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Thajuddin F, Ashok C, Thajuddin SF, Nooruddin T, Dharumadurai D, Babalola OO. Whole-genome sequence of Limnospira fusiformis NRMCF6962, isolated from lake water. Microbiol Resour Announc 2024:e0085524. [PMID: 39400141 DOI: 10.1128/mra.00855-24] [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: 08/04/2024] [Accepted: 09/24/2024] [Indexed: 10/15/2024] Open
Abstract
The economically important Cyanobacterial genus Limnospira is commercially utilized as a dietary supplement and nutraceutical agent. We present the whole-genome sequence of Limnospira fusiformis NRMCF6962 and was isolated from Kondakarla Ava Lake of Visakhapatnam, Andhra Pradesh, India.
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Affiliation(s)
- Fayaazuddin Thajuddin
- National Repository for Microalgae and Cyanobacteria - Freshwater (NRMC-F) (Sponsored by the DBT, Govt. of India), Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
- Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Chandru Ashok
- Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | | | - Thajuddin Nooruddin
- National Repository for Microalgae and Cyanobacteria - Freshwater (NRMC-F) (Sponsored by the DBT, Govt. of India), Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Dhanasekaran Dharumadurai
- National Repository for Microalgae and Cyanobacteria - Freshwater (NRMC-F) (Sponsored by the DBT, Govt. of India), Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
- Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
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de Oliva BHD, do Nascimento AB, de Oliveira JP, Guidone GHM, Schoeps BL, Silva LC, Barbosa MGL, Montini VH, de Oliveira Junior AG, Rocha SPD. Genomic insights into a Proteus mirabilis strain inducing avian cellulitis. Braz J Microbiol 2024:10.1007/s42770-024-01508-6. [PMID: 39235714 DOI: 10.1007/s42770-024-01508-6] [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: 05/16/2024] [Accepted: 08/28/2024] [Indexed: 09/06/2024] Open
Abstract
Proteus mirabilis, a microorganism distributed in soil, water, and animals, is clinically known for causing urinary tract infections in humans. However, recent studies have linked it to skin infections in broiler chickens, termed avian cellulitis, which poses a threat to animal welfare. While Avian Pathogenic Escherichia coli (APEC) is the primary cause of avian cellulitis, few cases of P. mirabilis involvement are reported, raising questions about the factors facilitating such occurrences. This study employed a pan-genomic approach to investigate whether unique genes exist in P. mirabilis strains causing avian cellulitis. The genome of LBUEL-A33, a P. mirabilis strain known to cause this infection, was assembled, and compared with other P. mirabilis strains isolated from poultry and other sources. Additionally, in silico serogroup analysis was conducted. Results revealed numerous genes unique to the LBUEL-A33 strain. No function in cellulitis was identified for these genes, and in silico investigation of the virulence potential of LBUEL-A33's exclusive proteins proved inconclusive. These findings support that multiple factors are necessary for P. mirabilis to cause avian cellulitis. Furthermore, this species likely employs its own unique arsenal of virulence factors, as many identified mechanisms are analogous to those of E. coli. While antigenic gene clusters responsible for serogroups were identified, no clear trend was observed, and the gene cluster of LBUEL-A33 did not show homology with any sequenced Proteus serogroups. These results reinforce the understanding that this disease is multifactorial, necessitating further research to unravel the mechanisms and underpin the development of control and prevention strategies.
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Affiliation(s)
- Bruno Henrique Dias de Oliva
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PO-BOX 6001, Londrina, 86051-980, Paraná, Brazil
| | - Arthur Bossi do Nascimento
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PO-BOX 6001, Londrina, 86051-980, Paraná, Brazil
| | - João Paulo de Oliveira
- Laboratory of Microbial Biotechnology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Gustavo Henrique Migliorini Guidone
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PO-BOX 6001, Londrina, 86051-980, Paraná, Brazil
| | - Beatriz Lernic Schoeps
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PO-BOX 6001, Londrina, 86051-980, Paraná, Brazil
| | - Luana Carvalho Silva
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PO-BOX 6001, Londrina, 86051-980, Paraná, Brazil
| | - Mario Gabriel Lopes Barbosa
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PO-BOX 6001, Londrina, 86051-980, Paraná, Brazil
| | - Victor Hugo Montini
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PO-BOX 6001, Londrina, 86051-980, Paraná, Brazil
| | | | - Sérgio Paulo Dejato Rocha
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PO-BOX 6001, Londrina, 86051-980, Paraná, Brazil.
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Gingras L, Piché LC, Saucier L, Vincent AT. The complete genomic sequence of the type strain Brochothrix thermosphacta DSM 20171 highlights a diversity of prophages in this species. Microbiol Resour Announc 2024; 13:e0023924. [PMID: 38953337 PMCID: PMC11321008 DOI: 10.1128/mra.00239-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024] Open
Abstract
The bacterium Brochothrix thermosphacta is a known muscle food spoiler. Here, the complete genome sequence of the B. thermosphacta type strain, DSM 20171, is reported. Prediction of prophages and genomic islands reveals an unsuspected diversity in this bacterial species that deserves further investigation.
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Affiliation(s)
- Loic Gingras
- Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada
| | - Laurie C. Piché
- Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada
| | - Linda Saucier
- Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Quebec, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels, Faculté des Sciences de L'agriculture et de l'Alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche en infectiologie porcine et avicole, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
| | - Antony T. Vincent
- Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels, Faculté des Sciences de L'agriculture et de l'Alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche en infectiologie porcine et avicole, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, Quebec, Canada
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Dos Santos A, Schultz J, Almeida Trapp M, Modolon F, Romanenko A, Kumar Jaiswal A, Gomes L, Rodrigues-Filho E, Rosado AS. Investigating Polyextremophilic Bacteria in Al Wahbah Crater, Saudi Arabia: A Terrestrial Model for Life on Saturn's Moon Enceladus. ASTROBIOLOGY 2024; 24:824-838. [PMID: 39159439 DOI: 10.1089/ast.2024.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
The study of extremophilic microorganisms has sparked interest in understanding extraterrestrial microbial life. Such organisms are fundamental for investigating life forms on Saturn's icy moons, such as Enceladus, which is characterized by potentially habitable saline and alkaline niches. Our study focused on the salt-alkaline soil of the Al Wahbah crater in Saudi Arabia, where we identified microorganisms that could be used as biological models to understand potential life on Enceladus. The search involved isolating 48 bacterial strains, sequencing the genomes of two thermo-haloalkaliphilic strains, and characterizing them for astrobiological application. A deeper understanding of the genetic composition and functional capabilities of the two novel strains of Halalkalibacterium halodurans provided valuable insights into their survival strategies and the presence of coding genes and pathways related to adaptations to environmental stressors. We also used mass spectrometry with a molecular network approach, highlighting various classes of molecules, such as phospholipids and nonproteinogenic amino acids, as potential biosignatures. These are essential features for understanding life's adaptability under extreme conditions and could be used as targets for biosignatures in upcoming missions exploring Enceladus' orbit. Furthermore, our study reinforces the need to look at new extreme environments on Earth that might contribute to the astrobiology field.
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Affiliation(s)
- Alef Dos Santos
- Department of Chemistry, Federal University of São Carlos, São Carlos, Brazil
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Júnia Schultz
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marilia Almeida Trapp
- Analytical Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Fluvio Modolon
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrii Romanenko
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Arun Kumar Jaiswal
- Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Lucas Gomes
- Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Alexandre Soares Rosado
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Kalizang'oma A, Swarthout TD, Mwalukomo TS, Kamng’ona A, Brown C, Msefula J, Demetriou H, Chan JM, Roalfe L, Obolski U, Lourenço J, Goldblatt D, Chaguza C, French N, Heyderman RS. Clonal Expansion of a Streptococcus pneumoniae Serotype 3 Capsule Variant Sequence Type 700 With Enhanced Vaccine Escape Potential After 13-Valent Pneumococcal Conjugate Vaccine Introduction. J Infect Dis 2024; 230:e189-e198. [PMID: 39052729 PMCID: PMC11272040 DOI: 10.1093/infdis/jiae040] [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: 12/13/2022] [Accepted: 01/21/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Streptococcus pneumoniae serotype 3 remains a problem globally. Malawi introduced 13-valent pneumococcal conjugate vaccine (PCV13) in 2011, but there has been no direct protection against serotype 3 carriage. We explored whether vaccine escape by serotype 3 is due to clonal expansion of a lineage with a competitive advantage. METHODS The distribution of serotype 3 Global Pneumococcal Sequence Clusters (GPSCs) and sequence types (STs) globally was assessed using sequences from the Global Pneumococcal Sequencing Project. Whole-genome sequences of 135 serotype 3 carriage isolates from Blantyre, Malawi (2015-2019) were analyzed. Comparative analysis of the capsule locus, entire genomes, antimicrobial resistance, and phylogenetic reconstructions were undertaken. Opsonophagocytosis was evaluated using serum samples from vaccinated adults and children. RESULTS Serotype 3 GPSC10-ST700 isolates were most prominent in Malawi. Compared with the prototypical serotype 3 capsular polysaccharide locus sequence, 6 genes are absent, with retention of capsule polysaccharide biosynthesis. This lineage is characterized by increased antimicrobial resistance and lower susceptibility to opsonophagocytic killing. CONCLUSIONS A serotype 3 variant in Malawi has genotypic and phenotypic characteristics that could enhance vaccine escape and clonal expansion after post-PCV13 introduction. Genomic surveillance among high-burden populations is essential to improve the effectiveness of next-generation pneumococcal vaccines.
