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Pilar AVC, Petronella N, Dussault FM, Verster AJ, Bekal S, Levesque RC, Goodridge L, Tamber S. Similar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries. BMC Genomics 2020; 21:377. [PMID: 32471418 PMCID: PMC7257147 DOI: 10.1186/s12864-020-06780-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/13/2020] [Indexed: 12/14/2022] Open
Abstract
Background Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presence of background microflora that may present as Salmonella (false positives). False positive isolates belonging to the genus Citrobacter can be difficult to distinguish from Salmonella due to similarities in their genetics, cell surface antigens, and other phenotypes. In order to understand the genetic basis of these similarities, a comparative genomic approach was used to define the pan-, core, accessory, and unique coding sequences of a representative population of Salmonella and Citrobacter strains. Results Analysis of the genomic content of 58 S. enterica strains and 37 Citrobacter strains revealed the presence of 31,130 and 1540 coding sequences within the pan- and core genome of this population. Amino acid sequences unique to either Salmonella (n = 1112) or Citrobacter (n = 195) were identified and revealed potential niche-specific adaptations. Phylogenetic network analysis of the protein families encoded by the pan-genome indicated that genetic exchange between Salmonella and Citrobacter may have led to the acquisition of similar traits and also diversification within the genera. Conclusions Core genome analysis suggests that the Salmonella enterica and Citrobacter populations investigated here share a common evolutionary history. Comparative analysis of the core and pan-genomes was able to define the genetic features that distinguish Salmonella from Citrobacter and highlight niche specific adaptations.
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Affiliation(s)
| | - Nicholas Petronella
- Bureau of Food Surveillance and Science Integration, Health Canada, Ottawa, Ontario, Canada
| | - Forest M Dussault
- Bureau of Food Surveillance and Science Integration, Health Canada, Ottawa, Ontario, Canada
| | - Adrian J Verster
- Bureau of Food Surveillance and Science Integration, Health Canada, Ottawa, Ontario, Canada
| | - Sadjia Bekal
- Laboratoire de santé publique du Québec, Ste-Anne-de-Bellevue, Quebec, Canada
| | - Roger C Levesque
- Institute for Integrative and Systems Biology (IBIS), Université Laval, Quebec, Quebec, Canada
| | - Lawrence Goodridge
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec, Canada.,Food Science Department, University of Guelph, Guelph, Ontario, Canada
| | - Sandeep Tamber
- Bureau of Microbial Hazards, Health Canada, Ottawa, Ontario, Canada.
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2
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Wang X, Zhu S, Zhao JH, Bao HX, Liu H, Ding TM, Liu GR, Li YG, Johnston RN, Cao FL, Tang L, Liu SL. Genetic boundaries delineate the potential human pathogen Salmonella bongori into discrete lineages: divergence and speciation. BMC Genomics 2019; 20:930. [PMID: 31801462 PMCID: PMC6894293 DOI: 10.1186/s12864-019-6259-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Salmonella bongori infect mainly cold-blooded hosts, but infections by S. bongori in warm-blooded hosts have been reported. We hypothesized that S. bongori might have diverged into distinct phylogenetic lineages, with some being able to infect warm-blooded hosts. RESULTS To inspect the divergence status of S. bongori, we first completely sequenced the parakeet isolate RKS3044 and compared it with other sequenced S. bongori strains. We found that RKS3044 contained a novel T6SS encoded in a pathogenicity island-like structure, in addition to a T6SS encoded in SPI-22, which is common to all S. bongori strains so far reported. This novel T6SS resembled the SPI-19 T6SS of the warm-blooded host infecting Salmonella Subgroup I lineages. Genomic sequence comparisons revealed different genomic sequence amelioration events among the S. bongori strains, including a unique CTAG tetranucleotide degeneration pattern in RKS3044, suggesting non-overlapping gene pools between RKS3044 and other S. bongori lineages/strains leading to their independent accumulation of genomic variations. We further proved the existence of a clear-cut genetic boundary between RKS3044 and the other S. bongori lineages/strains analyzed in this study. CONCLUSIONS The warm-blooded host-infecting S. bongori strain RKS3044 has diverged with distinct genomic features from other S. bongori strains, including a novel T6SS encoded in a previously not reported pathogenicity island-like structure and a unique genomic sequence degeneration pattern. These findings alert cautions about the emergence of new pathogens originating from non-pathogenic ancestors by acquiring specific pathogenic traits.
