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Shevtsov A, Izbanova U, Amirgazin A, Kairzhanova A, Dauletov A, Kiyan V, Vergnaud G. Genetic Homogeneity of Francisella tularensis subsp. mediasiatica Strains in Kazakhstan. Pathogens 2024; 13:581. [PMID: 39057808 PMCID: PMC11279412 DOI: 10.3390/pathogens13070581] [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: 06/15/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Tularemia is an acute febrile disease caused by the Gram-negative bacillus Francisella tularensis. Based on genetic and phenotypic characteristics, three subspecies are distinguished: tularensis, holarctica, and mediasiatica. F. tularensis subsp. mediasiatica remains the least studied subspecies. Over the past decade, new foci of distribution of F. tularensis subsp. mediasiatica have been discovered in Russia (Siberia), expanding the possible distribution area by thousands of kilometers. This article provides whole genome single nucleotide polymorphism (wgSNP) and polymorphic tandem repeats (MLVA) analyses of 28 mediasiatica strains isolated between 1965 and 2004 in Kazakhstan. Despite high genetic homogeneity, MLVA with eleven loci (MLVA11) demonstrates a high discriminatory ability (diversity index, 0.9497). The topological structure of the trees based on wgSNP and MLVA is not comparable; however, clustering remains congruent for most outbreaks, with the exception of two strains from one outbreak that are identical in terms of wgSNP but differ at three tandem repeat loci. Based on wgSNP, the strains are assigned to one of the three currently known mediasiatica sublineages, lineage M.I, together with other historical strains maintained in collections in Russia and Sweden. wgSNP shows limited previously unknown genetic diversity, with the M.I lineage size being only 118 SNPs. The wgSNP genotype is not strongly correlated with year and place of isolation.
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Affiliation(s)
- Alexandr Shevtsov
- National Center for Biotechnology, Astana 010000, Kazakhstan; (A.A.); (A.K.); (A.D.); (V.K.)
| | - Uinkul Izbanova
- Aikimbayev’s National Scientific Center for Especially Dangerous Infections, Almaty 050000, Kazakhstan
| | - Asylulan Amirgazin
- National Center for Biotechnology, Astana 010000, Kazakhstan; (A.A.); (A.K.); (A.D.); (V.K.)
| | - Alma Kairzhanova
- National Center for Biotechnology, Astana 010000, Kazakhstan; (A.A.); (A.K.); (A.D.); (V.K.)
| | - Ayan Dauletov
- National Center for Biotechnology, Astana 010000, Kazakhstan; (A.A.); (A.K.); (A.D.); (V.K.)
| | - Vladimir Kiyan
- National Center for Biotechnology, Astana 010000, Kazakhstan; (A.A.); (A.K.); (A.D.); (V.K.)
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
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Degabriel M, Valeva S, Boisset S, Henry T. Pathogenicity and virulence of Francisella tularensis. Virulence 2023; 14:2274638. [PMID: 37941380 PMCID: PMC10653695 DOI: 10.1080/21505594.2023.2274638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023] Open
Abstract
Tularaemia is a zoonotic disease caused by the Gram-negative bacterium, Francisella tularensis. Depending on its entry route into the organism, F. tularensis causes different diseases, ranging from life-threatening pneumonia to less severe ulceroglandular tularaemia. Various strains with different geographical distributions exhibit different levels of virulence. F. tularensis is an intracellular bacterium that replicates primarily in the cytosol of the phagocytes. The main virulence attribute of F. tularensis is the type 6 secretion system (T6SS) and its effectors that promote escape from the phagosome. In addition, F. tularensis has evolved a peculiar envelope that allows it to escape detection by the immune system. In this review, we cover tularaemia, different Francisella strains, and their pathogenicity. We particularly emphasize the intracellular life cycle, associated virulence factors, and metabolic adaptations. Finally, we present how F. tularensis largely escapes immune detection to be one of the most infectious and lethal bacterial pathogens.
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Affiliation(s)
- Manon Degabriel
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, LYON, France
| | - Stanimira Valeva
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, LYON, France
| | - Sandrine Boisset
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, LYON, France
- Univ. Grenoble Alpes, CHU Grenoble Alpes, CNRS, CEA, UMR5075, Institut de Biologie Structurale, Grenoble, France
| | - Thomas Henry
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Univ Lyon, LYON, France
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de Vries MC, Hoeve-Bakker BJA, van den Beld MJC, Hendriks ACA, Harpal ASD, Noomen RCEA, Reubsaet FAG. Identification of Francisella tularensis Subspecies in a Clinical Setting Using MALDI-TOF MS: An In-House Francisella Library and Biomarkers. Microorganisms 2023; 11:microorganisms11040905. [PMID: 37110328 PMCID: PMC10146885 DOI: 10.3390/microorganisms11040905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Francisella tularensis is a zoonotic bacterium that is endemic in large parts of the world. It is absent in the standard library of the most applied matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems: the Vitek MS and the Bruker Biotyper system. The additional Bruker MALDI Biotyper Security library contains F. tularensis without subspecies differentiation. The virulence of F. tularensis differs between the subspecies. The F. tularensis subspecies (ssp.) tularensis is highly pathogenic, whereas the subspecies holarctica displays lower virulence and subspecies novicida and F. tularensis ssp. mediasiatica are hardly virulent. To differentiate the Francisellaceae and the F. tularensis-subspecies, an in-house Francisella library was built with the Bruker Biotyper system and validated together with the existing Bruker databases. In addition, specific biomarkers were defined based on the main spectra of the Francisella strains supplemented with in silico genome data. Our in-house Francisella library accurately differentiates the F. tularensis subspecies and the other Francisellaceae. The biomarkers correctly differentiate the various species within the genus Francisella and the F. tularensis subspecies. These MALDI-TOF MS strategies can successfully be applied in a clinical laboratory setting as a fast and specific method to identify F. tularensis to subspecies level.
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Du Y, Yan Z, Song K, Jin J, Xiao L, Sun Z, Tan Y, Zhang P, Du Z, Yang R, Zhao Y, Song Y. Development and evaluation of a multiplex droplet digital polymerase chain reaction method for simultaneous detection of five biothreat pathogens. Front Microbiol 2022; 13:970973. [PMID: 35966705 PMCID: PMC9366144 DOI: 10.3389/fmicb.2022.970973] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Biothreat agents pose a huge threat to human and public health, necessitating the development of rapid and highly sensitive detection approaches. This study establishes a multiplex droplet digital polymerase chain reaction (ddPCR) method for simultaneously detecting five high-risk bacterial biothreats: Yersinia pestis, Bacillus anthracis, Brucella spp., Burkholderia pseudomallei, and Francisella tularensis. Unlike conventional multiplex real-time PCR (qPCR) methods, the multiplex ddPCR assay was developed using two types of probe fluorophores, allowing the assay to perform with a common two-color ddPCR system. After optimization, the assay performance was evaluated, showing a lower limit of detection (LOD) (0.1–1.0 pg/μL) and good selectivity for the five bacteria targets. The multiplex assay’s ability to simultaneously detect two or more kinds of targets in a sample was also demonstrated. The assay showed strong sample tolerance when testing simulated soil samples; the LOD for bacteria in soil was 2 × 102–2 × 103 colony-forming unit (CFU)/100 mg soil (around 5–50 CFU/reaction), which was 10-fold lower than that of the single-target qPCR method. When testing simulated soil samples at bacterial concentrations of 2 × 103–2 × 104 CFU/100 mg soil, the assay presented a higher sensitivity (100%, 35/35) than that of the qPCR method (65.71%, 23/35) and a good specificity (100%, 15/15). These results suggest that the developed 5-plex ddPCR method is more sensitive than conventional qPCR methods and is potentially suitable for rapidly detecting or screening the five selected bacterial biothreats in suspicious samples.
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Affiliation(s)
- Yipu Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- The First Department, General Hospital of Northern Theater Command, Shenyang, China
| | - Ziheng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Junyan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Liting Xiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Zhulin Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Pingping Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yong Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- *Correspondence: Yong Zhao,
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- Yajun Song,
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Yue Y, Puniya BL, Helikar T, Girardo B, Hinrichs SH, Larson MA. Arginine Catabolism and Polyamine Biosynthesis Pathway Disparities Within Francisella tularensis Subpopulations. Front Microbiol 2022; 13:890856. [PMID: 35794913 PMCID: PMC9251427 DOI: 10.3389/fmicb.2022.890856] [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: 03/06/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Francisella tularensis is a highly infectious zoonotic pathogen with as few as 10 organisms causing tularemia, a disease that is fatal if untreated. Although F. tularensis subspecies tularensis (type A) and subspecies holarctica (type B) share over 99.5% average nucleotide identity, notable differences exist in genomic organization and pathogenicity. The type A clade has been further divided into subtypes A.I and A.II, with A.I strains being recognized as some of the most virulent bacterial pathogens known. In this study, we report on major disparities that exist between the F. tularensis subpopulations in arginine catabolism and subsequent polyamine biosynthesis. The genes involved in these pathways include the speHEA and aguAB operons, along with metK. In the hypervirulent F. tularensis A.I clade, such as the A.I prototype strain SCHU S4, these genes were found to be intact and highly transcribed. In contrast, both subtype A.II and type B strains have a truncated speA gene, while the type B clade also has a disrupted aguA and truncated aguB. Ablation of the chromosomal speE gene that encodes a spermidine synthase reduced subtype A.I SCHU S4 growth rate, whereas the growth rate of type B LVS was enhanced. These results demonstrate that spermine synthase SpeE promotes faster replication in the F. tularensis A.I clade, whereas type B strains do not rely on this enzyme for in vitro fitness. Our ongoing studies on amino acid and polyamine flux within hypervirulent A.I strains should provide a better understanding of the factors that contribute to F. tularensis pathogenicity.
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Affiliation(s)
- Yinshi Yue
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Benjamin Girardo
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Steven H. Hinrichs
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Marilynn A. Larson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
- *Correspondence: Marilynn A. Larson,
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Shibata K, Shimizu T, Nakahara M, Ito E, Legoux F, Fujii S, Yamada Y, Furutani-Seiki M, Lantz O, Yamasaki S, Watarai M, Shirai M. The intracellular pathogen Francisella tularensis escapes from adaptive immunity by metabolic adaptation. Life Sci Alliance 2022; 5:5/10/e202201441. [PMID: 35667686 PMCID: PMC9170078 DOI: 10.26508/lsa.202201441] [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: 03/10/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
This study shows that metabolic adaptation allows the intracellular bacterial pathogen Francisella tularensis to escape recognition by the host adaptive immunity. Intracellular pathogens lose many metabolic genes during their evolution from free-living bacteria, but the pathogenic consequences of their altered metabolic programs on host immunity are poorly understood. Here, we show that a pathogenic strain of Francisella tularensis subsp. tularensis (FT) has five amino acid substitutions in RibD, a converting enzyme of the riboflavin synthetic pathway responsible for generating metabolites recognized by mucosal-associated invariant T (MAIT) cells. Metabolites from a free-living strain, F. tularensis subsp. novicida (FN), activated MAIT cells in a T-cell receptor (TCR)–dependent manner, whereas introduction of FT-type ribD to the free-living strain was sufficient to attenuate this activation in both human and mouse MAIT cells. Intranasal infection in mice showed that the ribDFT-expressing FN strain induced impaired Th1-type MAIT cell expansion and resulted in reduced bacterial clearance and worsened survival compared with the wild-type free-living strain FN. These results demonstrate that F. tularensis can acquire immune evasion capacity by alteration of metabolic programs during evolution.
