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He J, Yang Z, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Sun D, Tian B, He Y, Wu Z, Cheng A, Zhu D. Integrative and conjugative elements of Pasteurella multocida: Prevalence and signatures in population evolution. Virulence 2024; 15:2359467. [PMID: 38808732 PMCID: PMC11141479 DOI: 10.1080/21505594.2024.2359467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
Pasteurella multocida (P. multocida) is a bacterial pathogen responsible for a range of infections in humans and various animal hosts, causing significant economic losses in farming. Integrative and conjugative elements (ICEs) are important horizontal gene transfer elements, potentially enabling host bacteria to enhance adaptability by acquiring multiple functional genes. However, the understanding of ICEs in P. multocida and their impact on the transmission of this pathogen remains limited. In this study, 42 poultry-sourced P. multocida genomes obtained by high-throughput sequencing together with 393 publicly available P. multocida genomes were used to analyse the horizontal transfer of ICEs. Eighty-two ICEs were identified in P. multocida, including SXT/R391 and Tn916 subtypes, as well as three subtypes of ICEHin1056 family, with the latter being widely prevalent in P. multocida and carrying multiple resistance genes. The correlations between insertion sequences and resistant genes in ICEs were also identified, and some ICEs introduced the carbapenem gene blaOXA-2 and the bleomycin gene bleO to P. multocida. Phylogenetic and collinearity analyses of these bioinformatics found that ICEs in P. multocida were transmitted vertically and horizontally and have evolved with host specialization. These findings provide insight into the transmission and evolution mode of ICEs in P. multocida and highlight the importance of understanding these elements for controlling the spread of antibiotic resistance.
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Affiliation(s)
- Jiao He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Bin Tian
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Yu He
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Zhen Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Veterinary Medicine and Immunology, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Sicence and Technology Department of Sichuan Province, Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
- International Joint Research Center for Animal Disease Prevention and Control of Sichuan Province, Chengdu, Sichuan, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, Sichuan, China
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Majeau A, Dumonteil E, Herrera C. Identification of highly conserved Trypanosoma cruzi antigens for the development of a universal serological diagnostic assay. Emerg Microbes Infect 2024; 13:2315964. [PMID: 38381980 PMCID: PMC10883094 DOI: 10.1080/22221751.2024.2315964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/04/2024] [Indexed: 02/23/2024]
Abstract
Chagas Disease is an important neglected tropical disease caused by Trypanosoma cruzi. There is no gold standard for diagnosis and commercial serological tests perform poorly in certain locations. By aligning T. cruzi genomes covering parasite genetic and geographic diversity, we identified highly conserved proteins that could serve as universal antigens for improved diagnosis. Their antigenicity was tested in high-density peptide microarrays using well-characterized plasma samples, including samples presenting true infections but discordant serology. Individual and combination of epitopes were also evaluated in peptide-ELISAs. We identified >1400 highly conserved T. cruzi proteins evaluated in microarrays. Remarkably, T. cruzi positive controls had a different epitope recognition profile compared to serologically discordant samples. In particular, multiple T. cruzi antigens used in current tests and their strain-variants, and novel epitopes thought to be broadly antigenic failed to be recognized by discordant samples. Nonetheless, >2000 epitopes specifically recognized by IgGs from both positive controls and discordant samples were identified. Evaluation of selected peptides in ELISA further illustrated the extensive variation in antibody profiles among subjects and a peptide combination could outperform a commercial ELISA, increasing assay sensitivity from 52.3% to 72.7%. Individual variation in antibody profiles rather than T. cruzi diversity appears to be the main factor driving differences in serological diagnostic performance according to geography, which will be important to further elucidate. ELISA with a combination of peptides recognized by a greater number of individuals could better capture infections, and further development may lead to an optimal antigen mixture for a universal diagnostic assay.
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Affiliation(s)
- Alicia Majeau
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, New Orleans, LA, USA
| | - Eric Dumonteil
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, New Orleans, LA, USA
| | - Claudia Herrera
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, New Orleans, LA, USA
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3
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Syazwan SA, Mohd-Farid A, Yih Lee S, Mohamed R. Comparative analysis of mitochondrial genomes in Ceratocystis fimbriata complex across diverse hosts. Gene 2024; 921:148539. [PMID: 38710292 DOI: 10.1016/j.gene.2024.148539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/16/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
The decline ofAcacia mangiumWilld. in Malaysia, especially in Sabah since 2010, is primarily due to Ceratocystiswilt and canker disease (CWCD) caused by theCeratocystis fimbriataEllis & Halst. complex. This study was aimed to investigate the mitochondrial genome architecture of two differentC. fimbriatacomplex isolates from Malaysia: one fromA. mangiumin Pahang (FRIM1162) and another fromEucalyptus pellitain Sarawak (FRIM1441). This research employed Next-Generation Sequencing (NGS) to contrast genomes from diverse hosts with nine additional mitochondrial sequences, identifying significant genetic diversity and mutational hotspots in the mitochondrial genome alignment. The mitochondrial genome-based phylogenetic analysis revealed a significant genetic relationship between the studied isolates and theC. fimbriatacomplex in the South American Subclade, indicating that theC. fimbriatacomplex discovered in Malaysia isC. manginecans. The comparative mitochondrial genome demonstrates the adaptability of the complex due to mobile genetic components and genomic rearrangements in the studiedfungal isolates. This research enhances our knowledge of the genetic diversity and evolutionary patterns within theC. fimbriatacomplex, aiding in a deeper understanding of fungal disease development and host adaption processes. The acquired insights are crucial for creating specific management strategies for CWCD, improving the overall understanding of fungal disease evolution and control.
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Affiliation(s)
- Samsuddin Ahmad Syazwan
- Mycology and Pathology Branch, Forest Health and Conservation Programme, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia; Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, 43400 Serdang, Selangor, Malaysia.
| | - Ahmad Mohd-Farid
- Mycology and Pathology Branch, Forest Health and Conservation Programme, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia.
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, 71800 Nilai, Negeri Sembilan, Malaysia.
| | - Rozi Mohamed
- Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, 43400 Serdang, Selangor, Malaysia.
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4
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Sevilla-Navarro S, Otero J, López-Pérez J, Torres-Boncompte J, Prucha T, De Gussem M, Silva D, Burgan J, Catalá-Gregori P, Cortés P, Llagostera M. Limited Emergence of Salmonella enterica Serovar Infantis Variants with Reduced Phage Susceptibility in PhagoVet-Treated Broilers. Animals (Basel) 2024; 14:2352. [PMID: 39199885 PMCID: PMC11350853 DOI: 10.3390/ani14162352] [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: 07/18/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/01/2024] Open
Abstract
Salmonella enterica serovar Infantis (S. Infantis) poses a growing issue in the poultry sector, with phage-based products emerging as a safe and effective control measure. This study investigated the emergence of reduced-phage-susceptibility variants (RPSV) of S. Infantis in PhagoVet-treated broilers, given that RPSV could undermine phage treatment efficacy. The bacteriophages in the PhagoVet product were characterized using transmission electron microscopy (TEM), genome sequencing, and infection profiling. Furthermore, two broiler trials were conducted: a challenge group (T1) and a challenge-and-treated group (T2). The S. Infantis infective dose was set at 104 and 106 colony-forming units (CFUs) per animal, with PhagoVet administration at 106 and 108 plaque-forming units (PFUs) per animal, in Trials 1 and 2, respectively. The results revealed that the four PhagoVet bacteriophages belonged to different genera. PhagoVet evidenced broad-spectrum efficacy against 271 strains representing 18 Salmonella serovars. In Trial 1, PhagoVet reduced bacterial counts in feces to nearly undetectable levels by day 42, with no RPSV detected. However, in Trial 2, three and five RPSVs were detected in feces and ceca, respectively. Consequently, PhagoVet demonstrated efficacy against S. Infantis in broilers, and the potential impact of RPSV is deemed unlikely to compromise its efficacy.
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Affiliation(s)
- Sandra Sevilla-Navarro
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), 12539 Alquerias NP, Castellón, Spain; (S.S.-N.); (J.T.-B.); (P.C.-G.)
| | - Jennifer Otero
- Molecular Microbiology Group, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain; (J.O.); (J.L.-P.); (M.L.)
| | - Júlia López-Pérez
- Molecular Microbiology Group, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain; (J.O.); (J.L.-P.); (M.L.)
| | - Jan Torres-Boncompte
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), 12539 Alquerias NP, Castellón, Spain; (S.S.-N.); (J.T.-B.); (P.C.-G.)
| | - Tiago Prucha
- VETWORKS BVBA, Knokstraat 38, 9880 Poeke, Belgium; (T.P.); (M.D.G.)
| | | | - Daniela Silva
- ALS Life Sciences Portugal, Zona Industrial de Tondela ZIM II lote 6, 3460-070 Tondela, Portugal; (D.S.); (J.B.)
| | - Julia Burgan
- ALS Life Sciences Portugal, Zona Industrial de Tondela ZIM II lote 6, 3460-070 Tondela, Portugal; (D.S.); (J.B.)
| | - Pablo Catalá-Gregori
- Centro de Calidad Avícola y Alimentación Animal de la Comunidad Valenciana (CECAV), 12539 Alquerias NP, Castellón, Spain; (S.S.-N.); (J.T.-B.); (P.C.-G.)
| | - Pilar Cortés
- Molecular Microbiology Group, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain; (J.O.); (J.L.-P.); (M.L.)
| | - Montserrat Llagostera
- Molecular Microbiology Group, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain; (J.O.); (J.L.-P.); (M.L.)
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5
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Ikhimiukor OO, Zac Soligno NI, Akintayo IJ, Marcovici MM, Souza SSR, Workman A, Martin IW, Andam CP. Clonal background and routes of plasmid transmission underlie antimicrobial resistance features of bloodstream Klebsiella pneumoniae. Nat Commun 2024; 15:6969. [PMID: 39138200 PMCID: PMC11322185 DOI: 10.1038/s41467-024-51374-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Bloodstream infections caused by the opportunistic pathogen Klebsiella pneumoniae are associated with adverse health complications and high mortality rates. Antimicrobial resistance (AMR) limits available treatment options, thus exacerbating its public health and clinical burden. Here, we aim to elucidate the population structure of K. pneumoniae in bloodstream infections from a single medical center and the drivers that facilitate the dissemination of AMR. Analysis of 136 short-read genome sequences complemented with 12 long-read sequences shows the population consisting of 94 sequence types (STs) and 99 clonal groups, including globally distributed multidrug resistant and hypervirulent clones. In vitro antimicrobial susceptibility testing and in silico identification of AMR determinants reveal high concordance (90.44-100%) for aminoglycosides, beta-lactams, carbapenems, cephalosporins, quinolones, and sulfonamides. IncF plasmids mediate the clonal (within the same lineage) and horizontal (between lineages) transmission of the extended-spectrum beta-lactamase gene blaCTX-M-15. Nearly identical plasmids are recovered from isolates over a span of two years indicating long-term persistence. The genetic determinants for hypervirulence are carried on plasmids exhibiting genomic rearrangement, loss, and/or truncation. Our findings highlight the importance of considering both the genetic background of host strains and the routes of plasmid transmission in understanding the spread of AMR in bloodstream infections.
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Affiliation(s)
- Odion O Ikhimiukor
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
| | - Nicole I Zac Soligno
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Ifeoluwa J Akintayo
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Michael M Marcovici
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Stephanie S R Souza
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Adrienne Workman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Isabella W Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
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6
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Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA. An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense. Nat Commun 2024; 15:6955. [PMID: 39138193 PMCID: PMC11322646 DOI: 10.1038/s41467-024-51346-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
The prevalence of multidrug resistant (MDR) bacterial infections continues to rise as the development of antibiotics needed to combat these infections remains stagnant. MDR enterococci are a major contributor to this crisis. A potential therapeutic approach for combating MDR enterococci is bacteriophage (phage) therapy, which uses lytic viruses to infect and kill pathogenic bacteria. While phages that lyse some strains of MDR enterococci have been identified, other strains display high levels of resistance and the mechanisms underlying this resistance are poorly defined. Here, we use a CRISPR interference (CRISPRi) screen to identify a genetic locus found on a mobilizable plasmid from Enterococcus faecalis involved in phage resistance. This locus encodes a putative serine recombinase followed by a Type IV restriction enzyme (TIV-RE) that we show restricts the replication of phage phi47 in vancomycin-resistant E. faecalis. We further find that phi47 evolves to overcome restriction by acquiring a missense mutation in a TIV-RE inhibitor protein. We show that this inhibitor, termed type IV restriction inhibiting factor A (tifA), binds and inactivates diverse TIV-REs. Overall, our findings advance our understanding of phage defense in drug-resistant E. faecalis and provide mechanistic insight into how phages evolve to overcome antiphage defense systems.
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Affiliation(s)
- Nathan P Bullen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Cydney N Johnson
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Shelby E Andersen
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Garima Arya
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA
| | - Sonia R Marotta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - Peter R Weigele
- Research Department, New England Biolabs, Ipswich, MA, 01938, USA
| | - John C Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4L8, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School-Anschutz Medical Campus, School of Medicine, Aurora, CO, 80045, USA.
