes belonging to B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis, and identified 25 strains that carry 29 total CRISPR-Cas systems. We identify various Type I and Type II CRISPR-Cas systems that are widespread in this species, notably I-C, I-E, and II-C. Noteworthy, Type I-C systems showed extended CRISPR arrays, with extensive spacer diversity. We show how these hypervariable loci can be used to gain insights into strain origin, evolution and phylogeny, and can provide discriminatory sequences to distinguish even clonal isolates. By investigating CRISPR spacer sequences, we reveal their origin and implicate phages and prophages as drivers of CRISPR immunity expansion in this species, with redundant targeting of select prophages. Analysis of CRISPR spacer origin also revealed novel PAM sequences. Our results suggest that CRISPR-Cas immune systems are instrumental in mounting diversified viral resistance in B. longum, and show that these sequences are useful for typing across three subspecies.
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Affiliation(s)
- Claudio Hidalgo-Cantabrana
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, IPLA-CSIC, Villaviciosa, Spain
| | - Alexandra B. Crawley
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Borja Sanchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, IPLA-CSIC, Villaviciosa, Spain
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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15
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Stout E, Klaenhammer T, Barrangou R. CRISPR-Cas Technologies and Applications in Food Bacteria. Annu Rev Food Sci Technol 2017; 8:413-437. [DOI: 10.1146/annurev-food-072816-024723] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity.
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Affiliation(s)
- Emily Stout
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Todd Klaenhammer
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
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16
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Zhang X, Yin T, Du X, Yang W, Huang J, Jiao X. Occurrence and genotypes of Campylobacter species in broilers during the rearing period. Avian Pathol 2016; 46:215-223. [PMID: 27766896 DOI: 10.1080/03079457.2016.1248374] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Poultry are the main source of Campylobacter infection worldwide. To obtain information on Campylobacter-infected flocks and create a reference for preventing and controlling Campylobacter at farm level, Campylobacter isolates were recovered from broilers and the environments of nine chicken flocks in two farms during growth. The genetic relationship between the Campylobacter isolates was determined using multilocus sequence typing. Flocks were colonized as early as 3 weeks after introduction to the farm. The highest colonization rate was more than 90% and occurred 4-6 weeks after introduction to the farm. Quantitative data showed that the highest Campylobacter loads appeared at 1-2 weeks after initial colonization. Campylobacter loads in cloacal swabs in four flocks were significantly higher at 5 weeks than at 3 weeks (P < 0.05). Multilocus sequence typing of 171 selected isolates revealed 20 sequence types (STs), which consisted of 12 STs for Campylobacter jejuni and eight for Campylobacter coli isolates. The STs of the Campylobacter isolates recovered from farm 1 were more diversified than those from farm 2. The STs of environmental samples were highly consistent with those of the cloacal swab samples. The consistency between Campylobacter STs in the environmental and cloacal swab samples suggested that the environment might be one of the main sources of infection. Thus, our study highlights the prevalence and contamination load of Campylobacter in broilers during their rearing period and emphasizes the need for control and prevention measures for Campylobacter infection in broilers, which is also important for human health.
