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Zhao M, Zhai Y, Zai X, Mao Y, Hu E, Wei Z, Li Y, Li K, Liu Y, Xu J, Yu R, Chen W. Comparative evaluation of protective immunity against Francisella tularensis induced by subunit or adenovirus-vectored vaccines. Front Cell Infect Microbiol 2023; 13:1195314. [PMID: 37305410 PMCID: PMC10248143 DOI: 10.3389/fcimb.2023.1195314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
Tularemia is a highly contagious disease caused by infection with Francisella tularensis (Ft), a pathogenic intracellular gram-negative bacterium that infects a wide range of animals and causes severe disease and death in people, making it a public health concern. Vaccines are the most effective way to prevent tularemia. However, there are no Food and Drug Administration (FDA)-approved Ft vaccines thus far due to safety concerns. Herein, three membrane proteins of Ft, Tul4, OmpA, and FopA, and a molecular chaperone, DnaK, were identified as potential protective antigens using a multifactor protective antigen platform. Moreover, the recombinant DnaK, FopA, and Tul4 protein vaccines elicited a high level of IgG antibodies but did not protect against challenge. In contrast, protective immunity was elicited by a replication-defective human type 5 adenovirus (Ad5) encoding the Tul4, OmpA, FopA, and DnaK proteins (Ad5-Tul4, Ad5-OmpA, Ad5-FopA, and Ad5-DnaK) after a single immunization, and all Ad5-based vaccines stimulated a Th1-biased immune response. Moreover, intramuscular and intranasal vaccination with Ad5-Tul4 using the prime-boost strategy effectively eliminated Ft lung, spleen and liver colonization and provided nearly 80% protection against intranasal challenge with the Ft live vaccine strain (LVS). Only intramuscular, not intranasal vaccination, with Ad5-Tul4 protected mice from intraperitoneal challenge. This study provides a comprehensive comparison of protective immunity against Ft provided by subunit or adenovirus-vectored vaccines and suggests that mucosal vaccination with Ad5-Tul4 may yield desirable protective efficacy against mucosal infection, while intramuscular vaccination offers greater overall protection against intraperitoneal tularemia.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Rui Yu
- *Correspondence: Rui Yu, ; Wei Chen,
| | - Wei Chen
- *Correspondence: Rui Yu, ; Wei Chen,
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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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Neubert K, Zuchantke E, Leidenfrost RM, Wünschiers R, Grützke J, Malorny B, Brendebach H, Al Dahouk S, Homeier T, Hotzel H, Reinert K, Tomaso H, Busch A. Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures. BMC Genomics 2021; 22:822. [PMID: 34773979 PMCID: PMC8590783 DOI: 10.1186/s12864-021-08115-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/12/2021] [Indexed: 02/08/2023] Open
Abstract
Background We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation “short-read” and third-generation “long-read” sequencing methods. Results We focused on short-read assemblers, hybrid assemblers, and analysis of the genomic structure with particular emphasis on insertion sequences and the Francisella pathogenicity island. The A5-miseq pipeline performed best for MiSeq data, Mira for Ion Torrent data, and ABySS for HiSeq data from eight short-read assembly methods. Two approaches were applied to benchmark long-read and hybrid assembly strategies: long-read-first assembly followed by correction with short reads (Canu/Pilon, Flye/Pilon) and short-read-first assembly along with scaffolding based on long reads (Unicyler, SPAdes). Hybrid assembly can resolve large repetitive regions best with a “long-read first” approach. Conclusions Genomic structures of the Francisella pathogenicity islands frequently showed misassembly. Insertion sequences (IS) could be used to perform an evolutionary conservation analysis. A phylogenetic structure of insertion sequences and the evolution within the clades elucidated the clade structure of the highly conservative F. tularensis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08115-x.
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Affiliation(s)
- Kerstin Neubert
- Department of Mathematics and Computer Science, Algorithmic Bioinformatics, Freie Universität Berlin, Institute of Computer Science, Takustr. 9, 14195, Berlin, Germany.,German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Eric Zuchantke
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany
| | - Robert Maximilian Leidenfrost
- Department of Biotechnology and Chemistry, Mittweida University of Applied Sciences, Technikumplatz 17a, 09648, Mittweida, Germany
| | - Röbbe Wünschiers
- Department of Biotechnology and Chemistry, Mittweida University of Applied Sciences, Technikumplatz 17a, 09648, Mittweida, Germany
| | - Josephine Grützke
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Holger Brendebach
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Sascha Al Dahouk
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Timo Homeier
- Friedrich-Loeffler-Institut, Institute of Epidemiology, Südufer, 10 17493, Greifswald, Insel Riems, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany
| | - Knut Reinert
- Department of Mathematics and Computer Science, Algorithmic Bioinformatics, Freie Universität Berlin, Institute of Computer Science, Takustr. 9, 14195, Berlin, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany
| | - Anne Busch
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany. .,Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Jena, Germany.