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Wang J, Kan S, Kong J, Nie L, Fan W, Ren Y, Reeve W, Mower JP, Wu Z. Accumulation of Large Lineage-Specific Repeats Coincides with Sequence Acceleration and Structural Rearrangement in Plantago Plastomes. Genome Biol Evol 2024; 16:evae177. [PMID: 39190481 PMCID: PMC11354287 DOI: 10.1093/gbe/evae177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Repeats can mediate rearrangements and recombination in plant mitochondrial genomes and plastid genomes. While repeat accumulations are linked to heightened evolutionary rates and complex structures in specific lineages, debates persist regarding the extent of their influence on sequence and structural evolution. In this study, 75 Plantago plastomes were analyzed to investigate the relationships between repeats, nucleotide substitution rates, and structural variations. Extensive repeat accumulations were associated with significant rearrangements and inversions in the large inverted repeats (IRs), suggesting that repeats contribute to rearrangement hotspots. Repeats caused infrequent recombination that potentially led to substoichiometric shifting, supported by long-read sequencing. Repeats were implicated in elevating evolutionary rates by facilitating localized hypermutation, likely through DNA damage and repair processes. This study also observed a decrease in nucleotide substitution rates for loci translocating into IRs, supporting the role of biased gene conversion in maintaining lower substitution rates. Combined with known parallel changes in mitogenomes, it is proposed that potential dysfunction in nuclear-encoded genes associated with DNA replication, recombination, and repair may drive the evolution of Plantago organellar genomes. These findings contribute to understanding how repeats impact organellar evolution and stability, particularly in rapidly evolving plant lineages.
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Affiliation(s)
- Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
- College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Marine College, Shandong University, Weihai 264209, China
| | - Jiali Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Liyun Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Weishu Fan
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonglin Ren
- College of Environmental and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Wayne Reeve
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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8
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Zhou P, Lei WS, Shi YK, Liu YZ, Luo Y, Li JH, Xiang XG. Plastome Evolution, Phylogenomics, and DNA Barcoding Investigation of Gastrochilus (Aeridinae, Orchidaceae), with a Focus on the Systematic Position of Haraella retrocalla. Int J Mol Sci 2024; 25:8500. [PMID: 39126069 PMCID: PMC11312641 DOI: 10.3390/ijms25158500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
Gastrochilus is an orchid genus containing about 70 species in tropical and subtropical Asia with high morphological diversity. The phylogenetic relationships among this genus have not been fully resolved, and the plastome evolution has not been investigated either. In this study, five plastomes of Gastrochilus were newly reported, and sixteen plastomes of Gastrochilus were used to conduct comparative and phylogenetic analyses. Our results showed that the Gastrochilus plastomes ranged from 146,183 to 148,666 bp, with a GC content of 36.7-36.9%. There were 120 genes annotated, consisting of 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. Additionally, the repeat sequences and codon usage bias of Gastrochilus plastomes were highly conserved. Twenty hypervariable regions were selected as potential DNA barcodes. The phylogenetic relationships within Gastrochilus were well resolved based on the whole plastome, especially among main clades. Furthermore, both molecular and morphological data strongly supported Haraella retrocalla as a member of Gastrochilus (G. retrocallus).
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Affiliation(s)
- Peng Zhou
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Wan-Shun Lei
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Ying-Kang Shi
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Yi-Zhen Liu
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
| | - Yan Luo
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666300, China;
| | - Ji-Hong Li
- Kadoorie Farm and Botanic Garden, Hong Kong Lam Kam Road, Tai Po, New Territories, Hong Kong 999077, China;
| | - Xiao-Guo Xiang
- Key Laboratory of Poyang Lake Environment and Resource Utilization Ministry of Education, School of Life Sciences, Nanchang University, Nanchang 330031, China; (P.Z.); (W.-S.L.); (Y.-K.S.); (Y.-Z.L.)
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9
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Wang X, Wang D, Zhang R, Qin X, Shen X, You C. Morphological Structure Identification, Comparative Mitochondrial Genomics and Population Genetic Analysis toward Exploring Interspecific Variations and Phylogenetic Implications of Malus baccata 'ZA' and Other Species. Biomolecules 2024; 14:912. [PMID: 39199300 DOI: 10.3390/biom14080912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 09/01/2024] Open
Abstract
Malus baccata, a valuable germplasm resource in the genus Malus, is indigenous to China and widely distributed. However, little is known about the lineage composition and genetic basis of 'ZA', a mutant type of M. baccata. In this study, we compared the differences between 'ZA' and wild type from the perspective of morphology and ultrastructure and analyzed their chloroplast pigment content based on biochemical methods. Further, the complete mitogenome of M. baccata 'ZA' was assembled and obtained by next-generation sequencing. Subsequently, its molecular characteristics were analyzed using Geneious, MISA-web, and CodonW toolkits. Furthermore, by examining 106 Malus germplasms and 42 Rosaceae species, we deduced and elucidated the evolutionary position of M. baccata 'ZA', as well as interspecific variations among different individuals. In comparison, the total length of the 'ZA' mitogenome (GC content: 45.4%) is 374,023 bp, which is approximately 2.33 times larger than the size (160,202 bp) of the plastome (GC: 36.5%). The collinear analysis results revealed abundant repeats and genome rearrangements occurring between different Malus species. Additionally, we identified 14 plastid-driven fragment transfer events. A total of 54 genes have been annotated in the 'ZA' mitogenome, including 35 protein-coding genes, 16 tRNAs, and three rRNAs. By calculating nucleotide polymorphisms and selection pressure for 24 shared core mitochondrial CDSs from 42 Rosaceae species (including 'ZA'), we observed that the nad3 gene exhibited minimal variation, while nad4L appeared to be evolving rapidly. Population genetics analysis detected a total of 1578 high-quality variants (1424 SNPs, 60 insertions, and 94 deletions; variation rate: 1/237) among samples from 106 Malus individuals. Furthermore, by constructing phylogenetic trees based on both Malus and Rosaceae taxa datasets, it was preliminarily demonstrated that 'ZA' is closely related to M. baccata, M. sieversii, and other proximate species in terms of evolution. The sequencing data obtained in this study, along with our findings, contribute to expanding the mitogenomic resources available for Rosaceae research. They also hold reference significance for molecular identification studies as well as conservation and breeding efforts focused on excellent germplasms.
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Affiliation(s)
- Xun Wang
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Daru Wang
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Ruifen Zhang
- Qingdao Apple Rootstock Research and Development Center, Qingdao Academy of Agricultural Sciences, Qingdao 266100, China
| | - Xin Qin
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Xiang Shen
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Chunxiang You
- Apple Technology Innovation Center of Shandong Province, Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, National Key Laboratory of Wheat Improvement, College of Horticultural Science and Engineering, Shandong Agricultural University, Taian 271018, China
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10
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Yao Y, Imirzalioglu C, Falgenhauer L, Falgenhauer J, Heinmüller P, Domann E, Chakraborty T. Plasmid-Mediated Spread of Carbapenem Resistance in Enterobacterales: A Three-Year Genome-Based Survey. Antibiotics (Basel) 2024; 13:682. [PMID: 39199982 PMCID: PMC11350871 DOI: 10.3390/antibiotics13080682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/19/2024] [Accepted: 07/19/2024] [Indexed: 09/01/2024] Open
Abstract
The worldwide emergence and dissemination of carbapenem-resistant Gram-negative bacteria (CRGNB) is a challenging problem of antimicrobial resistance today. Outbreaks with CRGNB have severe consequences for both the affected healthcare settings as well as the patients with infection. Thus, bloodstream infections caused by metallo-ß-lactamase-producing Enterobacterales can often have clinical implications, resulting in high mortality rates due to delays in administering effective treatment and the limited availability of treatment options. The overall threat of CRGNB is substantial because carbapenems are used to treat infections caused by ESBL-producing Enterobacterales which also exist with high frequency within the same geographical regions. A genome-based surveillance of 589 CRGNB from 61 hospitals across the federal state Hesse in Germany was implemented using next-generation sequencing (NGS) technology to obtain a high-resolution landscape of carbapenem-resistant isolates over a three-year period (2017-2019). The study examined all reportable CRGNB isolates submitted by participating hospitals. This included isolates carrying known carbapenemases (435) together with carbapenem-resistant non-carbapenemase producers (154). Predominant carbapenemase producers included Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii and Acinetobacter baumannii. Over 80% of 375 carbapenem-resistant determinants including KPC-, NDM-, VIM- and OXA-48-like ones detected in 520 Enterobacterales were plasmid-encoded, and half of these were dominated by a few incompatibility (Inc) types, viz., IncN, IncL/M, IncFII and IncF(K). Our results revealed that plasmids play an extraordinary role in the dissemination of carbapenem resistance in the heterogeneous CRGNB population. The plasmids were also associated with several multispecies dissemination events and local outbreaks throughout the study period, indicating the substantial role of horizontal gene transfer in carbapenemase spread. Furthermore, due to vertical and horizontal plasmid transfer, this can have an impact on implant-associated infections and is therefore important for antibiotic-loaded bone cement and drug-containing devices in orthopedic surgery. Future genomic surveillance projects should increase their focus on plasmid characterization.
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Affiliation(s)
- Yancheng Yao
- Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (C.I.); (L.F.); (J.F.); (T.C.)
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (C.I.); (L.F.); (J.F.); (T.C.)
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (C.I.); (L.F.); (J.F.); (T.C.)
- Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
- Hessisches Landesamt für Gesundheit und Pflege (HLfGP), Heinrich-Hertz-Strasse 5, 35683 Dillenburg, Germany;
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (C.I.); (L.F.); (J.F.); (T.C.)
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
- Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Petra Heinmüller
- Hessisches Landesamt für Gesundheit und Pflege (HLfGP), Heinrich-Hertz-Strasse 5, 35683 Dillenburg, Germany;
| | - Eugen Domann
- Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (C.I.); (L.F.); (J.F.); (T.C.)
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
- Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (C.I.); (L.F.); (J.F.); (T.C.)
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, 35392 Giessen, Germany
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11
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Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA. An enterococcal phage protein broadly inhibits type IV restriction enzymes involved in antiphage defense. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.16.567456. [PMID: 38014348 PMCID: PMC10680825 DOI: 10.1101/2023.11.16.567456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The prevalence of multidrug resistant (MDR) bacterial infections continues to rise as the development of antibiotics needed to combat these infections remains stagnant. MDR enterococci are a major contributor to this crisis. A potential therapeutic approach for combating MDR enterococci is bacteriophage (phage) therapy, which uses lytic viruses to infect and kill pathogenic bacteria. While phages that lyse some strains of MDR enterococci have been identified, other strains display high levels of resistance and the mechanisms underlying this resistance are poorly defined. Here, we use a CRISPR interference (CRISPRi) screen to identify a genetic locus found on a mobilizable plasmid from Enterococcus faecalis involved in phage resistance. This locus encodes a putative serine recombinase followed by a Type IV restriction enzyme (TIV-RE) that we show restricts the replication of phage phi47 in E. faecalis. We further find that phi47 evolves to overcome restriction by acquiring a missense mutation in a TIV-RE inhibitor protein. We show that this inhibitor, termed type IV restriction inhibiting factor A (tifA), binds and inactivates diverse TIV-REs. Overall, our findings advance our understanding of phage defense in drug-resistant E. faecalis and provide mechanistic insight into how phages evolve to overcome antiphage defense systems.
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Affiliation(s)
- Nathan P. Bullen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Shelby E. Andersen
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Garima Arya
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Sonia R. Marotta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, USA, 01938
| | - Peter R. Weigele
- Research Department, New England Biolabs, Ipswich, MA, USA, 01938
| | - John C. Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
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12
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Ogawa M, Matsutani M, Katayama T, Takada N, Noda S, Takahashi M, Kageyama D, Hanaoka N, Ebihara H. Discovery of a novel spotted fever group Rickettsia, "Candidatus Rickettsia kedanie," in unfed larval chigger mites, Leptotrombidium scutellare. Microbiol Immunol 2024. [PMID: 38977291 DOI: 10.1111/1348-0421.13161] [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: 02/09/2024] [Revised: 06/03/2024] [Accepted: 06/11/2024] [Indexed: 07/10/2024]
Abstract
Spotted fever group (SFG) rickettsia, the causative agent of SFG rickettsiosis, is predominantly carried by ticks, whereas Orientia tsutusgamushi, the causative agent of scrub typhus, is primarily transmitted by chigger mites in Japan. In this study, we attempted to isolate intracellular eubacteria from Leptotrombidium scutellare, a major vector of O. tsutsugamushi; moreover, we isolated an SFG rickettsia using a mosquito-derived cell line. Draft genome sequences of this unique isolate, by applying criteria for species delimitation, classified this isolate as a novel strain, proposed as "Rickettsia kedanie." Further genetic analysis identified conserved virulence factors, and the isolate successfully propagated in mammalian cells, suggesting its ability to cause diseases in humans. The presence of SFG rickettsia in unfed larvae implies potential dual-pathogen carriage and reflects a symbiotic relationship similar to that between the mites and O. tsutsugamushi, indicating possibility of its transovarial transmission from female adults. Furthermore, conserved genomic similarity of the novel isolate to known SFG rickettsia suggests potential multiple hosts, including chiggers and ticks. In the natural environment, ticks, chigger mites, and wild animals may carry new isolates, complicating the infection cycle and increasing the transmission risks to humans. This discovery challenges the conventional association of SFG rickettsia with ticks, emphasizing its implications for research and disease control. However, this study was confined to a particular species of chigger mites and geographic area, underscoring the necessity for additional studies to comprehend the ecological dynamics, host interactions, and health implications linked to this newly identified SFG rickettsia.