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Affiliation(s)
- Kensuke Shibata
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan .,Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Ophthalmology, Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takashi Shimizu
- Joint Faculty of Veterinary Medicine, Laboratory of Veterinary Public Health, Yamaguchi University, Yamaguchi, Japan
| | - Mashio Nakahara
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Emi Ito
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | | | - Shotaro Fujii
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Yuka Yamada
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Makoto Furutani-Seiki
- Systems Biochemistry in Pathology and Regeneration, Graduate School of Medicine, Yamaguchi University, Ube, Japan
| | - Olivier Lantz
- INSERM U932, PSL University, Laboratoire d'Immunologie Clinique, Centre d'Investigation Clinique en Biothérapie, Institut Curie (CIC-BT1428), Paris, France
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Division of Molecular Design, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Masahisa Watarai
- Joint Faculty of Veterinary Medicine, Laboratory of Veterinary Public Health, Yamaguchi University, Yamaguchi, Japan
| | - Mutsunori Shirai
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Yamaguchi, Japan
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Balasubramanian D, López-Pérez M, Grant TA, Ogbunugafor CB, Almagro-Moreno S. Molecular mechanisms and drivers of pathogen emergence. Trends Microbiol 2022; 30:898-911. [DOI: 10.1016/j.tim.2022.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022]
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Mjølnerød EB, Nilsen HK, Gulla S, Riborg A, Bottolfsen KL, Wiklund T, Christiansen D, López Romalde JÁ, Scholz F, Colquhoun DJ. Multilocus sequence analysis reveals different lineages of Pseudomonas anguilliseptica associated with disease in farmed lumpfish (Cyclopterus lumpus L.). PLoS One 2021; 16:e0259725. [PMID: 34807918 PMCID: PMC8608339 DOI: 10.1371/journal.pone.0259725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022] Open
Abstract
The bacterium Pseudomonas anguilliseptica has in recent years emerged as a serious threat to production of lumpfish in Norway. Little is known about the population structure of this bacterium despite its association with disease in a wide range of different fish species throughout the world. The phylogenetic relationships between 53 isolates, primarily derived from diseased lumpfish, but including a number of reference strains from diverse geographical origins and fish species, were reconstructed by Multi-Locus Sequence Analysis (MLSA) using nine housekeeping genes (rpoB, atpD, gyrB, rpoD, ileS, aroE, carA, glnS and recA). MLSA revealed a high degree of relatedness between the studied isolates, altough the seven genotypes identified formed three main phylogenetic lineages. While four genotypes were identified amongst Norwegian lumpfish isolates, a single genotype dominated, irrespective of geographic origin. This suggests the existence of a dominant genotype associated with disease in production of lumpfish in Norwegian aquaculture. Elucidation of the population structure of the bacterium has provided valuable information for potential future vaccine development.
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Affiliation(s)
| | | | - Snore Gulla
- Norwegian Veterinary Institute, Oslo, Norway
| | - Andreas Riborg
- Norwegian Veterinary Institute, Oslo, Norway
- Vaxxinova AS, Bergen, Norway
| | | | - Tom Wiklund
- Laboratory of Aquatic Pathobiology, Environmental and Marine Biology, Åbo Akademi University, Turku, Finland
| | - Debes Christiansen
- Food and Veterinary Agency, National Reference Laboratory for Fish Diseases, Tórshavn, Faroe Islands
| | - Jesús Ángel López Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Duncan John Colquhoun
- University of Bergen, Institute of Biological Science, Bergen, Norway
- Norwegian Veterinary Institute, Oslo, Norway
- * E-mail:
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Bachert BA, Richardson JB, Mlynek KD, Klimko CP, Toothman RG, Fetterer DP, Luquette AE, Chase K, Storrs JL, Rogers AK, Cote CK, Rozak DA, Bozue JA. Development, Phenotypic Characterization and Genomic Analysis of a Francisella tularensis Panel for Tularemia Vaccine Testing. Front Microbiol 2021; 12:725776. [PMID: 34456897 PMCID: PMC8386241 DOI: 10.3389/fmicb.2021.725776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/21/2021] [Indexed: 11/23/2022] Open
Abstract
Francisella tularensis is one of several biothreat agents for which a licensed vaccine is needed to protect against this pathogen. To aid in the development of a vaccine protective against pneumonic tularemia, we generated and characterized a panel of F. tularensis isolates that can be used as challenge strains to assess vaccine efficacy. Our panel consists of both historical and contemporary isolates derived from clinical and environmental sources, including human, tick, and rabbit isolates. Whole genome sequencing was performed to assess the genetic diversity in comparison to the reference genome F. tularensis Schu S4. Average nucleotide identity analysis showed >99% genomic similarity across the strains in our panel, and pan-genome analysis revealed a core genome of 1,707 genes, and an accessory genome of 233 genes. Three of the strains in our panel, FRAN254 (tick-derived), FRAN255 (a type B strain), and FRAN256 (a human isolate) exhibited variation from the other strains. Moreover, we identified several unique mutations within the Francisella Pathogenicity Island across multiple strains in our panel, revealing unexpected diversity in this region. Notably, FRAN031 (Scherm) completely lacked the second pathogenicity island but retained virulence in mice. In contrast, FRAN037 (Coll) was attenuated in a murine pneumonic tularemia model and had mutations in pdpB and iglA which likely led to attenuation. All of the strains, except FRAN037, retained full virulence, indicating their effectiveness as challenge strains for future vaccine testing. Overall, we provide a well-characterized panel of virulent F. tularensis strains that can be utilized in ongoing efforts to develop an effective vaccine against pneumonic tularemia to ensure protection is achieved across a range F. tularensis strains.
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Affiliation(s)
- Beth A. Bachert
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Joshua B. Richardson
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Kevin D. Mlynek
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Christopher P. Klimko
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Ronald G. Toothman
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - David P. Fetterer
- Division of Biostatistics, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Andrea E. Luquette
- Biodefense Reference Material Repository, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Kitty Chase
- Biodefense Reference Material Repository, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Jessica L. Storrs
- Biodefense Reference Material Repository, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Ashley K. Rogers
- Biodefense Reference Material Repository, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Christopher K. Cote
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - David A. Rozak
- Biodefense Reference Material Repository, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Joel A. Bozue
- Division of Bacteriology, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
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10
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Golovliov I, Bäckman S, Granberg M, Salomonsson E, Lundmark E, Näslund J, Busch JD, Birdsell D, Sahl JW, Wagner DM, Johansson A, Forsman M, Thelaus J. Long-Term Survival of Virulent Tularemia Pathogens outside a Host in Conditions That Mimic Natural Aquatic Environments. Appl Environ Microbiol 2021; 87:e02713-20. [PMID: 33397692 PMCID: PMC8104992 DOI: 10.1128/aem.02713-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/17/2020] [Indexed: 01/22/2023] Open
Abstract
Francisella tularensis, the causative agent of the zoonotic disease tularemia, can cause seasonal outbreaks of acute febrile illness in humans with disease peaks in late summer to autumn. Interestingly, its mechanisms for environmental persistence between outbreaks are poorly understood. One hypothesis is that F. tularensis forms biofilms in aquatic environments. We utilized two fully virulent wild-type strains: FSC200 (Francisella tularensis subsp. holarctica) and Schu S4 (Francisella tularensis subsp. tularensis) and three control strains, the attenuated live vaccine strain (LVS; F. tularensis subsp. holarctica), a Schu S4 ΔwbtI mutant that is documented to form biofilms, and the low-virulence strain U112 of the closely related species Francisella novicida Strains were incubated in saline solution (0.9% NaCl) microcosms for 24 weeks at both 4°C and 20°C, whereupon viability and biofilm formation were measured. These temperatures were selected to approximate winter and summer temperatures of fresh water in Scandinavia, respectively. U112 and Schu S4 ΔwbtI formed biofilms, but F. tularensis strains FSC200 and Schu S4 and the LVS did not. All strains exhibited prolonged viability at 4°C compared to 20°C. U112 and FSC200 displayed remarkable long-term persistence at 4°C, with only 1- and 2-fold log reductions, respectively, of viable cells after 24 weeks. Schu S4 exhibited lower survival, yielding no viable cells by week 20. At 24 weeks, cells from FSC200, but not from Schu S4, were still fully virulent in mice. Taken together, these results demonstrate biofilm-independent, long-term survival of pathogenic F. tularensis subsp. holarctica in conditions that mimic overwinter survival in aquatic environments.IMPORTANCE Tularemia, a disease caused by the environmental bacterium Francisella tularensis, is characterized by acute febrile illness. F. tularensis is highly infectious: as few as 10 organisms can cause human disease. Tularemia is not known to be spread from person to person. Rather, all human infections are independently acquired from the environment via the bite of blood-feeding arthropods, ingestion of infected food or water, or inhalation of aerosolized bacteria. Despite the environmental origins of human disease events, the ecological factors governing the long-term persistence of F. tularensis in nature between seasonal human outbreaks are poorly understood. The significance of our research is in identifying conditions that promote long-term survival of fully virulent F. tularensis outside a mammalian host or insect vector. These conditions are similar to those found in natural aquatic environments in winter and provide important new insights on how F. tularensis may persist long-term in the environment.
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Affiliation(s)
- Igor Golovliov
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Stina Bäckman
- Division of CBRN Defence and Security, Swedish Defence Research Agency FOI, Umeå, Sweden
| | - Malin Granberg
- Division of CBRN Defence and Security, Swedish Defence Research Agency FOI, Umeå, Sweden
| | - Emelie Salomonsson
- Division of CBRN Defence and Security, Swedish Defence Research Agency FOI, Umeå, Sweden
| | - Eva Lundmark
- Division of CBRN Defence and Security, Swedish Defence Research Agency FOI, Umeå, Sweden
| | - Jonas Näslund
- Division of CBRN Defence and Security, Swedish Defence Research Agency FOI, Umeå, Sweden
| | - Joseph D Busch
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Dawn Birdsell
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Anders Johansson
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Mats Forsman
- Division of CBRN Defence and Security, Swedish Defence Research Agency FOI, Umeå, Sweden
| | - Johanna Thelaus
- Division of CBRN Defence and Security, Swedish Defence Research Agency FOI, Umeå, Sweden
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11
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Glinšek Biškup U, Kogoj R, Korva M, Knap N, Cerar T, Knapič T, Petrovec M, Avšič-Županc T. Characterization of Tularemia Cases in Slovenia with Multiple-Locus Variable-Number Tandem Repeat Analysis. Vector Borne Zoonotic Dis 2021; 21:351-357. [PMID: 33601964 PMCID: PMC8086403 DOI: 10.1089/vbz.2020.2711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Francisella tularensis is the etiologic agent of tularemia, a bacterial zoonotic disease. The genome of F. tularensis shows a recent evolutionary change, especially in reservoirs. Variable number of tandem repeats (VNTR) is described as a high-speed molecular clock and can thus be used as a high-resolution typing system. The main objective of our study was to investigate the molecular diversity of F. tularensis strains and reveal possible sources of infection. Using real-time PCR targeting the ISFtu2 region, we successfully amplified targeted DNA in 13/31 Slovenian patients with a clinical diagnosis of tularemia, and with PCR targeting the fopA gene, we obtained 11/13 PCR products. Sequencing revealed that all samples were identified as F. tularensis subsp. holarctica. We successfully obtained one F. tularensis isolate from a lymph node aspirate by culture on chocolate agar. Our isolate was clustered into major clade B12 (subclade B43). We optimized VNTR typing to be used directly on clinical samples. Multiple-locus VNTR analysis (MLVA) revealed five unique MLVA types; 45.5% samples had the same MLVA type, another 27.3% shared a different MLVA type, and each of the remaining had a unique MLVA type. Most samples differed at only two VNTR markers (Ft-M03 and Ft-M06). Additionally, we investigated samples from small mammals (n = 532) and Ixodes ricinus ticks (n = 232) captured in the same geographical area in which patients with tularemia were found. No F. tularensis DNA was detected in samples of small mammals or I. ricinus ticks. The diversity of MLVA types in Slovenia was high, despite the small region, but most of the samples from the same region shared the same MLVA type. Our results suggest that MLVA is a useful tool for quick molecular characterization of F. tularensis directly from patient samples, especially when investigating geographically localized outbreaks.
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Affiliation(s)
- Urška Glinšek Biškup
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Miša Korva
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Cerar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tea Knapič
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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12
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Öhrman C, Sahl JW, Sjödin A, Uneklint I, Ballard R, Karlsson L, McDonough RF, Sundell D, Soria K, Bäckman S, Chase K, Brindefalk B, Sozhamannan S, Vallesi A, Hägglund E, Ramirez-Paredes JG, Thelaus J, Colquhoun D, Myrtennäs K, Birdsell D, Johansson A, Wagner DM, Forsman M. Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis. Microorganisms 2021; 9:146. [PMID: 33440900 PMCID: PMC7826819 DOI: 10.3390/microorganisms9010146] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/01/2021] [Accepted: 01/04/2021] [Indexed: 12/21/2022] Open
Abstract
In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.
