1
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Seabaugh JA, Anderson DM. Pathogenicity and virulence of Yersinia. Virulence 2024; 15:2316439. [PMID: 38389313 PMCID: PMC10896167 DOI: 10.1080/21505594.2024.2316439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
The genus Yersinia includes human, animal, insect, and plant pathogens as well as many symbionts and harmless bacteria. Within this genus are Yersinia enterocolitica and the Yersinia pseudotuberculosis complex, with four human pathogenic species that are highly related at the genomic level including the causative agent of plague, Yersinia pestis. Extensive laboratory, field work, and clinical research have been conducted to understand the underlying pathogenesis and zoonotic transmission of these pathogens. There are presently more than 500 whole genome sequences from which an evolutionary footprint can be developed that details shared and unique virulence properties. Whereas the virulence of Y. pestis now seems in apparent homoeostasis within its flea transmission cycle, substantial evolutionary changes that affect transmission and disease severity continue to ndergo apparent selective pressure within the other Yersiniae that cause intestinal diseases. In this review, we will summarize the present understanding of the virulence and pathogenesis of Yersinia, highlighting shared mechanisms of virulence and the differences that determine the infection niche and disease severity.
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Affiliation(s)
- Jarett A. Seabaugh
- Department of Veterinary Pathobiology, University of Missouri, Columbia, USA
| | - Deborah M. Anderson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, USA
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2
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Kalalah AA, Koenig SSK, Feng P, Bosilevac JM, Bono JL, Eppinger M. Pathogenomes of Shiga Toxin Positive and Negative Escherichia coli O157:H7 Strains TT12A and TT12B: Comprehensive Phylogenomic Analysis Using Closed Genomes. Microorganisms 2024; 12:699. [PMID: 38674643 PMCID: PMC11052207 DOI: 10.3390/microorganisms12040699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/18/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Shiga toxin-producing Escherichia coli are zoonotic pathogens that cause food-borne human disease. Among these, the O157:H7 serotype has evolved from an enteropathogenic O55:H7 ancestor through the displacement of the somatic gene cluster and recurrent toxigenic conversion by Shiga toxin-converting bacteriophages. However, atypical strains that lack the Shiga toxin, the characteristic virulence hallmark, are circulating in this lineage. For this study, we analyzed the pathogenome and virulence inventories of the stx+ strain, TT12A, isolated from a patient with hemorrhagic colitis, and its respective co-isolated stx- strain, TT12B. Sequencing the genomes to closure proved critical to the cataloguing of subtle strain differentiating sequence and structural polymorphisms at a high-level of phylogenetic accuracy and resolution. Phylogenomic profiling revealed SNP and MLST profiles similar to the near clonal outbreak isolates. Their prophage inventories, however, were notably different. The attenuated atypical non-shigatoxigenic status of TT12B is explained by the absence of both the ΦStx1a- and ΦStx2a-prophages carried by TT12A, and we also recorded further alterations in the non-Stx prophage complement. Phenotypic characterization indicated that culture growth was directly impacted by the strains' distinct lytic phage complement. Altogether, our phylogenomic and phenotypic analyses show that these intimately related isogenic strains are on divergent Stx(+/stx-) evolutionary paths.
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Affiliation(s)
- Anwar A. Kalalah
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
| | - Peter Feng
- U.S. Food and Drug Administration (FDA), College Park, MD 20740, USA
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - James L. Bono
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX 78249, USA
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3
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Suntsov VV. Molecular phylogenies of the plague microbe Yersinia pestis: an environmental assessment. AIMS Microbiol 2023; 9:712-723. [PMID: 38173967 PMCID: PMC10758575 DOI: 10.3934/microbiol.2023036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/26/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024] Open
Abstract
Two approaches are applied to studies of the phylogeny of the plague microbe Yersinia pestis, i.e., the reconstruction of its history: Molecular genetic (MG) and ecological (ECO). The MG approach dominates. Phylogenies created with MG and ECO methods are not congruent. MG conclusions contradict the known facts and patterns of ecology, biogeography, paleontology, etc. We discuss some obvious contradictions and inconsistencies and suggest that real phylogenies of the plague microbe can be constructed only on the basis of the integration of MG and ECO approaches.
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Affiliation(s)
- Victor V. Suntsov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow 119071, Russia
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4
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Yang R, Atkinson S, Chen Z, Cui Y, Du Z, Han Y, Sebbane F, Slavin P, Song Y, Yan Y, Wu Y, Xu L, Zhang C, Zhang Y, Hinnebusch BJ, Stenseth NC, Motin VL. Yersinia pestis and Plague: some knowns and unknowns. ZOONOSES (BURLINGTON, MASS.) 2023; 3:5. [PMID: 37602146 PMCID: PMC10438918 DOI: 10.15212/zoonoses-2022-0040] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Since its first identification in 1894 during the third pandemic in Hong Kong, there has been significant progress of understanding the lifestyle of Yersinia pestis, the pathogen that is responsible for plague. Although we now have some understanding of the pathogen's physiology, genetics, genomics, evolution, gene regulation, pathogenesis and immunity, there are many unknown aspects of the pathogen and its disease development. Here, we focus on some of the knowns and unknowns relating to Y. pestis and plague. We notably focus on some key Y. pestis physiological and virulence traits that are important for its mammal-flea-mammal life cycle but also its emergence from the enteropathogen Yersinia pseudotuberculosis. Some aspects of the genetic diversity of Y. pestis, the distribution and ecology of plague as well as the medical countermeasures to protect our population are also provided. Lastly, we present some biosafety and biosecurity information related to Y. pestis and plague.
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Affiliation(s)
- Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Steve Atkinson
- School of Life Sciences, Centre for Biomolecular Science, University of Nottingham, Nottingham, United Kingdom
| | - Ziqi Chen
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Yujun Cui
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Zongmin Du
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yanping Han
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Florent Sebbane
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Philip Slavin
- Division of History and Politics, University of Stirling, Stirling FK9 4LJ, UK
| | - Yajun Song
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yanfeng Yan
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Yarong Wu
- Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Lei Xu
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - Chutian Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Yun Zhang
- Vanke School of Public Health, Tsinghua University, Beijing 100084, China
| | - B. Joseph Hinnebusch
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, Montana, USA
| | - Nils Chr. Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Vladimir L. Motin
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
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Cao S, Jiao Y, Jiang W, Wu Y, Qin S, Ren Y, You Y, Tan Y, Guo X, Chen H, Zhang Y, Wu G, Wang T, Zhou Y, Song Y, Cui Y, Shao F, Yang R, Du Z. Subversion of GBP-mediated host defense by E3 ligases acquired during Yersinia pestis evolution. Nat Commun 2022; 13:4526. [PMID: 35927280 PMCID: PMC9352726 DOI: 10.1038/s41467-022-32218-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/18/2022] [Indexed: 01/22/2023] Open
Abstract
Plague has caused three worldwide pandemics in history, including the Black Death in medieval ages. Yersinia pestis, the etiological agent of plague, has evolved a powerful arsenal to disrupt host immune defenses during evolution from enteropathogenic Y. pseudotuberculosis. Here, we find that two functionally redundant E3 ligase of Y. pestis, YspE1 and YspE2, can be delivered via type III secretion injectisome into host cytosol where they ubiquitinate multiple guanylate-binding proteins (GBPs) for proteasomal degradation. However, Y. pseudotuberculosis has no such capability due to lacking functional YspE1/2 homologs. YspE1/2-mediated GBP degradations significantly promote the survival of Y. pestis in macrophages and strongly inhibit inflammasome activation. By contrast, Gbpchr3−/−, chr5−/− macrophages exhibit much lowered inflammasome activation independent of YspE1/2, accompanied with an enhanced replication of Y. pestis. Accordingly, Gbpchr3−/−, chr5−/− mice are more susceptible to Y. pestis. We demonstrate that Y. pestis utilizes E3 ligases to subvert GBP-mediated host defense, which appears to be newly acquired by Y. pestis during evolution. Guanylate-binding proteins (GBPs) recognize pathogen containing vacuoles, leading to lysis of this intracellular niche and induction of inflammasomes. Here, Cao et al. show that Y. pestis, the causative agent of plague, secret two functionally redundant E3 ligase, YspE1 and YspE2, into the host’s cytosol to ubiquitinate multiple GBPs for proteasomal degradation to subvert host immune defense. This capability appears to be newly acquired by Y. pestis during evolution, since its closely related progenitor Y. pseudotuberculosis is unable to do so.
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Affiliation(s)
- Shiyang Cao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Yang Jiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Wei Jiang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Si Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Yifan Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Yang You
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Xiao Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Hongyan Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Yuan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Gengshan Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Tong Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Yazhou Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China
| | - Feng Shao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China.
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071, Beijing, China.