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Affiliation(s)
- Akuzike Kalizang'oma
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Todd D Swarthout
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Thandie S Mwalukomo
- School of Medicine and Oral Health, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Arox Kamng’ona
- School of Life Sciences and Allied Health Professionals, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Comfort Brown
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Jacquline Msefula
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
| | - Hayley Demetriou
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Jia Mun Chan
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Lucy Roalfe
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Uri Obolski
- Porter School of the Environment and Earth Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Jose Lourenço
- Faculdade de Ciências, BioISI, Universidade de Lisboa, Lisbon, Portugal
| | - David Goldblatt
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Chrispin Chaguza
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut, USA
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, USA
| | - Neil French
- Institute of Infection, Veterinary and Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, United Kingdom
| | - Robert S Heyderman
- NIHR Mucosal Pathogens Research Unit, Research Department of Infection, Division of Infection and Immunity, University College London, London, United Kingdom
- Pneumonia and Meningitis Pathogens Associate Research Group, Malawi-Liverpool-Wellcome Research Programme, Blantyre, Malawi
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Chekesa B, Singh H, Gonzalez-Juarbe N, Vashee S, Wiscovitch-Russo R, Dupont CL, Girma M, Kerro O, Gumi B, Ameni G. Pangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia. PLoS One 2024; 19:e0304060. [PMID: 39052555 PMCID: PMC11271921 DOI: 10.1371/journal.pone.0304060] [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: 03/06/2024] [Accepted: 05/06/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND The lineage 4 (L4) of Mycobacterium tuberculosis (MTB) is not only globally prevalent but also locally dominant, surpassing other lineages, with lineage 2 (L2) following in prevalence. Despite its widespread occurrence, factors influencing the expansion of L4 and its sub-lineages remain poorly understood both at local and global levels. Therefore, this study aimed to conduct a pan-genome and identify genomic signatures linked to the elevated prevalence of L4 sublineages among extrapulmonary TB (EPTB) patients in western Ethiopia. METHODS A cross-sectional study was conducted at an institutional level involving confirmed cases of extrapulmonary tuberculosis (EPTB) patients from August 5, 2018, to December 30, 2019. A total of 75 MTB genomes, classified under lineage 4 (L4), were used for conducting pan-genome and genome-wide association study (GWAS) analyses. After a quality check, variants were identified using MTBseq, and genomes were de novo assembled using SPAdes. Gene prediction and annotation were performed using Prokka. The pan-genome was constructed using GET_HOMOLOGUES, and its functional analysis was carried out with the Bacterial Pan-Genome Analysis tool (BPGA). For GWAS analysis, Scoary was employed with Benjamini-Hochberg correction, with a significance threshold set at p-value ≤ 0.05. RESULTS The analysis revealed a total of 3,270 core genes, predominantly associated with orthologous groups (COG) functions, notably in the categories of '[R] General function prediction only' and '[I] Lipid transport and metabolism'. Conversely, functions related to '[N] Cell motility' and '[Q] Secondary metabolites biosynthesis, transport, and catabolism' were primarily linked to unique and accessory genes. The pan-genome of MTB L4 was found to be open. Furthermore, the GWAS study identified genomic signatures linked to the prevalence of sublineages L4.6.3 and L4.2.2.2. CONCLUSIONS Apart from host and environmental factors, the sublineage of L4 employs distinct virulence factors for successful dissemination in western Ethiopia. Given that the functions of these newly identified genes are not well understood, it is advisable to experimentally validate their roles, particularly in the successful transmission of specific L4 sublineages over others.
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Affiliation(s)
- Basha Chekesa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Collage of Natural and Computational Science, Wallaga University, Nekemte, Ethiopia
| | - Harinder Singh
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - Sanjay Vashee
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | | | - Musse Girma
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Oudessa Kerro
- Institute of Agriculture, The University of Tennessee, Tennessee, Knoxville, United States of America
| | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
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Mian S, Machado ACZ, Hoshino RT, Mosela M, Higashi AY, Shimizu GD, Teixeira GM, Nogueira AF, Giacomin RM, Ribeiro LAB, Koltun A, de Assis R, Gonçalves LSA. Complete genome sequence of Bacillus velezensis strain Ag109, a biocontrol agent against plant-parasitic nematodes and Sclerotinia sclerotiorum. BMC Microbiol 2024; 24:194. [PMID: 38849775 PMCID: PMC11157790 DOI: 10.1186/s12866-024-03282-9] [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: 05/17/2023] [Accepted: 03/28/2024] [Indexed: 06/09/2024] Open
Abstract
Soybean is the main oilseed cultivated worldwide. Even though Brazil is the world's largest producer and exporter of soybean, its production is severely limited by biotic factors. Soil borne diseases are the most damaging biotic stressors since they significantly reduce yield and are challenging to manage. In this context, the present study aimed to evaluate the potential of a bacterial strain (Ag109) as a biocontrol agent for different soil pathogens (nematodes and fungi) of soybean. In addition, the genome of Ag109 was wholly sequenced and genes related to secondary metabolite production and plant growth promotion were mined. Ag109 showed nematode control in soybean and controlled 69 and 45% of the populations of Meloidogyne javanica and Pratylenchus brachyurus, respectively. Regarding antifungal activity, these strains showed activity against Macrophomia phaseolina, Rhizoctonia solani, and Sclerotinia sclerotiorum. For S. sclerotiorum, this strain increased the number of healthy plants and root dry mass compared to the control (with inoculation). Based on the average nucleotide identity and digital DNA-DNA hybridization, this strain was identified as Bacillus velezensis. Diverse clusters of specific genes related to secondary metabolite biosynthesis and root growth promotion were identified, highlighting the potential of this strain to be used as a multifunctional microbial inoculant that acts as a biological control agent while promoting plant growth in soybean.
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Affiliation(s)
- Silas Mian
- Agronomy Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | | | - Rodrigo Thibes Hoshino
- Agronomy Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - Mirela Mosela
- Microbiology Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - Allan Yukio Higashi
- Agronomy Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - Gabriel Danilo Shimizu
- Agronomy Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | - Gustavo Manoel Teixeira
- Microbiology Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
| | | | - Renata Mussoi Giacomin
- Biology Department, Universidade Estadual Do Centro Oeste, Guarapuava, Paraná, 85015-430, Brazil
| | | | - Alessandra Koltun
- Center for Molecular Biology and Genetic Engineering, UNICAMP, Campinas, São Paulo, 13083-875, Brazil
| | - Rafael de Assis
- Agronomy Department, Universidade Estadual de Londrina, Londrina, Paraná, 86097-570, Brazil
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Talat A, Khan F, Khan AU. Genome analyses of colistin-resistant high-risk bla NDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings. BMC Microbiol 2024; 24:174. [PMID: 38769479 PMCID: PMC11103832 DOI: 10.1186/s12866-024-03306-4] [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: 12/19/2023] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Colistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT). RESULTS This study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek®2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC = 4 μg/mL), while broth microdilution identified 48 (MIC = 32-128 μg/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357). CONCLUSION The global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.
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Affiliation(s)
- Absar Talat
- Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Fatima Khan
- Microbiology Department, JNMC and Hospital, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Withatanung P, Janesomboon S, Vanaporn M, Muangsombut V, Charoensudjai S, Baker DJ, Wuthiekanun V, Galyov EE, Clokie MRJ, Gundogdu O, Korbsrisate S. Induced Burkholderia prophages detected from the hemoculture: a biomarker for Burkholderia pseudomallei infection. Front Microbiol 2024; 15:1361121. [PMID: 38633694 PMCID: PMC11022660 DOI: 10.3389/fmicb.2024.1361121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/11/2024] [Indexed: 04/19/2024] Open
Abstract
Bacteriophages (phages), viruses that infect bacteria, are found in abundance not only in the environment but also in the human body. The use of phages for the diagnosis of melioidosis, a tropical infectious disease caused by Burkholderia pseudomallei, is emerging as a promising novel approach, but our understanding of conditions under which Burkholderia prophages can be induced remains limited. Here, we first demonstrated the isolation of Burkholderia phages from the hemocultures of melioidosis patients. The B. pseudomallei-positive hemoculture bottles were filtered to remove bacteria, and then phages were isolated and purified by spot and double agar overlay plaque assays. Forty blood samples (hemoculture-confirmed melioidosis) were tested, and phages were found in 30% of the samples. Transmission electron microscopy and genome analysis of the isolated phages, vB_HM387 and vB_HM795, showed that both phages are Myoviruses. These two phages were stable at a pH of 5-7 and temperatures of 25-37°C, suggesting their ability to survive in human blood. The genome sizes of vB_HM387 and vB_HM795 are 36.3 and 44.0 kb, respectively. A phylogenetic analysis indicated that vB_HM387 has homologs, but vB_HM795 is a novel Myovirus, suggesting the heterogeneity of Burkholderia phages in melioidosis patients. The key finding that Burkholderia phages could be isolated from the blood of melioidosis patients highlights the potential application of phage-based assays by detecting phages in blood as a pathogen-derived biomarker of infection.