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Affiliation(s)
- Caroline Öhrman
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - Andreas Sjödin
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Ingrid Uneklint
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Rebecca Ballard
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - Linda Karlsson
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Ryelan F. McDonough
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - David Sundell
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Kathleen Soria
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - Stina Bäckman
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Kitty Chase
- US Army Medical Research Institute, Fort Detrick, MD 21702, USA;
| | - Björn Brindefalk
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Shanmuga Sozhamannan
- Logistics Management Institute supporting Defense Biological Product Assurance Office (DBPAO) Joint Project Lead, CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD 21702, USA;
| | - Adriana Vallesi
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy;
| | - Emil Hägglund
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Jose Gustavo Ramirez-Paredes
- Ridgeway Biologicals Limited a Ceva Santé Animale Company, Units 1-3 Old Station Business Park, Compton, Berkshire, England RG20 6NE, UK;
| | - Johanna Thelaus
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Duncan Colquhoun
- Fish Health Research Group, Norwegian Veterinary Institute, Oslo, Pb 750 Sentrum, 23 N-0106 Oslo, Norway;
| | - Kerstin Myrtennäs
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
| | - Dawn Birdsell
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - Anders Johansson
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 85 Umeå, Sweden;
| | - David M. Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA; (J.W.S.); (R.B.); (R.F.M.); (K.S.); (D.B.); (D.M.W.)
| | - Mats Forsman
- CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden; (C.Ö.); (A.S.); (I.U.); (L.K.); (D.S.); (S.B.); (B.B.); (E.H.); (J.T.); (K.M.)
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13
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Xie Z. The Methods and Tools for Mobile Genetic Element Detection and their Application to Systems Medicine. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11537-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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14
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Evaluation of the Biotoxis qPCR Detection Kit for Francisella tularensis Detection in Clinical and Environmental Samples. J Clin Microbiol 2020; 59:JCM.01434-20. [PMID: 33115844 DOI: 10.1128/jcm.01434-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/16/2020] [Indexed: 11/20/2022] Open
Abstract
Rapid and reliable detection and identification of Francisella tularensis (a tier 1 select agent) are of primary interest for both medical and biological threat surveillance purposes. The Biotoxis qPCR detection kit is a real-time quantitative PCR (qPCR) assay designed for the detection of Bacillus anthracis, Yersinia pestis, and F. tularensis in environmental or biological samples. Here, we evaluated its performance for detecting F. tularensis in comparison to previously validated qPCR assays. The Biotoxis qPCR was positive for 87/87 F. tularensis subsp. holarctica (type B) strains but also for F. tularensis subsp. novicida It was negative for Francisella philomiragia and 24/24 strains belonging to other bacterial species. For 31 tularemia clinical specimens, the Biotoxis qPCR displayed a sensitivity between 90.32% and 96.55%, compared to qPCR tests targeting ISFtu2 or a type B-specific DNA sequence, respectively. All 30 nontularemia clinical specimens were Biotoxis qPCR negative. For water samples, the Biotoxis qPCR limit of detection was 1,000 CFU/liter of F. tularensis For 57 environmental water samples collected in France, the Biotoxis qPCR was positive for 6/15 samples positive for ISFtu2 qPCR and 4/4 positive for type B qPCR. In conclusion, the Biotoxis qPCR detection kit demonstrated good performances for F. tularensis detection in various biological and environmental samples, although cross-amplification of F. tularensis subsp. novicida must be considered. This plate format assay could be useful to test a large number of clinical or environmental specimens, especially in the context of natural or intentional tularemia outbreaks.
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15
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Control of Francisella tularensis Virulence at Gene Level: Network of Transcription Factors. Microorganisms 2020; 8:microorganisms8101622. [PMID: 33096715 PMCID: PMC7588896 DOI: 10.3390/microorganisms8101622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/14/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene transcription is the initial step in the complex process that controls gene expression within bacteria. Transcriptional control involves the joint effort of RNA polymerases and numerous other regulatory factors. Whether global or local, positive or negative, regulators play an essential role in the bacterial cell. For instance, some regulators specifically modify the transcription of virulence genes, thereby being indispensable to pathogenic bacteria. Here, we provide a comprehensive overview of important transcription factors and DNA-binding proteins described for the virulent bacterium Francisella tularensis, the causative agent of tularemia. This is an unexplored research area, and the poorly described networks of transcription factors merit additional experimental studies to help elucidate the molecular mechanisms of pathogenesis in this bacterium, and how they contribute to disease.
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16
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Busch A, Homeier-Bachmann T, Abdel-Glil MY, Hackbart A, Hotzel H, Tomaso H. Using affinity propagation clustering for identifying bacterial clades and subclades with whole-genome sequences of Francisella tularensis. PLoS Negl Trop Dis 2020; 14:e0008018. [PMID: 32991594 PMCID: PMC7523947 DOI: 10.1371/journal.pntd.0008018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 12/27/2019] [Indexed: 12/31/2022] Open
Abstract
By combining a reference-independent SNP analysis and average nucleotide identity (ANI) with affinity propagation clustering (APC), we developed a significantly improved methodology allowing resolving phylogenetic relationships, based on objective criteria. These bioinformatics tools can be used as a general ruler to determine phylogenetic relationships and clustering of bacteria, exemplary done with Francisella (F.) tularensis. Molecular epidemiology of F. tularensis is currently assessed mostly based on laboratory methods and molecular analysis. The high evolutionary stability and the clonal nature makes Francisella ideal for subtyping with single nucleotide polymorphisms (SNPs). Sequencing and real-time PCR can be used to validate the SNP analysis. We investigate whole-genome sequences of 155 F. tularensis subsp. holarctica isolates. Phylogenetic testing was based on SNPs and average nucleotide identity (ANI) as reference independent, alignment-free methods taking small-scale and large-scale differences within the genomes into account. Especially the whole genome SNP analysis with kSNP3.0 allowed deciphering quite subtle signals of systematic differences in molecular variation. Affinity propagation clustering (APC) resulted in three clusters showing the known clades B.4, B.6, and B.12. These data correlated with the results of real-time PCR assays targeting canSNPs loci. Additionally, we detected two subtle sub-clusters. SplitsTree was used with standard-setting using the aligned SNPs from Parsnps. Together APC, HierBAPS, and SplitsTree enabled us to generate hypotheses about epidemiologic relationships between bacterial clusters and describing the distribution of isolates. Our data indicate that the choice of the typing technique can increase our understanding of the pathogenesis and transmission of diseases with the eventual for prevention. This is opening perspectives to be applied to other bacterial species. The data provide evidence that Germany might be the collision zone where the clade B.12, also known as the East European clade, overlaps with the clade B.6, also known as the Iberian clade. Described methods allow generating a new, more detailed perspective for F. tularensis subsp. holarctica phylogeny. These results may encourage to determine phylogenetic relationships and clustering of other bacteria the same way.
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Affiliation(s)
- Anne Busch
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
- * E-mail:
| | - Timo Homeier-Bachmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Mostafa Y. Abdel-Glil
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Anja Hackbart
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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17
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Kumar R, Bröms JE, Sjöstedt A. Exploring the Diversity Within the Genus Francisella - An Integrated Pan-Genome and Genome-Mining Approach. Front Microbiol 2020; 11:1928. [PMID: 32849479 PMCID: PMC7431613 DOI: 10.3389/fmicb.2020.01928] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/22/2020] [Indexed: 01/13/2023] Open
Abstract
Pan-genome analysis is a powerful method to explore genomic heterogeneity and diversity of bacterial species. Here we present a pan-genome analysis of the genus Francisella, comprising a dataset of 63 genomes and encompassing clinical as well as environmental isolates from distinct geographic locations. To determine the evolutionary relationship within the genus, we performed phylogenetic whole-genome studies utilizing the average nucleotide identity, average amino acid identity, core genes and non-recombinant loci markers. Based on the analyses, the phylogenetic trees obtained identified two distinct clades, A and B and a diverse cluster designated C. The sizes of the pan-, core-, cloud-, and shell-genomes of Francisella were estimated and compared to those of two other facultative intracellular pathogens, Legionella and Piscirickettsia. Francisella had the smallest core-genome, 692 genes, compared to 886 and 1,732 genes for Legionella and Piscirickettsia respectively, while the pan-genome of Legionella was more than twice the size of that of the other two genera. Also, the composition of the Francisella Type VI secretion system (T6SS) was analyzed. Distinct differences in the gene content of the T6SS were identified. In silico approaches performed to identify putative substrates of these systems revealed potential effectors targeting the cell wall, inner membrane, cellular nucleic acids as well as proteins, thus constituting attractive targets for site-directed mutagenesis. The comparative analysis performed here provides a comprehensive basis for the assessment of the phylogenomic relationship of members of the genus Francisella and for the identification of putative T6SS virulence traits.
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Affiliation(s)
- Rajender Kumar
- Department of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Jeanette E Bröms
- Department of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Anders Sjöstedt
- Department of Clinical Microbiology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
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18
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Ramirez-Paredes JG, Larsson P, Thompson KD, Penman DJ, Busse HJ, Öhrman C, Sjödin A, Soto E, Richards RH, Adams A, Colquhoun DJ. Reclassification of Francisella noatunensis subsp. orientalis Ottem et al. 2009 as Francisella orientalis sp. nov., Francisella noatunensis subsp. chilensis subsp. nov. and emended description of Francisella noatunensis. Int J Syst Evol Microbiol 2020; 70:2034-2048. [PMID: 32160147 DOI: 10.1099/ijsem.0.004009] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Francisella noatunensis is a fastidious facultative intracellular bacterial pathogen that causes 'piscine francisellosis', a serious disease affecting both marine and fresh water farmed and wild fish worldwide. Currently two F. noatunensis subspecies are recognized, i.e. F. noatunensis subsp. noatunensis and F. noatunensis subsp. orientalis. In the present study, the taxonomy of F. noatunensis was revisited using a polyphasic approach, including whole genome derived parameters such as digital DNA-DNA hybridization, whole genome average nucleotide identity (wg-ANIm), whole genome phylogenetic analysis, whole genome G+C content, metabolic fingerprinting and chemotaxonomic analyses. The results indicated that isolates belonging to F. noatunensis subsp. orientalis represent a phenotypically and genetically homogenous taxon, clearly distinguishable from F. noatunensis subsp. noatunensis that fulfils requirements for separate species status. We propose, therefore, elevation of F. noatunensis subsp. orientalis to the species rank as Francisella orientalis sp. nov. with the type strain remaining as Ehime-1T (DSM 21254T=LMG 24544T). Furthermore, we identified sufficient phenotypic and genetic differences between F. noatunensis subsp. noatunensis recovered from diseased farmed Atlantic salmon in Chile and those isolated from wild and farmed Atlantic cod in Northern Europe to warrant proposal of the Chilean as a novel F. noatunensis subspecies, i.e. Francisella noatunensis subsp. chilensis subsp. nov. with strain PQ1106T (CECT 9798T=NCTC14375T) as the type strain. Finally, we emend the description of F. noatunensis by including further metabolic information and the description of atypical strains.