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Affiliation(s)
- Xiaoyan Zhang
- a Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , Jiangsu , People's Republic of China
| | - Tiantian Yin
- a Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , Jiangsu , People's Republic of China
| | - Xueqing Du
- a Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , Jiangsu , People's Republic of China
| | - Wenbin Yang
- a Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , Jiangsu , People's Republic of China
| | - Jinlin Huang
- a Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , Jiangsu , People's Republic of China
| | - Xinan Jiao
- a Jiangsu Key Lab of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou University , Yangzhou , Jiangsu , People's Republic of China
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17
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Llarena AK, Zhang J, Vehkala M, Välimäki N, Hakkinen M, Hänninen ML, Roasto M, Mäesaar M, Taboada E, Barker D, Garofolo G, Cammà C, Di Giannatale E, Corander J, Rossi M. Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion. Microb Genom 2016; 2:e000088. [PMID: 28348829 PMCID: PMC5359405 DOI: 10.1099/mgen.0.000088] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/12/2016] [Indexed: 01/05/2023] Open
Abstract
The decreased costs of genome sequencing have increased the capability to apply whole-genome sequencing to epidemiological surveillance of zoonotic Campylobacter jejuni. However, knowledge of the genetic diversity of this bacteria is vital for inferring relatedness between epidemiologically linked isolates and a necessary prerequisite for correct application of this methodology. To address this issue in C. jejuni we investigated the spatial and temporal signals in the genomes of a major clonal complex and generalist lineage, ST-45 CC, by analysing the population structure and genealogy as well as applying genome-wide association analysis of 340 isolates from across Europe collected over a wide time range. The occurrence and strength of the geographical signal varied between sublineages and followed the clonal frame when present, while no evidence of a temporal signal was found. Certain sublineages of ST-45 formed discrete and genetically isolated clades containing isolates with extremely similar genomes regardless of time and location of sampling. Based on a separate data set, these monomorphic genotypes represent successful C. jejuni clones, possibly spread around the globe by rapid animal (migrating birds), food or human movement. In addition, we observed an incongruence between the genealogy of the strains and multilocus sequence typing (MLST), challenging the existing clonal complex definition and the use of whole-genome gene-by-gene hierarchical nomenclature schemes for C. jejuni.
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Affiliation(s)
- Ann-Katrin Llarena
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ji Zhang
- Institute of Veterinary, Animal & Biomedical Sciences, College of Sciences, Massey University, Palmerstone North, New Zealand
| | - Minna Vehkala
- Department of Mathematics and Statistics, Faculty of Science, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Marjaana Hakkinen
- Food and Feed Microbiology Research Unit, Research and Laboratory Department, Finnish Food Safety Authority Evira, Helsinki, Finland
| | - Marja-Liisa Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Mati Roasto
- Department of Food Hygiene, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Mihkel Mäesaar
- Department of Food Hygiene, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Veterinary and Food Laboratory, VFL, Tartu, Estonia
| | - Eduardo Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, c/o Animal Diseases Research Institute, Lethbridge, Canada
| | - Dillon Barker
- National Microbiology Laboratory, Public Health Agency of Canada, c/o Animal Diseases Research Institute, Lethbridge, Canada
| | - Giuliano Garofolo
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise ‘G. Caporale’, Teramo, Italy
| | - Cesare Cammà
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise ‘G. Caporale’, Teramo, Italy
| | - Elisabetta Di Giannatale
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise ‘G. Caporale’, Teramo, Italy
| | - Jukka Corander
- Institute of Basic Medical Sciences, Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Mirko Rossi
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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18
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Perez M, Juniper SK. Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers. Appl Environ Microbiol 2016; 82:5197-205. [PMID: 27316954 PMCID: PMC4988177 DOI: 10.1128/aem.00953-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The symbiotic relationship between vestimentiferan tubeworms and their intracellular chemosynthetic bacteria is one of the more noteworthy examples of adaptation to deep-sea hydrothermal vent environments. The tubeworm symbionts have never been cultured in the laboratory. Nucleotide sequences from the small subunit rRNA gene suggest that the intracellular symbionts of the eastern Pacific vent tubeworms Oasisia alvinae, Riftia pachyptila, Tevnia jerichonana, and Ridgeia piscesae belong to the same phylotype of gammaproteobacteria, "Candidatus Endoriftia persephone." Comparisons of symbiont genomes between the East Pacific Rise tubeworms R. pachyptila and T. jerichonana confirmed that these two hosts share the same symbionts. Two Ridgeia symbiont genomes were assembled from trophosome metagenomes from worms collected from the Juan de Fuca Ridge (one and five individuals, respectively). We compared these assemblies to those of the sequenced Riftia and Tevnia symbionts. Pangenome composition, genome-wide comparisons of the nucleotide sequences, and pairwise comparisons of 2,313 orthologous genes indicated that "Ca Endoriftia persephone" symbionts are structured on large geographical scales but also on smaller scales and possibly through host specificity. IMPORTANCE Remarkably, the intracellular symbionts of four to six species of eastern Pacific vent tubeworms all belong to the same phylotype of gammaproteobacteria, "Candidatus Endoriftia persephone." Understanding the structure, dynamism, and interconnectivity of "Ca Endoriftia persephone" populations is important to advancing our knowledge of the ecology and evolution of their host worms, which are often keystone species in vent communities. In this paper, we present the first genomes for symbionts associated with the species R. piscesae, from the Juan de Fuca Ridge. We then combine these genomes with published symbiont genomes from the East Pacific Rise tubeworms R. pachyptila and T. jerichonana to develop a portrait of the "Ca Endoriftia persephone" pangenome and an initial outline of symbiont population structure in the different host species. Our study is the first to apply genome-wide comparisons of "Ca Endoriftia persephone" assemblies in the context of population genetics and molecular evolution.