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Allué-Guardia A, Koenig SSK, Martinez RA, Rodriguez AL, Bosilevac JM, Feng† P, Eppinger M. Pathogenomes and variations in Shiga toxin production among geographically distinct clones of Escherichia coli O113:H21. Microb Genom 2022; 8. [PMID: 35394418 PMCID: PMC9453080 DOI: 10.1099/mgen.0.000796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Infections with globally disseminated Shiga toxin-producing Escherichia coli (STEC) of the O113:H21 serotype can progress to severe clinical complications, such as hemolytic uremic syndrome (HUS). Two phylogeographically distinct clonal complexes have been established by multi locus sequence typing (MLST). Infections with ST-820 isolates circulating exclusively in Australia have caused severe human disease, such as HUS. Conversely, ST-223 isolates prevalent in the US and outside Australia seem to rarely cause severe human disease but are frequent contaminants. Following a genomic epidemiology approach, we wanted to gain insights into the underlying cause for this disparity. We examined the plasticity in the genome make-up and Shiga toxin production in a collection of 20 ST-820 and ST-223 strains isolated from produce, the bovine reservoir, and clinical cases. STEC are notorious for assembly into fragmented draft sequences when using short-read sequencing technologies due to the extensive and partly homologous phage complement. The application of long-read technology (LRT) sequencing yielded closed reference chromosomes and plasmids for two representative ST-820 and ST-223 strains. The established high-resolution framework, based on whole genome alignments, single nucleotide polymorphism (SNP)-typing and MLST, includes the chromosomes and plasmids of other publicly available O113:H21 sequences and allowed us to refine the phylogeographical boundaries of ST-820 and ST-223 complex isolates and to further identify a historic non-shigatoxigenic strain from Mexico as a quasi-intermediate. Plasmid comparison revealed strong correlations between the strains' featured pO113 plasmid genotypes and chromosomally inferred ST, which suggests coevolution of the chromosome and virulence plasmids. Our pathogenicity assessment revealed statistically significant differences in the Stx2a-production capabilities of ST-820 as compared to ST-223 strains under RecA-induced Stx phage mobilization, a condition that mimics Stx-phage induction. These observations suggest that ST-820 strains may confer an increased pathogenic potential in line with the strain-associated epidemiological metadata. Still, some of the tested ST-223 cultures sourced from contaminated produce or the bovine reservoir also produced Stx at levels comparable to those of ST-820 isolates, which calls for awareness and for continued surveillance of this lineage.
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Affiliation(s)
- Anna Allué-Guardia
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Sara S. K. Koenig
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Ricardo A. Martinez
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
| | - Armando L. Rodriguez
- University of Texas at San Antonio, Research Computing Support Group, San Antonio, TX, USA
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Peter Feng†
- U.S. Food and Drug Administration (FDA), College Park, MD, USA
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX, USA
- South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, USA
- *Correspondence: Mark Eppinger,
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7
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Cummins EA, Hall RJ, McInerney JO, McNally A. Prokaryote pangenomes are dynamic entities. Curr Opin Microbiol 2022; 66:73-78. [PMID: 35104691 DOI: 10.1016/j.mib.2022.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/24/2022]
Abstract
Prokaryote pangenomes are influenced heavily by environmental factors and the opportunity for gene gain and loss events. As the field of pangenome analysis has expanded, so has the need to fully understand the complexity of how eco-evolutionary dynamics shape pangenomes. Here, we describe current models of pangenome evolution and discuss their suitability and accuracy. We suggest that pangenomes are dynamic entities under constant flux, highlighting the influence of two-way interactions between pangenome and environment. New classifications of core and accessory genes are also considered, underscoring the need for continuous evaluation of nomenclature in a fast-moving field. We conclude that future models of pangenome evolution should incorporate eco-evolutionary dynamics to fully encompass their dynamic, changeable nature.
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Affiliation(s)
- Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - James O McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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8
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Silva-Andrade C, Martin AJ, Garrido D. Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance. Microorganisms 2022; 10:microorganisms10020213. [PMID: 35208668 PMCID: PMC8879937 DOI: 10.3390/microorganisms10020213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023] Open
Abstract
Clostridium baratii strains are rare opportunistic pathogens associated with botulism intoxication. They have been isolated from foods, soil and be carried asymptomatically or cause botulism outbreaks. Is not taxonomically related to Clostridium botulinum, but some strains are equipped with BoNT/F7 cluster. Despite their relationship with diseases, our knowledge regarding the genomic features and phylogenetic characteristics is limited. We analyzed the pangenome of C. baratii to understand the diversity and genomic features of this species. We compared existing genomes in public databases, metagenomes, and one newly sequenced strain isolated from an asymptomatic subject. The pangenome was open, indicating it comprises genetically diverse organisms. The core genome contained 28.49% of the total genes of the pangenome. Profiling virulence factors confirmed the presence of phospholipase C in some strains, a toxin capable of disrupting eukaryotic cell membranes. Furthermore, the genomic analysis indicated significant horizontal gene transfer (HGT) events as defined by the presence of prophage genomes. Seven strains were equipped with BoNT/F7 cluster. The active site was conserved in all strains, identifying a missing 7-aa region upstream of the active site in C. baratii genomes. This analysis could be important to advance our knowledge regarding opportunistic clostridia and better understand their contribution to disease.
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Affiliation(s)
- Claudia Silva-Andrade
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile;
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Alberto J. Martin
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago 8580000, Chile;
- Correspondence: (A.J.M.); (D.G.)
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Correspondence: (A.J.M.); (D.G.)
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9
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Eppinger M, Almería S, Allué-Guardia A, Bagi LK, Kalalah AA, Gurtler JB, Fratamico PM. Genome Sequence Analysis and Characterization of Shiga Toxin 2 Production by Escherichia coli O157:H7 Strains Associated With a Laboratory Infection. Front Cell Infect Microbiol 2022; 12:888568. [PMID: 35770066 PMCID: PMC9234449 DOI: 10.3389/fcimb.2022.888568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/03/2022] [Indexed: 11/21/2022] Open
Abstract
A laboratory-acquired E. coli O157:H7 infection with associated severe sequelae including hemolytic uremic syndrome occurred in an individual working in the laboratory with a mixture of nalidixic acid-resistant (NalR) O157:H7 mutant strains in a soil-biochar blend. The patient was hospitalized and treated with an intravenous combination of metronidazole and levofloxacin. The present study investigated the source of this severe laboratory acquired infection and further examined the influence of the antibiotics used during treatment on the expression and production of Shiga toxin. Genomes of two Stx2a-and eae-positive O157:H7 strains isolated from the patient's stool were sequenced along with two pairs of the wt strains and their derived NalR mutants used in the laboratory experiments. High-resolution SNP typing determined the strains' individual genetic relatedness and unambiguously identified the two laboratory-derived NalR mutant strains as the source of the researcher's life-threatening disease, rather than a conceivable ingestion of unrelated O157:H7 isolates circulating at the same time. It was further confirmed that in sublethal doses, the antibiotics increased toxin expression and production. Our results support a simultaneous co-infection with clinical strains in the laboratory, which were the causative agents of previous O157:H7 outbreaks, and further that the administration of antibiotics may have impacted the outcome of the infection.
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Affiliation(s)
- Mark Eppinger
- Department of Molecular Microbiology and Immunology (MMI), University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Sonia Almería
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
| | - Anna Allué-Guardia
- Department of Molecular Microbiology and Immunology (MMI), University of Texas at San Antonio, San Antonio, TX, United States
| | - Lori K Bagi
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
| | - Anwar A Kalalah
- Department of Molecular Microbiology and Immunology (MMI), University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases (STCEID), San Antonio, TX, United States
| | - Joshua B Gurtler
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
| | - Pina M Fratamico
- United States (US) Department of Agriculture (USDA), Agricultural Research Service (ARS), Eastern Regional Research Center, Wyndmoor, PA, United States
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10
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Suntsov VV. Host Aspect of Territorial Expansion of the Plague Microbe Yersinia pestis from the Populations of the Tarbagan Marmot (Marmota sibirica). BIOL BULL+ 2021. [DOI: 10.1134/s1062359021080288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Proteogenomic discovery of sORF-encoded peptides associated with bacterial virulence in Yersinia pestis. Commun Biol 2021; 4:1248. [PMID: 34728737 PMCID: PMC8563848 DOI: 10.1038/s42003-021-02759-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 10/08/2021] [Indexed: 11/08/2022] Open
Abstract
Plague caused by Yersinia pestis is one of the deadliest diseases. However, many molecular mechanisms of bacterial virulence remain unclear. This study engaged in the discovery of small open reading frame (sORF)-encoded peptides (SEPs) in Y. pestis. An integrated proteogenomic pipeline was established, and an atlas containing 76 SEPs was described. Bioinformatic analysis indicated that 20% of these SEPs were secreted or localized to the transmembrane and that 33% contained functional domains. Two SEPs, named SEPs-yp1 and -yp2 and encoded in noncoding regions, were selected by comparative peptidomics analysis under host-specific environments and high-salinity stress. They displayed important roles in the regulation of antiphagocytic capability in a thorough functional assay. Remarkable attenuation of virulence in mice was observed in the SEP-deleted mutants. Further global proteomic analysis indicated that SEPs-yp1 and -yp2 affected the bacterial metabolic pathways, and SEP-yp1 was associated with the bacterial virulence by modulating the expression of key virulence factors of the Yersinia type III secretion system. Our study provides a rich resource for research on Y. pestis and plague, and the findings on SEP-yp1 and SEP-yp2 shed light on the molecular mechanism of bacterial virulence. Shiyang Cao, Xinyue Liu, Yin Huang, and Yanfeng Yan et al. utilized an integrated proteogenomic approach to describe an atlas of small open reading frame-encoded peptides (SEPs) in the pathogen, Yersinia pestis. They demonstrate that two of these SEPs are associated with regulation of bacterial virulence, and altogether develop a valuable resource for future research into Y. pestis physiology.
