1
|
Berni M, Bolzoni L, Menozzi I, Dodi A, Bracchi C, Morganti M, Scaltriti E, Pongolini S, Tambassi M. Salmonella Derby adaptation to swine and simultaneous attenuation for humans go through decay of Salmonella Pathogenicity Island I. Microbiol Spectr 2023; 11:e0189923. [PMID: 37800927 PMCID: PMC10715017 DOI: 10.1128/spectrum.01899-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/09/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE This study integrated population data with in vitro assessment of virulence phenotypes to unveil that a considerable part of the global population of Salmonella Derby is evolving to enhance its host adaptation to the swine host and that this evolution is simultaneously increasing its attenuation for humans. The study shows that the fixation of deleterious mutations in SPI-1 has a role in this process. This evidence indicates that SPI-1 has a key role for S. Derby virulence in humans but not for its circulation in swine. The results show that genes generally considered essential for Salmonella pathogenesis do not play the same key role for all Salmonella serovars or lineages and/or all hosts. The study helps in understanding the molecular mechanisms underlying the ecology and host adaptation of Salmonella showing that the adaptation process can vary for different types of Salmonella and hosts.
Collapse
Affiliation(s)
- Melissa Berni
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Luca Bolzoni
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Ilaria Menozzi
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Alessandra Dodi
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Chiara Bracchi
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Marina Morganti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Stefano Pongolini
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Martina Tambassi
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna (IZSLER), Parma, Italy
| |
Collapse
|
2
|
Antoine L, Bahena-Ceron R, Devi Bunwaree H, Gobry M, Loegler V, Romby P, Marzi S. RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence. Genes (Basel) 2021; 12:1125. [PMID: 34440299 PMCID: PMC8394870 DOI: 10.3390/genes12081125] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 12/19/2022] Open
Abstract
RNA modifications are involved in numerous biological processes and are present in all RNA classes. These modifications can be constitutive or modulated in response to adaptive processes. RNA modifications play multiple functions since they can impact RNA base-pairings, recognition by proteins, decoding, as well as RNA structure and stability. However, their roles in stress, environmental adaptation and during infections caused by pathogenic bacteria have just started to be appreciated. With the development of modern technologies in mass spectrometry and deep sequencing, recent examples of modifications regulating host-pathogen interactions have been demonstrated. They show how RNA modifications can regulate immune responses, antibiotic resistance, expression of virulence genes, and bacterial persistence. Here, we illustrate some of these findings, and highlight the strategies used to characterize RNA modifications, and their potential for new therapeutic applications.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Stefano Marzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67000 Strasbourg, France; (L.A.); (R.B.-C.); (H.D.B.); (M.G.); (V.L.); (P.R.)
| |
Collapse
|
3
|
Yang T, Zhong J, Zhang J, Li C, Yu X, Xiao J, Jia X, Ding N, Ma G, Wang G, Yue L, Liang Q, Sheng Y, Sun Y, Huang H, Chen F. Pan-Genomic Study of Mycobacterium tuberculosis Reflecting the Primary/Secondary Genes, Generality/Individuality, and the Interconversion Through Copy Number Variations. Front Microbiol 2018; 9:1886. [PMID: 30177918 PMCID: PMC6109687 DOI: 10.3389/fmicb.2018.01886] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/27/2018] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) has surpassed HIV as the leading infectious disease killer worldwide since 2014. The main pathogen, Mycobacterium tuberculosis (Mtb), contains ~4,000 genes that account for ~90% of the genome. However, it is still unclear which of these genes are primary/secondary, which are responsible for generality/individuality, and which interconvert during evolution. Here we utilized a pan-genomic analysis of 36 Mtb genomes to address these questions. We identified 3,679 Mtb core (i.e., primary) genes, determining their phenotypic generality (e.g., virulence, slow growth, dormancy). We also observed 1,122 dispensable and 964 strain-specific secondary genes, reflecting partially shared and lineage-/strain-specific individualities. Among which, five L2 lineage-specific genes might be related to the increased virulence of the L2 lineage. Notably, we discovered 28 Mtb “Super Core Genes” (SCGs: more than a copy in at least 90% strains), which might be of increased importance, and reflected the “super phenotype generality.” Most SCGs encode PE/PPE, virulence factors, antigens, and transposases, and have been verified as playing crucial roles in Mtb pathogenicity. Further investigation of the 28 SCGs demonstrated the interconversion among SCGs, single-copy core, dispensable, and strain-specific genes through copy number variations (CNVs) during evolution; different mutations on different copies highlight the delicate adaptive-evolution regulation amongst Mtb lineages. This reflects that the importance of genes varied through CNVs, which might be driven by selective pressure from environment/host-adaptation. In addition, compared with Mycobacterium bovis (Mbo), Mtb possesses 48 specific single core genes that partially reflect the differences between Mtb and Mbo individuality.
Collapse
Affiliation(s)
- Tingting Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Zhong
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Cuidan Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinmiao Jia
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Ding
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Guannan Ma
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Guirong Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Liya Yue
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Qian Liang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Yongjie Sheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Yanhong Sun
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Collaborative Innovation Center for Genetics and Development, Beijing, China
| |
Collapse
|
5
|
Ben Zakour NL, Beatson SA, van den Broek AHM, Thoday KL, Fitzgerald JR. Comparative genomics of the Staphylococcus intermedius group of animal pathogens. Front Cell Infect Microbiol 2012; 2:44. [PMID: 22919635 PMCID: PMC3417630 DOI: 10.3389/fcimb.2012.00044] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 03/15/2012] [Indexed: 11/29/2022] Open
Abstract
The Staphylococcus intermedius group consists of three closely related coagulase-positive bacterial species including S. intermedius, Staphylococcus pseudintermedius, and Staphylococcus delphini. S. pseudintermedius is a major skin pathogen of dogs, which occasionally causes severe zoonotic infections of humans. S. delphini has been isolated from an array of different animals including horses, mink, and pigeons, whereas S. intermedius has been isolated only from pigeons to date. Here we provide a detailed analysis of the S. pseudintermedius whole genome sequence in comparison to high quality draft S. intermedius and S. delphini genomes, and to other sequenced staphylococcal species. The core genome of the SIG was highly conserved with average nucleotide identity (ANI) between the three species of 93.61%, which is very close to the threshold of species delineation (95% ANI), highlighting the close-relatedness of the SIG species. However, considerable variation was identified in the content of mobile genetic elements, cell wall-associated proteins, and iron and sugar transporters, reflecting the distinct ecological niches inhabited. Of note, S. pseudintermedius ED99 contained a clustered regularly interspaced short palindromic repeat locus of the Nmeni subtype and S. intermedius contained both Nmeni and Mtube subtypes. In contrast to S. intermedius and S. delphini and most other staphylococci examined to date, S. pseudintermedius contained at least nine predicted reverse transcriptase Group II introns. Furthermore, S. pseudintermedius ED99 encoded several transposons which were largely responsible for its multi-resistant phenotype. Overall, the study highlights extensive differences in accessory genome content between closely related staphylococcal species inhabiting distinct host niches, providing new avenues for research into pathogenesis and bacterial host-adaptation.
Collapse
Affiliation(s)
- Nouri L Ben Zakour
- The Roslin Institute and Edinburgh Infectious Diseases, The University of Edinburgh Edinburgh, UK
| | | | | | | | | |
Collapse
|