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Affiliation(s)
- Patoo Withatanung
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sujintana Janesomboon
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Muthita Vanaporn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Veerachat Muangsombut
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Dave J. Baker
- Science Operations, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Edouard E. Galyov
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ozan Gundogdu
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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10
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Zorec TM, Alm E, Lind Karlberg M, Advani R, Hošnjak L, Poljak M. Comprehensive analysis of 66 complete molluscum contagiosum virus (MOCV) genomes: characterization and functional annotation of 47 novel complete MOCV genomes, including the first genome of MOCV genotype 3, and a proposal for harmonized MOCV genotyping indexing. mBio 2023; 14:e0222423. [PMID: 37947415 PMCID: PMC10746250 DOI: 10.1128/mbio.02224-23] [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: 08/26/2023] [Accepted: 10/05/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Four molluscum contagiosum virus (MOCV) genotypes (MOCV1-4) and four subtype variants were partially characterized using restriction enzyme profiling in the 1980s/1990s, but complete genome sequences of only MOCV1 and MOCV2 are available. The evolutionary pathways whereby genotypes/subtype variants with unavailable sequences emerged and whether all MOCVs can be detected using current diagnostic approaches remain unclear. We fully characterized 47 novel complete MOCV genomes, including the first complete MOCV3 genome, expanding the number of fully characterized genomes to 66. For reliably classifying the novel non-MOCV1/2 genomes, we developed and validated a framework for matching sequence-derived restriction maps with those defining MOCV subtypes in pioneering studies. Six phylogenetic subgroups (PG1-6) were identified, PG5 representing a novel MOCV2 subtype. The phylogenetic subgroups diverged from the prototype lineages following large-scale recombination events and hinted at partial sequence content of MOCV4 and direction of recombinant transfer in the events spawning PG5 and yet undetected MOCV1vb variant.
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Affiliation(s)
- Tomaž Mark Zorec
- Laboratory for Molecular Microbiology and Slovenian HIV/AIDS Reference Center, Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Erik Alm
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | | | - Reza Advani
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Lea Hošnjak
- Laboratory for Molecular Microbiology and Slovenian HIV/AIDS Reference Center, Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Laboratory for Molecular Microbiology and Slovenian HIV/AIDS Reference Center, Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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11
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Girijan SK, Pillai D, Devika R. Complete genome sequence analysis of multi-drug resistant Klebsiella pneumoniae THK strain isolated from aquaculture farm in Kerala, India. 3 Biotech 2023; 13:394. [PMID: 37970451 PMCID: PMC10643474 DOI: 10.1007/s13205-023-03820-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/11/2023] [Indexed: 11/17/2023] Open
Abstract
The emergence of microorganisms with resistance toward antibiotics has been widely recognized as a growing hazard to public health. Here, we report the whole genome sequence of Klebsiella pneumoniae strain THK, which was isolated from an aquaculture farm in Kerala, India. Standard disc diffusion and strip methods were used for antibiotic susceptibility testing and minimum inhibitory concentration detection. The isolate showed high level of resistance against beta-lactam, aminoglycosides, fluoroquinolones, macrolides, tetracyclines, chloramphenicol, sulfonamides, and cephalosporin class of antibiotics, but were sensitive to carbapenem and polymyxins. The whole genome sequence analysis revealed that the final assembly of THK strain consisted of 30 contigs of 5, 199,186 bp including four plasmid sequences plasmid_690 (1 contig), plasmid_710 (9 contigs), plasmid_1222 (6 contigs), and plasmid_1528 (1 contig). Sequence analysis revealed that the isolate has a number of genes encoding for antibiotic resistance and virulence. The findings indicated that antibiotics present in aquatic environments at sub-inhibitory concentrations increase the selection pressure affecting the cell function of even normal aquatic microorganisms to change the genetic expression of virulence factors or acquire resistance genes through various transfer mechanisms. This strain would be of significant interest for thorough comparative genomic study, given the known vast diversity of pathogenic and antibiotic resistance potentials.
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Affiliation(s)
- Sneha Kalasseril Girijan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Panangad, Kochi, Kerala India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Panangad, Kochi, Kerala India
| | - Raj Devika
- National Institute of Oceanography, Regional Centre, Kochi, Kerala India
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12
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Prithvisagar KS, Gollapalli P, D’Souza C, Rai P, Karunasagar I, Karunasagar I, Ballamoole KK. Genome analysis of clinical genotype Vibrio vulnificus isolated from seafood in Mangaluru Coast, India provides insights into its pathogenicity. Vet Q 2023; 43:1-17. [PMID: 37478018 PMCID: PMC10438861 DOI: 10.1080/01652176.2023.2240389] [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: 11/29/2022] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023] Open
Abstract
Vibrio vulnificus an opportunistic human pathogen native to marine/estuarine environment, is one of the leading causes of death due to seafood consumption and exposure of wounds to seawater worldwide. The present study involves the whole genome sequence analysis of an environmental strain of V. vulnificus (clinical genotype) isolated from seafood along the Mangaluru coast of India. The sequenced genome data was subjected to in-silico analysis of phylogeny, virulence genes, antimicrobial resistance determinants, and secretary proteins using suitable bioinformatics tools. The sequenced isolate had an overall genome length of 4.8 Mb and GC content of 46% with 4400 coding DNA sequences. The sequenced strain belongs to a new sequence type (Multilocus sequence typing) and was also found to branch with a phylogenetic lineage that groups the most infectious strains of V. vulnificus. The seafood isolate had complete genes involved in conferring serum resistance yet showed limited serum resistance. The study identified several genes against the antibiotics that are commonly used in their treatment, highlighting the need for alternative treatments. Also, the secretory protein analysis revealed genes associated with major pathways like ABC transporters, two-component systems, quorum sensing, biofilm formation, cationic antimicrobial peptide (CAMP) resistance, and others that play a critical role in the pathogenesis of the V. vulnificus. To the best of our knowledge, this is the first report of a detailed analysis of the genomic information of a V. vulnificus isolated from the Indian subcontinent and provides evidence that raises public health concerns about the safety of seafood.
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Affiliation(s)
- Kattapuni Suresh Prithvisagar
- Department of Infectious Diseases and Microbial Genomics, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, India
| | - Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, Nitte (Deemed to be University), Mangaluru, India
| | - Caroline D’Souza
- Department of Infectious Diseases and Microbial Genomics, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, India
| | - Praveen Rai
- Department of Infectious Diseases and Microbial Genomics, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, India
| | - Iddya Karunasagar
- Department of Infectious Diseases and Microbial Genomics, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, India
| | - Indrani Karunasagar
- Department of Infectious Diseases and Microbial Genomics, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, India
| | - Krishna Kumar Ballamoole
- Department of Infectious Diseases and Microbial Genomics, Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Mangaluru, India
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13
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Marcoux PÉ, Girard SB, Fournier KC, Tardif CA, Gosselin A, Charette SJ. Interaction of pAsa5 and pAsa8 Plasmids in Aeromonas salmonicida subsp. salmonicida. Microorganisms 2023; 11:2685. [PMID: 38004697 PMCID: PMC10673383 DOI: 10.3390/microorganisms11112685] [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: 10/08/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The plasmid known as pAsa5 is present in Aeromonas salmonicida subsp. salmonicida, a fish pathogen. The pAsa5 plasmid carries genes that are essential for the bacterium's virulence. Recombination events are known to occur in pAsa5, resulting in the loss of certain segments or the acquisition of additional genetic elements. For example, the transposon carried by the large pAsa8 plasmid was found to be inserted into the pAsa5 plasmid in the SHY16-3432 strain, enabling the addition of antibiotic resistance genes to this plasmid, which does not normally possess any. In this study, we present the isolation of additional strains carrying pAsa8. Further analyses of these strains revealed that a fusion between pAsa5 and the complete version of pAsa8 is possible. The pAsa8 transposon insertion in pAsa5 seen in the SHY16-3432 strain appears to be an aberrant event compared to the fusion of the two full-length plasmids. A 22-nucleotide sequence, present in both plasmids, serves as the site for the fusion of the two plasmids. Moreover, it is possible to introduce pAsa8 through conjugation into naive strains of A. salmonicida subsp. salmonicida and once the plasmid is within a new strain, the fusion with pAsa5 is detectable. This study reveals a previously unexplored aspect of pAsa5 plasmid biology, highlighting an additional risk for the spread of antibiotic resistance genes in A. salmonicida subsp. salmonicida.