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12
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Susat J, Lübke H, Immel A, Brinker U, Macāne A, Meadows J, Steer B, Tholey A, Zagorska I, Gerhards G, Schmölcke U, Kalniņš M, Franke A, Pētersone-Gordina E, Teßman B, Tõrv M, Schreiber S, Andree C, Bērziņš V, Nebel A, Krause-Kyora B. A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis. Cell Rep 2021; 35:109278. [PMID: 34192537 DOI: 10.1016/j.celrep.2021.109278] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/18/2020] [Accepted: 05/28/2021] [Indexed: 11/18/2022] Open
Abstract
A 5,000-year-old Yersinia pestis genome (RV 2039) is reconstructed from a hunter-fisher-gatherer (5300-5050 cal BP) buried at Riņņukalns, Latvia. RV 2039 is the first in a series of ancient strains that evolved shortly after the split of Y. pestis from its antecessor Y. pseudotuberculosis ∼7,000 years ago. The genomic and phylogenetic characteristics of RV 2039 are consistent with the hypothesis that this very early Y. pestis form was most likely less transmissible and maybe even less virulent than later strains. Our data do not support the scenario of a prehistoric pneumonic plague pandemic, as suggested previously for the Neolithic decline. The geographical and temporal distribution of the few prehistoric Y. pestis cases reported so far is more in agreement with single zoonotic events.
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Affiliation(s)
- Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany
| | - Harald Lübke
- Centre for Baltic and Scandinavian Archaeology (ZBSA), Schleswig-Holstein State Museums Foundation Schloss Gottorf, Schlossinsel 1, 24837 Schleswig, Germany
| | - Alexander Immel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany
| | - Ute Brinker
- Centre for Baltic and Scandinavian Archaeology (ZBSA), Schleswig-Holstein State Museums Foundation Schloss Gottorf, Schlossinsel 1, 24837 Schleswig, Germany
| | - Aija Macāne
- Department of Historical Studies, University of Gothenburg, PO Box 200, SE405 30 Göteborg, Sweden
| | - John Meadows
- Centre for Baltic and Scandinavian Archaeology (ZBSA), Schleswig-Holstein State Museums Foundation Schloss Gottorf, Schlossinsel 1, 24837 Schleswig, Germany; Leibniz Laboratory for AMS Dating and Isotope Research, Kiel University, Max-Eyth-Str. 11-13, 24118 Kiel, Germany
| | - Britta Steer
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Niemannsweg 11, 24105 Kiel, Germany
| | - Andreas Tholey
- Systematic Proteomics & Bioanalytics, Institute for Experimental Medicine, Kiel University, Niemannsweg 11, 24105 Kiel, Germany
| | - Ilga Zagorska
- Institute of Latvian History, University of Latvia, Kalpaka bulv. 4, 1050 Riga, Latvia
| | - Guntis Gerhards
- Institute of Latvian History, University of Latvia, Kalpaka bulv. 4, 1050 Riga, Latvia
| | - Ulrich Schmölcke
- Centre for Baltic and Scandinavian Archaeology (ZBSA), Schleswig-Holstein State Museums Foundation Schloss Gottorf, Schlossinsel 1, 24837 Schleswig, Germany
| | - Mārcis Kalniņš
- Institute of Latvian History, University of Latvia, Kalpaka bulv. 4, 1050 Riga, Latvia
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany
| | | | - Barbara Teßman
- Berlin Society of Anthropology, Ethnology and Prehistory, c/o Museum of Pre- and Protohistory, Geschwister-Scholl-Str. 6, 10117 Berlin, Germany
| | - Mari Tõrv
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Jakobi 2, 51005 Tartu, Estonia
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany; Department of General Internal Medicine, University Hospital Schleswig-Holstein, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany
| | - Christian Andree
- Research Center of Medical History, Kiel University, Breiter Weg 10, 24105 Kiel, Germany
| | - Valdis Bērziņš
- Institute of Latvian History, University of Latvia, Kalpaka bulv. 4, 1050 Riga, Latvia
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany.
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13
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Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani. BMC Genomics 2020; 21:449. [PMID: 32600255 PMCID: PMC7325237 DOI: 10.1186/s12864-020-06863-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/22/2020] [Indexed: 11/11/2022] Open
Abstract
Background Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.
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14
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Petro CD, Duncan JK, Seldina YI, Allué-Guardia A, Eppinger M, Riddle MS, Tribble DR, Johnson RC, Dalgard CL, Sukumar G, Connor P, Boisen N, Melton-Celsa AR. Genetic and Virulence Profiles of Enteroaggregative Escherichia coli (EAEC) Isolated From Deployed Military Personnel (DMP) With Travelers' Diarrhea. Front Cell Infect Microbiol 2020; 10:200. [PMID: 32509590 PMCID: PMC7251025 DOI: 10.3389/fcimb.2020.00200] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/16/2020] [Indexed: 02/01/2023] Open
Abstract
To discern if there was a particular genotype associated with clinical enteroaggregative Escherichia coli (EAEC) strains isolated from deployed military personnel (DMP) with travelers' diarrhea (TD), we characterized a collection of EAEC from DMP deployed to Afghanistan, Djibouti, Kenya, or Honduras. Although we did not identify a specific EAEC genotype associated with TD in DMP, we found that EAEC isolated at the first clinic visit were more likely to encode the dispersin gene aap than EAEC collected at follow-up visits. A majority of the EAEC isolates were typical EAEC that adhered to HEp-2 cells, formed biofilms, and harbored genes for aggregative adherence fimbriae (AAF), AggR, and serine protease autotransporters of Enterobacteriaceae (SPATEs). A separate subset of the EAEC had aggR and genes for SPATEs but encoded a gene highly homologous to that for CS22, a fimbriae more commonly found in enterotoxigenic E. coli. None of these CS22-encoding EAEC formed biofilms in vitro or adhered to HEp-2 cells. Whole genome sequence and single nucleotide polymorphism analyses demonstrated that most of the strains were genetically diverse, but that a few were closely related. Isolation of these related strains occurred within days to more than a year apart, a finding that suggests a persistent source and genomic stability. In an ampicillin-treated mouse model we found that an agg4A+ aar- isolate formed a biofilm in the intestine and caused reduced weight gain in mice, whereas a strain that did not form an in vivo biofilm caused no morbidity. Our diverse strain collection from DMP displays the heterogeneity of EAEC strains isolated from human patients, and our mouse model of infection indicated the genotype agg4A+ aar– and/or capacity to form biofilm in vivo may correlate to disease severity.
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Affiliation(s)
- Courtney D Petro
- Department of Microbiology and Immunolgy, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Jeffrey K Duncan
- Department of Microbiology and Immunolgy, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Yuliya I Seldina
- Walter Reed National Military Medical Center, Bethesda, MD, United States
| | - Anna Allué-Guardia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Mark Eppinger
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Mark S Riddle
- Department of Preventative Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - David R Tribble
- Department of Preventative Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Ryan C Johnson
- Department of Preventative Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Clifton L Dalgard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Gauthaman Sukumar
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Collaborative Health Initiative Research Program, Henry Jackson Foundation, Bethesda, MD, United States
| | - Patrick Connor
- Military Enteric Disease Group, Academic Department of Military Medicine, Birmingham, United Kingdom
| | - Nadia Boisen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Angela R Melton-Celsa
- Department of Microbiology and Immunolgy, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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15
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Nyong EC, Zaia SR, Allué-Guardia A, Rodriguez AL, Irion-Byrd Z, Koenig SSK, Feng P, Bono JL, Eppinger M. Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes. Front Microbiol 2020; 11:619. [PMID: 32351476 PMCID: PMC7175801 DOI: 10.3389/fmicb.2020.00619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
The toxigenic conversion of Escherichia coli strains by Shiga toxin-converting (Stx) bacteriophages were prominent and recurring events in the stepwise evolution of enterohemorrhagic E. coli (EHEC) O157:H7 from an enteropathogenic (EPEC) O55:H7 ancestor. Atypical, attenuated isolates have been described for both non-sorbitol fermenting (NSF) O157:H7 and SF O157:NM serotypes, which are distinguished by the absence of Stx, the characteristic virulence hallmark of Stx-producing E. coli (STEC). Such atypical isolates either never acquired Stx-phages or may have secondarily lost stx during the course of infection, isolation, or routine subculture; the latter are commonly referred to as LST (Lost Shiga Toxin)-isolates. In this study we analyzed the genomes of 15 NSF O157:H7 and SF O157:NM strains from North America, Europe, and Asia that are characterized by the absence of stx, the virulence hallmark of STEC. The individual genomic basis of the Stx (-) phenotype has remained largely undetermined as the majority of STEC genomes in public genome repositories were generated using short read technology and are in draft stage, posing a major obstacle for the high-resolution whole genome sequence typing (WGST). The application of LRT (long-read technology) sequencing provided us with closed genomes, which proved critical to put the atypical non-shigatoxigenic NSF O157:H7 and SF O157:NM strains into the phylogenomic context of the stepwise evolutionary model. Availability of closed chromosomes for representative Stx (-) NSF O157:H7 and SF O157:NM strains allowed to describe the genomic basis and individual evolutionary trajectories underlying the absence of Stx at high accuracy and resolution. The ability of LRT to recover and accurately assemble plasmids revealed a strong correlation between the strains' featured plasmid genotype and chromosomally inferred clade, which suggests the coevolution of the chromosome and accessory plasmids. The identified ancestral traits in the pSFO157 plasmid of NSF O157:H7 strain LSU-61 provided additional evidence for its intermediate status. Taken together, these observations highlight the utility of LRTs for advancing our understanding of EHEC O157:H7/NM pathogenome evolution. Insights into the genomic and phenotypic plasticity of STEC on a lineage- and genome-wide scale are foundational to improve and inform risk assessment, biosurveillance, and prevention strategies.