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Affiliation(s)
- Motohiko Ogawa
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Minenosuke Matsutani
- Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, Japan
| | - Takashi Katayama
- Planning and Information Division, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Nobuhiro Takada
- Department of Pathological Sciences, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Shinichi Noda
- Research Center for the Pacific Islands, Kagoshima University, Kagoshima, Japan
| | - Mamoru Takahashi
- Department of Anesthesiology, Saitama Medical University, Saitama, Japan
| | - Daisuke Kageyama
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Nozomu Hanaoka
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideki Ebihara
- Department of Virology I, National Institute of Infectious Diseases, Tokyo, Japan
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13
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Sukee T, Koehler AV, Webster BL, Gauci CG, Fogarty CE, Ponder WF, Gasser RB, Young ND. Mitochondrial genome of the fluke pond snail, Austropeplea cf. brazieri (Gastropoda: Lymnaeidae). Parasit Vectors 2024; 17:283. [PMID: 38956636 PMCID: PMC11218368 DOI: 10.1186/s13071-024-06358-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Lymnaeid snails of the genus Austropeplea are an important vector of the liver fluke (Fasciola hepatica), contributing to livestock production losses in Australia and New Zealand. However, the species status within Austropeplea is ambiguous due to heavy reliance on morphological analysis and a relative lack of genetic data. This study aimed to characterise the mitochondrial genome of A. cf. brazieri, an intermediate host of liver fluke in eastern Victoria. METHODS The mitochondrial genome was assembled and annotated from a combination of second- and third-generation sequencing data. For comparative purposes, we performed phylogenetic analyses of the concatenated nucleotide sequences of the mitochondrial protein-coding genes, cytochrome c oxidase subunit 1 and 16S genes. RESULTS The assembled mt genome was 13,757 base pairs and comprised 37 genes, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The mt genome length, gene order and nucleotide compositions were similar to related species of lymnaeids. Phylogenetic analyses of the mt nucleotide sequences placed A. cf. brazieri within the same clade as Orientogalba ollula with strong statistical supports. Phylogenies of the cox1 and 16S mt sequences were constructed due to the wide availability of these sequences representing the lymnaeid taxa. As expected in both these phylogenies, A. cf. brazieri clustered with other Austropeplea sequences, but the nodal supports were low. CONCLUSIONS The representative mt genome of A. cf. brazieri should provide a useful resource for future molecular, epidemiology and parasitological studies of this socio-economically important lymnaeid species.
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Affiliation(s)
- Tanapan Sukee
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia
| | - Anson V Koehler
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia
| | | | - Charles G Gauci
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia
| | - Conor E Fogarty
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia
| | | | - Robin B Gasser
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia
| | - Neil D Young
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia.
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14
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Doré G, Barloy D, Barloy-Hubler F. De Novo Hybrid Assembly Unveils Multi-Chromosomal Mitochondrial Genomes in Ludwigia Species, Highlighting Genomic Recombination, Gene Transfer, and RNA Editing Events. Int J Mol Sci 2024; 25:7283. [PMID: 39000388 PMCID: PMC11242644 DOI: 10.3390/ijms25137283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/16/2024] Open
Abstract
Biological invasions have been identified as the fifth cause of biodiversity loss, and their subsequent dispersal represents a major ecological challenge. The aquatic invasive species Ludwigia grandiflora subsp. hexapetala (Lgh) and Ludwigia peploides subsp. montevidensis (Lpm) are largely distributed in aquatic environments in North America and in Europe. However, they also present worrying terrestrial forms that are able to colonize wet meadows. To comprehend the mechanisms of the terrestrial adaptation of Lgh and Lpm, it is necessary to develop their genomic resources, which are currently poorly documented. We performed de novo assembly of the mitogenomes of Lgh and Lpm through hybrid assemblies, combining short reads (SR) and/or long reads (LR) before annotating both mitogenomes. We successfully assembled the mitogenomes of Lgh and Lpm into two circular molecules each, resulting in a combined total length of 711,578 bp and 722,518 bp, respectively. Notably, both the Lgh and Lpm molecules contained plastome-origin sequences, comprising 7.8% of the mitochondrial genome length. Additionally, we identified recombinations that were mediated by large repeats, suggesting the presence of multiple alternative conformations. In conclusion, our study presents the first high-quality mitogenomes of Lpm and Lgh, which are the only ones in the Myrtales order found as two circular molecules.
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Affiliation(s)
- Guillaume Doré
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, INRAE, IFREMER, 35042 Rennes, France
| | - Dominique Barloy
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, INRAE, IFREMER, 35042 Rennes, France
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15
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Rodea M GE, González-Villalobos E, Espinoza-Mellado MDR, Hernández-Chiñas U, Eslava-Campos CA, Balcázar JL, Molina-López J. Genomic analysis of a novel phage vB_SenS_ST1UNAM with lytic activity against Salmonella enterica serotypes. Diagn Microbiol Infect Dis 2024; 109:116305. [PMID: 38643675 DOI: 10.1016/j.diagmicrobio.2024.116305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/09/2024] [Accepted: 04/12/2024] [Indexed: 04/23/2024]
Abstract
In this study, we present the complete annotated genome of a novel Salmonella phage, vB_SenS_ST1UNAM. This phage exhibits lytic activity against several Salmonella enterica serotypes, such as S. Typhi, S. Enteritidis, and S. Typhimurium strains, which are major causes of foodborne illness worldwide. Its genome consists of a linear, double-stranded DNA of 47,877 bp with an average G+C content of 46.6%. A total of 85 coding regions (CDS) were predicted, of which only 43 CDS were functionally assigned. Neither genes involved in the regulation of lysogeny, nor antibiotic resistance genes were identified. This phage harbors a lytic cassette that encodes a type II-holin and a Rz/Rz1-like spanin complex, along with a restriction-modification evasion system and a depolymerase that degrades Salmonella exopolysaccharide. Moreover, the comparative analysis with closely related phage genomes revealed that vB_SenS_ST1UNAM represents a novel genus, for which the genus "Gomezvirus" within the subfamily "ST1UNAM-like" is proposed.
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Affiliation(s)
- Gerardo E Rodea M
- Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación. Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720 Mexico City, Mexico; Unidad de Investigación en Enfermedades Infecciosas Área de Genética Bacteriana, Hospital Infantil de México Federico Gómez, Ciudad de México, México
| | - Edgar González-Villalobos
- Laboratorio de Epidemiología Molecular División de Investigación, departamento de Salud Pública, Facultad de Medicina UNAM, C.P. 06720 Mexico City, Mexico
| | - María Del Rosario Espinoza-Mellado
- Central de Instrumentación de Microscopía, Depto. Investigación, Instituto Politécnico Nacional-Escuela Nacional de Ciencias Biológicas (IPN-ENCB), Prolongación de Carpio y Plan de Ayala, Mexico City 11340, México
| | - Ulises Hernández-Chiñas
- Unidad Periférica de Investigación Básica y Clínica en Enfermedades Infecciosas; Departamento de Salud Pública/División de Investigación, Facultad de Medicina, UNAM, C.P. 04510. Mexico City, Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación. Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720 Mexico City, Mexico
| | - Carlos Alberto Eslava-Campos
- Unidad Periférica de Investigación Básica y Clínica en Enfermedades Infecciosas; Departamento de Salud Pública/División de Investigación, Facultad de Medicina, UNAM, C.P. 04510. Mexico City, Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación. Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720 Mexico City, Mexico
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA). 17003, Girona, Spain; University of Girona. 17004 Girona, Spain
| | - José Molina-López
- Unidad Periférica de Investigación Básica y Clínica en Enfermedades Infecciosas; Departamento de Salud Pública/División de Investigación, Facultad de Medicina, UNAM, C.P. 04510. Mexico City, Mexico; Laboratorio de Patogenicidad Bacteriana, Unidad de Hemato-Oncología e Investigación. Hospital Infantil de México Federico Gómez/Facultad de Medicina UNAM, C.P. 06720 Mexico City, Mexico.
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16
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Fernandez JE, Egli A, Overesch G, Perreten V. Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution. Nat Commun 2024; 15:5526. [PMID: 38951499 PMCID: PMC11217367 DOI: 10.1038/s41467-024-49644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
An international collection of Staphylococcus aureus of clonal complex (CC) 398 from diverse hosts spanning all continents and a 30 year-period is studied based on whole-genome sequencing (WGS) data. The collection consists of publicly available genomic data from 2994 strains and 134 recently sequenced Swiss methicillin-resistant S. aureus (MRSA) CC398 strains. A time-calibrated phylogeny reveals the presence of distinct phylogroups present in Asia, North and South America and Europe. European MRSA diverged from methicillin-susceptible S. aureus (MSSA) at the beginning of the 1950s. Two major European phylogroups (EP4 and EP5), which diverged approximately 1974, are the main drivers of MRSA CC398 spread in Europe. Within EP5, an emergent MRSA lineage spreading among the European horse population (EP5-Leq) diverged approximately 1996 from the pig lineage (EP5-Lpg), and also contains human-related strains. EP5-Leq is characterized by staphylococcal cassette chromosome mec (SCCmec) IVa and spa type t011 (CC398-IVa-t011), and EP5-Lpg by CC398-SCCmecVc-t011. The lineage-specific antibiotic resistance and virulence gene patterns are mostly mediated by the acquisition of mobile genetic elements like SCCmec, S. aureus Genomic Islands (SaGIs), prophages and transposons. Different combinations of virulence factors are present on S. aureus pathogenicity islands (SaPIs), and novel antimicrobial resistance gene containing elements are associated with certain lineages expanding in Europe. This WGS-based analysis reveals the actual evolutionary trajectory and epidemiological trend of the international MRSA CC398 population considering host, temporal, geographical and molecular factors. It provides a baseline for global WGS-based One-Health studies of adaptive evolution of MRSA CC398 as well as for local outbreak investigations.
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Affiliation(s)
- Javier Eduardo Fernandez
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Adrian Egli
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Gudrun Overesch
- Center for Zoonoses, Animal Bacterial Diseases and Antimicrobial Resistance, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Division of Molecular Bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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17
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Ma Y, López‐Pujol J, Yan D, Zhou Z, Deng Z, Niu J. Complete chloroplast genomes of the hemiparasitic genus Cymbaria: Insights into comparative analysis, development of molecular markers, and phylogenetic relationships. Ecol Evol 2024; 14:e11677. [PMID: 38962021 PMCID: PMC11221886 DOI: 10.1002/ece3.11677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 05/18/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
The hemiparasitic tribe Cymbarieae (Orobanchaceae) plays a crucial role in elucidating the initial stage of the transition from autotrophism to heterotrophism. However, the complete chloroplast genome of the type genus Cymbaria has yet to be reported. In addition, the traditional Mongolian medicine Cymbaria daurica is frequently subjected to adulteration or substitution because of the minor morphological differences with Cymbaria mongolica. In this study, the complete chloroplast genomes of the two Cymbaria species were assembled and annotated, and those of other published 52 Orobanchaceae species were retrieved for comparative analyses. We found that the Cymbaria chloroplast genomes are characterized by pseudogenization or loss of stress-relevant genes (ndh) and a unique rbcL-matK inversion. Unlike the high variability observed in holoparasites, Cymbaria and other hemiparasites exhibit high similarity to autotrophs in genome size, guanine-cytosine (GC) content, and intact genes. Notably, four pairs of specific DNA barcodes were developed and validated to distinguish the medicinal herb from its adulterants. Phylogenetic analyses revealed that the genus Cymbaria and the Schwalbea-Siphonostegia clade are grouped into the tribe Cymbarieae, which forms a sister clade to the remaining Orobanchaceae parasitic lineages. Moreover, the diversification of monophyletic Cymbaria occurred during the late Miocene (6.72 Mya) in the Mongol-Chinese steppe region. Our findings provide valuable genetic resources for studying the phylogeny of Orobanchaceae and plant parasitism, and genetic tools to validate the authenticity of the traditional Mongolian medicine "Xinba.".
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Affiliation(s)
- Yang Ma
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Jordi López‐Pujol
- Botanic Institute of Barcelona (IBB)CSIC‐CMCNBBarcelonaSpain
- Escuela de Ciencias AmbientalesUniversidad Espíritu Santo (UEES)SamborondónEcuador
| | - Dongqing Yan
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Zhen Zhou
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Zekun Deng
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
| | - Jianming Niu
- School of Ecology and EnvironmentInner Mongolia UniversityHohhotChina
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian PlateauHohhotChina
- Inner Mongolia Key Laboratory of Grassland Ecology and the Candidate State Key Laboratory of Ministry of Science and TechnologyHohhotChina
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18
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Barrett CF, Pace MC, Corbett CW. Plastid genome evolution in leafless members of the orchid subfamily Orchidoideae, with a focus on Degranvillea dermaptera. AMERICAN JOURNAL OF BOTANY 2024; 111:e16370. [PMID: 38989916 DOI: 10.1002/ajb2.16370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 07/12/2024]
Abstract
PREMISE Leafless, heterotrophic plants are prime examples of organismal modification, the genomic consequences of which have received considerable interest. In particular, plastid genomes (plastomes) are being sequenced at a high rate, allowing continual refinement of conceptual models of reductive evolution in heterotrophs. However, numerous sampling gaps exist, hindering the ability to conduct comprehensive phylogenomic analyses in these plants. METHODS Using floral tissue from an herbarium specimen, we sequenced and analyzed the plastome of Degranvillea dermaptera, a rarely collected, leafless orchid species from South America about which little is known, including its phylogenetic affinities. RESULTS The plastome is the most reduced of those sequenced among the orchid subfamily Orchidoideae. In Degranvillea, it has lost the majority of genes found in leafy autotrophic species, is structurally rearranged, and has similar gene content to the most reduced plastomes among the orchids. We found strong evidence for the placement of Degranvillea within the subtribe Spiranthinae using models that explicitly account for heterotachy, or lineage-specific evolutionary rate variation over time. We further found evidence of relaxed selection on several genes and of correlations among substitution rates and several other "traits" of the plastome among leafless members of orchid subfamily Orchidoideae. CONCLUSIONS Our findings advance knowledge on the phylogenetic relationships and paths of plastid genome evolution among the orchids, which have experienced more independent transitions to heterotrophy than any other plant family. This study demonstrates the importance of herbarium collections in comparative genomics of poorly known species of conservation concern.