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Affiliation(s)
- Jose Gustavo Ramirez-Paredes
- Ridgeway Biologicals Ltd. a Ceva Santé Animale Company, Units 1-3 Old Station Business Park, Compton, Berkshire, England, RG20 6NE, UK
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
- Present address: Ridgeway Biologicals Ltd. a Ceva Santé Animale Company, Units 1-3 Old Station Business Park, Compton, Berkshire, England, RG20 6NE, UK
| | - Pär Larsson
- Swedish Defence Research Agency (FOI), CBRN Defence and Security, Umeå, Sweden
- Department of Medical Biosciences, Umea University, Umeå, Sweden
| | - Kim D Thompson
- Aquaculture Research Group, Moredun Research Institute, Edinburgh, Scotland, EH26 0PZ, UK
| | - David J Penman
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Hans-Jürgen Busse
- Institute of Microbiology, Veterinary University, Vienna, A-1160 Wien, Austria
| | - Caroline Öhrman
- Swedish Defence Research Agency (FOI), CBRN Defence and Security, Umeå, Sweden
| | - Andreas Sjödin
- Swedish Defence Research Agency (FOI), CBRN Defence and Security, Umeå, Sweden
| | - Esteban Soto
- Department of Medicine and Epidemiology, University of California Davis, School of Veterinary Medicine, Davis, California, 95616, USA
| | - Randolph H Richards
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Alexandra Adams
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Duncan J Colquhoun
- Fish Health Research Group, Norwegian Veterinary Institute, Oslo, Pb 750 Sentrum, N-0106 Oslo, Norway
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19
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Dean SN, Milton ME, Cavanagh J, van Hoek ML. Francisella novicida Two-Component System Response Regulator BfpR Modulates iglC Gene Expression, Antimicrobial Peptide Resistance, and Biofilm Production. Front Cell Infect Microbiol 2020; 10:82. [PMID: 32232010 PMCID: PMC7082314 DOI: 10.3389/fcimb.2020.00082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 02/18/2020] [Indexed: 12/20/2022] Open
Abstract
Response regulators are a critical part of the two-component system of gene expression regulation in bacteria, transferring a signal from a sensor kinase into DNA binding activity resulting in alteration of gene expression. In this study, we investigated a previously uncharacterized response regulator in Francisella novicida, FTN_1452 that we have named BfpR (Biofilm-regulating Francisella protein Regulator, FTN_1452). In contrast to another Francisella response regulator, QseB/PmrA, BfpR appears to be a negative regulator of biofilm production, and also a positive regulator of antimicrobial peptide resistance in this bacterium. The protein was crystallized and X-ray crystallography studies produced a 1.8 Å structure of the BfpR N-terminal receiver domain revealing interesting insight into its potential interaction with the sensor kinase. Structural analysis of BfpR places it in the OmpR/PhoP family of bacterial response regulators along with WalR and ResD. Proteomic and transcriptomic analyses suggest that BfpR overexpression affects expression of the critical Francisella virulence factor iglC, as well as other proteins in the bacterium. We demonstrate that mutation of bfpR is associated with an antimicrobial peptide resistance phenotype, a phenotype also associated with other response regulators, for the human cathelicidin peptide LL-37 and a sheep antimicrobial peptide SMAP-29. F. novicida with mutated bfpR replicated better than WT in intracellular infection assays in human-derived macrophages suggesting that the down-regulation of iglC expression in bfpR mutant may enable this intracellular replication to occur. Response regulators have been shown to play important roles in the regulation of bacterial biofilm production. We demonstrate that F. novicida biofilm formation was highly increased in the bfpR mutant, corresponding to altered glycogen synthesis. Waxworm infection experiments suggest a role of BfpR as a negative modulator of iglC expression with de-repression by Mg2+. In this study, we find that the response regulator BfpR may be a negative regulator of biofilm formation, and a positive regulator of antimicrobial peptide resistance in F. novicida.
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Affiliation(s)
- Scott N Dean
- National Center for Biodefense and Infectious Diseases, and School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Morgan E Milton
- Department of Biochemistry and Molecular Biology, The Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - John Cavanagh
- Department of Biochemistry and Molecular Biology, The Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Monique L van Hoek
- National Center for Biodefense and Infectious Diseases, and School of Systems Biology, George Mason University, Manassas, VA, United States
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Nau GJ, Horzempa J, O’Dee D, Brown MJ, Russo BC, Hernandez A, Dillon ST, Cheng J, Kane LP, Sanker S, Hukriede NA. A predicted Francisella tularensis DXD-motif glycosyltransferase blocks immune activation. Virulence 2019; 10:643-656. [PMID: 31314675 PMCID: PMC6650193 DOI: 10.1080/21505594.2019.1631662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 06/07/2019] [Indexed: 02/04/2023] Open
Abstract
Pathogens enhance their survival during infections by manipulating host defenses. Francisella tularensis evades innate immune responses, which we have found to be dependent on an understudied gene ybeX (FTL_0883/FTT_0615c). To understand the function of YbeX, we sought protein interactors in F. tularensis subsp. holarctica live vaccine strain (LVS). An unstudied Francisella protein co-immunoprecipitated with recombinant YbeX, which is a predicted glycosyltransferase with a DXD-motif. There are up to four genomic copies of this gene with identical sequence in strains of F. tularensis pathogenic to humans, despite ongoing genome decay. Disruption mutations were generated by intron insertion into all three copies of this glycosyltransferase domain containing gene in LVS, gdcA1-3. The resulting strains stimulated more cytokines from macrophages in vitro than wild-type LVS and were attenuated in two in vivo infection models. GdcA was released from LVS during culture and was sufficient to block NF-κB activation when expressed in eukaryotic cells. When co-expressed in zebrafish, GdcA and YbeX were synergistically lethal to embryo development. Glycosyltransferases with DXD-motifs are found in a variety of pathogens including NleB, an Escherichia coli type-III secretion system effector that inhibits NF-κB by antagonizing death receptor signaling. To our knowledge, GdcA is the first DXD-motif glycosyltransferase that inhibits NF-κB in immune cells. Together, these findings suggest DXD-motif glycosyltransferases may be a conserved virulence mechanism used by pathogenic bacteria to remodel host defenses.
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Affiliation(s)
- Gerard J. Nau
- Division of Infectious Diseases, Alpert Medical School of Brown University, Providence, RI, USA
| | - Joseph Horzempa
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, WV, USA
| | - Dawn O’Dee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Matthew J. Brown
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Brian C. Russo
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Ana Hernandez
- Division of Infectious Diseases, Alpert Medical School of Brown University, Providence, RI, USA
| | - Simon T. Dillon
- Beth Israel Deaconess Medical Center Genomics, Proteomics, and Systems Biology Center, Harvard Medical School, Boston, MA, USA
| | - Jing Cheng
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lawrence P. Kane
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Subramaniam Sanker
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Neil A. Hukriede
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Critical Care Nephrology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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21
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Abstract
Microbial populations exchange genetic material through a process called homologous recombination. Although this process has been studied in particular organisms, we lack an understanding of its differential impact over the genome and across microbes with different life-styles. We used a common analytical framework to assess this process in a representative set of microorganisms. Our results uncovered important trends. First, microbes with different lifestyles are differentially impacted, with endosymbionts and obligate pathogens being those less prone to undergo this process. Second, certain genetic elements such as restriction-modification systems seem to be associated with higher rates of recombination. Most importantly, recombined genomes show the footprints of natural selection in which recombined regions preferentially contain genes that can be related to specific ecological adaptations. Taken together, our results clarify the relative contributions of factors modulating homologous recombination and show evidence for a clear a role of this process in shaping microbial genomes and driving ecological adaptations. Homologous recombination (HR) enables the exchange of genetic material between and within species. Recent studies suggest that this process plays a major role in the microevolution of microbial genomes, contributing to core genome homogenization and to the maintenance of cohesive population structures. However, we still have a very poor understanding of the possible adaptive roles of intraspecific HR and of the factors that determine its differential impact across clades and lifestyles. Here we used a unified methodological framework to assess HR in 338 complete genomes from 54 phylogenetically diverse and representative prokaryotic species, encompassing different lifestyles and a broad phylogenetic distribution. Our results indicate that lifestyle and presence of restriction-modification (RM) machineries are among the main factors shaping HR patterns, with symbionts and intracellular pathogens having the lowest HR levels. Similarly, the size of exchanged genomic fragments correlated with the presence of RM and competence machineries. Finally, genes exchanged by HR showed functional enrichments which could be related to adaptations to different environments and ecological strategies. Taken together, our results clarify the factors underlying HR impact and suggest important adaptive roles of genes exchanged through this mechanism. Our results also revealed that the extent of genetic exchange correlated with lifestyle and some genomic features. Moreover, the genes in exchanged regions were enriched for functions that reflected specific adaptations, supporting identification of HR as one of the main evolutionary mechanisms shaping prokaryotic core genomes.
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22
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Xie Z, Tang H. ISEScan: automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics 2018; 33:3340-3347. [PMID: 29077810 DOI: 10.1093/bioinformatics/btx433] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 07/04/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation The insertion sequence (IS) elements are the smallest but most abundant autonomous transposable elements in prokaryotic genomes, which play a key role in prokaryotic genome organization and evolution. With the fast growing genomic data, it is becoming increasingly critical for biology researchers to be able to accurately and automatically annotate ISs in prokaryotic genome sequences. The available automatic IS annotation systems are either providing only incomplete IS annotation or relying on the availability of existing genome annotations. Here, we present a new IS elements annotation pipeline to address these issues. Results ISEScan is a highly sensitive software pipeline based on profile hidden Markov models constructed from manually curated IS elements. ISEScan performs better than existing IS annotation systems when tested on prokaryotic genomes with curated annotations of IS elements. Applying it to 2784 prokaryotic genomes, we report the global distribution of IS families across taxonomic clades in Archaea and Bacteria. Availability and implementation ISEScan is implemented in Python and released as an open source software at https://github.com/xiezhq/ISEScan. Contact hatang@indiana.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhiqun Xie
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
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23
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Thelaus J, Lundmark E, Lindgren P, Sjödin A, Forsman M. Galleria mellonella Reveals Niche Differences Between Highly Pathogenic and Closely Related Strains of Francisella spp. Front Cell Infect Microbiol 2018; 8:188. [PMID: 29922601 PMCID: PMC5996057 DOI: 10.3389/fcimb.2018.00188] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/15/2018] [Indexed: 11/13/2022] Open
Abstract
Francisella tularensis, a highly virulent bacteria that causes the zoonotic disease tularemia, is considered a potential agent of biological warfare and bioterrorism. Although the host range for several species within the Francisella is known, little is known about the natural reservoirs of various Francisella species. The lack of knowledge regarding the environmental fates of these pathogens greatly reduces the possibilities for microbial risk assessments. The greater wax moth (Galleria mellonella) is an insect of the order Lepidoptera that has been used as an alternative model to study microbial infection during recent years. The aim of this study was to evaluate G. mellonella as a model system for studies of human pathogenic and closely related opportunistic and non-pathogenic strains within the Francisella genus. The employed G. mellonella larvae model demonstrated differences in lethality between human pathogenic and human non-pathogenic or opportunistic Francisella species. The F. novicida, F. hispaniensis and F. philomiragia strains were significantly more virulent in the G. mellonella model than the strains of human pathogens F. t. holarctica and F. t. tularensis. Our data show that G. mellonella is a possible in vivo model of insect immunity for studies of both opportunistic and virulent lineages of Francisella spp., that produces inverse results regarding lethality in G. mellonella and incapacitating disease in humans. The results provide insight into the potential host specificity of F. tularensis and closely related members of the same genus, thus increasing our present understanding of Francisella spp. ecology.
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Matz LM, Kamdar KY, Holder ME, Metcalf GA, Weissenberger GM, Meng Q, Vee V, Han Y, Muzny DM, Gibbs RA, Johnson CL, Revell PA, Petrosino JF. Challenges of Francisella classification exemplified by an atypical clinical isolate. Diagn Microbiol Infect Dis 2018; 90:241-247. [PMID: 29329757 PMCID: PMC5857240 DOI: 10.1016/j.diagmicrobio.2017.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/30/2017] [Accepted: 11/30/2017] [Indexed: 01/09/2023]
Abstract
The accumulation of sequenced Francisella strains has made it increasingly apparent that the 16S rRNA gene alone is not enough to stratify the Francisella genus into precise and clinically useful classifications. Continued whole-genome sequencing of isolates will provide a larger base of knowledge for targeted approaches with broad applicability. Additionally, examination of genomic information on a case-by-case basis will help resolve outstanding questions regarding strain stratification. We report the complete genome sequence of a clinical isolate, designated here as F. novicida-like strain TCH2015, acquired from the lymph node of a 6-year-old male. Two features were atypical for F. novicida: exhibition of functional oxidase activity and additional gene content, including proposed virulence determinants. These differences, which could potentially impact virulence and clinical diagnosis, emphasize the need for more comprehensive methods to profile Francisella isolates. This study highlights the value of whole-genome sequencing, which will lead to a more robust database of environmental and clinical genomes and inform strategies to improve detection and classification of Francisella strains.