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Affiliation(s)
- Emmanuel C. Nyong
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Sam R. Zaia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Anna Allué-Guardia
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Armando L. Rodriguez
- Research Computing Support Group, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Zaina Irion-Byrd
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Sara S. K. Koenig
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | | | - James L. Bono
- United States Meat Animal Research Center, Agricultural Research Service, United States Department of Agriculture (ARS-USDA), Clay Center, NE, United States
| | - Mark Eppinger
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
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16
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Gargis AS, Cherney B, Conley AB, McLaughlin HP, Sue D. Rapid Detection of Genetic Engineering, Structural Variation, and Antimicrobial Resistance Markers in Bacterial Biothreat Pathogens by Nanopore Sequencing. Sci Rep 2019; 9:13501. [PMID: 31534162 PMCID: PMC6751186 DOI: 10.1038/s41598-019-49700-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 08/27/2019] [Indexed: 01/10/2023] Open
Abstract
Widespread release of Bacillus anthracis (anthrax) or Yersinia pestis (plague) would prompt a public health emergency. During an exposure event, high-quality whole genome sequencing (WGS) can identify genetic engineering, including the introduction of antimicrobial resistance (AMR) genes. Here, we developed rapid WGS laboratory and bioinformatics workflows using a long-read nanopore sequencer (MinION) for Y. pestis (6.5 h) and B. anthracis (8.5 h) and sequenced strains with different AMR profiles. Both salt-precipitation and silica-membrane extracted DNA were suitable for MinION WGS using both rapid and field library preparation methods. In replicate experiments, nanopore quality metrics were defined for genome assembly and mutation analysis. AMR markers were correctly detected and >99% coverage of chromosomes and plasmids was achieved using 100,000 raw sequencing reads. While chromosomes and large and small plasmids were accurately assembled, including novel multimeric forms of the Y. pestis virulence plasmid, pPCP1, MinION reads were error-prone, particularly in homopolymer regions. MinION sequencing holds promise as a practical, front-line strategy for on-site pathogen characterization to speed the public health response during a biothreat emergency.
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Affiliation(s)
- Amy S Gargis
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
| | - Blake Cherney
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrew B Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, Georgia, USA
| | - Heather P McLaughlin
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - David Sue
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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17
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Keller M, Spyrou MA, Scheib CL, Neumann GU, Kröpelin A, Haas-Gebhard B, Päffgen B, Haberstroh J, Ribera I Lacomba A, Raynaud C, Cessford C, Durand R, Stadler P, Nägele K, Bates JS, Trautmann B, Inskip SA, Peters J, Robb JE, Kivisild T, Castex D, McCormick M, Bos KI, Harbeck M, Herbig A, Krause J. Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750). Proc Natl Acad Sci U S A 2019; 116:12363-12372. [PMID: 31164419 PMCID: PMC6589673 DOI: 10.1073/pnas.1820447116] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium's spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.
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Affiliation(s)
- Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
- State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Christiana L Scheib
- Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom
- Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Andreas Kröpelin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Friedrich Schiller University Jena, 07743 Jena, Germany
| | | | - Bernd Päffgen
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, 80799 Munich, Germany
| | - Jochen Haberstroh
- Bavarian State Department of Monuments and Sites, 80539 Munich, Germany
| | | | - Claude Raynaud
- CNRS, UMR5140, Archéologie des Sociétés Méditerranéennes, 34199 Montpellier, France
| | - Craig Cessford
- Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom
| | - Raphaël Durand
- Service d'Archéologie Préventive de l'Agglomération de Bourges Plus, 18023 Bourges Cedex, France
| | - Peter Stadler
- Department of Pre- and Protohistory, University of Vienna, 1190 Vienna, Austria
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Jessica S Bates
- Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom
| | - Bernd Trautmann
- State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany
| | - Sarah A Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, United Kingdom
| | - Joris Peters
- State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany
- ArchaeoBioCenter, Ludwig Maximilian University Munich, 80539 Munich, Germany
- Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig Maximilian University Munich, 80539 Munich, Germany
| | - John E Robb
- Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom
| | - Toomas Kivisild
- Department of Archaeology, University of Cambridge, Cambridge CB2 3ER, United Kingdom
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | | | - Michael McCormick
- Initiative for the Science of the Human Past, Department of History, Harvard University, Cambridge, MA 02138
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 07745 Jena, Germany
| | - Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Michaela Harbeck
- State Collection of Anthropology and Palaeoanatomy Munich, Staatliche Naturwissenschaftliche Sammlungen Bayerns, 80333 Munich, Germany;
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, 07745 Jena, Germany
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18
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Liu J, Zeng Q, Wang M, Cheng A, Liu M, Zhu D, Chen S, Jia R, Zhao XX, Wu Y, Yang Q, Zhang S, Liu Y, Yu Y, Zhang L, Chen X. Comparative genome-scale modelling of the pathogenic Flavobacteriaceae species Riemerella anatipestifer in China. Environ Microbiol 2019; 21:2836-2851. [PMID: 31004458 DOI: 10.1111/1462-2920.14635] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 04/17/2019] [Indexed: 12/14/2022]
Abstract
Riemerella anatipestifer (RA) is a gram-negative bacterium that has a high potential to infect waterfowl. Although more and more genomes of RA have been generated comparaed to genomic analysis of RA still remains at the level of individual species. In this study, we analysed the pan-genome of 27 RA virulent isolates to reveal the intraspecies genomic diversity from various aspects. The multi-locus sequence typing (MLST) analysis suggests that the geographic origin of R. anatipestifer is Guangdong province, China. Results of pan-genome analysis revealed an open pan-genome for all 27 species with the sizes of 2967 genes. We identified 387 genes among 555 unique genes originated by horizontal gene transfer. Further studies showed 204 strain-specific HGT genes were predicted as virulent proteins. Screening the 1113 core genes in RA through subtractive genomic approach, 70 putative vaccine targets out of 125 non-cytoplasmic proteins have been predicted. Further analysis of these non A. platyrhynchos homologous proteins predicted that 56 essential proteins as drug target with more interaction partners were involved in unique metabolic pathways of RA. In conclusion, the present study indicated the essence and the diversity of RA and also provides useful information for identification of vaccine and drugs candidates in future.