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Affiliation(s)
- Craig F Barrett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, 26506, WV, USA
| | - Matthew C Pace
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, 10458, NY, USA
| | - Cameron W Corbett
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, 26506, WV, USA
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Masséglia S, René-Martellet M, Rates M, Hizo-Teufel C, Fingerle V, Margos G, Bailly X. Development and validation of a multi-target TaqMan qPCR method for detection of Borrelia burgdorferi sensu lato. J Microbiol Methods 2024; 222:106941. [PMID: 38714225 DOI: 10.1016/j.mimet.2024.106941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/05/2024] [Accepted: 04/30/2024] [Indexed: 05/09/2024]
Abstract
Reliable detection of bacteria belonging to the Borrelia burgdorferi sensu lato species complex in vertebrate reservoirs, tick vectors, and patients is key to answer questions regarding Lyme borreliosis epidemiology. Nevertheless, the description of characteristics of qPCRs for the detection of B. burgdorferi s. l. are often limited. This study covers the development and validation of two duplex taqman qPCR assays used to target four markers on the chromosome of genospecies of B. burgdorferi s. l. Analytical specificity was determined with a panel of spirochete strains. qPCR characteristics were specified using water or tick DNA spiked with controlled quantities of the targeted DNA sequences of B. afzelii, B. burgdorferi sensu stricto or B. bavariensis. The effectiveness of detection results was finally evaluated using DNA extracted from ticks and biopsies from mammals whose infectious status had been determined by other detection assays. The developed qPCR assays allow exclusive detection of B. burgdorferi s. l. with the exception of the M16 marker which also detect relapsing fever Borreliae. The limit of detection is between 10 and 40 copies per qPCR reaction depending on the sample type, the B. burgdorferi genospecies and the targeted marker. Detection tests performed on various kind of samples illustrated the accuracy and robustness of our qPCR assays. Within the defined limits, this multi-target qPCR method allows a versatile detection of B. burgdorferi s. l., regardless of the genospecies and the sample material analyzed, with a sensitivity that would be compatible with most applications and a reproducibility of 100% under measurement conditions of limits of detection, thereby limiting result ambiguities.
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Affiliation(s)
- Sébastien Masséglia
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, F-63122 Saint-Genès-Champanelle, France.
| | - Magalie René-Martellet
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, F-63122 Saint-Genès-Champanelle, France; Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, F-69280 Marcy l'Etoile, France
| | - Maxime Rates
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, F-63122 Saint-Genès-Champanelle, France; Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, F-69280 Marcy l'Etoile, France
| | - Cecilia Hizo-Teufel
- Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia, Veterinärstr. 2, 85764 Oberschleissheim, Germany
| | - Volker Fingerle
- Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia, Veterinärstr. 2, 85764 Oberschleissheim, Germany
| | - Gabriele Margos
- Bavarian Health and Food Safety Authority, German National Reference Centre for Borrelia, Veterinärstr. 2, 85764 Oberschleissheim, Germany
| | - Xavier Bailly
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, F-63122 Saint-Genès-Champanelle, France
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20
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Raustad N, Dai Y, Iinishi A, Mohapatra A, Soo MW, Hay E, Hernandez GM, Geisinger E. A phosphorylation signal activates genome-wide transcriptional control by BfmR, the global regulator of Acinetobacter resistance and virulence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.16.599214. [PMID: 38948834 PMCID: PMC11212878 DOI: 10.1101/2024.06.16.599214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The nosocomial pathogen Acinetobacter baumannii is a major threat to human health. The sensor kinase-response regulator system, BfmS-BfmR, is essential to multidrug resistance and virulence in the bacterium and represents a potential antimicrobial target. Important questions remain about how the system controls resistance and pathogenesis. Although BfmR knockout alters expression of >1000 genes, its direct regulon is undefined. Moreover, how phosphorylation controls the regulator is unclear. Here, we address these problems by combining mutagenesis, ChIP-seq, and in vitro phosphorylation to study the functions of phospho-BfmR. We show that phosphorylation is required for BfmR-mediated gene regulation, antibiotic resistance, and sepsis development in vivo. Consistent with activating the protein, phosphorylation induces dimerization and target DNA affinity. Integrated analysis of genome-wide binding and transcriptional profiles of BfmR led to additional key findings: (1) Phosphorylation dramatically expands the number of genomic sites BfmR binds; (2) DNA recognition involves a direct repeat motif widespread across promoters; (3) BfmR directly regulates 303 genes as activator (eg, capsule, peptidoglycan, and outer membrane biogenesis) or repressor (pilus biogenesis); (4) BfmR controls several non-coding sRNAs. These studies reveal the centrality of a phosphorylation signal in driving A. baumannii disease and disentangle the extensive pathogenic gene-regulatory network under its control.
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Affiliation(s)
- Nicole Raustad
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Yunfei Dai
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Akira Iinishi
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Arpita Mohapatra
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Mark W. Soo
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Everett Hay
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | | | - Edward Geisinger
- Department of Biology, Northeastern University, Boston, MA 02115, USA
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21
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Atkins H, Sabharwal B, Boger L, Stegman N, Kula A, Wolfe AJ, Banerjee S, Putonti C. Evidence of Lactobacillus strains shared between the female urinary and vaginal microbiota. Microb Genom 2024; 10:001267. [PMID: 38949867 PMCID: PMC11316553 DOI: 10.1099/mgen.0.001267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/14/2024] [Indexed: 07/02/2024] Open
Abstract
Lactobacillus species are common inhabitants of the 'healthy' female urinary and vaginal communities, often associated with a lack of symptoms in both anatomical sites. Given identification by prior studies of similar bacterial species in both communities, it has been hypothesized that the two microbiotas are in fact connected. Here, we carried out whole-genome sequencing of 49 Lactobacillus strains, including 16 paired urogenital samples from the same participant. These strains represent five different Lactobacillus species: L. crispatus, L. gasseri, L. iners, L. jensenii, and L. paragasseri. Average nucleotide identity (ANI), alignment, single-nucleotide polymorphism (SNP), and CRISPR comparisons between strains from the same participant were performed. We conducted simulations of genome assemblies and ANI comparisons and present a statistical method to distinguish between unrelated, related, and identical strains. We found that 50 % of the paired samples have identical strains, evidence that the urinary and vaginal communities are connected. Additionally, we found evidence of strains sharing a common ancestor. These results establish that microbial sharing between the urinary tract and vagina is not limited to uropathogens. Knowledge that these two anatomical sites can share lactobacilli in females can inform future clinical approaches.
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Affiliation(s)
- Haley Atkins
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA
| | - Baani Sabharwal
- Department of Molecular Environmental Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Leah Boger
- Data Science Program, Loyola University Chicago, Chicago, IL, USA
| | - Natalie Stegman
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA
| | - Alexander Kula
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Swarnali Banerjee
- Data Science Program, Loyola University Chicago, Chicago, IL, USA
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
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Lakhova TN, Tsygichko AA, Klimenko AI, Ismailov VY, Vasiliev GV, Asaturova AM, Lashin SA. Assembly and Genome Annotation of Different Strains of Apple Fruit Moth Virus ( Cydia pomonella granulovirus). Int J Mol Sci 2024; 25:7146. [PMID: 39000263 PMCID: PMC11240899 DOI: 10.3390/ijms25137146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 07/16/2024] Open
Abstract
Cydia pomonella granulovirus is a natural pathogen for Cydia pomonella that is used as a biocontrol agent of insect populations. The study of granulovirus virulence is of particular interest since the development of resistance in natural populations of C. pomonella has been observed during the long-term use of the Mexican isolate CpGV. In our study, we present the genomes of 18 CpGV strains endemic to southern Russia and from Kazakhstan, as well as a strain included in the commercial preparation "Madex Twin", which were sequenced and analyzed. We performed comparative genomic analysis using several tools. From comparisons at the level of genes and protein products that are involved in the infection process of virosis, synonymous and missense substitution variants have been identified. The average nucleotide identity has demonstrated a high similarity with other granulovirus genomes of different geographic origins. Whole-genome alignment of the 18 genomes relative to the reference revealed regions of low similarity. Analysis of gene repertoire variation has shown that BZR GV 4, BZR GV 6, and BZR GV L-7 strains have been the closest in gene content to the commercial "Madex Twin" strain. We have confirmed two deletions using read depth coverage data in regions lacking genes shown by homology analysis for granuloviruses BZR GV L-4 and BZR GV L-6; however, they are not related to the known genes causing viral pathogenicity. Thus, we have isolated novel CpGV strains and analyzed their potential as strains producing highly effective bioinsecticides against C. pomonella.
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Affiliation(s)
- Tatiana N. Lakhova
- Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.K.); (S.A.L.)
- Department of Mathematics and Mechanics, Mathematical Center, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aleksandra A. Tsygichko
- Federal State Budgetary Scientific Institution, Federal Research Center of Biological Plant Protection, 350039 Krasnodar, Russia; (A.A.T.); (A.M.A.)
| | - Alexandra I. Klimenko
- Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.K.); (S.A.L.)
- Department of Mathematics and Mechanics, Mathematical Center, Novosibirsk State University, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Vladimir Y. Ismailov
- Federal State Budgetary Scientific Institution, Federal Research Center of Biological Plant Protection, 350039 Krasnodar, Russia; (A.A.T.); (A.M.A.)
| | - Gennady V. Vasiliev
- Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.K.); (S.A.L.)
| | - Anzhela M. Asaturova
- Federal State Budgetary Scientific Institution, Federal Research Center of Biological Plant Protection, 350039 Krasnodar, Russia; (A.A.T.); (A.M.A.)
| | - Sergey A. Lashin
- Kurchatov Genomic Centre of Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.I.K.); (S.A.L.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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23
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Kaur J, Verma H, Kaur J, Lata P, Dhingra GG, Lal R. In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium. Curr Microbiol 2024; 81:233. [PMID: 38904756 DOI: 10.1007/s00284-024-03762-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/22/2024]
Abstract
The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.
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Affiliation(s)
- Jasvinder Kaur
- Department of Zoology, Gargi College, Siri Fort Road, New Delhi, 110049, India.
| | - Helianthous Verma
- Department of Zoology, Ramjas College, University of Delhi, New Delhi, 110007, India
| | - Jaspreet Kaur
- Department of Zoology, Maitreyi College, University of Delhi, New Delhi, 110021, India
| | - Pushp Lata
- Department of Zoology, University of Delhi, New Delhi, 110007, India
| | - Gauri Garg Dhingra
- Department of Zoology, Kirori Mal College, University of Delhi, New Delhi, 110007, India
| | - Rup Lal
- Acharya Narendra Dev College, University of Delhi, New Delhi, 110019, India.
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24
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Yuan L, Ni Y, Chen H, Li J, Lu Q, Wang L, Zhang X, Yue J, Yang H, Liu C. Comparative chloroplast genomes study of five officinal Ardisia Species: Unraveling interspecific diversity and evolutionary insights in Ardisia. Gene 2024; 912:148349. [PMID: 38460806 DOI: 10.1016/j.gene.2024.148349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/11/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Ardisia S.W. (Primulaceae), naturally distributed in tropical and subtropical regions, has edible and medicinal values and is prevalent in clinical and daily use in China. More genetic information for distinct species delineation is needed to support the development and utilization of the genus Ardisia. We sequenced, annotated, and compared the chloroplast genomes of five Ardisia species: A. brunnescens, A. pusilla, A. squamulosa, A. crenata, and A. brevicaulis in this study. We found a typical quadripartite structure in all five chloroplast genomes, with lengths ranging from 155,045 to 156,943 bp. Except for A. pusilla, which lacked the ycf15 gene, the other four Ardisia species contained 114 unique genes, including 79 protein-coding genes, 30 tRNAs, and four rRNAs. In addition, the rps19 pseudogene gene was present only in A. brunnescens. Five highly variable DNA barcodes were identified for five Ardisia species, including trnT-GGU-psbD, trnT-UGU-trnL-UAA, rps4-trnT-UGU, rpl32-trnL-UAG, and rpoB-trnC-GAA. The RNA editiing sites of protein-coding genes in the five Ardisia plastome were characterized and compared, and 274 (A. crenata)-288 (A. brevicaulis) were found. The results of the phylogenetic analysis were consistent with the morphological classification. Sequence alignment and phylogenetic analysis showed that ycf15 genes were highly divergent in Primulaceae. Reconstructions of ancestral character states indicated that leaf margin morphology is critical for classifying the genus Ardisia, with a rodent-like character being the most primitive. These results provide valuable information on the taxonomy and evolution of Ardisia plants.
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Affiliation(s)
- Lichai Yuan
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Ni
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Haimei Chen
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jingling Li
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Qianqi Lu
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong, China.
| | - Xinyi Zhang
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jingwen Yue
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Heyu Yang
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Chang Liu
- Institute of Medicine Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Enav H, Paz I, Ley RE. Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution. Nat Biotechnol 2024:10.1038/s41587-024-02276-2. [PMID: 38898177 DOI: 10.1038/s41587-024-02276-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/10/2024] [Indexed: 06/21/2024]
Abstract
Microbial species diversify into strains through single-nucleotide mutations and structural changes, such as recombination, insertions and deletions. Most strain-comparison methods quantify differences in single-nucleotide polymorphisms (SNPs) and are insensitive to structural changes. However, recombination is an important driver of phenotypic diversification in many species, including human pathogens. We introduce SynTracker, a tool that compares microbial strains using genome synteny-the order of sequence blocks in homologous genomic regions-in pairs of metagenomic assemblies or genomes. Genome synteny is a rich source of genomic information untapped by current strain-comparison tools. SynTracker has low sensitivity to SNPs, has no database requirement and is robust to sequencing errors. It outperforms existing tools when tracking strains in metagenomic data and is particularly suited for phages, plasmids and other low-data contexts. Applied to single-species datasets and human gut metagenomes, SynTracker, combined with an SNP-based tool, detects strains enriched in either point mutations or structural changes, providing insights into microbial evolution in situ.