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Affiliation(s)
- Maëva Perez
- School of Earth and Ocean Sciences, University of Victoria, Victoria, BC, Canada
| | - S Kim Juniper
- School of Earth and Ocean Sciences, University of Victoria, Victoria, BC, Canada Department of Biology, University of Victoria, Victoria, BC, Canada
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19
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Klein-Jöbstl D, Sofka D, Iwersen M, Drillich M, Hilbert F. Multilocus Sequence Typing and Antimicrobial Resistance of Campylobacter jejuni Isolated from Dairy Calves in Austria. Front Microbiol 2016; 7:72. [PMID: 26870027 PMCID: PMC4737881 DOI: 10.3389/fmicb.2016.00072] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 01/15/2016] [Indexed: 11/13/2022] Open
Abstract
Human campylobacteriosis is primarily associated with poultry but also cattle. In this study, 55 Campylobacter jejuni strains isolated from 382 dairy calves’ feces were differentiated by multilocus sequence typing and tested for antimicrobial resistance. The most prevalent sequence type (ST) was ST883 (20.0%), followed by ST48 (14.5%), and ST50 (9.1%). In contrast to ST48 and ST50, ST883 has rarely been described in cattle previously. Furthermore, risk factor analysis was performed for the presence of the most prevalent STs in these calves. Multiple regression analysis revealed that the type of farm (organic vs. conventional) and calf housing (place, and individual vs. group) were identified as significantly (p < 0.05) associated with the presence of ST883 in calves, and ST50 was associated with calf diarrhea. Antimicrobial resistance was detected in 58.2% of the isolates. Most of the resistant isolates (81.3%) were resistant to more than one antimicrobial. Most frequently, resistance to ciprofloxacin (49.1%), followed by nalidixic acid (42.8%), and tetracycline (14.5%) was observed. The results of the present study support the hypothesis that dairy calves may serve as a potential reservoir for C. jejuni and pose a risk for transmission, including antimicrobial resistant isolates to the environment and to humans.