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Affiliation(s)
- Jibin Liu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China
| | - Qiurui Zeng
- School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xin-Xin Zhao
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yunya Liu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiaoyue Chen
- Institute of Preventive Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, 611130, China.,Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
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19
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McLaughlin HP, Sue D. Rapid antimicrobial susceptibility testing and β-lactam-induced cell morphology changes of Gram-negative biological threat pathogens by optical screening. BMC Microbiol 2018; 18:218. [PMID: 30563467 PMCID: PMC6299660 DOI: 10.1186/s12866-018-1347-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND For Yersinia pestis, Burkholderia pseudomallei, and Burkholderia mallei, conventional broth microdilution (BMD) is considered the gold standard for antimicrobial susceptibility testing (AST) and, depending on the species, requires an incubation period of 16-20 h, or 24-48 h according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. After a diagnosis of plague, melioidosis or glanders during an outbreak or after an exposure event, the timely distribution of appropriate antibiotics for treatment or post-exposure prophylaxis of affected populations could reduce mortality rates. RESULTS Herein, we developed and evaluated a rapid, automated susceptibility test for these Gram-negative bacterial pathogens based on time-lapse imaging of cells incubating in BMD microtitre drug panels using an optical screening instrument (oCelloScope). In real-time, the instrument screened each inoculated well containing broth with various concentrations of antibiotics published by CLSI for primary testing: ciprofloxacin (CIP), doxycycline (DOX) and gentamicin (GEN) for Y. pestis; imipenem (IPM), ceftazidime (CAZ) and DOX for B. mallei; and IPM, DOX, CAZ, amoxicillin-clavulanic acid (AMC) and trimethoprim-sulfamethoxazole (SXT) for B. pseudomallei. Based on automated growth kinetic data, the time required to accurately determine susceptibility decreased by ≥70% for Y. pestis and ≥ 50% for B. mallei and B. pseudomallei compared to the times required for conventional BMD testing. Susceptibility to GEN, IPM and DOX could be determined in as early as three to six hours. In the presence of CAZ, susceptibility based on instrument-derived growth values could not be determined for the majority of B. pseudomallei and B. mallei strains tested. Time-lapse video imaging of these cultures revealed that the formation of filaments in the presence of this cephalosporin at inhibitory concentrations was detected as growth. Other β-lactam-induced cell morphology changes, such as the formation of spheroplasts and rapid cell lysis, were also observed and appear to be strain- and antibiotic concentration-dependent. CONCLUSIONS A rapid, functional AST was developed and real-time video footage captured β-lactam-induced morphologies of wild-type B. mallei and B. pseudomallei strains in broth. Optical screening reduced the time to results required for AST of three Gram-negative biothreat pathogens using clinically relevant, first-line antibiotics compared to conventional BMD.
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Affiliation(s)
- Heather P. McLaughlin
- Laboratory of Preparedness and Response Branch, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS-H17-5, Atlanta, GA 30333 USA
| | - David Sue
- Laboratory of Preparedness and Response Branch, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road NE, MS-H17-5, Atlanta, GA 30333 USA
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20
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Rascovan N, Sjögren KG, Kristiansen K, Nielsen R, Willerslev E, Desnues C, Rasmussen S. Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline. Cell 2018; 176:295-305.e10. [PMID: 30528431 DOI: 10.1016/j.cell.2018.11.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/10/2018] [Accepted: 11/01/2018] [Indexed: 12/30/2022]
Abstract
Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.
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Affiliation(s)
- Nicolás Rascovan
- Aix Marseille Université, UMR MEPHI, CNRS FRE2013, IRD 198, AP-HM, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France.
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kristian Kristiansen
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Rasmus Nielsen
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Eske Willerslev
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Christelle Desnues
- Aix Marseille Université, UMR MEPHI, CNRS FRE2013, IRD 198, AP-HM, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, 2800 Kongens Lyngby, Denmark.
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21
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Nikiforov KA, Morozov OA, Nosov NY, Kukleva LM, Yeroshenko GA, Kutyrev VV. Population Structure, Taxonomy, and Genetic Features of Yersinia pestis Strains of the Central Asian Subspecies. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418100101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Dai R, Wei B, Xiong H, Yang X, Peng Y, He J, Jin J, Wang Y, Zha X, Zhang Z, Liang Y, Zhang Q, Xu J, Wang Z, Li W. Human plague associated with Tibetan sheep originates in marmots. PLoS Negl Trop Dis 2018; 12:e0006635. [PMID: 30114220 PMCID: PMC6095483 DOI: 10.1371/journal.pntd.0006635] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 06/25/2018] [Indexed: 11/21/2022] Open
Abstract
The Qinghai-Tibet plateau is a natural plague focus and is the largest such focus in China. In this area, while Marmota himalayana is the primary host, a total of 18 human plague outbreaks associated with Tibetan sheep (78 cases with 47 deaths) have been reported on the Qinghai-Tibet plateau since 1956. All of the index infectious cases had an exposure history of slaughtering or skinning diseased or dead Tibetan sheep. In this study, we sequenced and compared 38 strains of Yersinia pestis isolated from different hosts, including humans, Tibetan sheep, and M. himalayana. Phylogenetic relationships were reconstructed based on genome-wide single-nucleotide polymorphisms identified from our isolates and reference strains. The phylogenetic relationships illustrated in our study, together with the finding that the Tibetan sheep plague clearly lagged behind the M. himalayana plague, and a previous study that identified the Tibetan sheep as a plague reservoir with high susceptibility and moderate sensitivity, indicated that the human plague was transmitted from Tibetan sheep, while the Tibetan sheep plague originated from marmots. Tibetan sheep may encounter this infection by contact with dead rodents or through being bitten by fleas originating from M. himalayana during local epizootics. Plague is mainly a disease of wild rodents, and their parasitic fleas are considered the transmitting vectors. However, human plague originating from Ovis aries (Tibetan sheep) is found in the Qinghai-Tibet plateau in China, where Marmota. himalayana is the primary plague host. Tibetan sheep-related human plague infection is always associated with slaughtering or skinning diseased or dead Tibetan sheep. The plague in Tibetan sheep clearly lags that in M. himalayana. In this study, we performed a genome-wide single nucleotide polymorphism analysis of Tibetan sheep-related plague events, including pathogens isolated from humans, Tibetan sheep, and marmots. Through genomic analysis, together with the epidemiological connections, we confirmed that human plague came from Tibetan sheep, and the Tibetan sheep plague originated from marmots. Tibetan sheep account for about 1/3 of the total number of sheep in China. Tibetan sheep and goats are important domestic livestock on the Qinghai-Tibet plateau. Therefore, the hazards of Tibetan sheep plague should not be underestimated.
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Affiliation(s)
- Ruixia Dai
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Baiqing Wei
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Haoming Xiong
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Xiaoyan Yang
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Yao Peng
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Jian He
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Juan Jin
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Yumeng Wang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Xi Zha
- Center for Disease Control and Prevention of Tibet Autonomous Region, Lhasa, China
| | - Zhikai Zhang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Ying Liang
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Qingwen Zhang
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Jianguo Xu
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
| | - Zuyun Wang
- Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Wei Li
- National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Hangzhou, China
- * E-mail:
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23
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Investigation of Yersinia pestis and Yersinia pseudotuberculosis strains from Georgia and neighboring countries in the Caucasus by high-density SNP microarray. Arch Microbiol 2018; 200:1345-1355. [PMID: 29974157 DOI: 10.1007/s00203-018-1545-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/06/2018] [Accepted: 06/22/2018] [Indexed: 11/27/2022]
Abstract
Yersinia pestis, the causative agent of plague, is a recently evolved clone of the enteropathogenic bacterium Yersinia pseudotuberculosis. Y. pestis has been extensively studied for decades; however, there are insufficient data about the intra-species diversity of this microorganism in certain parts of the world, including the Caucasus region. Using a high-density single-nucleotide polymorphism (SNP) microarray, we genotyped a total of 46 Y. pestis isolates from two plague foci in Georgia and neighboring Caucasus countries together with 12 Y. pseudotuberculosis isolates from Georgia. The genotyping microarray captured a total of 13,525 SNP positions across the Y. pestis and Y. pseudotuberculosis genomes and plasmids with high-throughput capability and superior reproducibility. From this analysis, we confirmed the presence of two independent and relatively distant phylogenetic groups of Y. pestis in the Caucasus region. The signature SNP patterns identified from this study will allow assay development for plague surveillance and pseudotuberculosis diagnostics.
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24
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Genesis of Flea-Born Transmission of Plague Microbe, Yersinia pestis: Two Approachs – Molecular-Genetic and Ecological Ones. PROBLEMS OF PARTICULARLY DANGEROUS INFECTIONS 2018. [DOI: 10.21055/0370-1069-2018-2-37-44] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two approaches to studying the origin and transmission mechanism of the flea-borne plague pathogen, Yersinia pestis: molecular-genetic and ecological ones – are considered in this review. The molecular genetic approach is based on saltation evolutionary ideology and relies upon the phenomenon of horizontal gene transfer of pla and ymt as critical evolutionary events. Further deletion of some structural and regulatory genes optimized “blockage” mechanism of transmission. The Ecological approach is based on the modern synthetic theory of evolution. It posits a gradual population-genetic transformation in the Marmot – Flea (Marmota sibirica – Oropsylla silantiewi) transitional (heterothermal, heteroimmune) host-parasite system in Late Pleistocene – Holocene epochs. The best prospects for disclosing the mechanisms of evolutionary formation of flea-borne Y. pestis transmission consist in the synthesis of molecular-genetic and ecological approaches.
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25
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Bochkareva OO, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva VA, Artamonova II, Gelfand MS. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ 2018; 6:e4545. [PMID: 29607260 PMCID: PMC5877447 DOI: 10.7717/peerj.4545] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/07/2018] [Indexed: 12/20/2022] Open
Abstract
Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content.