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Affiliation(s)
- L M Matz
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| | - K Y Kamdar
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Cancer and Hematology Centers, Texas Children's Hospital, Houston, TX, USA
| | - M E Holder
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - G A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - G M Weissenberger
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Q Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - V Vee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Y Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - D M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - R A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - C L Johnson
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA; Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - P A Revell
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA; Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - J F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
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25
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Busch A, Thomas P, Zuchantke E, Brendebach H, Neubert K, Gruetzke J, Al Dahouk S, Peters M, Hotzel H, Neubauer H, Tomaso H. Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis. Front Microbiol 2018; 9:344. [PMID: 29593661 PMCID: PMC5859110 DOI: 10.3389/fmicb.2018.00344] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/12/2018] [Indexed: 12/30/2022] Open
Abstract
Francisella (F.) tularensis is a highly virulent, Gram-negative bacterial pathogen and the causative agent of the zoonotic disease tularemia. Here, we generated, analyzed and characterized a high quality circular genome sequence of the F. tularensis subsp. holarctica strain 12T0050 that caused fatal tularemia in a hare. Besides the genomic structure, we focused on the analysis of oriC, unique to the Francisella genus and regulating replication in and outside hosts and the first report on genomic DNA methylation of a Francisella strain. The high quality genome was used to establish and evaluate a diagnostic whole genome sequencing pipeline. A genotyping strategy for F. tularensis was developed using various bioinformatics tools for genotyping. Additionally, whole genome sequences of F. tularensis subsp. holarctica isolates isolated in the years 2008–2015 in Germany were generated. A phylogenetic analysis allowed to determine the genetic relatedness of these isolates and confirmed the highly conserved nature of F. tularensis subsp. holarctica.
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Affiliation(s)
- Anne Busch
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Prasad Thomas
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Eric Zuchantke
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Holger Brendebach
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Kerstin Neubert
- Algorithmic Bioinformatics, Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Josephine Gruetzke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Sascha Al Dahouk
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Martin Peters
- Standort Arnsberg, Chemisches und Veterinäruntersuchungsamt Westfalen, Arnsberg, Germany
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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26
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Mortimer TD, Weber AM, Pepperell CS. Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis. mSystems 2018; 3:e00108-17. [PMID: 29404424 PMCID: PMC5790871 DOI: 10.1128/msystems.00108-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death by an infectious disease, and global TB control efforts are increasingly threatened by drug resistance in Mycobacterium tuberculosis. Unlike most bacteria, where lateral gene transfer is an important mechanism of resistance acquisition, resistant M. tuberculosis arises solely by de novo chromosomal mutation. Using whole-genome sequencing data from two natural populations of M. tuberculosis, we characterized the population genetics of known drug resistance loci using measures of diversity, population differentiation, and convergent evolution. We found resistant subpopulations to be less diverse than susceptible subpopulations, consistent with ongoing transmission of resistant M. tuberculosis. A subset of resistance genes ("sloppy targets") were characterized by high diversity and multiple rare variants; we posit that a large genetic target for resistance and relaxation of purifying selection contribute to high diversity at these loci. For "tight targets" of selection, the path to resistance appeared narrower, evidenced by single favored mutations that arose numerous times in the phylogeny and segregated at markedly different frequencies in resistant and susceptible subpopulations. These results suggest that diverse genetic architectures underlie drug resistance in M. tuberculosis and that combined approaches are needed to identify causal mutations. Extrapolating from patterns observed for well-characterized genes, we identified novel candidate variants involved in resistance. The approach outlined here can be extended to identify resistance variants for new drugs, to investigate the genetic architecture of resistance, and when phenotypic data are available, to find candidate genetic loci underlying other positively selected traits in clonal bacteria. IMPORTANCEMycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a significant burden on global health. Antibiotic treatment imposes strong selective pressure on M. tuberculosis populations. Identifying the mutations that cause drug resistance in M. tuberculosis is important for guiding TB treatment and halting the spread of drug resistance. Whole-genome sequencing (WGS) of M. tuberculosis isolates can be used to identify novel mutations mediating drug resistance and to predict resistance patterns faster than traditional methods of drug susceptibility testing. We have used WGS from natural populations of drug-resistant M. tuberculosis to characterize effects of selection for advantageous mutations on patterns of diversity at genes involved in drug resistance. The methods developed here can be used to identify novel advantageous mutations, including new resistance loci, in M. tuberculosis and other clonal pathogens.
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Affiliation(s)
- Tatum D. Mortimer
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Alexandra M. Weber
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Caitlin S. Pepperell
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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27
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Liu Q, Xin YH, Zhou YG, Chen WX. Multilocus sequence analysis of homologous recombination and diversity in Arthrobacter sensu lato named species and glacier-inhabiting strains. Syst Appl Microbiol 2017; 41:23-29. [PMID: 29129356 DOI: 10.1016/j.syapm.2017.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/30/2017] [Accepted: 08/19/2017] [Indexed: 10/18/2022]
Abstract
Members of the bacterial genus Arthrobacter sensu lato are Gram-positive actinomycetes distributed worldwide and found in numerous environments including soil, water, glacier ice, and sewage. Homologous recombination is an important driving force in bacterial evolution, but its impact on Arthrobacter sensu lato evolution is poorly understood. We evaluated homologous recombination among 41 Arthrobacter sensu lato named species, using multilocus sequence analysis (MLSA). A high level of recombination was found, associated with strong diversification and a reticulate evolutionary pattern of Arthrobacter sensu lato. We also collected a total of 31 cold-adapted Arthrobacter sensu lato strains from two cold glaciers located in northwest China and two temperate glaciers in southwest China, and evaluated their diversity and population structure by MLSA. The glacier strains displayed high diversity, but rates of recombination among the four glacier groups were quite low, indicating that barriers to homologous recombination formed in the past among the populations on different glaciers. Our findings indicate that historical glaciation events shaped the contemporary distributions, taxonomic relationships, and phylogeographic patterns of Arthrobacter sensu lato species on glaciers.
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Affiliation(s)
- Qing Liu
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu-Hua Xin
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yu-Guang Zhou
- China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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28
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Mortimer TD, Annis DS, O’Neill MB, Bohr LL, Smith TM, Poinar HN, Mosher DF, Pepperell CS. Adaptation in a Fibronectin Binding Autolysin of Staphylococcus saprophyticus. mSphere 2017; 2:e00511-17. [PMID: 29202045 PMCID: PMC5705806 DOI: 10.1128/msphere.00511-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/13/2017] [Indexed: 12/18/2022] Open
Abstract
Human-pathogenic bacteria are found in a variety of niches, including free-living, zoonotic, and microbiome environments. Identifying bacterial adaptations that enable invasive disease is an important means of gaining insight into the molecular basis of pathogenesis and understanding pathogen emergence. Staphylococcus saprophyticus, a leading cause of urinary tract infections, can be found in the environment, food, animals, and the human microbiome. We identified a selective sweep in the gene encoding the Aas adhesin, a key virulence factor that binds host fibronectin. We hypothesize that the mutation under selection (aas_2206A>C) facilitates colonization of the urinary tract, an environment where bacteria are subject to strong shearing forces. The mutation appears to have enabled emergence and expansion of a human-pathogenic lineage of S. saprophyticus. These results demonstrate the power of evolutionary genomic approaches in discovering the genetic basis of virulence and emphasize the pleiotropy and adaptability of bacteria occupying diverse niches. IMPORTANCEStaphylococcus saprophyticus is an important cause of urinary tract infections (UTI) in women; such UTI are common, can be severe, and are associated with significant impacts to public health. In addition to being a cause of human UTI, S. saprophyticus can be found in the environment, in food, and associated with animals. After discovering that UTI strains of S. saprophyticus are for the most part closely related to each other, we sought to determine whether these strains are specially adapted to cause disease in humans. We found evidence suggesting that a mutation in the gene aas is advantageous in the context of human infection. We hypothesize that the mutation allows S. saprophyticus to survive better in the human urinary tract. These results show how bacteria found in the environment can evolve to cause disease.
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Affiliation(s)
- Tatum D. Mortimer
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Douglas S. Annis
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Mary B. O’Neill
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Lindsey L. Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Tracy M. Smith
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario, Canada
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Deane F. Mosher
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin, USA
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29
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Déraspe M, Raymond F, Boisvert S, Culley A, Roy PH, Laviolette F, Corbeil J. Phenetic Comparison of Prokaryotic Genomes Using k-mers. Mol Biol Evol 2017; 34:2716-2729. [PMID: 28957508 PMCID: PMC5850840 DOI: 10.1093/molbev/msx200] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets.
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Affiliation(s)
- Maxime Déraspe
- Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Université Laval, Quebec City, QC, Canada
| | - Frédéric Raymond
- Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada
| | | | - Alexander Culley
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Quebec City, QC, Canada
| | - Paul H. Roy
- Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC, Canada
- Département de Biochimie, Microbiologie et Bio-informatique, Université Laval, Quebec City, QC, Canada
| | - François Laviolette
- Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada
- Département d’Informatique et de Génie Logiciel, Université Laval, Quebec City, QC, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie, CHU de Québec-Université Laval, Quebec City, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Quebec City, QC, Canada
- Département de Médecine Moléculaire, Université Laval, Quebec City, QC, Canada
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30
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Brenz Y, Winther-Larsen HC, Hagedorn M. Expanding Francisella models: Pairing up the soil amoeba Dictyostelium with aquatic Francisella. Int J Med Microbiol 2017; 308:32-40. [PMID: 28843671 DOI: 10.1016/j.ijmm.2017.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/31/2017] [Accepted: 08/04/2017] [Indexed: 12/19/2022] Open
Abstract
The bacterial genus Francisella comprises highly pathogenic species that infect mammals, arthropods, fish and protists. Understanding virulence and host defense mechanisms of Francisella infection relies on multiple animal and cellular model systems. In this review, we want to summarize the most commonly used Francisella host model platforms and highlight novel, alternative model systems using aquatic Francisella species. Established mouse and macrophage models contributed extensively to our understanding of Francisella infection. However, murine and human cells display significant differences in their response to Francisella infection. The zebrafish and the amoeba Dictyostelium are well-established model systems for host-pathogen interactions and open up opportunities to investigate bacterial virulence and host defense. Comparisons between model systems using human and fish pathogenic Francisella species revealed shared virulence strategies and pathology between them. Hence, zebrafish and Dictyostelium might complement current model systems to find new vaccine candidates and contribute to our understanding of Francisella infection.
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Affiliation(s)
- Yannick Brenz
- Department of Parasitology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany.
| | - Hanne C Winther-Larsen
- Centre for Integrative Microbial Evolution (CIME) and Department of Pharmaceutical Biosciences, University of Oslo, Sem Sælands vei 3, 0371 Oslo, Norway.
| | - Monica Hagedorn
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, 28759 Bremen, Germany.
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31
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Ramakrishnan G. Iron and Virulence in Francisella tularensis. Front Cell Infect Microbiol 2017; 7:107. [PMID: 28421167 PMCID: PMC5378763 DOI: 10.3389/fcimb.2017.00107] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/16/2017] [Indexed: 12/12/2022] Open
Abstract
Francisella tularensis, the causative agent of tularemia, is a Gram-negative bacterium that infects a variety of cell types including macrophages, and propagates with great efficiency in the cytoplasm. Iron, essential for key enzymatic and redox reactions, is among the nutrients required to support this pathogenic lifestyle and the bacterium relies on specialized mechanisms to acquire iron within the host environment. Two distinct pathways for iron acquisition are encoded by the F. tularensis genome- a siderophore-dependent ferric iron uptake system and a ferrous iron transport system. Genes of the Fur-regulated fslABCDEF operon direct the production and transport of the siderophore rhizoferrin. Siderophore biosynthesis involves enzymes FslA and FslC, while export across the inner membrane is mediated by FslB. Uptake of the rhizoferrin- ferric iron complex is effected by the siderophore receptor FslE in the outer membrane in a TonB-independent process, and FslD is responsible for uptake across the inner membrane. Ferrous iron uptake relies largely on high affinity transport by FupA in the outer membrane, while the Fur-regulated FeoB protein mediates transport across the inner membrane. FslE and FupA are paralogous proteins, sharing sequence similarity and possibly sharing structural features as well. This review summarizes current knowledge of iron acquisition in this organism and the critical role of these uptake systems in bacterial pathogenicity.
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Affiliation(s)
- Girija Ramakrishnan
- Department of Medicine/Division of Infectious Diseases, University of VirginiaCharlottesville, VA, USA
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32
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Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection. Appl Environ Microbiol 2017; 83:AEM.02589-16. [PMID: 27881415 DOI: 10.1128/aem.02589-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
Abstract
Francisella tularensis is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 7 new Francisella genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features-for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected Francisella bacteria. IMPORTANCE DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics, and environmental surveillance, for which response times must be short. Many new Francisella isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate F. tularensis from clinical and environmental Francisella isolates and provide a knowledge base for future comparison of Francisella organisms identified in clinical samples or environmental surveys.