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Affiliation(s)
- Pierre-Étienne Marcoux
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Sarah B. Girard
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Kim C. Fournier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Catherine A. Tardif
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Ariane Gosselin
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Steve J. Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC G1V 0A6, Canada; (P.-É.M.); (K.C.F.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC G1V 0A6, Canada
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC G1V 4G5, Canada
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14
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Srivastava N, Shiburaj S, Khare SK. Pan-genomic comparison of a potential solvent-tolerant alkaline protease-producing Exiguobacterium sp. TBG-PICH-001 isolated from a marine habitat. 3 Biotech 2023; 13:371. [PMID: 37854939 PMCID: PMC10579205 DOI: 10.1007/s13205-023-03796-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023] Open
Abstract
The identification and applicability of bacteria are inconclusive until comprehended with genomic repositories. Our isolate, Exiguobacterium sp. TBG-PICH-001 exhibited excellent halo- and organic solvent tolerance with simultaneous production of alkaline protease/s (0.512 IU/mL). The crude protease (1 IU) showed a 43.57% degradation of whey protein. The bulk proteins in the whey were hydrolyzed to smaller peptides which were evident in the SDS-PAGE profile. With such characteristics, the isolate became interesting for its genomic studies. The TBG-PICH-001 genome was found to be 3.14 Mb in size with 17 contigs and 47.33% GC content. The genome showed 3176 coding genes, and 2699 genes were characterized for their functionality. The Next-Generation-Sequencing of the genome identified only the isolate's genus; hence we attempted to delineate its species position. The genomes of the isolate and other representative Exiguobacterium spp. were compared based on orthologous genes (Orthovenn2 server). A pan-genomic analysis revealed the match of TBG-PICH-001 with 15 uncharacterized Exiguobacterium genomes at the species level. All these collectively matched with Exiguobacterium indicum, and the results were reconfirmed through phylogenetic studies. Further, the Exiguobacterium indicum genomes were engaged for homology studies rendering 11 classes of protease genes. Two putative proteases (Zinc metalloprotease and Serine protease) obtained from homology were checked for PCR amplification using genomic DNA of TBG-PICH-001 and other Exiguobacterium genomes. The results showed amplification only in the Exiguobacterium indicum genome. These protease genes, after sequencing, were matched with the TBG-PICH-001 genome. Their presence in its whole genome experimentally validated the study. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03796-5.
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Affiliation(s)
- Nitin Srivastava
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016 India
| | - Sugathan Shiburaj
- Department of Botany, University of Kerala, Palayam, Thiruvananthapuram, Kerala 695034 India
| | - Sunil Kumar Khare
- Enzyme and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016 India
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15
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Ariute JC, Coelho-Rocha ND, Dantas CWD, de Vasconcelos LAT, Profeta R, de Jesus Sousa T, de Souza Novaes A, Galotti B, Gomes LG, Gimenez EGT, Diniz C, Dias MV, de Jesus LCL, Jaiswal AK, Tiwari S, Carvalho R, Benko-Iseppon AM, Brenig B, Azevedo V, Barh D, Martins FS, Aburjaile F. Probiogenomics of Leuconostoc Mesenteroides Strains F-21 and F-22 Isolated from Human Breast Milk Reveal Beneficial Properties. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10170-7. [PMID: 37804433 DOI: 10.1007/s12602-023-10170-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 10/09/2023]
Abstract
Bacteria of the Leuconostoc genus are Gram-positive bacteria that are commonly found in raw milk and persist in fermented dairy products and plant food. Studies have already explored the probiotic potential of L. mesenteroides, but not from a probiogenomic perspective, which aims to explore the molecular features responsible for their phenotypes. In the present work, probiogenomic approaches were applied in strains F-21 and F-22 of L. mesenteroides isolated from human milk to assess their biosafety at the molecular level and to correlate molecular features with their potential probiotic characteristics. The complete genome of strain F-22 is 1.99 Mb and presents one plasmid, while the draft genome of strain F-21 is 1.89 Mb and presents four plasmids. A high percentage of average nucleotide identity among other genomes of L. mesenteroides (≥ 96%) corroborated the previous taxonomic classification of these isolates. Genomic regions that influence the probiotic properties were identified and annotated. Both strains exhibited wide genome plasticity, cell adhesion ability, proteolytic activity, proinflammatory and immunomodulation capacity through interaction with TLR-NF-κB and TLR-MAPK pathway components, and no antimicrobial resistance, denoting their potential to be candidate probiotics. Further, the strains showed bacteriocin production potential and the presence of acid, thermal, osmotic, and bile salt resistance genes, indicating their ability to survive under gastrointestinal stress. Taken together, our results suggest that L. mesenteroides F-21 and F-22 are promising candidates for probiotics in the food and pharmaceutical industries.
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Affiliation(s)
- Juan Carlos Ariute
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Nina Dias Coelho-Rocha
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Carlos Willian Dias Dantas
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Larissa Amorim Tourinho de Vasconcelos
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Rodrigo Profeta
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Thiago de Jesus Sousa
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Ane de Souza Novaes
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Bruno Galotti
- Laboratory of Biotherapeutic Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Lucas Gabriel Gomes
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Enrico Giovanelli Toccani Gimenez
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- Graduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Carlos Diniz
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Mariana Vieira Dias
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Luís Cláudio Lima de Jesus
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Arun Kumar Jaiswal
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Sandeep Tiwari
- Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, 40231-300, Brazil
| | - Rodrigo Carvalho
- Department of Biochemistry and Biophysics, Institute of Health Sciences, Federal University of Bahia, Salvador, Bahia, 40231-300, Brazil
| | - Ana Maria Benko-Iseppon
- Laboratory of Plants Genetics and Biotechnology, Genetics Department, Biosciences Center, Federal University of Pernambuco, Recife, Pernambuco, 50740-600, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, 721172, India
| | - Flaviano S Martins
- Laboratory of Biotherapeutic Agents, Department of Microbiology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Flavia Aburjaile
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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16
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Hurtado R, Barh D, de Jesus LCL, Canário Viana MV, Tiwari S, Aburjaile FF, Carhuaricra Huaman DE, Brenig B, Hernández LM, Azevedo V. The genomic approach of antimicrobial resistance of Salmonella Typhimurium isolates from guinea pigs in Lima, Peru. Res Microbiol 2023; 174:104086. [PMID: 37307910 DOI: 10.1016/j.resmic.2023.104086] [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: 12/07/2022] [Revised: 05/12/2023] [Accepted: 05/27/2023] [Indexed: 06/14/2023]
Abstract
Salmonella Typhimurium is an important agent of foodborne diseases. In Peru, the emergence of multidrug-resistant isolates of S. Typhimurium from the food chain could be linked to guinea pig farming as a potential reservoir and their uncontrolled antibiotic treatment against salmonellosis. In this study, we performed the sequencing, genomic diversity, and characterization of resistance elements transmitted by isolates from farm and meat guinea pigs. The genomic diversity and antimicrobial resistance of S. Typhimurium isolates were performed using nucleotide similarity, cgMLST, serotyping, phylogenomic analyses, and characterization of resistance plasmids. We found at least four populations of isolates from farm guinea pigs and four populations from meat guinea pigs without finding isolated transmission between both resources. Genotypic resistance to antibiotics was observed in at least 50% of the isolates. Among the farm guinea pig isolates, ten were found to be resistant to nalidixic acid, and two isolates exhibited multidrug resistance to aminoglycosides, tetracycline-fluoroquinolone (carrying strA-strB-tetA-tetB genes and gyrA S83F mutation), or trimethoprim-sulfonamide (carrying AaadA1-drfA15-sul1 genes). Additionally, two isolates from the meat source were resistant to fluoroquinolones (one of which had enrofloxacin resistance). The transmissible resistance plasmids with insertion sequences (IS) such as IncI-gamma-K1-ISE3-IS6, IncI1-I (alpha)-IS21-Tn10, and Col (pHAD28) were commonly found in isolates belonging to the HC100-9757 cluster from both guinea pigs and human hosts. Altogether, our work provides resistance determinants profiles and Salmonella sp. circulating lineages using WGS data that can promote better sanitary control and adequate antimicrobial prescription.
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Affiliation(s)
- Raquel Hurtado
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Debmalya Barh
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil; Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, 721172, India.
| | - Luís Cláudio Lima de Jesus
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Marcus Vinicius Canário Viana
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Sandeep Tiwari
- Pós-graduação em Microbiologia, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahía, Brazil; Programa de Pós-graduação em Imunologia, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahía, Brazil.
| | - Flávia Figueira Aburjaile
- Preventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Dennis E Carhuaricra Huaman
- SANIGEN, Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, San Borja, Lima, 15021, Peru.
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany.
| | - Lenin Maturrano Hernández
- SANIGEN, Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, San Borja, Lima, 15021, Peru.
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
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Vincent AT, Bergeron RP, Piché LC, Prado D, Saucier L. Genomic Characterization of a Tetracycline-Resistant Strain of Brochothrix thermosphacta Highlights Plasmids Partially Shared between Various Strains. Genes (Basel) 2023; 14:1731. [PMID: 37761871 PMCID: PMC10531132 DOI: 10.3390/genes14091731] [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: 07/31/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
The Gram-positive bacterium Brochothrix thermosphacta is a spoilage agent commonly found on meat products. While the tet(L) gene, which confers resistance to tetracycline, has been identified in certain strains of B. thermosphacta, only a limited number of studies have investigated this gene and its potential presence on mobile DNA elements. This study aims to analyze the tetracycline-resistant strain B. thermosphacta BT469 at the genomic level to gain insight into the molecular determinants responsible for this resistance. Three plasmids have been identified in the strain: pBT469-1, which contains a tetR gene; pBT469-2, which harbours the tet(L) gene responsible for tetracycline resistance; and pBT469-3, which carries genes encoding for a thioredoxin and a phospholipase A2. Homology searches among sequences in public databases have revealed that the plasmid pBT469-2 is currently unique to the BT469 strain. However, the pBT469-1 plasmid is also found in three other strains of B. thermosphacta. Notably, sequences similar to pBT469-1 and pBT469-2 were also found in other bacterial genera, suggesting that these plasmids may be part of a diverse family present in several bacterial genera. Interestingly, sequences of various strains of B. thermosphacta show a high level of similarity with pBT469-3, suggesting that variants of this plasmid could be frequently found in this bacterium.