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Affiliation(s)
- Daniela Klein-Jöbstl
- Clinical Unit for Herd Health Management, University Clinic for Ruminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna Vienna, Austria
| | - Dmitri Sofka
- Institute of Meat Hygiene, Meat Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna Vienna, Austria
| | - Michael Iwersen
- Clinical Unit for Herd Health Management, University Clinic for Ruminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna Vienna, Austria
| | - Marc Drillich
- Clinical Unit for Herd Health Management, University Clinic for Ruminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna Vienna, Austria
| | - Friederike Hilbert
- Institute of Meat Hygiene, Meat Technology and Food Science, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna Vienna, Austria
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20
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Pohjola L, Nykäsenoja S, Kivistö R, Soveri T, Huovilainen A, Hänninen ML, Fredriksson-Ahomaa M. Zoonotic Public Health Hazards in Backyard Chickens. Zoonoses Public Health 2016; 63:420-30. [PMID: 26752227 DOI: 10.1111/zph.12247] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 01/31/2023]
Abstract
Backyard poultry has become increasingly popular in industrialized countries. In addition to keeping chickens for eggs and meat, owners often treat the birds as pets. However, several pathogenic enteric bacteria have the potential for zoonotic transmission from poultry to humans but very little is known about the occurrence of zoonotic pathogens in backyard flocks. The occurrence and the antimicrobial resistance of Salmonella enterica, Campylobacter spp., Listeria monocytogenes and enteropathogenic Yersinia spp. was studied in 51 voluntary backyard chicken farms in Finland during October 2012 and January 2013. Campylobacter isolates were further characterized by pulsed-field gel electrophoresis (PFGE), and the occurrence of ESBL/AmpC-producing E. coli was investigated. The findings from this study indicate that backyard chickens are a reservoir of Campylobacter jejuni strains and a potential source of C. jejuni infection for humans. Backyard chickens can also carry L. monocytogenes, although their role as a primary reservoir is questionable. Campylobacter coli, Yersinia pseudotuberculosis and Salmonella enterica were only found sporadically in the faecal and environmental samples of backyard poultry in Finland. No Yersinia enterocolitica carrying the virulence plasmid was isolated. All pathogens were highly susceptible to most of the antimicrobials studied. Only a few AmpC- and no ESBL-producing E. coli were found.
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Affiliation(s)
- L Pohjola
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Saarentaus, Finland
| | - S Nykäsenoja
- Research and Laboratory Department, Food and Feed Microbiology Research Unit, Finnish Food Safety Authority Evira, Helsinki, Finland
| | - R Kivistö
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - T Soveri
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Saarentaus, Finland
| | - A Huovilainen
- Veterinary Virology, Finnish Food Safety Authority Evira, Helsinki, Finland
| | - M L Hänninen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - M Fredriksson-Ahomaa
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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21
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Abstract
Bacteria occur ubiquitously in nature and are broadly relevant throughout the food supply chain, with diverse and variable tolerance levels depending on their origin, biological role, and impact on the quality and safety of the product as well as on the health of the consumer. With increasing knowledge of and accessibility to the microbial composition of our environments, food supply, and host-associated microbiota, our understanding of and appreciation for the ratio of beneficial to undesirable bacteria are rapidly evolving. Therefore, there is a need for tools and technologies that allow definite, accurate, and high-resolution identification and typing of various groups of bacteria that include beneficial microbes such as starter cultures and probiotics, innocuous commensals, and undesirable pathogens and spoilage organisms. During the transition from the current molecular biology-based PFGE (pulsed-field gel electrophoresis) gold standard to the increasingly accessible omics-level whole-genome sequencing (WGS) N-gen standard, high-resolution technologies such as CRISPR-based genotyping constitute practical and powerful alternatives that provide valuable insights into genome microevolution and evolutionary trajectories. Indeed, several studies have shown potential for CRISPR-based typing of industrial starter cultures, health-promoting probiotic strains, animal commensal species, and problematic pathogens. Emerging CRISPR-based typing methods open new avenues for high-resolution typing of a broad range of bacteria and constitute a practical means for rapid tracking of a diversity of food-associated microbes.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695; .,Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Edward G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802;
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22
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Qi Z, Cui Y, Zhang Q, Yang R. Taxonomy of Yersinia pestis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 918:35-78. [PMID: 27722860 DOI: 10.1007/978-94-024-0890-4_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This chapter summarized the taxonomy and typing works of Yersinia pestis since it's firstly identified in Hong Kong in 1894. Phenotyping methods that based on phenotypic characteristics, including biotyping, serotyping, antibiogram analysis, bacteriocin typing, phage typing, and plasmid typing, were firstly applied in classification of Y. pestis in subspecies level. And then, with the advancement of molecular biological technology, the methods based on outer membrane protein profiles, fatty acid composition, and bacterial mass fingerprinting were also used to identify the populations within Y. pestis. However, Y. pestis is a highly homogenous species; therefore, the above typing methods could only provide low resolution, e.g., only one serotype and one phage type were observed for the whole species. Since the 1990s, molecular typing based on DNA variations, including single-nucleotide polymorphism, gene gain/loss, variable-number tandem repeats, clustered regularly interspaced short palindromic repeat, etc., was introduced and improved the resolution and robust of typing result. Especially in recent years, genotyping-based whole-genome-wide variations were successfully employed in Y. pestis, which built the "gold standard" of typing scheme of the species and could distinguish the samples under the strain level. The taxonomy and typing works leaved us enormous polymorphism data; therefore, a comprehensive fingerprint database of Y. pestis was needed to collect and standardize these data, for facilitating future works on evolution, plague surveillance and control, anti-bioterrorism, and microbial forensic researches.