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Devault AM, Mortimer TD, Kitchen A, Kiesewetter H, Enk JM, Golding GB, Southon J, Kuch M, Duggan AT, Aylward W, Gardner SN, Allen JE, King AM, Wright G, Kuroda M, Kato K, Briggs DE, Fornaciari G, Holmes EC, Poinar HN, Pepperell CS. A molecular portrait of maternal sepsis from Byzantine Troy. eLife 2017; 6. [PMID: 28072390 PMCID: PMC5224923 DOI: 10.7554/elife.20983] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/24/2016] [Indexed: 12/14/2022] Open
Abstract
Pregnancy complications are poorly represented in the archeological record, despite their importance in contemporary and ancient societies. While excavating a Byzantine cemetery in Troy, we discovered calcified abscesses among a woman’s remains. Scanning electron microscopy of the tissue revealed ‘ghost cells’, resulting from dystrophic calcification, which preserved ancient maternal, fetal and bacterial DNA of a severe infection, likely chorioamnionitis. Gardnerella vaginalis and Staphylococcus saprophyticus dominated the abscesses. Phylogenomic analyses of ancient, historical, and contemporary data showed that G. vaginalis Troy fell within contemporary genetic diversity, whereas S. saprophyticus Troy belongs to a lineage that does not appear to be commonly associated with human disease today. We speculate that the ecology of S. saprophyticus infection may have differed in the ancient world as a result of close contacts between humans and domesticated animals. These results highlight the complex and dynamic interactions with our microbial milieu that underlie severe maternal infections. DOI:http://dx.doi.org/10.7554/eLife.20983.001 Why and how have some bacteria evolved to cause illness in humans? One way to study bacterial evolution is to search for ancient samples of bacteria and use DNA sequencing technology to investigate how modern bacteria have changed from their ancestors. Understanding the evolution process may help researchers to understand how some bacteria become resistant to the antibiotics designed to kill them. Complications that occur during pregnancy, including bacterial infections, have long been a major cause of death for women. Now, Devault, Mortimer et al. have been able to sequence the DNA of bacteria found in tissue collected from a woman buried 800 years ago in a cemetery in Troy. Some of the woman’s tissues had been well preserved because they had calcified (probably as the result of infection), which preserved their structure in a mineralized layer. Two mineralized “nodules” in the body appear to be the remains of abscesses. Some of the human DNA in the nodules came from a male, suggesting that the woman was pregnant with a boy and that the abscesses formed in placental tissue. Sequencing the DNA of the bacteria in the abscess allowed Devault, Mortimer et al. to diagnose the woman’s infection, which was caused by two types of bacteria. One species, called Gardnerella vaginalis, is found in modern pregnancy-related infections. The DNA of the ancient samples was similar to that of modern bacteria. The other bacteria species was an ancient form of Staphylococcus saprophyticus, a type of bacteria that causes urinary tract infections. However, the DNA of the ancient S. saprophyticus bacteria is quite different to that of the bacteria found in modern humans. Instead, their DNA sequence appears more similar to forms of the bacteria that infect currently livestock. As humans lived closely with their livestock at the time the woman lived, her infection may be due to a type of bacteria that passed easily between humans and animals. Overall, the results suggest that the disease-causing properties of bacteria can arise from a wide range of sources. In addition, Devault, Mortimer et al. have demonstrated that certain types of tissue found in archeological remains are a potential gold mine of information about the evolution of bacteria and other microbes found in the human body. DOI:http://dx.doi.org/10.7554/eLife.20983.002
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Affiliation(s)
- Alison M Devault
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,MYcroarray, Ann Arbor, United States
| | - Tatum D Mortimer
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, United States
| | - Andrew Kitchen
- Department of Anthropology, University of Iowa, Iowa City, United States
| | - Henrike Kiesewetter
- Project Troia, Institute of Prehistory, Early History, and Medieval Archaeology, Tübingen University, Tübingen, Germany
| | - Jacob M Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,MYcroarray, Ann Arbor, United States
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Canada
| | - John Southon
- Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, United States
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada
| | - William Aylward
- Molecular Archaeology Laboratory, Biotechnology Center, University of Wisconsin-Madison, Madison, United States.,Department of Classics and Ancient Near Eastern Studies, University of Wisconsin-Madison, Madison, United States
| | - Shea N Gardner
- Lawrence Livermore National Laboratory, Livermore, United States
| | - Jonathan E Allen
- Lawrence Livermore National Laboratory, Livermore, United States
| | - Andrew M King
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Gerard Wright
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kengo Kato
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Derek Eg Briggs
- Department of Geology and Geophysics, Yale University, New Haven, United States
| | - Gino Fornaciari
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Canada.,Department of Biology, McMaster University, Hamilton, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.,Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States.,Molecular Archaeology Laboratory, Biotechnology Center, University of Wisconsin-Madison, Madison, United States.,Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, United States
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34
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Affiliation(s)
- Petra Spidlova
- a Department of Molecular Pathology and Biology , Faculty of Military Health Sciences, University of Defence , Hradec Kralove , Czech Republic
| | - Jiri Stulik
- a Department of Molecular Pathology and Biology , Faculty of Military Health Sciences, University of Defence , Hradec Kralove , Czech Republic
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35
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Fuentealba P, Aros C, Latorre Y, Martínez I, Marshall S, Ferrer P, Albiol J, Altamirano C. Genome-scale metabolic reconstruction for the insidious bacterium in aquaculture Piscirickettsia salmonis. BIORESOURCE TECHNOLOGY 2017; 223:105-114. [PMID: 27788423 DOI: 10.1016/j.biortech.2016.10.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/04/2016] [Accepted: 10/11/2016] [Indexed: 06/06/2023]
Abstract
Piscirickettsia salmonis is a fish bacterium that causes the disease piscirickettsiosis in salmonids. This pathology is partially controlled by vaccines. The lack of knowledge has hindered its culture on laboratory and industrial scale. The study describes the metabolic phenotype of P. salmonis in culture. This study presents the first genome-scale model (iPF215) of the LF-89 strain of P. salmonis, describing the central metabolic pathway, biosynthesis and molecule degradation and transport mechanisms. The model was adjusted with experiment data, allowing the identification of the capacities that were not predicted by the automatic annotation of the genome sequences. The iPF215 model is comprised of 417 metabolites, 445 reactions and 215 genes, was used to reproduce the growth of P. salmonis (μmax 0.052±0.005h-1). The metabolic reconstruction of the P. salmonis LF-89 strain obtained in this research provides a baseline that describes the metabolic capacities of the bacterium and is the basis for developing improvements to its cultivation for vaccine formulation.
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Affiliation(s)
- Pablo Fuentealba
- Doctorado en Biotecnología, Pontificia Universidad Católica de Valparaíso - Universidad Federico Santa María, Valparaíso, Chile; Laboratorio of Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Camila Aros
- Laboratorio of Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Yesenia Latorre
- Laboratorio of Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Irene Martínez
- Laboratorio of Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Sergio Marshall
- Laboratorio of Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Curauma, Chile
| | - Pau Ferrer
- Laboratorio de Biología de Sistemas, Departamento Ingeniería Química, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Joan Albiol
- Laboratorio de Biología de Sistemas, Departamento Ingeniería Química, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Claudia Altamirano
- Laboratorio of Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile; CREAS CONICYT Regional GORE Valparaíso R0GI1004, Av. Universidad, Curauma, Chile.
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36
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Sensitive Detection of Francisella tularensis Directly from Whole Blood by Use of the GeneXpert System. J Clin Microbiol 2016; 55:291-301. [PMID: 27847371 DOI: 10.1128/jcm.01126-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/02/2016] [Indexed: 11/20/2022] Open
Abstract
Francisella tularensis is a potential bioterrorism agent that is highly infectious at very low doses. Diagnosis of tularemia by blood culture and nucleic acid-based diagnostic tests is insufficiently sensitive. Here, we demonstrate a highly sensitive F. tularensis assay that incorporates sample processing and detection into a single cartridge suitable for point-of-care detection. The assay limit of detection (LOD) and dynamic range were determined in a filter-based cartridge run on the GeneXpert system. F. tularensis DNA in buffer or CFU of F. tularensis was spiked into human or macaque blood. To simulate detection in human disease, the assay was tested on blood drawn from macaques infected with F. tularensis Schu S4 at daily intervals. Assay detection was compared to that with a conventional quantitative PCR (qPCR) assay and blood culture. The assay LOD was 0.1 genome equivalents (GE) per reaction and 10 CFU/ml F. tularensis in both human and macaque blood. In infected macaques, the assay detected F. tularensis on days 1 to 4 postinfection in 21%, 17%, 60%, and 83% of macaques, respectively, compared to conventional qPCR positivity rates of 0%, 0%, 30%, and 100% and CFU detection of blood culture at 0%, 0%, 0%, and 10% positive, respectively. Assay specificity was 100%. The new cartridge-based assay can rapidly detect F. tularensis in bloodstream infections directly in whole blood at the early stages of infection with a sensitivity that is superior to that of other methods. The simplicity of the automated testing procedures may make this test suitable for rapid point-of-care detection.
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37
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Dwibedi C, Birdsell D, Lärkeryd A, Myrtennäs K, Öhrman C, Nilsson E, Karlsson E, Hochhalter C, Rivera A, Maltinsky S, Bayer B, Keim P, Scholz HC, Tomaso H, Wittwer M, Beuret C, Schuerch N, Pilo P, Hernández Pérez M, Rodriguez-Lazaro D, Escudero R, Anda P, Forsman M, Wagner DM, Larsson P, Johansson A. Long-range dispersal moved Francisella tularensis into Western Europe from the East. Microb Genom 2016; 2:e000100. [PMID: 28348839 PMCID: PMC5359409 DOI: 10.1099/mgen.0.000100] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/22/2016] [Indexed: 01/31/2023] Open
Abstract
For many infections transmitting to humans from reservoirs in nature, disease dispersal patterns over space and time are largely unknown. Here, a reversed genomics approach helped us understand disease dispersal and yielded insight into evolution and biological properties of Francisella tularensis, the bacterium causing tularemia. We whole-genome sequenced 67 strains and characterized by single-nucleotide polymorphism assays 138 strains, collected from individuals infected 1947-2012 across Western Europe. We used the data for phylogenetic, population genetic and geographical network analyses. All strains (n=205) belonged to a monophyletic population of recent ancestry not found outside Western Europe. Most strains (n=195) throughout the study area were assigned to a star-like phylogenetic pattern indicating that colonization of Western Europe occurred via clonal expansion. In the East of the study area, strains were more diverse, consistent with a founder population spreading from east to west. The relationship of genetic and geographic distance within the F. tularensis population was complex and indicated multiple long-distance dispersal events. Mutation rate estimates based on year of isolation indicated null rates; in outbreak hotspots only, there was a rate of 0.4 mutations/genome/year. Patterns of nucleotide substitution showed marked AT mutational bias suggestive of genetic drift. These results demonstrate that tularemia has moved from east to west in Europe and that F. tularensis has a biology characterized by long-range geographical dispersal events and mostly slow, but variable, replication rates. The results indicate that mutation-driven evolution, a resting survival phase, genetic drift and long-distance geographical dispersal events have interacted to generate genetic diversity within this species.