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Affiliation(s)
- Antony T. Vincent
- Département des Sciences Animales, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Romain P. Bergeron
- Département des Sciences Animales, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada
- Site de Bourg-end-Bresse, IUT Lyon 1 Site de Bourg-en-Bresse, 01000 Bourg-en-Bresse, France
| | - Laurie C. Piché
- Département des Sciences Animales, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - David Prado
- Département des Sciences Animales, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Linda Saucier
- Département des Sciences Animales, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada
- Institut sur la Nutrition et les Aliments Fonctionnels, Faculté des Sciences de L’agriculture et de L’alimentation, Université Laval, Quebec City, QC G1V 0A6, Canada
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18
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Thirugnanam T, Dharumadurai D, Babalola OO. Draft Genome Sequence of Streptomyces moderatus DT446, Isolated from Root Nodules of Casuarina cunninghamiana. Microbiol Resour Announc 2023; 12:e0018123. [PMID: 37432108 PMCID: PMC10443386 DOI: 10.1128/mra.00181-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/04/2023] [Indexed: 07/12/2023] Open
Abstract
A putative plant growth-promoting endophytic Streptomyces moderatus strain, DT446, was isolated from the root nodules of Casuarina cunninghamiana in Tamil Nadu, India. We report a draft genome sequence for S. moderatus DT446, with 8,168,245 bp and a GC content of 70.9%.
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Affiliation(s)
- Thirumagal Thirugnanam
- Department of Microbiology, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | | | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
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19
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Naud S, Valles C, Abdillah A, Abou Chacra L, Mekhalif FZ, Ibrahim A, Caputo A, Baudoin JP, Gouriet F, Bittar F, Lagier JC, Ranque S, Fenollar F, Tidjani Alou M, Raoult D. Preliminary landscape of Candidatus Saccharibacteria in the human microbiome. Front Cell Infect Microbiol 2023; 13:1195679. [PMID: 37577371 PMCID: PMC10414567 DOI: 10.3389/fcimb.2023.1195679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date. Methods In this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics. Results Using Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples. Conclusion This study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.
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Affiliation(s)
- Sabrina Naud
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Camille Valles
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Abdourahim Abdillah
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Linda Abou Chacra
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Fatima Zouina Mekhalif
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Ahmad Ibrahim
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Aurelia Caputo
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Pierre Baudoin
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Frédérique Gouriet
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Fadi Bittar
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Stéphane Ranque
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Florence Fenollar
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, IHU Méditerranée InfectionMarseille, France
| | - Maryam Tidjani Alou
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
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20
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Silva NM, Romagnoli CL, Santiago CRDN, de Lacerda JPA, Leão SC, Digiampietri LA, Viana-Niero C. Multi-Approach Characterization of Novel Pyrene-Degrading Mycolicibacterium austroafricanum Isolates Lacking nid Genes. Microorganisms 2023; 11:1413. [PMID: 37374915 DOI: 10.3390/microorganisms11061413] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/21/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are chemical compounds that are widespread in the environment, arising from the incomplete combustion of organic material, as well as from human activities involving petrol exploitation, petrochemical industrial waste, gas stations, and environmental disasters. PAHs of high molecular weight, such as pyrene, have carcinogenic and mutagenic effects and are considered pollutants. The microbial degradation of PAHs occurs through the action of multiple dioxygenase genes (nid), which are localized in genomic island denominate region A, and cytochrome P450 monooxygenases genes (cyp) dispersed in the bacterial genome. This study evaluated pyrene degradation by five isolates of Mycolicibacterium austroafricanum using 2,6-dichlorophenol indophenol (DCPIP assay), gas chromatography/mass spectrometry (CG/MS), and genomic analyses. Two isolates (MYC038 and MYC040) exhibited pyrene degradation indexes of 96% and 88%, respectively, over a seven-day incubation period. Interestingly, the genomic analyses showed that the isolates do not have nid genes, which are involved in PAH biodegradation, despite their ability to degrade pyrene, suggesting that degradation may occur due to the presence of cyp150 genes, or even genes that have not yet been described. To the best of our knowledge, this is the first report of isolates without nid genes demonstrating the ability to degrade pyrene.
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Affiliation(s)
- Natalia Maria Silva
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | - Camila Lopes Romagnoli
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | | | - João Paulo Amorim de Lacerda
- Laboratory of Chemistry and Manufactured Products, Institute of Technological Research, São Paulo 05508-901, Brazil
| | - Sylvia Cardoso Leão
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo 04023-901, Brazil
| | | | - Cristina Viana-Niero
- Department of Microbiology, Immunology and Parasitology, Federal University of São Paulo, São Paulo 04023-901, Brazil
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21
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Salcedo-Mejía LA, Tapia-Chirinos S, Atarama-Orejuela J, Grabiel S, Villalobos E, Gómez-Sánchez M, Velazco-Peña R. Near-Complete Genome Sequence of White Spot Syndrome Virus Infecting Cultivated Shrimp (Penaeus vannamei) in Peru. Microbiol Resour Announc 2023:e0004023. [PMID: 37158747 DOI: 10.1128/mra.00040-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
White spot syndrome virus (WSSV) infects a broad range of aquatic animals, including the shrimp Penaeus vannamei. In this study, we report one genome sequence of WSSV present in shrimp on the north coast of Peru.
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Affiliation(s)
- Luis Alberto Salcedo-Mejía
- Laboratorio de Sanidad Acuícola, Sede Tumbes, Organismo Nacional de Sanidad Pesquera (SANIPES), Lima, Peru
| | - Stephanie Tapia-Chirinos
- Laboratorio de Sanidad Acuícola, Sede Tumbes, Organismo Nacional de Sanidad Pesquera (SANIPES), Lima, Peru
| | - Joel Atarama-Orejuela
- Laboratorio de Sanidad Acuícola, Sede Tumbes, Organismo Nacional de Sanidad Pesquera (SANIPES), Lima, Peru
| | - Sandra Grabiel
- Laboratorio de Sanidad Acuícola, Sede Tumbes, Organismo Nacional de Sanidad Pesquera (SANIPES), Lima, Peru
| | - Eduard Villalobos
- Laboratorio de Sanidad Acuícola, Sede Tumbes, Organismo Nacional de Sanidad Pesquera (SANIPES), Lima, Peru
| | - Muriel Gómez-Sánchez
- Laboratorio de Sanidad Acuícola, Sede Tumbes, Organismo Nacional de Sanidad Pesquera (SANIPES), Lima, Peru
| | - Rodolfo Velazco-Peña
- Laboratorio de Sanidad Acuícola, Sede Tumbes, Organismo Nacional de Sanidad Pesquera (SANIPES), Lima, Peru
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22
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Najjari A, Boussetta A, Youssef N, Linares-Pastén JA, Mahjoubi M, Belloum R, Sghaier H, Cherif A, Ouzari HI. Physiological and genomic insights into abiotic stress of halophilic archaeon Natrinema altunense 4.1R isolated from a saline ecosystem of Tunisian desert. Genetica 2023; 151:133-152. [PMID: 36795306 PMCID: PMC9995536 DOI: 10.1007/s10709-023-00182-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023]
Abstract
Halophilic archaea are polyextremophiles with the ability to withstand fluctuations in salinity, high levels of ultraviolet radiation, and oxidative stress, allowing them to survive in a wide range of environments and making them an excellent model for astrobiological research. Natrinema altunense 4.1R is a halophilic archaeon isolated from the endorheic saline lake systems, Sebkhas, located in arid and semi-arid regions of Tunisia. It is an ecosystem characterized by periodic flooding from subsurface groundwater and fluctuating salinities. Here, we assess the physiological responses and genomic characterization of N. altunense 4.1R to UV-C radiation, as well as osmotic and oxidative stresses. Results showed that the 4.1R strain is able to survive up to 36% of salinity, up to 180 J/m2 to UV-C radiation, and at 50 mM of H2O2, a resistance profile similar to Halobacterium salinarum, a strain often used as UV-C resistant model. In order to understand the genetic determinants of N. altunense 4.1R survival strategy, we sequenced and analyzed its genome. Results showed multiple gene copies of osmotic stress, oxidative stress, and DNA repair response mechanisms supporting its survivability at extreme salinities and radiations. Indeed, the 3D molecular structures of seven proteins related to responses to UV-C radiation (excinucleases UvrA, UvrB, and UvrC, and photolyase), saline stress (trehalose-6-phosphate synthase OtsA and trehalose-phosphatase OtsB), and oxidative stress (superoxide dismutase SOD) were constructed by homology modeling. This study extends the abiotic stress range for the species N. altunense and adds to the repertoire of UV and oxidative stress resistance genes generally known from haloarchaeon.