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Affiliation(s)
- Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Inbal Paz
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany.
- Cluster of Excellence EXC 2124: Controlling Microbes to Fight Infections (CMFI), University of Tübingen, Tübingen, Germany.
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Kellgren T, Dwibedi C, Widerström M, Sundell D, Öhrman C, Sjödin A, Monsen T, Rydén P, Johansson A. Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215. BMC Microbiol 2024; 24:215. [PMID: 38890594 PMCID: PMC11186124 DOI: 10.1186/s12866-024-03367-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND A multidrug-resistant lineage of Staphylococcus epidermidis named ST215 is a common cause of prosthetic joint infections and other deep surgical site infections in Northern Europe, but is not present elsewhere. The increasing resistance among S. epidermidis strains is a global concern. We used whole-genome sequencing to characterize ST215 from healthcare settings. RESULTS We completed the genome of a ST215 isolate from a Swedish hospital using short and long reads, resulting in a circular 2,676,787 bp chromosome and a 2,326 bp plasmid. The new ST215 genome was placed in phylogenetic context using 1,361 finished public S. epidermidis reference genomes. We generated 10 additional short-read ST215 genomes and 11 short-read genomes of ST2, which is another common multidrug-resistant lineage at the same hospital. We studied recombination's role in the evolution of ST2 and ST215, and found multiple recombination events averaging 30-50 kb. By comparing the results of antimicrobial susceptibility testing for 31 antimicrobial drugs with the genome content encoding antimicrobial resistance in the ST215 and ST2 isolates, we found highly similar resistance traits between the isolates, with 22 resistance genes being shared between all the ST215 and ST2 genomes. The ST215 genome contained 29 genes that were historically identified as virulence genes of S. epidermidis ST2. We established that in the nucleotide sequence stretches identified as recombination events, virulence genes were overrepresented in ST215, while antibiotic resistance genes were overrepresented in ST2. CONCLUSIONS This study features the extensive antibiotic resistance and virulence gene content in ST215 genomes. ST215 and ST2 lineages have similarly evolved, acquiring resistance and virulence through genomic recombination. The results highlight the threat of new multidrug-resistant S. epidermidis lineages emerging in healthcare settings.
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Affiliation(s)
- Therese Kellgren
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, SE, 90187, Sweden
| | - Chinmay Dwibedi
- Department of Clinical Microbiology and Molecular Infection Medicine Sweden (MIMS), Umeå University, 90185, Umeå, Sweden
| | - Micael Widerström
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden.
| | - David Sundell
- Division of CBRN Defence and Security, Swedish Defense Research Agency, 90182, Umeå, SE, Sweden
| | - Caroline Öhrman
- Division of CBRN Defence and Security, Swedish Defense Research Agency, 90182, Umeå, SE, Sweden
| | - Andreas Sjödin
- Division of CBRN Defence and Security, Swedish Defense Research Agency, 90182, Umeå, SE, Sweden
| | - Tor Monsen
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
| | - Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, SE, 90187, Sweden
| | - Anders Johansson
- Department of Clinical Microbiology and Molecular Infection Medicine Sweden (MIMS), Umeå University, 90185, Umeå, Sweden
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Alves J, Vrieling M, Ring N, Yebra G, Pickering A, Prajsnar TK, Renshaw SA, Fitzgerald JR. Experimental evolution of Staphylococcus aureus in macrophages: dissection of a conditional adaptive trait promoting intracellular survival. mBio 2024; 15:e0034624. [PMID: 38682911 PMCID: PMC11237485 DOI: 10.1128/mbio.00346-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/26/2024] [Indexed: 05/01/2024] Open
Abstract
Staphylococcus aureus is a major pathogen associated with important diseases in humans and animals. Macrophages are a key component of the innate immune response to S. aureus infection and play a major role in disease outcomes. To investigate the adaptive evolution of S. aureus in response to macrophages, we developed an experimental infection assay. S. aureus strains representing major human epidemic clones were passaged many times in a macrophage cell line, accumulating mutations in an array of genomic loci. Phenotypic analysis revealed the emergence of a lineage exhibiting increased survival in macrophages and human blood, and resistance to vancomycin. The evolved lineage exhibited a previously undescribed small colony variant (SCV) phenotype characterized by hyper-pigmentation, which resulted from a missense mutation in rsbW. Notably, the novel SCV was a conditional adaptive trait that was unstable in nutrient-replete conditions in vitro, rapidly converting from hyper-pigmented SCV to a non-pigmented large colony variant via spontaneous sigB deletion events. Importantly, we identified similar deletions in the genome sequences of a limited number of clinical S. aureus isolates from public databases, indicating that related events may occur during clinical infection. Experimental infection of zebrafish did not reveal a difference in virulence between parent and novel SCV but demonstrated an in vivo fitness cost for the compensatory sigB deletion events. Taken together, we report an experimental evolutionary approach for investigating bacterial innate immune cell interactions, revealing a conditional adaptation that promotes S. aureus survival in macrophages and resistance to vancomycin. IMPORTANCE Staphylococcus aureus is an important human bacterial pathogen. The host response to S. aureus involves the production of innate immune cells such as macrophages which are important for fighting infection. Here we report a new model of experimental evolution for studying how S. aureus can evade killing by macrophages. We identified a novel adaptive phenotype that promotes survival in macrophages and blood and resistance to antibiotics. The phenotype is lost rapidly upon growth in nutrient-rich conditions via disruption of the alternative sigma factor sigB, revealing a conditional niche-specific fitness advantage. Genomic analysis of clinical isolates suggests similar adaptations may occur during human infections. Our model may be used broadly to identify adaptations of S. aureus to the innate immune response.
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Affiliation(s)
- Joana Alves
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
| | - Manouk Vrieling
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
| | - Natalie Ring
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
| | - Gonzalo Yebra
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
| | - Amy Pickering
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
| | - Tomasz K. Prajsnar
- Florey Institute, Bateson Centre and Division of Clinical Medicine, School of Medicine and Population Health, Sheffield, United Kingdom
| | - Stephen A. Renshaw
- Florey Institute, Bateson Centre and Division of Clinical Medicine, School of Medicine and Population Health, Sheffield, United Kingdom
| | - J. Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, United Kingdom
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de Paula Baptista R, Tucker MS, Valente MJ, Srivastava SK, Chehab N, Li A, Shaik JS, Ramirez JD, Rosenthal BM, Khan A. Comparative genomics of Giardia duodenalis sub-assemblage AI beaver (Be-2) and human (WB-C6) strains show remarkable homozygosity, sequence similarity, and conservation of VSP genes. Sci Rep 2024; 14:13582. [PMID: 38866814 PMCID: PMC11169602 DOI: 10.1038/s41598-024-63783-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
Giardia duodenalis, a major cause of waterborne infection, infects a wide range of mammalian hosts and is subdivided into eight genetically well-defined assemblages named A through H. However, fragmented genomes and a lack of comparative analysis within and between the assemblages render unclear the molecular mechanisms controlling host specificity and differential disease outcomes. To address this, we generated a near-complete de novo genome of AI assemblage using the Oxford Nanopore platform by sequencing the Be-2 genome. We generated 148,144 long-reads with quality scores of > 7. The final genome assembly consists of only nine contigs with an N50 of 3,045,186 bp. This assembly agrees closely with the assembly of another strain in the AI assemblage (WB-C6). However, a critical difference is that a region previously placed in the five-prime region of Chr5 belongs to Chr4 of Be-2. We find a high degree of conservation in the ploidy, homozygosity, and the presence of cysteine-rich variant-specific surface proteins (VSPs) within the AI assemblage. Our assembly provides a nearly complete genome of a member of the AI assemblage of G. duodenalis, aiding population genomic studies capable of elucidating Giardia transmission, host range, and pathogenicity.
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Affiliation(s)
- Rodrigo de Paula Baptista
- Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Medicine, Weill Cornell Medicine College, New York, NY, 10065, USA
| | - Matthew S Tucker
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Matthew J Valente
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Subodh K Srivastava
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Nadya Chehab
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Alison Li
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Jahangheer S Shaik
- Insights and Analytics, Applied Data Science and Learning, Data Science Institute, Takeda, Cambridge, MA, 02142, USA
| | - Juan David Ramirez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Benjamin M Rosenthal
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Asis Khan
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA.
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29
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Tomasch J, Kopejtka K, Shivaramu S, Mujakić I, Koblížek M. On the evolution of chromosomal regions with high gene strand bias in bacteria. mBio 2024; 15:e0060224. [PMID: 38752745 PMCID: PMC11237797 DOI: 10.1128/mbio.00602-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/17/2024] [Indexed: 06/13/2024] Open
Abstract
On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of "hybrid" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell's information content.
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Affiliation(s)
- Jürgen Tomasch
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Karel Kopejtka
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Sahana Shivaramu
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Izabela Mujakić
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Michal Koblížek
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
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30
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Socarras KM, Marino MC, Earl JP, Ehrlich RL, Cramer NA, Mell JC, Sen B, Ahmed A, Marconi RT, Ehrlich GD. Characterization of the family-level Borreliaceae pan-genome and development of an episomal typing protocol. RESEARCH SQUARE 2024:rs.3.rs-4491589. [PMID: 38947078 PMCID: PMC11213207 DOI: 10.21203/rs.3.rs-4491589/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background The Borreliaceae family includes many obligate parasitic bacterial species which are etiologically associated with a myriad of zoonotic borrelioses including Lyme disease and vector-borne relapsing fevers. Infections by the Borreliaceae are difficult to detect by both direct and indirect methods, often leading to delayed and missed diagnoses. Efforts to improve diagnoses center around the development of molecular diagnostics (MDx), but due to deep tissue sequestration of the causative spirochaetes and the lack of persistent bacteremias, even MDx assays suffer from a lack of sensitivity. Additionally, the highly extensive genomic heterogeneity among isolates, even within the same species, contributes to the lack of assay sensitivity as single target assays cannot provide universal coverage. This within-species heterogeneity is partly due to differences in replicon repertoires and genomic structures that have likely arisen to support the complex Borreliaceae lifecycle in which these parasites have to survive in multiple hosts each with unique immune responses. Results We constructed a Borreliaceae family-level pangenome and characterized the phylogenetic relationships among the constituent taxa which supports the recent taxonomy of splitting the family into at least two genera. Gene content pro les were created for the majority of the Borreliaceae replicons, providing for the first time their unambiguous molecular typing. Conclusion Our characterization of the Borreliaceae pan-genome supports the splitting of the former Borrelia genus into two genera and provides for the phylogenetic placement of several non-species designated isolates. Mining this family-level pangenome will enable precision diagnostics corresponding to gene content-driven clinical outcomes while also providing targets for interventions.
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Affiliation(s)
- Kayla M Socarras
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Mary C Marino
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Joshua P Earl
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | | | - Nicholas A Cramer
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center
| | - Joshua C Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Bhaswati Sen
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Azad Ahmed
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Richard T Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center
| | - Garth D Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
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31
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Branger M, Leclercq SO. GenoFig: a user-friendly application for the visualization and comparison of genomic regions. Bioinformatics 2024; 40:btae372. [PMID: 38870520 PMCID: PMC11199195 DOI: 10.1093/bioinformatics/btae372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024] Open
Abstract
MOTIVATION Understanding the molecular evolutionary history of organisms usually requires visual comparison of genomic regions from related species or strains. Although several applications already exist to achieve this task, they are either too old, too limited, or too complex for most user's needs. RESULTS GenoFig is a graphical application for the visualization of prokaryotic genomic regions, intended to be as easy to use as possible and flexible enough to adapt to a variety of needs. GenoFig allows the personalized representation of annotations extracted from GenBank files in a consistent way across sequences, using regular expressions. It also provides several unique options to optimize the display of homologous regions between sequences, as well as other more classical features such as sequence GC percent or GC-skew representations. In summary, GenoFig is a simple, free, and highly configurable tool to explore the evolution of specific genomic regions in prokaryotes and to produce publication-ready figures. AVAILABILITY AND IMPLEMENTATION Genofig is fully available at https://forgemia.inra.fr/public-pgba/genofig under a GPL 3.0 license.
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Affiliation(s)
- Maxime Branger
- INRAE, Université de Tours, ISP, Nouzilly F-37380, France
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Queiroz VF, Rodrigues RAL, Abrahão JS. A taxonomic proposal for cedratviruses, orpheoviruses, and pithoviruses. Arch Virol 2024; 169:132. [PMID: 38822903 DOI: 10.1007/s00705-024-06055-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Orpheoviruses, cedratviruses, and pithoviruses are large DNA viruses that cluster together taxonomically within the order Pimascovirales of the phylum Nucleocytoviricota. However, they were not classified previously by the International Committee on Taxonomy of Viruses (ICTV). Here, we present a comprehensive analysis of the gene content, morphology, and phylogenomics of these viruses, providing data that underpinned the recent proposal to establish new taxa for their initial classification. The new taxonomy, which has now been ratified by the ICTV, includes the family Orpheoviridae and genus Alphaorpheovirus, the family Pithoviridae and genus Alphapithovirus, and the family Cedratviridae and genus Alphacedratvirus, aiming to formally catalogue the isolates covered in this study. Additionally, as per the newly adopted rules, we applied standardized binomial names for the virus species created to classify isolates with complete genome sequences available in public databases at the time of the proposal. The specific epithet of each virus species was chosen as a reference to the location where the exemplar virus was isolated.