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Affiliation(s)
- Chinmay Dwibedi
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Dawn Birdsell
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Adrian Lärkeryd
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Kerstin Myrtennäs
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Caroline Öhrman
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Elin Nilsson
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Edvin Karlsson
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Christian Hochhalter
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Andrew Rivera
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Sara Maltinsky
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Brittany Bayer
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
- Translational Genomics Research Institute North, Flagstaff AZ, USA
| | | | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses Friedrich-Loeffler, Institut Federal Research Institute for Animal Health, Jena, Germany
| | - Matthias Wittwer
- Biology Division, Spietz Laboratory, Federal Office for Civil Protection, Spietz, Switzerland
| | - Christian Beuret
- Biology Division, Spietz Laboratory, Federal Office for Civil Protection, Spietz, Switzerland
| | - Nadia Schuerch
- Biology Division, Spietz Laboratory, Federal Office for Civil Protection, Spietz, Switzerland
| | - Paola Pilo
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Marta Hernández Pérez
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
- Departamento de Ingeniería Agrícola y Forestal, Universidad de Valladolid, Palencia, Spain
| | | | - Raquel Escudero
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Anda
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Mats Forsman
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - David M. Wagner
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff AZ, USA
| | - Pär Larsson
- Division of CBRN Security and Defence, Swedish Defense Research Agency, Umeå, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology and the Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Correspondence Anders Johansson ()
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38
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Chou AY, Kennett NJ, Melillo AA, Elkins KL. Murine survival of infection with Francisella novicida and protection against secondary challenge is critically dependent on B lymphocytes. Microbes Infect 2016; 19:91-100. [PMID: 27965147 DOI: 10.1016/j.micinf.2016.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 10/13/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022]
Abstract
Respiratory infection of mice with Francisella novicida has recently been used as a model for the highly virulent human pathogen Francisella tularensis. Similar to F. tularensis, even small doses of F. novicida administered by respiratory routes are lethal for inbred laboratory mice. This feature obviously limits study of infection-induced immunity. Parenteral sublethal infections of mice with F. novicida are feasible, but the resulting immune responses are incompletely characterized. Here we use parenteral intradermal (i.d.) and intraperitoneal (i.p.) F. novicida infections of C57BL/6J mice to determine the role of B cells in controlling primary and secondary F. novicida infections. Despite developing comparable levels of F. novicida-primed T cells, B cell knockout mice were much more susceptible to both primary i.d. infection and secondary i.p. challenge than wild type (normal) C57BL/6J mice. Transfer of F. novicida-immune sera to either wild type C57BL/6J mice or to B cell knockout mice did not appreciably impact survival of subsequent lethal F. novicida challenge. However, F. novicida-immune mice that were depleted of T cells after priming but just before challenge survived and cleared secondary i.p. F. novicida challenge. Collectively these results indicate that B cells, if not serum antibodies, play a major role in controlling F. novicida infections in mice.
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Affiliation(s)
- Alicia Y Chou
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Rockville, MD 20852, United States
| | - Nikki J Kennett
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Rockville, MD 20852, United States
| | - Amanda A Melillo
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Rockville, MD 20852, United States
| | - Karen L Elkins
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Rockville, MD 20852, United States.
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39
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Periasamy S, Le HT, Duffy EB, Chin H, Harton JA. Inflammasome-Independent NLRP3 Restriction of a Protective Early Neutrophil Response to Pulmonary Tularemia. PLoS Pathog 2016; 12:e1006059. [PMID: 27926940 PMCID: PMC5142794 DOI: 10.1371/journal.ppat.1006059] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/13/2016] [Indexed: 11/26/2022] Open
Abstract
Francisella tularensis (Ft) causes a frequently fatal, acute necrotic pneumonia in humans and animals. Following lethal Ft infection in mice, infiltration of the lungs by predominantly immature myeloid cells and subsequent myeloid cell death drive pathogenesis and host mortality. However, following sub-lethal Ft challenge, more mature myeloid cells are elicited and are protective. In addition, inflammasome-dependent IL-1β and IL-18 are important for protection. As Nlrp3 appears dispensable for resistance to infection with Francisella novicida, we considered its role during infection with the virulent Type A strain SchuS4 and the attenuated Type B live vaccine strain LVS. Here we show that both in vitro macrophage and in vivo IL-1β and IL-18 responses to Ft LVS and SchuS4 involve both the Aim2 and Nlrp3 inflammasomes. However, following lethal infection with Francisella, IL-1r-, Caspase-1/11-, Asc- and Aim2-deficient mice exhibited increased susceptibility as expected, while Nlrp3-deficient mice were more resistant. Despite reduced levels of IL-1β and IL-18, in the absence of Nlrp3, Ft infected mice have dramatically reduced lung pathology, diminished recruitment and death of immature myeloid cells, and reduced bacterial burden in comparison to wildtype and inflammasome-deficient mice. Further, increased numbers of mature neutrophil appear in the lung early during lethal Ft infection in Nlrp3-deficient mice. Finally, Ft infection induces myeloid and lung stromal cell death that in part requires Nlrp3, is necrotic/necroptotic in nature, and drives host mortality. Thus, Nlrp3 mediates an inflammasome-independent process that restricts the appearance of protective mature neutrophils and promotes lethal necrotic lung pathology.
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Affiliation(s)
- Sivakumar Periasamy
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Hongnga T. Le
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Ellen B. Duffy
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Heather Chin
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
| | - Jonathan A. Harton
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, New York, United States of America
- * E-mail:
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Myrtennäs K, Marinov K, Johansson A, Niemcewicz M, Karlsson E, Byström M, Forsman M. Introduction and persistence of tularemia in Bulgaria. Infect Ecol Epidemiol 2016; 6:32838. [PMID: 27790972 PMCID: PMC5084392 DOI: 10.3402/iee.v6.32838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/14/2016] [Accepted: 09/20/2016] [Indexed: 12/23/2022] Open
Abstract
Introduction Outbreaks of the zoonotic disease tularemia occurred in north-east Bulgaria in the 1960s. Then came 30 years of epidemiological silence until new outbreaks occurred in west Bulgaria in the 1990s. To investigate how bacterial strains of Francisella tularensis causing tularemia in wildlife and humans in the 1960s and the 1990s were related, we explored their genetic diversity. Material and methods Ten F. tularensis genomes from the 1960s (n=3) and the 1990s (n=7) were sequenced, assigned to canonical single-nucleotide polymorphism (canSNP) clades, and compared to reference genomes. We developed four new canSNP polymerase chain reaction (PCR) assays based on the genome sequence information. Results and discussion The genetic analysis showed that the outbreaks in the 1960s as well as in the 1990s involved multiple clones and new genetic diversity. The smallest genetic difference found between any of the Bulgarian strains was five SNPs between the strains L2 and 81 isolated 43 years apart, indicating that F. tularensis may persist locally over long time periods without causing outbreaks. The existence of genetically highly similar strain-pairs isolated the same year in the same area from different hosts supports a hypothesis of local expansion of clones during outbreaks. Close relationship (two SNPs) was found between one strain isolated 1961 in northeast Bulgaria and one strain isolated 5 years before in USSR. Historical data coinciding with the actual time point describe the introduction of water rats from USSR into the Bulgarian outbreak area, which may explain the close genetic relationship and the origin of the outbreak. Conclusion Genome analysis of strains from two outbreaks in the 1960s and the 1990s provided valuable information on the genetic diversity and persistence of F. tularensis in Bulgaria.
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Affiliation(s)
- Kerstin Myrtennäs
- Department of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden;
| | - Krustyu Marinov
- Department of Microbiology, Military Medical Academy (MMA), Sofia, Bulgaria
| | - Anders Johansson
- Departments of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Marcin Niemcewicz
- Biological Threat Identification Center, Military Institute of Hygiene and Epidemiology (MIHE), Pulawy, Poland
| | - Edvin Karlsson
- Department of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Mona Byström
- Department of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
| | - Mats Forsman
- Department of CBRN Defence and Security, Swedish Defence Research Agency (FOI), Umeå, Sweden
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Rigard M, Bröms JE, Mosnier A, Hologne M, Martin A, Lindgren L, Punginelli C, Lays C, Walker O, Charbit A, Telouk P, Conlan W, Terradot L, Sjöstedt A, Henry T. Francisella tularensis IglG Belongs to a Novel Family of PAAR-Like T6SS Proteins and Harbors a Unique N-terminal Extension Required for Virulence. PLoS Pathog 2016; 12:e1005821. [PMID: 27602570 PMCID: PMC5014421 DOI: 10.1371/journal.ppat.1005821] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/20/2016] [Indexed: 12/12/2022] Open
Abstract
The virulence of Francisella tularensis, the etiological agent of tularemia, relies on an atypical type VI secretion system (T6SS) encoded by a genomic island termed the Francisella Pathogenicity Island (FPI). While the importance of the FPI in F. tularensis virulence is clearly established, the precise role of most of the FPI-encoded proteins remains to be deciphered. In this study, using highly virulent F. tularensis strains and the closely related species F. novicida, IglG was characterized as a protein featuring a unique α-helical N-terminal extension and a domain of unknown function (DUF4280), present in more than 250 bacterial species. Three dimensional modeling of IglG and of the DUF4280 consensus protein sequence indicates that these proteins adopt a PAAR-like fold, suggesting they could cap the T6SS in a similar way as the recently described PAAR proteins. The newly identified PAAR-like motif is characterized by four conserved cysteine residues, also present in IglG, which may bind a metal atom. We demonstrate that IglG binds metal ions and that each individual cysteine is required for T6SS-dependent secretion of IglG and of the Hcp homologue, IglC and for the F. novicida intracellular life cycle. In contrast, the Francisella-specific N-terminal α-helical extension is not required for IglG secretion, but is critical for F. novicida virulence and for the interaction of IglG with another FPI-encoded protein, IglF. Altogether, our data suggest that IglG is a PAAR-like protein acting as a bi-modal protein that may connect the tip of the Francisella T6SS with a putative T6SS effector, IglF. Francisella tularensis is a highly pathogenic bacterium causing tularemia. Its ability to cause disease is linked to its ability to replicate in the macrophage cytosol. The intracellular life cycle of Francisella is controlled by a type VI secretion system (T6SS), which is thought to inject effectors into the host cell to allow bacterial escape into the host cytosol. The molecular mechanisms behind this process are still largely unclear. In this work, we identify IglG as a protein with two important domains, one conserved in proteins from more than 250 bacterial species (DUF4280, renamed here as PAAR-like domain) and one specific for the Francisella genus. Using protein sequence analysis and three-dimensional structure predictions, comparative modeling and biochemistry approaches, our data demonstrate that IglG is a metal-binding protein that based on its PAAR-like domain might cap the VgrG spike of the T6SS and act as a membrane-puncturing protein. Furthermore, we identified that the Francisella-specific domain is directly involved in forming a protein complex with another virulence protein, IglF. This work, in addition to enhancing the molecular understanding of the Francisella T6SS, defines the features of the conserved DUF4280, a novel PAAR-like domain involved in type VI secretion (T6S) of many bacterial species.
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Affiliation(s)
- Mélanie Rigard
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jeanette E. Bröms
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Amandine Mosnier
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Maggy Hologne
- Institut des Sciences Analytiques, CNRS, UMR 5280, Université de Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, Villeurbanne, France
| | - Amandine Martin
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Lena Lindgren
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Claire Punginelli
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Claire Lays
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
| | - Olivier Walker
- Institut des Sciences Analytiques, CNRS, UMR 5280, Université de Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, Villeurbanne, France
| | - Alain Charbit
- Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche, Paris, France
- Institut Necker-Enfants Malades, Equipe 11: Pathogénie des Infections Systémiques, Paris, France
| | - Philippe Telouk
- University of Lyon, Lyon, France
- Laboratoire de Geologie de Lyon; Ecole Normale Supérieure de Lyon, Lyon, France
| | - Wayne Conlan
- National Research Council Canada, Human Health Therapeutics Portfolio, Ottawa, Ontario, Canada
| | - Laurent Terradot
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
- * E-mail: (LT); (AS); (TH)
| | - Anders Sjöstedt
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- * E-mail: (LT); (AS); (TH)
| | - Thomas Henry
- CIRI, International Center for Infectiology Research, Inserm U1111, CNRS, UMR5308, Lyon, France
- University of Lyon, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail: (LT); (AS); (TH)
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Karlsson E, Golovliov I, Lärkeryd A, Granberg M, Larsson E, Öhrman C, Niemcewicz M, Birdsell D, Wagner DM, Forsman M, Johansson A. Clonality of erythromycin resistance in Francisella tularensis. J Antimicrob Chemother 2016; 71:2815-23. [PMID: 27334667 DOI: 10.1093/jac/dkw235] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/17/2016] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVES We analysed diverse strains of Francisella tularensis subsp. holarctica to assess if its division into biovars I and II is associated with specific mutations previously linked to erythromycin resistance and to determine the distribution of this resistance trait across this subspecies. METHODS Three-hundred and fourteen F. tularensis subsp. holarctica strains were tested for erythromycin susceptibility and whole-genome sequences for these strains were examined for SNPs in genes previously associated with erythromycin resistance. Each strain was assigned to a global phylogenetic framework using genome-wide canonical SNPs. The contribution of a specific SNP to erythromycin resistance was examined using allelic exchange. The geographical distribution of erythromycin-resistant F. tularensis strains was further investigated by literature search. RESULTS There was a perfect correlation between biovar II strains (erythromycin resistance) and the phylogenetic group B.12. Only B.12 strains had an A → C SNP at position 2059 in the three copies of the rrl gene. Introducing 2059C into an rrl gene of an erythromycin-susceptible F. tularensis strain resulted in resistance. An additional 1144 erythromycin-resistant strains were identified from the scientific literature, all of them from Eurasia. CONCLUSIONS Erythromycin resistance in F. tularensis is caused by an A2059C rrl gene mutation, which exhibits a strictly clonal inheritance pattern found only in phylogenetic group B.12. This group is an extremely successful clone, representing the most common type of F. tularensis throughout Eurasia.