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Identification of an Attenuated Substrain of Francisella tularensis SCHU S4 by Phenotypic and Genotypic Analyses. Pathogens 2021; 10:pathogens10060638. [PMID: 34067337 PMCID: PMC8224608 DOI: 10.3390/pathogens10060638] [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: 04/16/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
Pneumonic tularemia is a highly debilitating and potentially fatal disease caused by inhalation of Francisella tularensis. Most of our current understanding of its pathogenesis is based on the highly virulent F. tularensis subsp. tularensis strain SCHU S4. However, multiple sources of SCHU S4 have been maintained and propagated independently over the years, potentially generating genetic variants with altered virulence. In this study, the virulence of four SCHU S4 stocks (NR-10492, NR-28534, NR-643 from BEI Resources and FTS-635 from Battelle Memorial Institute) along with another virulent subsp. tularensis strain, MA00-2987, were assessed in parallel. In the Fischer 344 rat model of pneumonic tularemia, NR-643 and FTS-635 were found to be highly attenuated compared to NR-10492, NR-28534, and MA00-2987. In the NZW rabbit model of pneumonic tularemia, NR-643 caused morbidity but not mortality even at a dose equivalent to 500x the LD50 for NR-10492. Genetic analyses revealed that NR-10492 and NR-28534 were identical to each other, and nearly identical to the reference SCHU S4 sequence. NR-643 and FTS-635 were identical to each other but were found to have nine regions of difference in the genomic sequence when compared to the published reference SCHU S4 sequence. Given the genetic differences and decreased virulence, NR-643/FTS-635 should be clearly designated as a separate SCHU S4 substrain and no longer utilized in efficacy studies to evaluate potential vaccines and therapeutics against tularemia.
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Larson MA, Abdalhamid B, Puniya BL, Helikar T, Kelley DW, Iwen PC. Differences in Blood-derived Francisella tularensis Type B Strains from Clinical Cases of Tularemia. Microorganisms 2020; 8:microorganisms8101515. [PMID: 33019689 PMCID: PMC7600085 DOI: 10.3390/microorganisms8101515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/26/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
Francisella tularensis can cause the zoonotic disease tularemia and is partitioned into subspecies due to differences in chromosomal organization and virulence. The subspecies holarctica (type B) is generally considered more clonal than the other subpopulations with moderate virulence compared to the hypervirulent A.I clade. We performed whole genome sequencing (WGS) on six type B strains isolated from the blood of patients with tularemia within a one-year period from the same United States region, to better understand the associated pathogenicity. The WGS data were compared to the prototype strain for this subspecies, specifically FSC200, which was isolated from a patient with tularemia in Europe. These findings revealed 520–528 single nucleotide polymorphisms (SNPs) between the six United States type B strains compared to FSC200, with slightly higher A+T content in the latter strain. In contrast, comparisons between the six type B isolates showed that five of the six type B isolates had only 4–22 SNPs, while one of the strains had 47–53 SNPs. Analysis of SNPs in the core genome for the six United States type B isolates and the FSC200 strain gave similar results, suggesting that some of these mutations may have been nonsynonymous, resulting in altered protein function and pathogenicity.
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Affiliation(s)
- Marilynn A. Larson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (B.A.); (D.W.K.); (P.C.I.)
- Correspondence: ; Tel.: +1-402-559-9115
| | - Baha Abdalhamid
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (B.A.); (D.W.K.); (P.C.I.)
| | - Bhanwar Lal Puniya
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (B.L.P.); (T.H.)
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (B.L.P.); (T.H.)
| | - David W. Kelley
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (B.A.); (D.W.K.); (P.C.I.)
| | - Peter C. Iwen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; (B.A.); (D.W.K.); (P.C.I.)
- Nebraska Public Health Laboratory, Omaha, NE 68198, USA
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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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Lai XH, Zhao LF, Chen XM, Ren Y. Rapid Identification and Characterization of Francisella by Molecular Biology and Other Techniques. Open Microbiol J 2016; 10:64-77. [PMID: 27335619 PMCID: PMC4899538 DOI: 10.2174/1874285801610010064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 11/22/2022] Open
Abstract
Francisella tularensis is the causative pathogen of tularemia and a
Tier 1 bioterror agent on the CDC list. Considering the fact that some
subpopulation of the F. tularensis strains is more virulent, more
significantly associated with mortality, and therefore poses more threat to
humans, rapid identification and characterization of this subpopulation strains
is of invaluable importance. This review summarizes the up-to-date developments
of assays for mainly detecting and characterizing F. tularensis and a
touch of caveats of some of the assays.
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Affiliation(s)
- Xin-He Lai
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Long-Fei Zhao
- College of Life Sciences, Key Laboratory of Plant-Microbe Interactions of Henan, Shangqiu Normal University, Shangqiu, Henan, 476000, PR China
| | - Xiao-Ming Chen
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China ; Department of Pediatric Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yi Ren
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, USA
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