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Affiliation(s)
- Afef Najjari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Ayoub Boussetta
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Noha Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Javier A Linares-Pastén
- Department of Biotechnology, Faculty of Engineering, Lunds Tekniska Högskola (LTH), Lund University, P. O. Box 124, 22100, Lund, Sweden.
| | - Mouna Mahjoubi
- University of Manouba, ISBST, LR11-ES31 BVBGR, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Rahma Belloum
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Haitham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Ariana, Tunisia
| | - Ameur Cherif
- University of Manouba, ISBST, LR11-ES31 BVBGR, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Hadda Imene Ouzari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
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Chromosomal Position of Ribosomal Protein Genes Affects Long-Term Evolution of Vibrio cholerae. mBio 2023; 14:e0343222. [PMID: 36861972 PMCID: PMC10127744 DOI: 10.1128/mbio.03432-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
It is unclear how gene order within the chromosome influences genome evolution. Bacteria cluster transcription and translation genes close to the replication origin (oriC). In Vibrio cholerae, relocation of s10-spc-α locus (S10), the major locus of ribosomal protein genes, to ectopic genomic positions shows that its relative distance to the oriC correlates to a reduction in growth rate, fitness, and infectivity. To test the long-term impact of this trait, we evolved 12 populations of V. cholerae strains bearing S10 at an oriC-proximal or an oriC-distal location for 1,000 generations. During the first 250 generations, positive selection was the main force driving mutation. After 1,000 generations, we observed more nonadaptative mutations and hypermutator genotypes. Populations fixed inactivating mutations at many genes linked to virulence: flagellum, chemotaxis, biofilm, and quorum sensing. Throughout the experiment, all populations increased their growth rates. However, those bearing S10 close to oriC remained the fittest, indicating that suppressor mutations cannot compensate for the genomic position of the main ribosomal protein locus. Selection and sequencing of the fastest-growing clones allowed us to characterize mutations inactivating, among other sites, flagellum master regulators. Reintroduction of these mutations into the wild-type context led to a ≈10% growth improvement. In conclusion, the genomic location of ribosomal protein genes conditions the evolutionary trajectory of V. cholerae. While genomic content is highly plastic in prokaryotes, gene order is an underestimated factor that conditions cellular physiology and evolution. A lack of suppression enables artificial gene relocation as a tool for genetic circuit reprogramming. IMPORTANCE The bacterial chromosome harbors several entangled processes such as replication, transcription, DNA repair, and segregation. Replication begins bidirectionally at the replication origin (oriC) until the terminal region (ter) organizing the genome along the ori-ter axis gene order along this axis could link genome structure to cell physiology. Fast-growing bacteria cluster translation genes near oriC. In Vibrio cholerae, moving them away was feasible but at the cost of losing fitness and infectivity. Here, we evolved strains harboring ribosomal genes close or far from oriC. Growth rate differences persisted after 1,000 generations. No mutation was able to compensate for the growth defect, showing that ribosomal gene location conditions their evolutionary trajectory. Despite the high plasticity of bacterial genomes, evolution has sculpted gene order to optimize the ecological strategy of the microorganism. We observed growth rate improvement throughout the evolution experiment that occurred at expense of energetically costly processes such the flagellum biosynthesis and virulence-related functions. From the biotechnological point of view, manipulation of gene order enables altering bacterial growth with no escape events.
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Lima A, Carolina Barbosa Caetano A, Hurtado Castillo R, Gonçalves Dos Santos R, Lucas Neres Rodrigues D, de Jesus Sousa T, Kato RB, Vinicius Canário Viana M, Cybelle Pinto Gomide A, Figueira Aburjaile F, Tiwari S, Jaiswal A, Gala-García A, Seyffert N, Luiz de Paula Castro T, Brenig B, Matiuzzi da Costa M, Maria Seles Dorneles E, Le Loir Y, Azevedo V. Comparative genomic analysis of ovine and other host associated isolates of Staphylococcus aureus exhibit the important role of mobile genetic elements and virulence factors in host adaptation. Gene 2023; 855:147131. [PMID: 36539044 DOI: 10.1016/j.gene.2022.147131] [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: 09/15/2022] [Revised: 12/01/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Staphylococcus aureus is the main etiological agent of mastitis in small ruminants worldwide. This disease has a difficult cure and possible relapse, leading to significant economic losses in production, milk quality and livestock. This study performed comparative genomic analyses between 73 S. aureus genomes from different hosts (human, bovine, pig and others). This work isolated and sequenced 12 of these genomes from ovine. This study contributes to the knowledge of genomic specialization and the role of specific genes in establishing infection in ovine mastitis-associated S. aureus. The genomes of S. aureus isolated from sheep maintained a higher representation when grouped with clonal complexes 130 and 133. The genomes showed high genetic similarity, the species pan-genome consisting of 4200 genes (central = 2008, accessory = 1559 and unique = 634). Among these, 277 unique genes were related to the genomes isolated from sheep, with 39.6 % as hypothetical proteins, 6.4 % as phages, 6.4 % as toxins, 2.9 % as transporters, and 44.7 % as related to other proteins. Furthermore, at the pathogen level, they showed 80 genes associated with virulence factors and 19 with antibiotic resistance shared in almost all isolates. Although S. aureus isolated from ovine showed susceptibility to antimicrobials in vitro, ten genes were predicted to be associated with antibiotic inactivation and efflux pump, suggesting resistance to gentamicin and penicillin. This work may contribute to identifying genes acquired by horizontal transfer and their role in host adaptation, virulence, bacterial resistance, and characterization of strains affecting ovine.
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Affiliation(s)
- Alessandra Lima
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Raquel Hurtado Castillo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Diego Lucas Neres Rodrigues
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thiago de Jesus Sousa
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rodrigo Bentes Kato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Anne Cybelle Pinto Gomide
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Flavia Figueira Aburjaile
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sandeep Tiwari
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Programa de Pós-graduação em Imunologia, Instituto De Biologia, Universidade Federal da Bahia, Salvador, BA, Brasil.; Programa de Pós-graduação em Microbiologia, Instituto De Biologia, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Arun Jaiswal
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alfonso Gala-García
- Faculdade de Odontologia, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Núbia Seyffert
- Programa de Pós-graduação em Imunologia, Instituto De Biologia, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Thiago Luiz de Paula Castro
- Programa de Pós-graduação em Imunologia, Instituto De Biologia, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany
| | - Mateus Matiuzzi da Costa
- Laboratório de Microbiologia e Imunologia Animal, Campus Ciências Agrárias, Universidade Federal do Vale do São Francisco (UNIVASF), Petrolina, Pernambuco, Brazil
| | - Elaine Maria Seles Dorneles
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Yves Le Loir
- Institut National de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Paris, France
| | - Vasco Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Escobedo S, Campelo AB, Umu ÖCO, López-González MJ, Rodríguez A, Diep DB, Martínez B. Resistance to the Bacteriocin Lcn972 Deciphered by Genome Sequencing. Microorganisms 2023; 11:microorganisms11020501. [PMID: 36838466 PMCID: PMC9964109 DOI: 10.3390/microorganisms11020501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
In view of the current threat of antibiotic resistance, new antimicrobials with low risk of resistance development are demanded. Lcn972 is a lactococcal bacteriocin that inhibits septum formation by binding to the cell wall precursor lipid II in Lactococcus. It has a species-specific spectrum of activity, making Lcn972 an attractive template to develop or improve existing antibiotics. The aim of this work was to identify mutations present in the Lcn972-resistant clone Lactococcus cremoris D1-20, previously evolved from the sensitive strain L. cremoris MG1614. Whole-genome sequencing and comparison over the reference genome L. cremoris MG1363 identified several unexpected mutations in the parental strain MG1614, likely selected during in-house propagation. In the Lcn972R clone, two previously identified mutations were mapped and confirmed. Additionally, another transposition event deregulating cellobiose uptake was identified along with three point mutations of unknown consequences for Lcn972 resistance. Two new independent evolution experiments exposing L. cremoris MG1614 to Lcn972 revealed transposition of IS981 into the LLMG_RS12285 locus as the predominant mutation selected by Lcn972. This event occurs early during evolution and was found in 100% of the evolved clones, while other mutations were not selected. Therefore, activation of LLMG_RS12285 coding for a putative anti-ECF (extra-cytoplasmic function) sigma factor is regarded as the main Lcn972 resistance factor in L. cremoris MG1614.