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Affiliation(s)
- Victória F Queiroz
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, MG, Brazil
| | - Rodrigo A L Rodrigues
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, MG, Brazil
| | - Jônatas Santos Abrahão
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, MG, Brazil.
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Dost C, Michling F, Kaimenyi D, Rij M, Wendland J. Isolation of Saccharomycopsis species from plant material. Microbiol Res 2024; 283:127691. [PMID: 38492364 DOI: 10.1016/j.micres.2024.127691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
Saccharomycopsis species are natural organic sulphur auxotrophs. Their genomes do not encode genes for the uptake and assimilation of sulphate and thus these species cannot grow on media lacking e.g. methionine. Due to the similarity between sulphate and selenate, uptake and assimilation of selenate occurs through the same pathway starting from sulphate transporters encoded by the homologs of the SUL1 and SUL2 genes in S. cerevisiae. Lack of these transporters renders Saccharomycopsis species resistant to selenate levels that are toxic to other microorganisms. We used this feature to enrich environmental samples for Saccharomycopsis species. This led to the isolation of S. schoenii, S. lassenensis and a hitherto undescribed Saccharomycopsis species with limited by-catch of other yeasts, mainly belonging to Metschnikowia and Hanseniaspora. We performed growth and predation assays to characterize the potential of these new isolates as predacious yeasts. Most Saccharomycopsis species are temperature sensitive and cannot grow at 37°C; with the exception of S. lassenensis strains. Predation assays with S. schoenii and S. cerevisiae as prey indicated that predation was enhanced at 20°C compared to 30°C. We crossed an American isolate of S. schoenii with our German isolate using marker directed breeding. Viable progeny indicated that both strains are interfertile and belong to the same biological species. S. lassenensis is heterothallic, while S. schoenii and the new Saccharomycopsis isolate, for which we suggest the name S. geisenheimensis sp. nov., are homothallic.
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Affiliation(s)
- Carmen Dost
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany; Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany
| | - Florian Michling
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany; Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany
| | - Davies Kaimenyi
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany
| | - Mareike Rij
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany
| | - Jürgen Wendland
- Department of Microbiology and Biochemistry, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany; Geisenheim Yeast Breeding Center, Hochschule Geisenheim University, Von-Lade-Strasse 1, Geisenheim 65366, Germany.
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Elrashedy A, Nayel M, Salama A, Zaghawa A, Abdelsalam NR, Hasan ME. Phylogenetic Analysis and Comparative Genomics of Brucella abortus and Brucella melitensis Strains in Egypt. J Mol Evol 2024; 92:338-357. [PMID: 38809331 PMCID: PMC11169049 DOI: 10.1007/s00239-024-10173-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Brucellosis is a notifiable disease induced by a facultative intracellular Brucella pathogen. In this study, eight Brucella abortus and eighteen Brucella melitensis strains from Egypt were annotated and compared with RB51 and REV1 vaccines respectively. RAST toolkit in the BV-BRC server was used for annotation, revealing genome length of 3,250,377 bp and 3,285,803 bp, 3289 and 3323 CDS, 48 and 49 tRNA genes, the same number of rRNA (3) genes, 583 and 586 hypothetical proteins, 2697 and 2726 functional proteins for B. abortus and B. melitensis respectively. B. abortus strains exhibit a similar number of candidate genes, while B. melitensis strains showed some differences, especially in the SRR19520422 Faiyum strain. Also, B. melitensis clarified differences in antimicrobial resistance genes (KatG, FabL, MtrA, MtrB, OxyR, and VanO-type) in SRR19520319 Faiyum and (Erm C and Tet K) in SRR19520422 Faiyum strain. Additionally, the whole genome phylogeny analysis proved that all B. abortus strains were related to vaccinated animals and all B. melitensis strains of Menoufia clustered together and closely related to Gharbia, Dameitta, and Kafr Elshiek. The Bowtie2 tool identified 338 (eight B. abortus) and 4271 (eighteen B. melitensis) single nucleotide polymorphisms (SNPs) along the genomes. These variants had been annotated according to type and impact. Moreover, thirty candidate genes were predicted and submitted at GenBank (24 in B. abortus) and (6 in B. melitensis). This study contributes significant insights into genetic variation, virulence factors, and vaccine-related associations of Brucella pathogens, enhancing our knowledge of brucellosis epidemiology and evolution in Egypt.
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Affiliation(s)
- Alyaa Elrashedy
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt.
| | - Mohamed Nayel
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Akram Salama
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Ahmed Zaghawa
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
| | - Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
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Hu X, He B, Liu Y, Ma S, Yu C. Genomic characterization of a novel ureolytic bacteria, Lysinibacillus capsici TSBLM, and its application to the remediation of acidic heavy metal-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:172170. [PMID: 38575034 DOI: 10.1016/j.scitotenv.2024.172170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/23/2024] [Accepted: 03/31/2024] [Indexed: 04/06/2024]
Abstract
Soil heavy metal contamination is an essential challenge in ecological and environmental management, especially for acidic soils. Microbially induced carbonate precipitation (MICP) is an effective and environmentally friendly remediation technology for heavy metal contaminated sites, and one of the key factors for its realization lies in the microorganisms. In this study, Lysinibacillus capsici TSBLM was isolated from heavy metal contaminated soil around a gold mine, and inferred to be a novel ureolytic bacteria after phylogenomic inference and genome characterization. The urease of L. capsici TSBLM was analyzed by genetic analysis and molecular docking, and further applied this bacteria to the remediation of Cu and Pb in solution and acidic soils to investigate its biomineralization mechanism and practical application. The results revealed L. capsici TSBLM possessed a comprehensive urease gene cluster ureABCEFGD, and the encoded urease docked with urea at the lowest binding energy site (ΔG = -3.43 kcal/mol) connected to three amino acids threonine, aspartic, and alanine. The urease of L. capsici TSBLM is synthesized intracellularly but mainly functions extracellularly. L. capsici TSBLM removes Cu/Pb from the solution by generating heavy metal carbonates or co-precipitating with CaCO3 vaterite. For acidic heavy metal-contaminated soil, the carbonate-bound states of Cu and Pb increased significantly from 7 % to 16 % and from 23 % to 35 % after 30 days by L. capsici TSBLM. Soil pH improved additionally. L. capsici TSBLM maintained the dominant status in the remediated soil after 30 days, demonstrating good environmental adaptability and curing persistence. The results provided new strain resources and practical application references for the remediation of acidic heavy metal contaminated soil based on MICP.
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Affiliation(s)
- Xuesong Hu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Banghua He
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Yingchao Liu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Suya Ma
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China
| | - Caihong Yu
- School of Chemical & Environmental Engineering, China University of Mining and Technology (Beijing), 100083 Beijing, China.
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Mansueto A, Good DJ. Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis. J Mol Evol 2024; 92:266-277. [PMID: 38683367 PMCID: PMC11169010 DOI: 10.1007/s00239-024-10165-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/20/2024] [Indexed: 05/01/2024]
Abstract
Ascorbic acid functions as an antioxidant and facilitates other biochemical processes such as collagen triple helix formation, and iron uptake by cells. Animals which endogenously produce ascorbic acid have a functional gulonolactone oxidase gene (GULO); however, humans have a GULO pseudogene (GULOP) and depend on dietary ascorbic acid. In this study, the conservation of GULOP sequences in the primate haplorhini suborder were investigated and compared to the GULO sequences belonging to the primates strepsirrhini suborder. Phylogenetic analysis suggested that the conserved GULOP exons in the haplorhini primates experienced a high rate of mutations following the haplorhini/strepsirrhini divergence. This high mutation rate has decreased during the evolution of the haplorhini primates. Additionally, indels of the haplorhini GULOP sequences were conserved across the suborder. A separate analysis for GULO sequences and well-conserved GULOP sequences focusing on placental mammals identified an in-frame GULO sequence in the Brazilian guinea pig, and a potential GULOP sequence in the pika. Similar to haplorhini primates, the guinea pig and lagomorph species have experienced a high substitution rate when compared to the mammals used in this study. A shared synteny to examine the conservation of local genes near GULO/GULOP identified a conserved inversion around the GULO/GULOP locus between the haplorhini and strepsirrhini primates. Fischer's exact test did not support an association between GULOP and the chromosomal inversion. Mauve alignment showed that the inversion of the length of the syntenic block that the GULO/GULOP genes belonged to was variable. However, there were frequent rearrangements around ~ 2 million base pairs adjacent to GULOP involving the KIF13B and MSRA genes. These data may suggest that genes acquiring deleterious mutations in the coding sequence may respond to these deleterious mutations with rapid substitution rates.
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Affiliation(s)
- Alexander Mansueto
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
- Department of Biological Sciences, Vanderbilt University, Nashvile, TN, USA
| | - Deborah J Good
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA.
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, 1981 Kraft Drive (0913), ILSB Room 1020, Blacksburg, VA, 24060, USA.
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Davison C, Tallman S, de Ste-Croix M, Antonio M, Oggioni MR, Kwambana-Adams B, Freund F, Beleza S. Long-term evolution of Streptococcus mitis and Streptococcus pneumoniae leads to higher genetic diversity within rather than between human populations. PLoS Genet 2024; 20:e1011317. [PMID: 38843312 PMCID: PMC11185502 DOI: 10.1371/journal.pgen.1011317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 06/18/2024] [Accepted: 05/23/2024] [Indexed: 06/19/2024] Open
Abstract
Evaluation of the apportionment of genetic diversity of human bacterial commensals within and between human populations is an important step in the characterization of their evolutionary potential. Recent studies showed a correlation between the genomic diversity of human commensal strains and that of their host, but the strength of this correlation and of the geographic structure among human populations is a matter of debate. Here, we studied the genomic diversity and evolution of the phylogenetically related oro-nasopharyngeal healthy-carriage Streptococcus mitis and Streptococcus pneumoniae, whose lifestyles range from stricter commensalism to high pathogenic potential. A total of 119 S. mitis genomes showed higher within- and among-host variation than 810 S. pneumoniae genomes in European, East Asian and African populations. Summary statistics of the site-frequency spectrum for synonymous and non-synonymous variation and ABC modelling showed this difference to be due to higher ancestral bacterial population effective size (Ne) in S. mitis, whose genomic variation has been maintained close to mutation-drift equilibrium across (at least many) generations, whereas S. pneumoniae has been expanding from a smaller ancestral bacterial population. Strikingly, both species show limited differentiation among human populations. As genetic differentiation is inversely proportional to the product of effective population size and migration rate (Nem), we argue that large Ne have led to similar differentiation patterns, even if m is very low for S. mitis. We conclude that more diversity within than among human populations and limited population differentiation must be common features of the human microbiome due to large Ne.
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Affiliation(s)
- Charlotte Davison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Sam Tallman
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Megan de Ste-Croix
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Fajara, The Gambia
- Centre for Epidemic Preparedness and Response, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Marco R. Oggioni
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Brenda Kwambana-Adams
- Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Fajara, The Gambia
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Malawi Liverpool Welcome Programme, Blantyre, Malawi
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Fabian Freund
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Noh S, Peck RF, Larson ER, Covitz RM, Chen A, Roy P, Hamilton MC, Dettmann RA. Facultative symbiont virulence determines horizontal transmission rate without host specificity in Dictyostelium discoideum social amoebas. Evol Lett 2024; 8:437-447. [PMID: 38818420 PMCID: PMC11134466 DOI: 10.1093/evlett/qrae001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/08/2024] [Accepted: 01/15/2024] [Indexed: 06/01/2024] Open
Abstract
In facultative symbioses, only a fraction of hosts are associated with symbionts. Specific host and symbiont pairings may be the result of host-symbiont coevolution driven by reciprocal selection or priority effects pertaining to which potential symbiont is associated with a host first. Distinguishing between these possibilities is important for understanding the evolutionary forces that affect facultative symbioses. We used the social amoeba, Dictyostelium discoideum, and its symbiont, Paraburkholderia bonniea, to determine whether ongoing coevolution affects which host-symbiont strain pairs naturally cooccur within a facultative symbiosis. Relative to other Paraburkholderia, including another symbiont of D. discoideum, P. bonniea features a reduced genome size that indicates a significant history of coevolution with its host. We hypothesized that ongoing host-symbiont coevolution would lead to higher fitness for naturally cooccurring (native) host and symbiont pairings compared to novel pairings. We show for the first time that P. bonniea symbionts can horizontally transmit to new amoeba hosts when hosts aggregate together during the social stage of their life cycle. Here we find evidence for a virulence-transmission trade-off without host specificity. Although symbiont strains were significantly variable in virulence and horizontal transmission rate, hosts and symbionts responded similarly to associations in native and novel pairings. We go on to identify candidate virulence factors in the genomes of P. bonniea strains that may contribute to variation in virulence. We conclude that ongoing coevolution is unlikely for D. discoideum and P. bonniea. The system instead appears to represent a stable facultative symbiosis in which naturally cooccurring P. bonniea host and symbiont pairings are the result of priority effects.