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Affiliation(s)
- Xiaoyu Wang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Songling Zhu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Jian-Hua Zhao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Hong-Xia Bao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Huidi Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Tie-Min Ding
- Department of Medicine and Food Engineering, Harbin Labor Technician College, Harbin, China
| | - Gui-Rong Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yong-Guo Li
- Department of Infectious Diseases, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Randal N. Johnston
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Feng-Lin Cao
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Le Tang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
- Department of Ecosystems and Public Health, University of Calgary, Calgary, Canada
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, 157 Baojian Road, Harbin, 150081 China
- HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
- Department of Infectious Diseases, The First Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
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3
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Distinct evolutionary origins of common multi-drug resistance phenotypes in Salmonella typhimurium DT104: a convergent process for adaptation under stress. Mol Genet Genomics 2019; 294:597-605. [PMID: 30710177 DOI: 10.1007/s00438-019-01531-5] [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: 06/22/2018] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
Abstract
Antimicrobial resistance makes pathogenic bacteria hard to control, but little is known about the general processes of resistance gain or loss. Here, we compared distinct S. typhimurium DT104 strains resistant to zero, two, five, or more of the tested antimicrobials. We found that common resistance phenotypes could be encoded by distinct genes, on SGI-1 or plasmid. We also demonstrated close clonality among all the tested non-resistant and differently resistant DT104 strains, demonstrating dynamic acquisition or loss (by total deletion or gradual decaying of multi-drug resistance gene clusters) of the genetic traits. These findings reflect convergent processes to make the bacteria resistant to multiple antimicrobials by acquiring the needed traits from stochastically available origins. When the antimicrobial stress is absent, the resistance genes may be dropped off quickly, so the bacteria can save the cost for maintaining unneeded genes. Therefore, this work reiterates the importance of strictly controlled use of antimicrobials.
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Tang L, Mastriani E, Zhou YJ, Zhu S, Fang X, Liu YP, Liu WQ, Li YG, Johnston RN, Guo Z, Liu GR, Liu SL. Differential degeneration of the ACTAGT sequence among Salmonella: a reflection of distinct nucleotide amelioration patterns during bacterial divergence. Sci Rep 2017; 7:10985. [PMID: 28887484 PMCID: PMC5591236 DOI: 10.1038/s41598-017-11226-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/21/2017] [Indexed: 12/01/2022] Open
Abstract
When bacteria diverge, they need to adapt to the new environments, such as new hosts or different tissues of the same host, by accumulating beneficial genomic variations, but a general scenario is unknown due to the lack of appropriate methods. Here we profiled the ACTAGT sequence and its degenerated forms (i.e., hexa-nucleotide sequences with one of the six nucleotides different from ACTAGT) in Salmonella to estimate the nucleotide amelioration processes of bacterial genomes. ACTAGT was mostly located in coding sequences but was also found in several intergenic regions, with its degenerated forms widely scattered throughout the bacterial genomes. We speculated that the distribution of ACTAGT and its degenerated forms might be lineage-specific as a consequence of different selection pressures imposed on ACTAGT at different genomic locations (in genes or intergenic regions) among different Salmonella lineages. To validate this speculation, we modelled the secondary structures of the ACTAGT-containing sequences conserved across Salmonella and many other enteric bacteria. Compared to ACTAGT at conserved regions, the degenerated forms were distributed throughout the bacterial genomes, with the degeneration patterns being highly similar among bacteria of the same phylogenetic lineage but radically different across different lineages. This finding demonstrates biased amelioration under distinct selection pressures among the bacteria and provides insights into genomic evolution during bacterial divergence.
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Affiliation(s)
- Le Tang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Department of Ecosystems and Public Health, University of Calgary, Calgary, Canada
| | - Emilio Mastriani
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yu-Jie Zhou
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Songling Zhu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xin Fang
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yang-Peng Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Wei-Qiao Liu
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- Department of Clinical Neurosciences, University of Calgary, Calgary, Canada
| | - Yong-Guo Li
- Department of Infectious Diseases of First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Randal N Johnston
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Zheng Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
| | - Gui-Rong Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China.
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
- Department of Infectious Diseases of First Affiliated Hospital, Harbin Medical University, Harbin, China.