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Affiliation(s)
- Susana Escobedo
- Instituto de Productos Lacteos de Asturias (IPLA), CSIC, 33300 Villaviciosa, Spain
| | - Ana B. Campelo
- Instituto de Productos Lacteos de Asturias (IPLA), CSIC, 33300 Villaviciosa, Spain
| | - Özgün C. O. Umu
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, 1432 Ås, Norway
| | | | - Ana Rodríguez
- Instituto de Productos Lacteos de Asturias (IPLA), CSIC, 33300 Villaviciosa, Spain
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Beatriz Martínez
- Instituto de Productos Lacteos de Asturias (IPLA), CSIC, 33300 Villaviciosa, Spain
- Correspondence: ; Tel.: +34-985-89-21-31
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26
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Quispe-Ricalde MA, Castelán-Sánchez HG, Meza-Rodríguez PM, Dávila-Ramos S, Sierra JL, Batista-Garcia R, Concha-Velasco F, Lucana SF, De Santa Cruz J, Zea V, Galarza M, Caceres-Rey O, Tsukayama P, Foronda P, Soto-Chambi BJ, Abreu N. Evidence of natural selection and dominance of SARS-CoV-2 variant Lambda (C.37) over variants of concern in Cusco, Peru. Arch Virol 2023; 168:88. [PMID: 36786950 PMCID: PMC9926449 DOI: 10.1007/s00705-022-05645-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/13/2022] [Indexed: 02/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage C.37 (Lambda) has spread rapidly in Peru and other Latin American countries. However, most studies in Peru have focused on Lima, the capital city, without knowing the dynamics of the spread of the variant in other departments. Cusco, Peru, is one of the most popular departments in the country for tourists, so the introduction of new variants of SARS-CoV-2 might occur despite closure of the borders. Therefore, in this work, we analyzed the variants circulating in Cusco. The aim of this work was to better understand the distribution of SARS-CoV-2 lineages circulating in Cusco and to characterize the genomes of these strains. To this end, 46 SARS-CoV-2 genomes from vaccinated and unvaccinated patients were sequenced in the first half of 2021. The genomes were analyzed using phylogenetic and natural selection methods. Phylogenetic trees from Cusco showed dominance of the Lambda lineage over the variants of concern (VOCs), and there was no clustering of variants by district. Natural selection analysis revealed mutations, mainly in the spike protein, at positions 75, 246, 247, 707, 769, and 1020. In addition, we found that unvaccinated patients accumulated more new mutations than did vaccinated patients, and these included the F101Y mutation in ORF7a, E419A in NSP3, a deletion in S (21,618-22,501), and a deletion in ORF3a (25,437-26,122).
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Affiliation(s)
- Maria Antonieta Quispe-Ricalde
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de San Antonio Abad del Cusco, Av. de La Cultura 733, C.P. 0800, Cusco, Perú.
| | - Hugo G Castelán-Sánchez
- Programa de Investigadoras e Investigadores por México. Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Crédito Constructo, Benito Juárez, Ciudad de México, C.P. 03940, México.
| | - Pablo M Meza-Rodríguez
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa, Cuernavaca, Morelos, C.P. 62209, México
| | - Sonia Dávila-Ramos
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa, Cuernavaca, Morelos, C.P. 62209, México
| | - José Luis Sierra
- Escuela de Postgrado, Universidad Nacional de San Antonio Abad del Cusco, Av. de La Cultura 733, Cusco, C.P. 0800, Perú
| | - Ramón Batista-Garcia
- Centro de Investigación en Dinámica Celular, Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Morelos. Av. Universidad 1001. Col. Chamilpa, Cuernavaca, Morelos, C.P. 62209, México
| | - Fátima Concha-Velasco
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
- Dirección de epidemiología e investigación. Gerencia regional de salud, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - Sonia Flores Lucana
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - José De Santa Cruz
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - Víctor Zea
- Laboratorio Regional de Referencia, Gerencia Regional de Salud Cusco, Av. de La Cultura 147, Cusco, C.P. 08003, Perú
| | - Marco Galarza
- Laboratorio de Referencia Nacional de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Perú
| | - Omar Caceres-Rey
- Laboratorio de Referencia Nacional de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Perú
| | - Pablo Tsukayama
- Laboratorio de Genómica Microbiana, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porres 15102, Lima, C.P. 15102, Perú
- Instituto de Medicina Tropical Alexander von Humboldt, Av. Honorio Delgado 430, San Martín de Porres, Lima, Peru
- Wellcome Sanger Institute, Saffron Walden, Cambridge, Reino Unido. Z.P. CB10 1SA, Hinxton, UK
| | - Pilar Foronda
- University Institute of Tropical Diseases and Public Health of the Canary Islands, Av. Astrofísico FranciscoSánchez, s/n, San Cristóbal de La Laguna, Tenerife, C.P.38200, Spain
| | - Brandon Jason Soto-Chambi
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de San Antonio Abad del Cusco, Av. de La Cultura 733, C.P. 0800, Cusco, Perú
| | - Nestor Abreu
- University Institute of Tropical Diseases and Public Health of the Canary Islands, Av. Astrofísico FranciscoSánchez, s/n, San Cristóbal de La Laguna, Tenerife, C.P.38200, Spain.
- NERTALAB, SL., C, /José Rodríguez Mouré, 4, Santa Cruz de Tenerife, Tenerife, C.P. 38008, España.
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Bartie KL, Ngô TPH, Bekaert M, Hoang Oanh DT, Hoare R, Adams A, Desbois AP. Aeromonas hydrophila ST251 and Aeromonas dhakensis are major emerging pathogens of striped catfish in Vietnam. Front Microbiol 2023; 13:1067235. [PMID: 36794008 PMCID: PMC9924233 DOI: 10.3389/fmicb.2022.1067235] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Introduction Aeromonads are ubiquitous in aquatic environments and several species are opportunistic pathogens of fish. Disease losses caused by motile Aeromonas species, particularly Aeromonas hydrophila, can be challenging in intensive aquaculture, such as at striped catfish (Pangasianodon hypophthalmus) farms in Vietnam. Outbreaks require antibiotic treatments, but their application is undesirable due to risks posed by resistance. Vaccines are an attractive prophylactic and they must protect against the prevalent strains responsible for ongoing outbreaks. Methods This present study aimed to characterize A. hydrophila strains associated with mortalities in striped catfish culture in the Mekong Delta by a polyphasic genotyping approach, with a view to developing more effective vaccines. Results During 2013-2019, 345 presumptive Aeromonas spp. isolates were collected at farms in eight provinces. Repetitive element sequence-based PCR, multi-locus sequence typing and whole-genome sequencing revealed most of the suspected 202 A. hydrophila isolates to belong to ST656 (n = 151), which corresponds to the closely-related species Aeromonas dhakensis, with a lesser proportion belonging to ST251 (n = 51), a hypervirulent lineage (vAh) of A. hydrophila already causing concern in global aquaculture. The A. dhakensis ST656 and vAh ST251 isolates from outbreaks possessed unique gene sets compared to published A. dhakensis and vAh ST251 genomes, including antibiotic-resistance genes. The sharing of resistance determinants to sulphonamides (sul1) and trimethoprim (dfrA1) suggests similar selection pressures acting on A. dhakensis ST656 and vAh ST251 lineages. The earliest isolate (a vAh ST251 from 2013) lacked most resistance genes, suggesting relatively recent acquisition and selection, and this underscores the need to reduce antibiotics use where possible to prolong their effectiveness. A novel PCR assay was designed and validated to distinguish A. dhakensis and vAh ST251 strains. Discussion This present study highlights for the first time A. dhakensis, a zoonotic species that can cause fatal human infection, to be an emerging pathogen in aquaculture in Vietnam, with widespread distribution in recent outbreaks of motile Aeromonas septicaemia in striped catfish. It also confirms vAh ST251 to have been present in the Mekong Delta since at least 2013. Appropriate isolates of A. dhakensis and vAh should be included in vaccines to prevent outbreaks and reduce the threat posed by antibiotic resistance.
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Affiliation(s)
- Kerry L. Bartie
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Thao P. H. Ngô
- Aquacultural Biotechnology Division, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | | | - Rowena Hoare
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Alexandra Adams
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Andrew P. Desbois
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
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28
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Viana MVC, Galdino JH, Profeta R, Oliveira M, Tavares L, de Castro Soares S, Carneiro P, Wattam AR, Azevedo V. Analysis of Corynebacterium silvaticum genomes from Portugal reveals a single cluster and a clade suggested to produce diphtheria toxin. PeerJ 2023; 11:e14895. [PMID: 36919166 PMCID: PMC10008321 DOI: 10.7717/peerj.14895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/24/2023] [Indexed: 03/11/2023] Open
Abstract
Background Corynebacterium silvaticum is a pathogenic, gram-positive bacterial species that causes caseous lymphadenitis in wild boars, domestic pigs and roe deer in Western Europe. It can affect animal production and cause zoonosis. Genome analysis has suggested that one strain from Portugal and one from Austria could probably produce the diphtheria toxin (DT), which inhibits protein synthesis and can cause death. Methods To further investigate the species genetic diversity and probable production of DT by Portuguese strains, eight isolates from this country were sequenced and compared to 38 public ones. Results Strains from Portugal are monophyletic, nearly identical, form a unique cluster and have 27 out of 36 known Corynebacterium virulence or niche factors. All of them lack a frameshift in the tox gene and were suggested to produce DT. A phylogenetic analysis shows that the species has diverged into two clades. Clade 1 is composed of strains that were suggested to have the ability to produce DT, represented by the monophyletic strains from Portugal and strain 05-13 from Austria. Clade 2 is composed of strains unable to produce DT due to a frameshifted tox gene. The second clade is represented by strains from Austria, Germany and Switzerland. Ten genome clusters were detected, in which strains from Germany are the most diverse. Strains from Portugal belong to an exclusive cluster. The pangenome has 2,961 proteins and is nearly closed (α = 0.968). Exclusive genes shared by clusters 1 and 2, and Portuguese strains are probably not related to disease manifestation as they share the same host but could play a role in their extra-host environmental adaptation. These results show the potential of the species to cause zoonosis, possibly diphtheria. The identified clusters, exclusively shaded genes, and exclusive STs identified in Portugal could be applied in the identification and epidemiology of the species.