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Affiliation(s)
- Olga O Bochkareva
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Natalia O Dranenko
- Department of Molecular and Chemical Physics, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Elena S Ocheredko
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - German M Kanevsky
- Higher Chemical College of the Russian Academy of Sciences, D. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - Yaroslav N Lozinsky
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | | | - Irena I Artamonova
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Mikhail S Gelfand
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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26
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Abstract
The adaptation phase of CRISPR-Cas immunity depends on the precise integration of short segments of foreign DNA (spacers) into a specific genomic location within the CRISPR locus by the Cas1-Cas2 integration complex. Although off-target spacer integration outside of canonical CRISPR arrays has been described in vitro, no evidence of non-specific integration activity has been found in vivo. Here, we show that non-canonical off-target integrations can occur within bacterial chromosomes at locations that resemble the native CRISPR locus by characterizing hundreds of off-target integration locations within Escherichia coli. Considering whether such promiscuous Cas1-Cas2 activity could have an evolutionary role through the genesis of neo-CRISPR loci, we combed existing CRISPR databases and available genomes for evidence of off-target integration activity. This search uncovered several putative instances of naturally occurring off-target spacer integration events within the genomes of Yersinia pestis and Sulfolobus islandicus. These results are important in understanding alternative routes to CRISPR array genesis and evolution, as well as in the use of spacer acquisition in technological applications.
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27
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Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration. Nat Microbiol 2018; 3:310-318. [PMID: 29379209 DOI: 10.1038/s41564-017-0097-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 12/11/2017] [Indexed: 01/09/2023]
Abstract
The adaptation phase of CRISPR-Cas immunity depends on the precise integration of short segments of foreign DNA (spacers) into a specific genomic location within the CRISPR locus by the Cas1-Cas2 integration complex. Although off-target spacer integration outside of canonical CRISPR arrays has been described in vitro, no evidence of non-specific integration activity has been found in vivo. Here, we show that non-canonical off-target integrations can occur within bacterial chromosomes at locations that resemble the native CRISPR locus by characterizing hundreds of off-target integration locations within Escherichia coli. Considering whether such promiscuous Cas1-Cas2 activity could have an evolutionary role through the genesis of neo-CRISPR loci, we combed existing CRISPR databases and available genomes for evidence of off-target integration activity. This search uncovered several putative instances of naturally occurring off-target spacer integration events within the genomes of Yersinia pestis and Sulfolobus islandicus. These results are important in understanding alternative routes to CRISPR array genesis and evolution, as well as in the use of spacer acquisition in technological applications.
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28
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Kiu R, Caim S, Alexander S, Pachori P, Hall LJ. Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors. Front Microbiol 2017; 8:2485. [PMID: 29312194 PMCID: PMC5733095 DOI: 10.3389/fmicb.2017.02485] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/29/2017] [Indexed: 01/08/2023] Open
Abstract
Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an "open" pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene) in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc), enterotoxin (cpe), and Perfringolysin O (pfo or pfoA), although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56) of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet) and anti-defensins genes (mprF) were consistently detected in silico (tet: 75%; mprF: 100%). However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.
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Affiliation(s)
- Raymond Kiu
- Gut Health and Food Safety, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Shabhonam Caim
- Gut Health and Food Safety, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | | | - Purnima Pachori
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Lindsay J. Hall
- Gut Health and Food Safety, Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
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29
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Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:5575-5599. [DOI: 10.1099/ijsem.0.001485] [Citation(s) in RCA: 556] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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30
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Giles TA, Greenwood AD, Tsangaras K, Giles TC, Barrow PA, Hannant D, Abu-Median AB, Yon L. Detection of a Yersinia pestis gene homologue in rodent samples. PeerJ 2016; 4:e2216. [PMID: 27602258 PMCID: PMC4991868 DOI: 10.7717/peerj.2216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/14/2016] [Indexed: 11/20/2022] Open
Abstract
A homologue to a widely used genetic marker, pla, for Yersinia pestis has been identified in tissue samples of two species of rat (Rattus rattus and Rattus norvegicus) and of mice (Mus musculus and Apodemus sylvaticus) using a microarray based platform to screen for zoonotic pathogens of interest. Samples were from urban locations in the UK (Liverpool) and Canada (Vancouver). The results indicate the presence of an unknown bacterium that shares a homologue for the pla gene of Yersinia pestis, so caution should be taken when using this gene as a diagnostic marker.
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Affiliation(s)
- Timothy A Giles
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research,Berlin,Germany; Department of Veterinary Medicine, Freie Universität Berlin,Berlin,Germany
| | - Kyriakos Tsangaras
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research,Berlin,Germany; Department of Translational Genetics, Cyprus Institute of Neurology and Genetics,Nicosia,Cyprus
| | - Tom C Giles
- The Advanced Data Analysis Centre, University of Nottingham, Leicestershire, United Kingdom
| | - Paul A Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Duncan Hannant
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Abu-Bakr Abu-Median
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
| | - Lisa Yon
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, Leicestershire, United Kingdom
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31
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Mao Y, Yang X, Liu Y, Yan Y, Du Z, Han Y, Song Y, Zhou L, Cui Y, Yang R. Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. Am J Trop Med Hyg 2016; 95:562-70. [PMID: 27382076 DOI: 10.4269/ajtmh.16-0215] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/17/2016] [Indexed: 12/16/2022] Open
Abstract
Yersinia pestis is among the most dangerous human pathogens, and systematic research of this pathogen is important in bacterial pathogenomics research. To fully interpret the biological functions, physiological characteristics, and pathogenesis of Y. pestis, a comprehensive annotation of its entire genome is necessary. The emergence of omics-based research has brought new opportunities to better annotate the genome of this pathogen. Here, the complete genome of Y. pestis strain 91001 was reannotated using genomics and proteogenomics data. One hundred and thirty-seven unreliable coding sequences were removed, and 41 homologous genes were relocated with their translational initiation sites, while the functions of seven pseudogenes and 392 hypothetical genes were revised. Moreover, annotations of noncoding RNAs, repeat sequences, and transposable elements have also been incorporated. The reannotated results are freely available at http://tody.bmi.ac.cn.
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Affiliation(s)
- Yiqing Mao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China. Center of Information Technology, Beijing Institute of Health and Medical Information, Beijing, People's Republic of China
| | - Xianwei Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yang Liu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, People's Republic of China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Lei Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
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Rusconi B, Sanjar F, Koenig SSK, Mammel MK, Tarr PI, Eppinger M. Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks. Front Microbiol 2016; 7:985. [PMID: 27446025 PMCID: PMC4928038 DOI: 10.3389/fmicb.2016.00985] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 06/08/2016] [Indexed: 01/29/2023] Open
Abstract
Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies.
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Affiliation(s)
- Brigida Rusconi
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
| | - Fatemeh Sanjar
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
| | - Sara S K Koenig
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
| | - Mark K Mammel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration Laurel, MD, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine St. Louis, MO, USA
| | - Mark Eppinger
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
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Oyston PCF, Williamson ED. Modern Advances against Plague. ADVANCES IN APPLIED MICROBIOLOGY 2016; 81:209-41. [PMID: 22958531 DOI: 10.1016/b978-0-12-394382-8.00006-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Plague has been a scourge of humanity, responsible for the deaths of millions. The etiological agent, Yersinia pestis, has evolved relatively recently from an enteropathogen, Yersinia pseudotuberculosis. The evolution of the plague pathogen has involved a complex series of genetic acquisitions, deletions, and rearrangements in its transition from an enteric niche to becoming a systemic, flea-vectored pathogen. With the advent of modern molecular biology techniques, we are starting to understand how the organism adapts to the diverse niches it encounters and how to combat the threat it poses.
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Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373. [PMID: 27071527 PMCID: PMC4829868 DOI: 10.1038/srep24373] [Citation(s) in RCA: 587] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/23/2016] [Indexed: 01/02/2023] Open
Abstract
Recent advances in ultra-high-throughput sequencing technology and metagenomics have led to a paradigm shift in microbial genomics from few genome comparisons to large-scale pan-genome studies at different scales of phylogenetic resolution. Pan-genome studies provide a framework for estimating the genomic diversity of the dataset, determining core (conserved), accessory (dispensable) and unique (strain-specific) gene pool of a species, tracing horizontal gene-flux across strains and providing insight into species evolution. The existing pan genome software tools suffer from various limitations like limited datasets, difficult installation/requirements, inadequate functional features etc. Here we present an ultra-fast computational pipeline BPGA (Bacterial Pan Genome Analysis tool) with seven functional modules. In addition to the routine pan genome analyses, BPGA introduces a number of novel features for downstream analyses like core/pan/MLST (Multi Locus Sequence Typing) phylogeny, exclusive presence/absence of genes in specific strains, subset analysis, atypical G + C content analysis and KEGG & COG mapping of core, accessory and unique genes. Other notable features include minimum running prerequisites, freedom to select the gene clustering method, ultra-fast execution, user friendly command line interface and high-quality graphics outputs. The performance of BPGA has been evaluated using a dataset of complete genome sequences of 28 Streptococcus pyogenes strains.