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Affiliation(s)
- Suegene Noh
- Biology Department, Colby College, Waterville, ME, United States
| | - Ron F Peck
- Biology Department, Colby College, Waterville, ME, United States
| | - Emily R Larson
- Biology Department, Colby College, Waterville, ME, United States
| | - Rachel M Covitz
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States
| | - Anna Chen
- Biology Department, Colby College, Waterville, ME, United States
| | - Prachee Roy
- Biology Department, Colby College, Waterville, ME, United States
| | - Marisa C Hamilton
- University Program in Genetics and Genomics, Duke University, Durham, NC, United States
| | - Robert A Dettmann
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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Macesic N, Dennis A, Hawkey J, Vezina B, Wisniewski JA, Cottingham H, Blakeway LV, Harshegyi T, Pragastis K, Badoordeen GZ, Bass P, Stewardson AJ, Dennison A, Spelman DW, Jenney AW, Peleg AY. Genomic investigation of multispecies and multivariant blaNDM outbreak reveals key role of horizontal plasmid transmission. Infect Control Hosp Epidemiol 2024; 45:709-716. [PMID: 38344902 PMCID: PMC11102827 DOI: 10.1017/ice.2024.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/10/2023] [Accepted: 12/28/2023] [Indexed: 05/18/2024]
Abstract
OBJECTIVES New Delhi metallo-β-lactamases (NDMs) are major contributors to the spread of carbapenem resistance globally. In Australia, NDMs were previously associated with international travel, but from 2019 we noted increasing incidence of NDM-positive clinical isolates. We investigated the clinical and genomic epidemiology of NDM carriage at a tertiary-care Australian hospital from 2016 to 2021. METHODS We identified 49 patients with 84 NDM-carrying isolates in an institutional database, and we collected clinical data from electronic medical record. Short- and long-read whole genome sequencing was performed on all isolates. Completed genome assemblies were used to assess the genetic setting of blaNDM genes and to compare NDM plasmids. RESULTS Of 49 patients, 38 (78%) were identified in 2019-2021 and only 11 (29%) of 38 reported prior travel, compared with 9 (82%) of 11 in 2016-2018 (P = .037). In patients with NDM infection, the crude 7-day mortality rate was 0% and the 30-day mortality rate was 14% (2 of 14 patients). NDMs were noted in 41 bacterial strains (ie, species and sequence type combinations). Across 13 plasmid groups, 4 NDM variants were detected: blaNDM-1, blaNDM-4, blaNDM-5, and blaNDM-7. We noted a change from a diverse NDM plasmid repertoire in 2016-2018 to the emergence of conserved blaNDM-1 IncN and blaNDM-7 IncX3 epidemic plasmids, with interstrain spread in 2019-2021. These plasmids were noted in 19 (50%) of 38 patients and 35 (51%) of 68 genomes in 2019-2021. CONCLUSIONS Increased NDM case numbers were due to local circulation of 2 epidemic plasmids with extensive interstrain transfer. Our findings underscore the challenges of outbreak detection when horizontal transmission of plasmids is the primary mode of spread.
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Affiliation(s)
- Nenad Macesic
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Adelaide Dennis
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | - Ben Vezina
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | - Jessica A. Wisniewski
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | - Hugh Cottingham
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | - Luke V. Blakeway
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | - Taylor Harshegyi
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | - Katherine Pragastis
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | - Gnei Zweena Badoordeen
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | - Pauline Bass
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | - Andrew J. Stewardson
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
| | | | - Denis W. Spelman
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
- Microbiology Unit, Alfred Hospital, Melbourne, Australia
| | - Adam W.J. Jenney
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
- Microbiology Unit, Alfred Hospital, Melbourne, Australia
| | - Anton Y. Peleg
- Department of Infectious Diseases, The Alfred Hospital and School of Translational Medicine, Monash University, Melbourne, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Australia
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Gu W, Wu S, Liu X, Wang L, Wang X, Qiu Q, Wang G. Algal-bacterial consortium promotes carbon sink formation in saline environment. J Adv Res 2024; 60:111-125. [PMID: 37597746 PMCID: PMC11156706 DOI: 10.1016/j.jare.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/26/2023] [Accepted: 08/05/2023] [Indexed: 08/21/2023] Open
Abstract
INTRODUCTION The level of atmospheric CO2 has continuously been increasing and the resulting greenhouse effects are receiving attention globally. Carbon removal from the atmosphere occurs naturally in various ecosystems. Among them, saline environments contribute significantly to the global carbon cycle. Carbonate deposits in the sediments of salt lakes are omnipresent, and the biological effects, especially driven by halophilic microalgae and bacteria, on carbonate formation remain to be elucidated. OBJECTIVES The present study aims to characterize the carbonates formed in saline environments and demonstrate the mechanisms underlying biological-driven CO2 removal via microalgal-bacterial consortium. METHODS The carbonates naturally formed in saline environments were collected and analyzed. Two saline representative organisms, the photosynthetic microalga Dunaliella salina and its mutualistic halophilic bacteria Nesterenkonia sp. were isolated from the inhabiting saline environment and co-cultivated to study their biological effects on carbonates precipitation and isotopic composition. During this process, electrochemical parameters and Ca2+ flux, and expression of genes related to CaCO3 formation were analyzed. Genome sequencing and metagenomic analysis were conducted to provide molecular evidence. RESULTS The results showed that natural saline sediments are enriched with CaCO3 and enrichment of genes related to photosynthesis and ureolysis. The co-cultivation stimulated 54.54% increase in CaCO3 precipitation and significantly promoted the absorption of external CO2 by 49.63%. A pH gradient was formed between the bacteria and algae culture, creating 150.22 mV of electronic potential, which might promote Ca2+ movement toward D. salina cells. Based on the results of lab-scale induction and 13C analysis, a theoretical calculation indicates a non-negligible amount of 0.16 and 2.3 Tg C/year carbon sequestration in China and global saline lakes, respectively. CONCLUSION The combined effects of these two typical representative species have contributed to the carbon sequestration in saline environments, by promoting Ca2+ influx and increase of pH via microalgal and bacterial metabolic processes.
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Affiliation(s)
- Wenhui Gu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Songcui Wu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Xuehua Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Lijun Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Xulei Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Qi Qiu
- Tianjin Changlu Hangu Saltern Co., LTD, 300480, China
| | - Guangce Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China.
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Ridgway R, Lu H, Blower TR, Evans NJ, Ainsworth S. Genomic and taxonomic evaluation of 38 Treponema prophage sequences. BMC Genomics 2024; 25:549. [PMID: 38824509 PMCID: PMC11144348 DOI: 10.1186/s12864-024-10461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 05/28/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Despite Spirochetales being a ubiquitous and medically important order of bacteria infecting both humans and animals, there is extremely limited information regarding their bacteriophages. Of the genus Treponema, there is just a single reported characterised prophage. RESULTS We applied a bioinformatic approach on 24 previously published Treponema genomes to identify and characterise putative treponemal prophages. Thirteen of the genomes did not contain any detectable prophage regions. The remaining eleven contained 38 prophage sequences, with between one and eight putative prophages in each bacterial genome. The prophage regions ranged from 12.4 to 75.1 kb, with between 27 and 171 protein coding sequences. Phylogenetic analysis revealed that 24 of the prophages formed three distinct sequence clusters, identifying putative myoviral and siphoviral morphology. ViPTree analysis demonstrated that the identified sequences were novel when compared to known double stranded DNA bacteriophage genomes. CONCLUSIONS In this study, we have started to address the knowledge gap on treponeme bacteriophages by characterising 38 prophage sequences in 24 treponeme genomes. Using bioinformatic approaches, we have been able to identify and compare the prophage-like elements with respect to other bacteriophages, their gene content, and their potential to be a functional and inducible bacteriophage, which in turn can help focus our attention on specific prophages to investigate further.
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Affiliation(s)
- Rachel Ridgway
- Department of Infection Biology and Microbiomes, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Cheshire, CH64 7TE, UK.
| | - Hanshuo Lu
- Department of Infection Biology and Microbiomes, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Nicholas James Evans
- Department of Infection Biology and Microbiomes, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Cheshire, CH64 7TE, UK
| | - Stuart Ainsworth
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool Science Park IC2, 146 Brownlow Hill, Liverpool, L3 5RF, UK
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Fernandez CM, Krockenberger MB, Ho SYW, Crowther MS, Mella VSA, Jelocnik M, Wilmott L, Higgins DP. Novel typing scheme reveals emergence and genetic diversity of Chlamydia pecorum at the local management scale across two koala populations. Vet Microbiol 2024; 293:110085. [PMID: 38581768 DOI: 10.1016/j.vetmic.2024.110085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
To overcome shortcomings in discriminating Chlamydia pecorum strains infecting the koala (Phascolarctos cinereus) at the local level, we developed a novel genotyping scheme for this pathogen to inform koala management at a fine-scale subpopulation level. We applied this scheme to two geographically distinct koala populations in New South Wales, Australia: the Liverpool Plains and the Southern Highlands to South-west Sydney (SHSWS). Our method provides greater resolution than traditional multi-locus sequence typing, and can be used to monitor strain emergence, movement, and divergence across a range of fragmented habitats. Within the Liverpool Plains population, suspected recent introduction of a novel strain was confirmed by an absence of genetic diversity at the earliest sampling events and limited diversity at recent sampling events. Across the partially fragmented agricultural landscape of the Liverpool Plains, diversity within a widespread sequence type suggests that this degree of fragmentation may hinder but not prevent spread. In the SHSWS population, our results suggest movement of a strain from the south, where diverse strains exist, into a previously Chlamydia-free area in the north, indicating the risk of expansion towards an adjacent Chlamydia-negative koala population in South-west Sydney. In the south of the SHSWS where koala subpopulations appear segregated, we found evidence of divergent strain evolution. Our tool can be used to infer the risks of strain introduction across fragmented habitats in population management, particularly through practices such as wildlife corridor constructions and translocations.
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Affiliation(s)
- Cristina M Fernandez
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mark B Krockenberger
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia; Sydney Infectious Diseases, The University of Sydney, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mathew S Crowther
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Valentina S A Mella
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Martina Jelocnik
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia; Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, QLD 4556, Australia
| | - Lachlan Wilmott
- NSW Department of Planning and Environment, Wollongong, NSW 2005, Australia
| | - Damien P Higgins
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia.
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Baysal Ö, Studholme DJ, Jimenez-Quiros C, Tör M. Genome sequence of the plant-growth-promoting bacterium Bacillus velezensis EU07. Access Microbiol 2024; 6:000762.v3. [PMID: 38868377 PMCID: PMC11165630 DOI: 10.1099/acmi.0.000762.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/17/2024] [Indexed: 06/14/2024] Open
Abstract
Many Gram-positive spore-forming rhizobacteria of the genus Bacillus show potential as biocontrol biopesticides that promise improved sustainability and ecological safety in agriculture. Here, we present a draft-quality genome sequence for Bacillus velezensis EU07, which shows growth-promotion in tomato plants and biocontrol against Fusarium head blight. We found that the genome of EU07 is almost identical to that of the commercially used strain QST713, but identified 46 single-nucleotide differences that distinguish these strains from each other. The availability of this genome sequence will facilitate future efforts to unravel the genetic and molecular basis for EU07's beneficial properties.
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Affiliation(s)
- Ömür Baysal
- Department of Molecular Biology and Genetics, Faculty of Science, Mugla Sitki Kocman University, 48000 Menteşe, Turkey
- Department of Biological Sciences, University of Worcester, Worcester, UK
| | | | | | - Mahmut Tör
- Department of Biological Sciences, University of Worcester, Worcester, UK
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Patel L, Ailloud F, Suerbaum S, Josenhans C. Single-base resolution quantitative genome methylation analysis in the model bacterium Helicobacter pylori by enzymatic methyl sequencing (EM-Seq) reveals influence of strain, growth phase, and methyl homeostasis. BMC Biol 2024; 22:125. [PMID: 38807090 PMCID: PMC11134628 DOI: 10.1186/s12915-024-01921-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND Bacterial epigenetics is a rapidly expanding research field. DNA methylation by diverse bacterial methyltransferases (MTases) contributes to genomic integrity and replication, and many recent studies extended MTase function also to global transcript regulation and phenotypic variation. Helicobacter pylori is currently one of those bacterial species which possess the highest number and the most variably expressed set of DNA MTases. Next-generation sequencing technologies can directly detect DNA base methylation. However, they still have limitations in their quantitative and qualitative performance, in particular for cytosine methylation. RESULTS As a complementing approach, we used enzymatic methyl sequencing (EM-Seq), a technology recently established that has not yet been fully evaluated for bacteria. Thereby, we assessed quantitatively, at single-base resolution, whole genome cytosine methylation for all methylated cytosine motifs in two different H. pylori strains and isogenic MTase mutants. EM-Seq reliably detected both m5C and m4C methylation. We demonstrated that three different active cytosine MTases in H. pylori provide considerably different levels of average genome-wide single-base methylation, in contrast to isogenic mutants which completely lost specific motif methylation. We found that strain identity and changed environmental conditions, such as growth phase and interference with methyl donor homeostasis, significantly influenced quantitative global and local genome-wide methylation in H. pylori at specific motifs. We also identified significantly hyper- or hypo-methylated cytosines, partially linked to overlapping MTase target motifs. Notably, we revealed differentially methylated cytosines in genome-wide coding regions under conditions of methionine depletion, which can be linked to transcript regulation. CONCLUSIONS This study offers new knowledge on H. pylori global and local genome-wide methylation and establishes EM-Seq for quantitative single-site resolution analyses of bacterial cytosine methylation.
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Affiliation(s)
- Lubna Patel
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Florent Ailloud
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Sebastian Suerbaum
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Christine Josenhans
- Max von Pettenkofer Institute, Chair for Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.