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5
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Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction. Sci Rep 2017; 7:43565. [PMID: 28262684 PMCID: PMC5337935 DOI: 10.1038/srep43565] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/23/2017] [Indexed: 01/14/2023] Open
Abstract
Highly conserved short sequences help identify functional genomic regions and facilitate genomic annotation. We used Salmonella as the model to search the genome for evolutionarily conserved regions and focused on the tetranucleotide sequence CTAG for its potentially important functions. In Salmonella, CTAG is highly conserved across the lineages and large numbers of CTAG-containing short sequences fall in intergenic regions, strongly indicating their biological importance. Computer modeling demonstrated stable stem-loop structures in some of the CTAG-containing intergenic regions, and substitution of a nucleotide of the CTAG sequence would radically rearrange the free energy and disrupt the structure. The postulated degeneration of CTAG takes distinct patterns among Salmonella lineages and provides novel information about genomic divergence and evolution of these bacterial pathogens. Comparison of the vertically and horizontally transmitted genomic segments showed different CTAG distribution landscapes, with the genome amelioration process to remove CTAG taking place inward from both terminals of the horizontally acquired segment.
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6
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Zhou YJ, Zhu S, Yang DH, Zhao DD, Li JJ, Liu SL. Characterization of Klebsiella sp. strain S1: a bacterial producer of secoisolariciresinol through biotransformation. Can J Microbiol 2016; 63:1-10. [PMID: 27819481 DOI: 10.1139/cjm-2016-0266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Secoisolariciresinol (SECO) is a lignan of potential therapeutic value for diseases such as cancer, but its use has been limited by the lack of ideal production methods, even though its precursors are abundant in plants, such as flaxseeds. Here, we report the characterization of a bacterial strain, S1, isolated from the human intestinal flora, which could produce secoisolariciresinol by biotransformation of precursors in defatted flaxseeds. This bacterium was a Gram-negative and facultatively anaerobic straight rod without capsules. Biochemical assays showed that it was negative for production of oxidase, lysine decarboxylase, ornithine decarboxylase, arginine dihydrolase, and β-glucolase. The G + C content of genomic DNA was 57.37 mol%. Phylogenetic analysis by 16S rRNA and rpoB gene sequences demonstrated S1's close relatedness to Klebsiella. No homologues were found for wzb or wzc (capsular genes), which may explain why Klebsiella sp. strain S1 does not have the capsule and was isolated from a healthy human individual. Based on the percentages of homologous genes with identical nucleotide sequences between the bacteria in comparison, we found that clear-cut genetic boundaries had been formed between S1 and any other Klebsiella strains compared, dividing them into distinct phylogenetic lineages. This work demonstrates that the intestinal Klebsiella, well known as important opportunistic pathogens prevalent in potentially fatal nosocomial infections, may contain lineages that are particularly beneficial to the human health.
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Affiliation(s)
- Yu-Jie Zhou
- a Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, People's Republic of China.,b HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, People's Republic of China
| | - Songling Zhu
- a Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, People's Republic of China.,b HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, People's Republic of China
| | - Dong-Hui Yang
- c Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing, People's Republic of China
| | - Dan-Dan Zhao
- a Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, People's Republic of China.,b HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, People's Republic of China
| | - Jia-Jing Li
- a Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, People's Republic of China.,b HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, People's Republic of China
| | - Shu-Lin Liu
- a Systemomics Center, College of Pharmacy, and Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, People's Republic of China.,b HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, People's Republic of China.,d Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
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7
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Wang CX, Zhu SL, Wang XY, Feng Y, Li B, Li YG, Johnston RN, Liu GR, Zhou J, Liu SL. Complete genome sequence of Salmonella enterica subspecies arizonae str. RKS2983. Stand Genomic Sci 2015; 10:30. [PMID: 26203341 PMCID: PMC4511000 DOI: 10.1186/s40793-015-0015-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/21/2015] [Indexed: 11/10/2022] Open
Abstract
Salmonella arizonae (also called Salmonella subgroup IIIa) is a Gram-negative, non-spore-forming, motile, rod-shaped, facultatively anaerobic bacterium. S. arizonae strain RKS2983 was isolated from a human in California, USA. S. arizonae lies somewhere between Salmonella subgroups I (human pathogens) and V (also called S. bongori; usually non-pathogenic to humans) and so is an ideal model organism for studies of bacterial evolution from non-human pathogen to human pathogens. We hence sequenced the genome of RKS2983 for clues of genomic events that might have led to the divergence and speciation of Salmonella into distinct lineages with diverse host ranges and pathogenic features. The 4,574,836 bp complete genome contains 4,203 protein-coding genes, 82 tRNA genes and 7 rRNA operons. This genome contains several characteristics not reported to date in Salmonella subgroup I or V and may provide information about the genetic divergence of Salmonella pathogens.