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Affiliation(s)
- Narendrakumar M Chaudhari
- Structural Biology &Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Vinod Kumar Gupta
- Structural Biology &Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Chitra Dutta
- Structural Biology &Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
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Abstract
This chapter summarizes researches on genome and evolution features of Yersinia pestis, the young pathogen that evolved from Y. pseudotuberculosis at least 5000 years ago. Y. pestis is a highly clonal bacterial species with closed pan-genome. Comparative genomic analysis revealed that genome of Y. pestis experienced highly frequent rearrangement and genome decay events during the evolution. The genealogy of Y. pestis includes five major branches, and four of them seemed raised from a "big bang" node that is associated with the Black Death. Although whole genome-wide variation of Y. pestis reflected a neutral evolutionary process, the branch length in the genealogical tree revealed over dispersion, which was supposedly caused by varied historical molecular clock that is associated with demographical effect by alternate cycles of enzootic disease and epizootic disease in sylvatic plague foci. In recent years, palaeomicrobiology researches on victims of the Black Death, and Justinian's plague verified that two historical pandemics were indeed caused by Y. pestis, but the etiological lineages might be extinct today.
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36
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Vogler AJ, Keim P, Wagner DM. A review of methods for subtyping Yersinia pestis: From phenotypes to whole genome sequencing. INFECTION GENETICS AND EVOLUTION 2015; 37:21-36. [PMID: 26518910 DOI: 10.1016/j.meegid.2015.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/23/2015] [Accepted: 10/24/2015] [Indexed: 12/28/2022]
Abstract
Numerous subtyping methods have been applied to Yersinia pestis with varying success. Here, we review the various subtyping methods that have been applied to Y. pestis and their capacity for answering questions regarding the population genetics, phylogeography, and molecular epidemiology of this important human pathogen. Methods are evaluated in terms of expense, difficulty, transferability among laboratories, discriminatory power, usefulness for different study questions, and current applicability in light of the advent of whole genome sequencing.
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Affiliation(s)
- Amy J Vogler
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA; Translational Genomics Research Institute North, Flagstaff, AZ 86001, USA.
| | - David M Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073, USA.
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Chen Y, Duan R, Li X, Li K, Liang J, Liu C, Qiu H, Xiao Y, Jing H, Wang X. Homology analysis and cross-immunogenicity of OmpA from pathogenic Yersinia enterocolitica, Yersinia pseudotuberculosis and Yersinia pestis. Mol Immunol 2015; 68:290-9. [PMID: 26435220 DOI: 10.1016/j.molimm.2015.09.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 09/15/2015] [Accepted: 09/22/2015] [Indexed: 11/19/2022]
Abstract
The outer membrane protein A (OmpA) is one of the intra-species conserved proteins with immunogenicity widely found in the family of Enterobacteriaceae. Here we first confirmed OmpA is conserved in the three pathogenic Yersinia: Yersinia pestis, Yersinia pseudotuberculosis and pathogenic Yersinia enterocolitica, with high homology at the nucleotide level and at the amino acid sequence level. The identity of ompA sequences for 262 Y. pestis strains, 134 Y. pseudotuberculosis strains and 219 pathogenic Y. enterocolitica strains are 100%, 98.8% and 97.7% similar. The main pattern of OmpA of pathogenic Yersinia are 86.2% and 88.8% identical at the nucleotide and amino acid sequence levels, respectively. Immunological analysis showed the immunogenicity of each OmpA and cross-immunogenicity of OmpA for pathogenic Yersinia where OmpA may be a vaccine candidate for Y. pestis and other pathogenic Yersinia.
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Affiliation(s)
- Yuhuang Chen
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Ran Duan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Xu Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Kewei Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Junrong Liang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Chang Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Haiyan Qiu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Yuchun Xiao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Huaiqi Jing
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China
| | - Xin Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing, China.
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Zimbler DL, Schroeder JA, Eddy JL, Lathem WW. Early emergence of Yersinia pestis as a severe respiratory pathogen. Nat Commun 2015; 6:7487. [PMID: 26123398 PMCID: PMC4491175 DOI: 10.1038/ncomms8487] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/12/2015] [Indexed: 11/09/2022] Open
Abstract
Yersinia pestis causes the fatal respiratory disease pneumonic plague. Y. pestis recently evolved from the gastrointestinal pathogen Y. pseudotuberculosis; however, it is not known at what point Y. pestis gained the ability to induce a fulminant pneumonia. Here we show that the acquisition of a single gene encoding the protease Pla was sufficient for the most ancestral, deeply rooted strains of Y. pestis to cause pneumonic plague, indicating that Y. pestis was primed to infect the lungs at a very early stage in its evolution. As Y. pestis further evolved, modern strains acquired a single amino-acid modification within Pla that optimizes protease activity. While this modification is unnecessary to cause pneumonic plague, the substitution is instead needed to efficiently induce the invasive infection associated with bubonic plague. These findings indicate that Y. pestis was capable of causing pneumonic plague before it evolved to optimally cause invasive infections in mammals.
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Affiliation(s)
- Daniel L Zimbler
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Jay A Schroeder
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Justin L Eddy
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Wyndham W Lathem
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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Rouli L, Merhej V, Fournier PE, Raoult D. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect 2015; 7:72-85. [PMID: 26442149 PMCID: PMC4552756 DOI: 10.1016/j.nmni.2015.06.005] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/16/2015] [Indexed: 01/18/2023] Open
Abstract
The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position. Pangenome is a new way of studying pathogenic bacteria. Pangenome can be used as a taxonomic tool. This review describes pangenome in the world of pathogenic bacteria.
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Affiliation(s)
- L Rouli
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - V Merhej
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - P-E Fournier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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40
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Tan SY, Dutta A, Jakubovics NS, Ang MY, Siow CC, Mutha NV, Heydari H, Wee WY, Wong GJ, Choo SW. YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia. BMC Bioinformatics 2015; 16:9. [PMID: 25591325 PMCID: PMC4384384 DOI: 10.1186/s12859-014-0422-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/11/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica. The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity. DESCRIPTION To facilitate the ongoing and future research of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia pestis. In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase. Besides incorporating existing tools, which include JavaScript-based genome browser (JBrowse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools: (1) Pairwise Genome Comparison tool (PGC) for comparing two user-selected genomes; (2) Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomics analysis of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica. CONCLUSIONS YersiniaBase offers free access to wide range of genomic data and analysis tools for the analysis of Yersinia. YersiniaBase can be accessed at http://yersinia.um.edu.my .
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Affiliation(s)
- Shi Yang Tan
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Avirup Dutta
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Nicholas S Jakubovics
- Center for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom.
| | - Mia Yang Ang
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Cheuk Chuen Siow
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Naresh Vr Mutha
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Hamed Heydari
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Faculty of Computer Science and Information Technology, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Wei Yee Wee
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Guat Jah Wong
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Siew Woh Choo
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, 50603, Kuala Lumpur, Malaysia.
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Vernikos G, Medini D, Riley DR, Tettelin H. Ten years of pan-genome analyses. Curr Opin Microbiol 2014; 23:148-54. [PMID: 25483351 DOI: 10.1016/j.mib.2014.11.016] [Citation(s) in RCA: 298] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 10/24/2022]
Abstract
Next generation sequencing technologies have engendered a genome sequence data deluge in public databases. Genome analyses have transitioned from single or few genomes to hundreds to thousands of genomes. Pan-genome analyses provide a framework for estimating the genomic diversity of the dataset at hand and predicting the number of additional whole genomes sequences that would be necessary to fully characterize that diversity. We review recent implementations of the pan-genome approach, its impact and limits, and we propose possible extensions, including analyses at the whole genome multiple sequence alignment level.
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Affiliation(s)
- George Vernikos
- Novartis (Hellas) S.A.C.I., 12th Km Athens-Lamia North Road, 14451 Metamorfossi, Athens, Greece
| | - Duccio Medini
- Novartis Vaccines Research, Via Fiorentina 1, 53100 Siena, Italy
| | - David R Riley
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA.
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42
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Barros MPS, França CT, Lins RHFB, Santos MDV, Silva EJ, Oliveira MBM, Silveira-Filho VM, Rezende AM, Balbino VQ, Leal-Balbino TC. Dynamics of CRISPR loci in microevolutionary process of Yersinia pestis strains. PLoS One 2014; 9:e108353. [PMID: 25265542 PMCID: PMC4180756 DOI: 10.1371/journal.pone.0108353] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Accepted: 08/27/2014] [Indexed: 12/19/2022] Open
Abstract
The potential use of CRISPR loci genotyping to elucidate population dynamics and microevolution of 146 Yersinia pestis strains from different biovars and locations was investigated in this work. The majority of strains from the Orientalis biovar presented specific spacer arrays, allowing for the establishment of a CRISPR signature for their respective isolates. Twenty-one new spacers were found in the Y. pestis strains from plague foci in Brazil. Ninety-three (64%) strains were grouped in the G1 genotype, whereas the others were distributed in 35 genotypes. This study allowed observing a microevolutionary process in a group of Y. pestis isolated from Brazil. We also identified specific genotypes of Y. pestis that were important for the establishment of the bacteria in plague foci in Brazil. The data have provided supporting evidence for the diversity and dynamics of CRISPR loci present in the genome of Y. pestis strains from plague foci in Brazil.