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Affiliation(s)
- Edvin Karlsson
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Igor Golovliov
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Adrian Lärkeryd
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Malin Granberg
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Eva Larsson
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Caroline Öhrman
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Marcin Niemcewicz
- Wojskowy Instytut Higieny i Epidemioligii, Biological Threat Identification and Countermeasure Center, Warsaw, Poland
| | - Dawn Birdsell
- Department of Biological Sciences and Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - David M Wagner
- Department of Biological Sciences and Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, USA
| | - Mats Forsman
- CBRN Defence and Security, Swedish Defence Research Agency, Umeå, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
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43
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Abstract
Francisella tularensis is the causative agent of the potentially lethal disease tularemia. Due to a low infectious dose and ease of airborne transmission, Francisella is classified as a category A biological agent. Despite the possible risk to public health, there is no safe and fully licensed vaccine. A potential vaccine candidate, an attenuated live vaccine strain, does not fulfil the criteria for general use. In this review, we will summarize existing and new candidates for live attenuated and subunit vaccines.
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44
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Towards Development of Improved Serodiagnostics for Tularemia by Use of Francisella tularensis Proteome Microarrays. J Clin Microbiol 2016; 54:1755-1765. [PMID: 27098957 DOI: 10.1128/jcm.02784-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/11/2016] [Indexed: 12/13/2022] Open
Abstract
Tularemia in humans is caused mainly by two subspecies of the Gram-negative facultative anaerobe Francisella tularensis: F. tularensis subsp. tularensis (type A) and F. tularensis subsp. holarctica (type B). The current serological test for tularemia is based on agglutination of whole organisms, and the reactive antigens are not well understood. Previously, we profiled the antibody responses in type A and B tularemia cases in the United States using a proteome microarray of 1,741 different proteins derived from the type A strain Schu S4. Fifteen dominant antigens able to detect antibodies to both types of infection were identified, although these were not validated in a different immunoassay format. Since type A and B subspecies are closely related, we hypothesized that Schu S4 antigens would also have utility for diagnosing type B tularemia caused by strains from other geographic locations. To test this, we probed the Schu S4 array with sera from 241 type B tularemia cases in Spain. Despite there being no type A strains in Spain, we confirmed the responses against some of the same potential serodiagnostic antigens reported previously, as well as determined the responses against additional potential serodiagnostic antigens. Five potential serodiagnostic antigens were evaluated on immunostrips, and two of these (FTT1696/GroEL and FTT0975/conserved hypothetical protein) discriminated between the Spanish tularemia cases and healthy controls. We conclude that antigens from the type A strain Schu S4 are suitable for detection of antibodies from patients with type B F. tularensis infections and that these can be used for the diagnosis of tularemia in a deployable format, such as the immunostrip.
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Abstract
Francisella tularensis is a facultative intracellular bacterium causing tularemia, a zoonotic disease. Francisella replicates in the macrophage cytosol and eventually triggers cytosolic immune responses. In murine macrophages, Francisella novicida and Francisella tularensis live vaccine strain lyse in the host cytosol and activate the cytosolic DNA receptor Aim2. Here, we review the mechanisms leading or contributing to Aim2 inflammasome activation, including the role of TLRs and of IFN signaling and the implication of the guanylate-binding proteins 2 and 5 in triggering cytosolic bacteriolysis. Furthermore, we present how this cytosolic Gram-negative bacterium escapes recognition by caspase-11 but can trigger a non-canonical caspase-8 inflammasome. In addition, we highlight the differences in inflammasome activation in murine and human cells with pyrin, NLRP3, and AIM2 involved in sensing Francisella in human phagocytes. From a bacterial prospective, we describe the hiding strategy of Francisella to escape recognition by innate sensors and to resist to bacteriolysis in the host cytosol. Finally, we discuss the inability of the inflammasome sensors to detect F. tularensis subspecies tularensis strains, making them highly pathogenic stealth microbes.
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46
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Scaffolding of a bacterial genome using MinION nanopore sequencing. Sci Rep 2015; 5:11996. [PMID: 26149338 PMCID: PMC4493687 DOI: 10.1038/srep11996] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 06/12/2015] [Indexed: 11/29/2022] Open
Abstract
Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program. The latter has highly advantageous portability and sequences samples by measuring changes in ionic current when single-stranded DNA molecules are translocated through nanopores. We show that the MinION system produces long reads with high mapability that can be used for scaffolding bacterial genomes, despite currently producing substantially higher error rates than PacBio reads. With further development we anticipate that MinION will be useful not only for assembling genomes, but also for rapid detection of organisms, potentially in the field.
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47
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Karadenizli A, Forsman M, Şimşek H, Taner M, Öhrman C, Myrtennäs K, Lärkeryd A, Johansson A, Özdemir L, Sjödin A. Genomic analyses of Francisella tularensis strains confirm disease transmission from drinking water sources, Turkey, 2008, 2009 and 2012. ACTA ACUST UNITED AC 2015; 20. [PMID: 26062561 DOI: 10.2807/1560-7917.es2015.20.21.21136] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Waterborne epidemics of tularaemia caused by Francisella tularensis are increasingly reported in Turkey. We have used whole genome sequencing to investigate if F. tularensis isolated from patients could be traced back to drinking water sources. Tonsil swabs from 33 patients diagnosed with oropharyngeal tularaemia in three outbreaks and 140 water specimens were analysed. F. tularensis subsp. holarctica was confirmed by microagglutination and PCR in 12 patients and five water specimens. Genomic analysis of three pairs of patient and water isolates from outbreaks in Sivas, Çorum, and Kocaeli showed the isolates to belong to two new clusters of the F. tularensis B.12 genetic clade. The clusters were defined by 19 and 15 single nucleotide polymorphisms (SNPs) in a multiple alignment based on 507 F. tularensis genomes. One synonymous SNP was chosen as a new canonical SNP (canSNP) for each cluster for future use in diagnostic assays. No SNP was identified between the genomes from the patient–water pair of isolates from Kocaeli, one SNP between the pair of isolates from Sivas, whereas the pair from Çorum differed at seven SNPs. These results illustrate the power of whole genome sequencing for tracing F. tularensis patient isolates back to their environmental source.
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Affiliation(s)
- A Karadenizli
- Department of Medical Microbiology, Kocaeli University, Kocaeli, Turkey
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48
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Larson MA, Nalbantoglu U, Sayood K, Zentz EB, Bartling AM, Francesconi SC, Fey PD, Dempsey MP, Hinrichs SH. Francisella tularensis Subtype A.II Genomic Plasticity in Comparison with Subtype A.I. PLoS One 2015; 10:e0124906. [PMID: 25918839 PMCID: PMC4412822 DOI: 10.1371/journal.pone.0124906] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/09/2015] [Indexed: 11/26/2022] Open
Abstract
Although Francisella tularensis is considered a monomorphic intracellular pathogen, molecular genotyping and virulence studies have demonstrated important differences within the tularensis subspecies (type A). To evaluate genetic variation within type A strains, sequencing and assembly of a new subtype A.II genome was achieved for comparison to other completed F. tularensis type A genomes. In contrast with the F. tularensis A.I strains (SCHU S4, FSC198, NE061598, and TI0902), substantial genomic variation was observed between the newly sequenced F. tularensis A.II strain (WY-00W4114) and the only other publically available A.II strain (WY96-3418). Genome differences between WY-00W4114 and WY96-3418 included three major chromosomal translocations, 1580 indels, and 286 nucleotide substitutions of which 159 were observed in predicted open reading frames and 127 were located in intergenic regions. The majority of WY-00W4114 nucleotide deletions occurred in intergenic regions, whereas most of the insertions and substitutions occurred in predicted genes. Of the nucleotide substitutions, 48 (30%) were synonymous and 111 (70%) were nonsynonymous. WY-00W4114 and WY96-3418 nucleotide polymorphisms were predominantly G/C to A/T allelic mutations, with WY-00W4114 having more A+T enrichment. In addition, the A.II genomes contained a considerably higher number of intact genes and longer repetitive sequences, including transposon remnants than the A.I genomes. Together these findings support the premise that F. tularensis A.II may have a fitness advantage compared to the A.I subtype due to the higher abundance of functional genes and repeated chromosomal sequences. A better understanding of the selective forces driving F. tularensis genetic diversity and plasticity is needed.
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Affiliation(s)
- Marilynn A. Larson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
| | - Ufuk Nalbantoglu
- Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Khalid Sayood
- Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Emily B. Zentz
- OpGen Inc., Gaithersburg, Maryland, United States of America
| | - Amanda M. Bartling
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | | | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Michael P. Dempsey
- United States Air Force School of Aerospace Medicine, Wright-Patterson Air Force Base, Ohio, United States of America
| | - Steven H. Hinrichs
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
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Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+"). PLoS One 2015; 10:e0123298. [PMID: 25856198 PMCID: PMC4391923 DOI: 10.1371/journal.pone.0123298] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/17/2015] [Indexed: 11/19/2022] Open
Abstract
The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.
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50
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Ramond E, Gesbert G, Guerrera IC, Chhuon C, Dupuis M, Rigard M, Henry T, Barel M, Charbit A. Importance of host cell arginine uptake in Francisella phagosomal escape and ribosomal protein amounts. Mol Cell Proteomics 2015; 14:870-81. [PMID: 25616868 PMCID: PMC4390266 DOI: 10.1074/mcp.m114.044552] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 01/19/2015] [Indexed: 11/06/2022] Open
Abstract
Upon entry into mammalian host cells, the pathogenic bacterium Francisella must import host cell arginine to multiply actively in the host cytoplasm. We identified and functionally characterized an arginine transporter (hereafter designated ArgP) whose inactivation considerably delayed bacterial phagosomal escape and intracellular multiplication. Intramacrophagic growth of the ΔargP mutant was fully restored upon supplementation of the growth medium with excess arginine, in both F. tularensis subsp. novicida and F. tularensis subsp. holarctica LVS, demonstrating the importance of arginine acquisition in these two subspecies. High-resolution mass spectrometry revealed that arginine limitation reduced the amount of most of the ribosomal proteins in the ΔargP mutant. In response to stresses such as nutritional limitation, repression of ribosomal protein synthesis has been observed in all kingdoms of life. Arginine availability may thus contribute to the sensing of the intracellular stage of the pathogen and to trigger phagosomal egress. All MS data have been deposited in the ProteomeXchange database with identifier PXD001584 (http://proteomecentral.proteomexchange.org/dataset/PXD001584).
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Affiliation(s)
- Elodie Ramond
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche; §INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Team 11. Paris, France
| | - Gael Gesbert
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche; §INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Team 11. Paris, France
| | - Ida Chiara Guerrera
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche; ¶Plateforme Protéome Institut Necker, PPN, Structure Fédérative de Recherche SFR Necker, Université Paris Descartes, Paris 75015 France
| | - Cerina Chhuon
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche; ¶Plateforme Protéome Institut Necker, PPN, Structure Fédérative de Recherche SFR Necker, Université Paris Descartes, Paris 75015 France
| | - Marion Dupuis
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche; §INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Team 11. Paris, France
| | - Mélanie Rigard
- ‖CIRI, Centre International de Recherche en Infectiologie, Lyon, France
| | - Thomas Henry
- ‖CIRI, Centre International de Recherche en Infectiologie, Lyon, France
| | - Monique Barel
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche; §INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Team 11. Paris, France
| | - Alain Charbit
- From the ‡Université Paris Descartes, Sorbonne Paris Cité, Bâtiment Leriche; §INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Team 11. Paris, France;
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