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Affiliation(s)
- Chun-Xiao Wang
- Genomics Research Center, Harbin Medical University, Harbin, China
| | - Song-Ling Zhu
- Genomics Research Center, Harbin Medical University, Harbin, China
| | - Xiao-Yu Wang
- Genomics Research Center, Harbin Medical University, Harbin, China
| | - Ye Feng
- Institute for Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Bailiang Li
- Genomics Research Center, Harbin Medical University, Harbin, China
| | - Yong-Guo Li
- Department of Infectious Diseases, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Randal N Johnston
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Gui-Rong Liu
- Genomics Research Center, Harbin Medical University, Harbin, China
| | - Jin Zhou
- Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, Harbin Medical University, Harbin, China
- Department of Infectious Diseases, The First Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
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8
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Tang L, Liu WQ, Fang X, Sun Q, Zhu SL, Wang CX, Wang XY, Li YG, Zhu DL, Sanderson KE, Johnston RN, Liu GR, Liu SL. CTAG-containing cleavage site profiling to delineate Salmonella into natural clusters. PLoS One 2014; 9:e103388. [PMID: 25137186 PMCID: PMC4138082 DOI: 10.1371/journal.pone.0103388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/30/2014] [Indexed: 11/24/2022] Open
Abstract
Background The bacterial genus Salmonella contains thousands of serotypes that infect humans or other hosts, causing mild gastroenteritis to potentially fatal systemic infections in humans. Pathogenically distinct Salmonella serotypes have been classified as individual species or as serological variants of merely one or two species, causing considerable confusion in both research and clinical settings. This situation reflects a long unanswered question regarding whether the Salmonella serotypes exist as discrete genetic clusters (natural species) of organisms or as phenotypic (e.g. pathogenic) variants of a single (or two) natural species with a continuous spectrum of genetic divergence among them. Our recent work, based on genomic sequence divergence analysis, has demonstrated that genetic boundaries exist among Salmonella serotypes, circumscribing them into clear-cut genetic clusters of bacteria. Methodologies/Principal Findings To further test the genetic boundary concept for delineating Salmonella into clearly defined natural lineages (e.g., species), we sampled a small subset of conserved genomic DNA sequences, i.e., the endonuclease cleavage sites that contain the highly conserved CTAG sequence such as TCTAGA for XbaI. We found that the CTAG-containing cleavage sequence profiles could be used to resolve the genetic boundaries as reliably and efficiently as whole genome sequence comparisons but with enormously reduced requirements for time and resources. Conclusions Profiling of CTAG sequence subsets reflects genetic boundaries among Salmonella lineages and can delineate these bacteria into discrete natural clusters.
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Affiliation(s)
- Le Tang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Wei-Qiao Liu
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Xin Fang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Qiang Sun
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Song-Ling Zhu
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Chun-Xiao Wang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xiao-Yu Wang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yong-Guo Li
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Department of Infectious Diseases of First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Da-Ling Zhu
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- College of Pharmacy, Daqing Campus, Harbin Medical University, Daqing, China
| | - Kenneth E. Sanderson
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Randal N. Johnston
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Gui-Rong Liu
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- * E-mail: grliu.natsumi@gmailcom (GRL); (SLL)
| | - Shu-Lin Liu
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences, Harbin Medical University, Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin Medical University, Harbin, China
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
- Department of Infectious Diseases of First Affiliated Hospital, Harbin Medical University, Harbin, China
- * E-mail: grliu.natsumi@gmailcom (GRL); (SLL)
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9
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Genomic comparison of Salmonella typhimurium DT104 with non-DT104 strains. Mol Genet Genomics 2013; 288:549-57. [PMID: 23933962 DOI: 10.1007/s00438-013-0762-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 06/15/2013] [Indexed: 10/26/2022]
Abstract
DT104 emerged as a new branch of Salmonella typhimurium with resistance to multiple antimicrobials. To reveal some general genomic features of DT104 for clues of evolutionary events possibly associated with the emergence of this relatively new type of this pathogen, we mapped 11 independent DT104 strains and compared them with non-DT104 S. typhimurium strains. We found that all 11 DT104 strains contained three insertions absent in non-DT104 strains, i.e., the previously reported ST104, ST104B and ST64B. However, SGI-1, a genomic island known to be responsible for DT104 multidrug resistance, was not present in all DT104 strains examined in this study: one DT104 strain did not contain SGI-1 but carried a 144 kb plasmid, suggesting possible evolutionary relationships between the two DNA elements in the development of antimicrobial resistance.