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Affiliation(s)
- Zhizhen Qi
- Qinghai Provincial Key Laboratory for Plague Control and Research, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai Province, 811602, China
| | - Yujun Cui
- Beijing Institute of Microbiology and Epidemiology, No. Dongdajie, Fengtai, Beijing, 100071, China
| | - Qingwen Zhang
- Qinghai Provincial Key Laboratory for Plague Control and Research, Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai Province, 811602, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, No. Dongdajie, Fengtai, Beijing, 100071, China.
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Pearson BM, Louwen R, van Baarlen P, van Vliet AHM. Differential Distribution of Type II CRISPR-Cas Systems in Agricultural and Nonagricultural Campylobacter coli and Campylobacter jejuni Isolates Correlates with Lack of Shared Environments. Genome Biol Evol 2015; 7:2663-79. [PMID: 26338188 PMCID: PMC4607530 DOI: 10.1093/gbe/evv174] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR (clustered regularly interspaced palindromic repeats)-Cas (CRISPR-associated) systems are sequence-specific adaptive defenses against phages and plasmids which are widespread in prokaryotes. Here we have studied whether phylogenetic relatedness or sharing of environmental niches affects the distribution and dissemination of Type II CRISPR-Cas systems, first in 132 bacterial genomes from 15 phylogenetic classes, ranging from Proteobacteria to Actinobacteria. There was clustering of distinct Type II CRISPR-Cas systems in phylogenetically distinct genera with varying G+C%, which share environmental niches. The distribution of CRISPR-Cas within a genus was studied using a large collection of genome sequences of the closely related Campylobacter species Campylobacter jejuni (N = 3,746) and Campylobacter coli (N = 486). The Cas gene cas9 and CRISPR-repeat are almost universally present in C. jejuni genomes (98.0% positive) but relatively rare in C. coli genomes (9.6% positive). Campylobacter jejuni and agricultural C. coli isolates share the C. jejuni CRISPR-Cas system, which is closely related to, but distinct from the C. coli CRISPR-Cas system found in C. coli isolates from nonagricultural sources. Analysis of the genomic position of CRISPR-Cas insertion suggests that the C. jejuni-type CRISPR-Cas has been transferred to agricultural C. coli. Conversely, the absence of the C. coli-type CRISPR-Cas in agricultural C. coli isolates may be due to these isolates not sharing the same environmental niche, and may be affected by farm hygiene and biosecurity practices in the agricultural sector. Finally, many CRISPR spacer alleles were linked with specific multilocus sequence types, suggesting that these can assist molecular epidemiology applications for C. jejuni and C. coli.
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Affiliation(s)
- Bruce M Pearson
- Institute of Food Research, Gut Health and Food Safety Programme, Norwich Research Park, Norwich, United Kingdom
| | - Rogier Louwen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter van Baarlen
- Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
| | - Arnoud H M van Vliet
- Institute of Food Research, Gut Health and Food Safety Programme, Norwich Research Park, Norwich, United Kingdom
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