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Affiliation(s)
- Maria Paloma S. Barros
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães (CPqAM/Fiocruz), Recife, PE, Brasil
- * E-mail:
| | - Camila T. França
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães (CPqAM/Fiocruz), Recife, PE, Brasil
| | - Rosanny Holanda F. B. Lins
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães (CPqAM/Fiocruz), Recife, PE, Brasil
- Departamento de Genética, Universidade Federal de Pernambuco (UFPE), Recife, PE, Brasil
| | - Milena Danda V. Santos
- Departamento de Bioquímica, Universidade Federal de Pernambuco (UFPE), Recife, PE, Brasil
| | - Ednaldo J. Silva
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães (CPqAM/Fiocruz), Recife, PE, Brasil
| | | | | | - Antônio M. Rezende
- Departamento de Microbiologia, Centro de Pesquisas Aggeu Magalhães (CPqAM/Fiocruz), Recife, PE, Brasil
| | - Valdir Q. Balbino
- Departamento de Genética, Universidade Federal de Pernambuco (UFPE), Recife, PE, Brasil
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Rouli L, MBengue M, Robert C, Ndiaye M, La Scola B, Raoult D. Genomic analysis of three African strains of Bacillus anthracis demonstrates that they are part of the clonal expansion of an exclusively pathogenic bacterium. New Microbes New Infect 2014; 2:161-9. [PMID: 25566394 PMCID: PMC4265047 DOI: 10.1002/nmi2.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/04/2014] [Accepted: 08/08/2014] [Indexed: 01/31/2023] Open
Abstract
Bacillus anthracis is the causative agent of anthrax and is classified as a
‘Category A’ biological weapon. Six complete genomes of
B. anthracis (A0248, Ames, Ames Ancestor, CDC684, H0491, and Sterne) are
currently available. In this report, we add three African strain genomes: Sen2Col2, Sen3 and Gmb1.
To study the pan-genome of B. anthracis, we used bioinformatics tools, such
as Cluster of Orthologous Groups, and performed phylogenetic analysis. We found that the three
African strains contained the pX01 and pX02 plasmids, the nonsense mutation in the
plcR gene and the four known prophages. These strains are most similar to the
CDC684 strain and belong to the A cluster. We estimated that the
B. anthracis pan-genome has 2893 core genes (99% of the genome size)
and 85 accessory genes. We validated the hypothesis that B. anthracis has a
closed pan-genome and found that the three African strains carry the two plasmids associated with
bacterial virulence. The pan-genome nature of B. anthracis confirms its lack
of exchange (similar to Clostridium tetani) and supports its exclusively pathogenic
role, despite its survival in the environment. Moreover, thanks to the study of the core content
single nucleotide polymorphisms, we can see that our three African strains diverged very recently
from the other B. anthracis strains.
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Affiliation(s)
- L Rouli
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
| | - M MBengue
- Laboratoire National d'Elevage et des Recherches Vétérinaires (LNERV), Institut Sénégalais de Recherches Agricoles (ISRA) Hann, Dakar, Senegal
| | - C Robert
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
| | - M Ndiaye
- Laboratoire de Biologie Cellulaire, Faculté des Sciences et Techniques de l'Université Cheikh Anta DIOP de Dakar (UCAD) Dakar, Senegal
| | - B La Scola
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095 Marseille, France
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44
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Skennerton CT, Barr JJ, Slater FR, Bond PL, Tyson GW. Expanding our view of genomic diversity in Candidatus Accumulibacter clades. Environ Microbiol 2014; 17:1574-85. [PMID: 25088527 DOI: 10.1111/1462-2920.12582] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/20/2014] [Accepted: 07/27/2014] [Indexed: 12/01/2022]
Abstract
Enhanced biological phosphorus removal (EBPR) is an important industrial wastewater treatment process mediated by polyphosphate-accumulating organisms (PAOs). Members of the genus Candidatus Accumulibacter are one of the most extensively studied PAO as they are commonly enriched in lab-scale EBPR reactors. Members of different Accumulibacter clades are often enriched through changes in reactor process conditions; however, the two currently sequenced Accumulibacter genomes show extensive metabolic similarity. Here, we expand our understanding of Accumulibacter genomic diversity through recovery of eight population genomes using deep metagenomics, including seven from phylogenetic clades with no previously sequenced representative. Comparative genomic analysis revealed a core of shared genes involved primarily in carbon and phosphorus metabolism; however, each Accumulibacter genome also encoded a substantial number of unique genes (> 700 genes). A major difference between the Accumulibacter clades was the type of nitrate reductase encoded and the capacity to perform subsequent steps in denitrification. The Accumulibacter clade IIF genomes also contained acetaldehyde dehydrogenase that may allow ethanol to be used as carbon source. These differences in metabolism between Accumulibacter genomes provide a molecular basis for niche differentiation observed in lab-scale reactors and may offer new opportunities for process optimization.
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Affiliation(s)
- Connor T Skennerton
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, St Lucia, QLD, 4072, Australia; Advanced Water Management Centre, University of Queensland, St Lucia, QLD, 4072, Australia
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45
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Liang Y, Xie F, Tang X, Wang M, Zhang E, Zhang Z, Cai H, Wang Y, Shen X, Zhao H, Yu D, Xia L, Hai R. Chromosomal rearrangement features of Yersinia pestis strains from natural plague foci in China. Am J Trop Med Hyg 2014; 91:722-8. [PMID: 25114008 DOI: 10.4269/ajtmh.13-0491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Yersinia pestis chromosome contains a large variety and number of insert sequences that have resulted in frequent chromosome rearrangement events. To identify the chromosomal rearrangement features of Y. pestis strains from five typical plague foci in China and study spontaneous DNA rearrangements potentially stabilized in certain lineages of Y. pestis genomes, we examined the linking mode of locally collinear blocks (LCBs) in 30 Y. pestis strains by a polymerase chain reaction-based method. Our results suggest most strains have relatively stable chromosomal arrangement patterns, and these rearrangement characteristics also have a very close relationship with the geographical origin. In addition, some LCB linking modes are only present in specific strains. We conclude Y. pestis chromosome rearrangement patterns may reflect the genetic features of specific geographical areas and can be applied to distinguish Y. pestis isolates; furthermore, most of the rearrangement events are stable in certain lineages of Y. pestis genomes.
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Affiliation(s)
- Ying Liang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Fang Xie
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Xinyuan Tang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Mei Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Enmin Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Zhikai Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Hong Cai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Yanhua Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Xiaona Shen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Hongqun Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Dongzheng Yu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Lianxu Xia
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
| | - Rong Hai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China; Qinghai Institute for Endemic Disease Control and Prevention, Xining, China
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46
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Eroshenko GA, Odinokov GN, Kukleva LM, Shavina NY, Guseva NP, Kutyrev VV. Genetic basis of the variability of nitrate reduction trait in Yersinia pestis strains. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414050044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Plague has been a scourge of mankind for centuries, and outbreaks continue to the present day. The virulence mechanisms employed by the etiological agent Yersinia pestis are reviewed in the context of the available prophylactic and therapeutic strategies for plague. Although antibiotics are available, resistance is emerging in this dangerous pathogen. Therapeutics used in the clinic are discussed and innovative approaches to the design and development of new therapeutic compounds are reviewed. Currently there is no licensed vaccine available for prevention of plague in the USA or western Europe, although both live attenuated strains and killed whole-cell extracts have been used historically. Live strains are still approved for human use in some parts of the world, such as the former Soviet Union, but poor safety profiles render them unacceptable to many countries. The development of safe, effective next-generation vaccines, including the recombinant subunit vaccine currently used in clinical trials is discussed.
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Affiliation(s)
- Petra C F Oyston
- Biomedical Sciences, Dstl Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
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48
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Suntsov VV. Ecological aspects of the origin of Yersinia pestis, causative agent of the plague: Concept of intermediate environment. CONTEMP PROBL ECOL+ 2014. [DOI: 10.1134/s1995425514010144] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Jakupciak JP, Wells JM, Karalus RJ, Pawlowski DR, Lin JS, Feldman AB. Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis. J Nucleic Acids 2013; 2013:801505. [PMID: 24455204 PMCID: PMC3877622 DOI: 10.1155/2013/801505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 11/18/2022] Open
Abstract
Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.
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Affiliation(s)
| | | | | | | | - Jeffrey S. Lin
- The Johns Hopkins University, Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| | - Andrew B. Feldman
- The Johns Hopkins University, Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
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50
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Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis. GENOME ANNOUNCEMENTS 2013; 1:1/6/e00926-13. [PMID: 24201203 PMCID: PMC3820784 DOI: 10.1128/genomea.00926-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Piscirickettsia salmonis is a Gram-negative intracellular fish pathogen that has a significant impact on the salmon industry. Here, we report the genome sequence of P. salmonis strain LF-89. This is the first draft genome sequence of P. salmonis, and it reveals interesting attributes, including flagellar genes, despite this bacterium being considered nonmotile.
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