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Tang L, Li Y, Deng X, Johnston RN, Liu GR, Liu SL. Defining natural species of bacteria: clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergence. BMC Genomics 2013; 14:489. [PMID: 23865772 PMCID: PMC3751360 DOI: 10.1186/1471-2164-14-489] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 07/15/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Bacteria are currently classified into arbitrary species, but whether they actually exist as discrete natural species was unclear. To reveal genomic features that may unambiguously group bacteria into discrete genetic clusters, we carried out systematic genomic comparisons among representative bacteria. RESULTS We found that bacteria of Salmonella formed tight phylogenetic clusters separated by various genetic distances: whereas over 90% of the approximately four thousand shared genes had completely identical sequences among strains of the same lineage, the percentages dropped sharply to below 50% across the lineages, demonstrating the existence of clear-cut genetic boundaries by a steep turning point in nucleotide sequence divergence. Recombination assays supported the genetic boundary hypothesis, suggesting that genetic barriers had been formed between bacteria of even very closely related lineages. We found similar situations in bacteria of Yersinia and Staphylococcus. CONCLUSIONS Bacteria are genetically isolated into discrete clusters equivalent to natural species.
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Affiliation(s)
- Le Tang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin, China
- Department of Biopharmaceutics, Harbin Medical University, 157 Baojian Road, Harbin 150081, China
| | - Yang Li
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
| | - Xia Deng
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
| | | | - Gui-Rong Liu
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin, China
- Department of Biopharmaceutics, Harbin Medical University, 157 Baojian Road, Harbin 150081, China
| | - Shu-Lin Liu
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin, China
- HMU-UCFM Centre for Infection and Genomics, Harbin, China
- Department of Biopharmaceutics, Harbin Medical University, 157 Baojian Road, Harbin 150081, China
- Microbiology and Infectious Diseases, University of Calgary, Calgary, Canada
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Zou QH, Li RQ, Wang YJ, Liu SL. Identification of genes to differentiate closely related Salmonella lineages. PLoS One 2013; 8:e55988. [PMID: 23441160 PMCID: PMC3575412 DOI: 10.1371/journal.pone.0055988] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 01/07/2013] [Indexed: 01/23/2023] Open
Abstract
Background Salmonella are important human and animal pathogens. Though highly related, the Salmonella lineages may be strictly adapted to different hosts or cause different diseases, from mild local illness like gastroenteritis to fatal systemic infections like typhoid. Therefore, rapid and accurate identification of Salmonella is essential for timely and correct diagnosis of Salmonella infections. The current identification methods such as 16S rRNA sequencing and multilocus sequence typing are expensive and time consuming. Additionally, these methods often do not have sufficient distinguishing resolution among the Salmonella lineages. Methodologies/Principal Findings We compared 27 completely sequenced Salmonella genomes to identify possible genomic features that could be used for differentiation of individual lineages. We concatenated 2372 core genes in each of the 27 genomes and constructed a neighbor-joining tree. On the tree, strains of each serotype were clustered tightly together and different serotypes were unambiguously separated with clear genetic distances, demonstrating systematic genomic divergence among the Salmonella lineages. We made detailed comparisons among the 27 genomes and identified distinct sets of genomic differences, including nucleotide variations and genomic islands (GIs), among the Salmonella lineages. Two core genes STM4261 and entF together could unambiguously distinguish all Salmonella lineages compared in this study. Additionally, strains of a lineage have a common set of GIs and closely related lineages have similar sets of GIs. Conclusions Salmonella lineages have accumulated distinct sets of mutations and laterally acquired DNA (e.g., GIs) in evolution. Two genes entF and STM4261 have diverged sufficiently among the Salmonella lineages to be used for their differentiation. Further investigation of the distinct sets of mutations and GIs will lead to novel insights into genomic evolution of Salmonella and greatly facilitate the elucidation of pathogeneses of Salmonella infections.
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Affiliation(s)
- Qing-Hua Zou
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ren-Qing Li
- Institute of Immunology, Beijing Center for Disease Control and Prevention, Beijing, China
| | - Ye-Jun Wang
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Department of Microbiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Genomics Research Center (one of The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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