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Ayalew LE, Mekuria ZH, Despres B, Saab ME, Ojha S. Genome Sequence Comparisons between Small and Large Colony Phenotypes of Equine Clinical Isolates of Arcanobacterium hippocoleae. Animals (Basel) 2024; 14:1609. [PMID: 38891657 PMCID: PMC11171008 DOI: 10.3390/ani14111609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Arcanobacterium hippocoleae is a Gram-positive fastidious bacterium and is occasionally isolated from the reproductive tract of apparently healthy mares (Equus caballus) or from mares with reproductive tract abnormalities. Apart from a few 16S rRNA gene-based GenBank sequences and one recent report on complete genome assembly, detailed genomic sequence and clinical experimental data are not available on the bacterium. Recently, we observed an unusual increase in the detection of the organism from samples associated with mare reproductive failures in Atlantic Canada. Two colony morphotypes (i.e., small, and large) were detected in culture media, which were identified as A. hippocoleae by MALDI-TOF mass spectrometry and 16S rRNA gene sequencing. Here, we report the whole genome sequencing and characterization of the morphotype variants. The genome length of the large phenotypes was between 2.42 and 2.43, and the small phenotype was 1.99 Mbs. The orthologous nucleotide identity between the large colony phenotypes was ~99%, and the large and small colony phenotypes was between 77.86 and 78.52%, which may warrant the classification of the two morphotypes into different species. Phylogenetic analysis based on 16S rRNA genes or concatenated housekeeping genes grouped the small and large colony variants into two different genotypic clusters. The UvrA protein, which is part of the nucleotide excision repair (NER) system, and 3-isopropoylmalate dehydratase small subunit protein expressed by the leuD gene were identified as potential virulence factors in the large and small colony morphotypes, respectively. However, detailed functional studies will be required to determine the exact roles of these and other identified hypothetical proteins in the cellular metabolism and potential pathogenicity of A. hippocoleae in mares.
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Affiliation(s)
- Lisanework E. Ayalew
- Atlantic Veterinary College, University of Prince Edward Island (UPEI), 550 University Ave, Charlottetown, PE C1A 4P3, Canada
| | - Zelalem H. Mekuria
- Global One Health Initiative (GOHI), The Ohio State University (OSU), Columbus, OH 43210, USA;
- Department of Veterinary Preventative Medicine, College of Veterinary Medicine, The Ohio State University (OSU), Columbus, OH 43210, USA
| | - Beatrice Despres
- Atlantic Veterinary College, University of Prince Edward Island (UPEI), 550 University Ave, Charlottetown, PE C1A 4P3, Canada
| | - Matthew E. Saab
- Atlantic Veterinary College, University of Prince Edward Island (UPEI), 550 University Ave, Charlottetown, PE C1A 4P3, Canada
| | - Shivani Ojha
- Atlantic Veterinary College, University of Prince Edward Island (UPEI), 550 University Ave, Charlottetown, PE C1A 4P3, Canada
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Liu S, Veranso-Libalah MC, Sukhorukov AP, Sun X, Nilova MV, Kushunina M, Mamut J, Wen Z. Phylogenetic placement of the monotypic Baolia (Amaranthaceae s.l.) based on morphological and molecular evidence. BMC PLANT BIOLOGY 2024; 24:456. [PMID: 38789931 PMCID: PMC11127444 DOI: 10.1186/s12870-024-05164-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/17/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Baolia H.W.Kung & G.L.Chu is a monotypic genus only known in Diebu County, Gansu Province, China. Its systematic position is contradictory, and its morphoanatomical characters deviate from all other Chenopodiaceae. Recent study has regarded Baolia as a sister group to Corispermoideae. We therefore sequenced and compared the chloroplast genomes of this species, and resolved its phylogenetic position based on both chloroplast genomes and marker sequences. RESULTS We sequenced 18 chloroplast genomes of 16 samples from two populations of Baolia bracteata and two Corispermum species. These genomes of Baolia ranged in size from 152,499 to 152,508 bp. Simple sequence repeats (SSRs) were primarily located in the LSC region of Baolia chloroplast genomes, and most of them consisted of single nucleotide A/T repeat sequences. Notably, there were differences in the types and numbers of SSRs between the two populations of B. bracteata. Our phylogenetic analysis, based on both complete chloroplast genomes from 33 species and a combination of three markers (ITS, rbcL, and matK) from 91 species, revealed that Baolia and Corispermoideae (Agriophyllum, Anthochlamys, and Corispermum) form a well-supported clade and sister to Acroglochin. According to our molecular dating results, a major divergence event between Acroglochin, Baolia, and Corispermeae occurred during the Middle Eocene, approximately 44.49 mya. Ancestral state reconstruction analysis showed that Baolia exhibited symplesiomorphies with those found in core Corispermoideae characteristics including pericarp and seed coat. CONCLUSIONS Comparing the chloroplast genomes of B. bracteata with those of eleven typical Chenopodioideae and Corispermoideae species, we observed a high overall similarity and a one notable noteworthy case of inversion of approximately 3,100 bp. of DNA segments only in two Atriplex and four Chenopodium species. We suggest that Corispermoideae should be considered in a broader sense, it includes Corispermeae (core Corispermoideae: Agriophyllum, Anthochlamys, and Corispermum), as well as two new monotypic tribes, Acroglochineae (Acroglochin) and Baolieae (Baolia).
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Affiliation(s)
- Shuai Liu
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Marie Claire Veranso-Libalah
- Biodiversität und Evolution der Pflanzen, Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 830052, München, Germany
| | - Alexander P Sukhorukov
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russian Federation.
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, 634050,, Russian Federation.
| | - Xuegang Sun
- College of Forestry, Gansu Agricultural University, Lanzhou, 730070, China
| | - Maya V Nilova
- Department of Higher Plants, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Maria Kushunina
- Laboratory Herbarium (TK), Tomsk State University, Tomsk, 634050,, Russian Federation
- Department of Plant Physiology, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Jannathan Mamut
- College of Life Sciences, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zhibin Wen
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Urumqi, 830011, China.
- Sino-Tajikistan Joint Laboratory for Conservation and Utilization of Biological Resources, Urumqi, 830011, China.
- The Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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Greenrod STE, Cazares D, Johnson S, Hector TE, Stevens EJ, MacLean RC, King KC. Warming alters life-history traits and competition in a phage community. Appl Environ Microbiol 2024; 90:e0028624. [PMID: 38624196 PMCID: PMC11107170 DOI: 10.1128/aem.00286-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024] Open
Abstract
Host-parasite interactions are highly susceptible to changes in temperature due to mismatches in species thermal responses. In nature, parasites often exist in communities, and responses to temperature are expected to vary between host-parasite pairs. Temperature change thus has consequences for both host-parasite dynamics and parasite-parasite interactions. Here, we investigate the impact of warming (37°C, 40°C, and 42°C) on parasite life-history traits and competition using the opportunistic bacterial pathogen Pseudomonas aeruginosa (host) and a panel of three genetically diverse lytic bacteriophages (parasites). We show that phages vary in their responses to temperature. While 37°C and 40°C did not have a major effect on phage infectivity, infection by two phages was restricted at 42°C. This outcome was attributed to disruption of different phage life-history traits including host attachment and replication inside hosts. Furthermore, we show that temperature mediates competition between phages by altering their competitiveness. These results highlight phage trait variation across thermal regimes with the potential to drive community dynamics. Our results have important implications for eukaryotic viromes and the design of phage cocktail therapies.IMPORTANCEMammalian hosts often elevate their body temperatures through fevers to restrict the growth of bacterial infections. However, the extent to which fever temperatures affect the communities of phages with the ability to parasitize those bacteria remains unclear. In this study, we investigate the impact of warming across a fever temperature range (37°C, 40°C, and 42°C) on phage life-history traits and competition using a bacterium (host) and bacteriophage (parasite) system. We show that phages vary in their responses to temperature due to disruption of different phage life-history traits. Furthermore, we show that temperature can alter phage competitiveness and shape phage-phage competition outcomes. These results suggest that fever temperatures have the potential to restrict phage infectivity and drive phage community dynamics. We discuss implications for the role of temperature in shaping host-parasite interactions more widely.
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Affiliation(s)
| | - Daniel Cazares
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Serena Johnson
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Tobias E. Hector
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Emily J. Stevens
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - R. Craig MacLean
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Kayla C. King
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C. Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae. PLoS One 2024; 19:e0302365. [PMID: 38768140 PMCID: PMC11104678 DOI: 10.1371/journal.pone.0302365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 04/03/2024] [Indexed: 05/22/2024] Open
Abstract
In this study of evolutionary relationships in the subfamily Rubioideae (Rubiaceae), we take advantage of the off-target proportion of reads generated via previous target capture sequencing projects based on nuclear genomic data to build a plastome phylogeny and investigate cytonuclear discordance. The assembly of off-target reads resulted in a comprehensive plastome dataset and robust inference of phylogenetic relationships, where most intratribal and intertribal relationships are resolved with strong support. While the phylogenetic results were mostly in agreement with previous studies based on plastome data, novel relationships in the plastid perspective were also detected. For example, our analyses of plastome data provide strong support for the SCOUT clade and its sister relationship to the remaining members of the subfamily, which differs from previous results based on plastid data but agrees with recent results based on nuclear genomic data. However, several instances of highly supported cytonuclear discordance were identified across the Rubioideae phylogeny. Coalescent simulation analysis indicates that while ILS could, by itself, explain the majority of the discordant relationships, plastome introgression may be the better explanation in some cases. Our study further indicates that plastomes across the Rubioideae are, with few exceptions, highly conserved and mainly conform to the structure, gene content, and gene order present in the majority of the flowering plants.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
| | | | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Bergius Foundation, The Royal Academy of Sciences, Stockholm, Sweden
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Vilela FP, Felice AG, Seribelli AA, Rodrigues DP, Soares SC, Allard MW, Falcão JP. Comparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil. PeerJ 2024; 12:e17306. [PMID: 38784399 PMCID: PMC11114117 DOI: 10.7717/peerj.17306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 04/04/2024] [Indexed: 05/25/2024] Open
Abstract
Background Salmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil's relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses. Methods Analyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Results wgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to biological processes, molecular functions, and cellular components were detected among Brazilian and non-Brazilian genomes. Conclusion The results presented using different genomic approaches emphasized the significant genomic similarity among Brazilian Salmonella Infantis genomes analyzed, suggesting wide distribution of closely related genotypes among diverse sources in Brazil. The data generated contributed to novel information regarding the genomic diversity of Brazilian and non-Brazilian Salmonella Infantis in comparison. The different genetically related subtypes of Salmonella Infantis from Brazil can either occur exclusively within the country, or also in other countries, suggesting that some exportation of the Brazilian genotypes may have already occurred.
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Affiliation(s)
- Felipe P. Vilela
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Andrei G. Felice
- Institute of Biological and Natural Sciences, Department of Microbiology, Immunology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Amanda A. Seribelli
- Medical School of Ribeirão Preto, Department of Cellular and Molecular Biology, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Dália P. Rodrigues
- Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Siomar C. Soares
- Institute of Biological and Natural Sciences, Department of Microbiology, Immunology and Parasitology, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America
| | - Juliana P. Falcão
- School of Pharmaceutical Sciences of Ribeirão Preto, Department of Clinical Analyses, Toxicology and Food Science, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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Liu J, Zang E, Tian Y, Zhang L, Li Y, Shi L, Xu L, Xiao P. Comparative chloroplast genomes: insights into the identification and phylogeny of rapid radiation genus Rhodiola. FRONTIERS IN PLANT SCIENCE 2024; 15:1404447. [PMID: 38799090 PMCID: PMC11116683 DOI: 10.3389/fpls.2024.1404447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]
Abstract
Rhodiola L. is a genus exhibiting rapid radiation and represents a typical case for studying plastid gene adaptation in species that spread from high altitudes to low altitudes. In this study, 23 samples of 18 Rhodiola species were collected from the Qinghai-Tibetan Plateau and five scattered alpine areas, and the plastid genomes (plastomes) of these species were sequenced, annotated, and compared between high-altitude and widely distributed groups. The plastomes of Rhodiola were found to be highly conserved in terms of gene size, content, and order but highly variable in several lineage-specific features, such as codon usage bias, IR boundary shifting, and distinct repeat sequence structures binding to SSRs. Codon usage in the genes of photosystem II exhibited an obvious preference, reflecting significant environmental adaptation pressures. In this study, three repeat regions compounded with trinucleotide and mononucleotide repeats were found for the first time in R. forrestii, R. himalensis, and R. yunnanensis. High-variability regions such as ndhF, ycf1, trnH-psbA, and rpoC1-rpoB were screened, laying the foundation for the precise identification of these species. The phylogenetic analysis revealed the occurrence of cyto-nuclear discordance, likely originating from the frequent interspecific hybridization events observed within Rhodiola species during rapid radiation. Dioecious and hermaphrodite species can be broadly categorized into two subclades, probably they have different environmental adaptation strategies in response to climate change. In addition, the phylogenetic tree supported the monophyly of R. forrestii and R. yunnanensis, which compose R. Sect. Pseudorhodiola. In conclusion, plastome data enrich the genetic information available for the Rhodiola genus and may provide insight into species migration events during climate change.
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Affiliation(s)
- Jinxin Liu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
| | - Erhuan Zang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Tian
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Liqiu Zhang
- School of Medicine and Pharmacy, Tonghua Normal University, Tonghua, China
| | - Yimin Li
- College of Pharmacy and Key Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Chinese Medicine, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Linchun Shi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
| | - Lijia Xu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
| | - Peigen Xiao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing, China
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