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Affiliation(s)
- Marcus Vinicius Canario Viana
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - José Henrique Galdino
- Department of Biological Sciences, State University of Southwest of Bahia, Jequié, Bahia, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Manuela Oliveira
- Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Luís Tavares
- Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Paulo Carneiro
- Department of Biological Sciences, State University of Southwest of Bahia, Jequié, Bahia, Brazil
| | - Alice Rebecca Wattam
- Biocomplexity Institute, University of Virginia, Charlottesville, VA, United States of America
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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29
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Pereira FL, Dorella FA, Castrejón-Nájera J, Reis FYT, Ortega C, Irgang R, Echeverría-Bugueño M, Avendaño-Herrera R, Figueiredo HCP. Comparative polyphasic characterization of Weissella strains isolated from beaked whale and rainbow trout (Oncorhynchus mykiss): confirmation of Weissella ceti sp. nov. and description of the novel Weissella tructae sp. nov. isolated from farmed rainbow trout. Braz J Microbiol 2022; 53:2263-2272. [PMID: 36307638 PMCID: PMC9679048 DOI: 10.1007/s42770-022-00856-5] [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: 04/18/2022] [Accepted: 10/04/2022] [Indexed: 01/13/2023] Open
Abstract
The weissellosis agent bacterium (WS08T = CBMAI 2730) was isolated from diseased rainbow trout (Oncorhynchus mykiss) in Brazil. The whole genome sequence of this strain was compared with the Mexican W-1 strain, also isolated from diseased rainbow trout, and with the Weissella ceti type strain CECT 7719 T (= 1119-1A-09 T = CCUG 59653 T), recovered from the beaked whale. Digital DNA-DNA hybridization pairwise analyses scored 98.7% between the Mexican W-1 and Brazilian WS08T but just 24.4% for both fish isolates compared to the W. ceti type strain CECT 7719 T. The 16S rRNA gene sequence comparisons with isolates of W. ceti, available at GenBank, were conducted. All rainbow trout-pathogenic isolates grouped close (97% bootstrap confirmation), but when this group was compared to the W. ceti type strain CECT 7719 T the similarity varied from 78.9 to 79.1%. Phenotypic assays were also conducted, and the W. ceti type strain diverged from WS08T and W-1 in the hydrolysis of aesculin, D-mannose, and potassium gluconate and in the hydrolysis of hippurate. Moreover, WS08T and W-1 showed weak growth at 5 °C whereas no growth was observed for W. ceti CECT 7719 T. The major fatty acids (> 10% total fatty acids) presented by WS08T and W-1 were summed feature 8 (C18:1 ω7c/C18:1 ω6c), summed feature 3 (C16:1 ω6c/C16:1ω7c), and C16:0. The results of phylogenetic and phenotypic analyses clearly differentiated the W. ceti CECT 7719 T type strain from the assessed pathogenic strains obtained from rainbow trout. Therefore, Weissella strains isolated from rainbow trout, here represented by strain WS08T (= CBMAI 2730), should be known as members of a novel species for which the name Weissella tructae sp. nov. is proposed.
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Affiliation(s)
- Felipe Luiz Pereira
- AQUAVETAQUAVET, Laboratory of Aquatic Animal Diseases, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
- IFC, Federal Institute of Santa Catarina, Camboriú, Santa Catarina, 88020-300, Brazil
| | - Fernanda Alves Dorella
- AQUAVETAQUAVET, Laboratory of Aquatic Animal Diseases, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Jésica Castrejón-Nájera
- CIESA, Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Universidad Autónoma del Estado de México (UAEM), Toluca, 50295, México
| | - Francisco Yan Tavares Reis
- AQUAVETAQUAVET, Laboratory of Aquatic Animal Diseases, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - César Ortega
- CIESA, Centro de Investigación y Estudios Avanzados en Salud Animal, Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Universidad Autónoma del Estado de México (UAEM), Toluca, 50295, México
| | - Rute Irgang
- Laboratorio de Patología de Organismos Acuáticos Y Biotecnología Acuícola, Facultad de Ciencias de La Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Macarena Echeverría-Bugueño
- Laboratorio de Patología de Organismos Acuáticos Y Biotecnología Acuícola, Facultad de Ciencias de La Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos Y Biotecnología Acuícola, Facultad de Ciencias de La Vida, Universidad Andrés Bello, Viña del Mar, Chile.
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad Andrés Bello, Viña del Mar, Chile.
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay, Chile.
| | - Henrique César Pereira Figueiredo
- AQUAVETAQUAVET, Laboratory of Aquatic Animal Diseases, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
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Genome Report of Emergent Fish Pathogen
Edwardsiella piscicida
Recovered from
Pseudoplatystoma corruscans
in Brazil. Microbiol Resour Announc 2022; 11:e0079622. [DOI: 10.1128/mra.00796-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Edwardsiella piscicida
is a Gram-negative bacteria belonging to the
Hafniaceae
family which affects several species of marine and freshwater fish. We present the complete genome of
E
.
piscicida
strain BEP80 recovered from the Brazilian catfish named Surubim (
Pseudoplatystoma corruscans
), consisting a chromosome of 3,883,256 bp and no plasmids.
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Bertê R, Teixeira GM, de Oliveira JP, Nicoletto MLA, da Silva DV, de Godoy GG, Sanches DS, de Resende JTV, Pereira UDP, Nunes da Rocha U, de Oliveira AG. Genome Mining Reveals High Biosynthetic Potential of Biocontrol Agent Bacillus velezensis B.BV10. Genes (Basel) 2022; 13:1984. [PMID: 36360221 PMCID: PMC9690179 DOI: 10.3390/genes13111984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 01/07/2024] Open
Abstract
The present study demonstrates the biocontrol potential of a plant growth-promoting bacterial strain using three different approaches: (i) an in vitro evaluation of antagonistic activity against important phytopathogenic fungi; (ii) an evaluation under greenhouse conditions with strawberry plants to assess the control of gray mold; and (iii) an in silico whole genome sequence mining to assign genetic features such as gene clusters or isolated genes to the strain activity. The in vitro assay showed that the B.BV10 strain presented antagonistic activity, inhibiting the mycelial growth in all the phytopathogenic fungi evaluated. The application of the Bacillus velezensis strain B.BV10 under greenhouse conditions reduced the presence of Botrytis cinerea and increased the mean fruit biomass. The genome of B.BV10 was estimated at 3,917,533 bp, with a GC content of 46.6% and 4088 coding DNA sequences, and was identified as B. velezensis. Biosynthetic gene clusters related to the synthesis of the molecules with antifungal activity were found in its genome. Genes related to the regulation/formation of biofilms, motility, and the important properties for the rhizospheric colonization were also found in the genome. The current study offers a comprehensive understanding of the genomic architecture and control activity of phytopathogenic fungi by the B. velezensis strain B.BV10 that may substantiate the industrialization of this strain in the future.
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Affiliation(s)
- Rosiana Bertê
- Department of Microbiology, Universidade Estadual de Londrina, Londrina 86057-970, PR, Brazil
| | - Gustavo Manoel Teixeira
- Department of Microbiology, Universidade Estadual de Londrina, Londrina 86057-970, PR, Brazil
| | - João Paulo de Oliveira
- Department of Microbiology, Universidade Estadual de Londrina, Londrina 86057-970, PR, Brazil
| | | | - Daniel Vieira da Silva
- Department of Microbiology, Universidade Estadual de Londrina, Londrina 86057-970, PR, Brazil
| | | | - Danilo Sipoli Sanches
- Computer Science Department, Universidade Tecnológica Federal do Paraná, Cornélio Procópio 86300000, PR, Brazil
| | | | - Ulisses de Padua Pereira
- Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Londrina 86057-970, PR, Brazil
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research–UFZ GmbH, 04318 Leipzig, Germany
| | - Admilton Gonçalves de Oliveira
- Department of Microbiology, Universidade Estadual de Londrina, Londrina 86057-970, PR, Brazil
- Laboratory of Electron Microscopy and Microanalysis, Universidade Estadual de Londrina, Londrina 86057-970, PR, Brazil
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32
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Draft Genome Sequence of Bacillus vallismortis Strain BL01, Isolated from
Artemisia lerchiana
Web. Roots. Microbiol Resour Announc 2022; 11:e0064722. [PMID: 36250876 PMCID: PMC9670946 DOI: 10.1128/mra.00647-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Some strains of Bacillus vallismortis have been reported to be efficient plant-growth-promoting bacteria as well as inducers of systemic resistance. Here, we report the draft genome sequence of Bacillus vallismortis strain BL01, isolated from the roots of Artemisia lerchiana Web.
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Mosela M, Andrade G, Massucato LR, de Araújo Almeida SR, Nogueira AF, de Lima Filho RB, Zeffa DM, Mian S, Higashi AY, Shimizu GD, Teixeira GM, Branco KS, Faria MV, Giacomin RM, Scapim CA, Gonçalves LSA. Bacillus velezensis strain Ag75 as a new multifunctional agent for biocontrol, phosphate solubilization and growth promotion in maize and soybean crops. Sci Rep 2022; 12:15284. [PMID: 36088482 PMCID: PMC9464197 DOI: 10.1038/s41598-022-19515-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Soybean and maize are some of the main drivers of Brazilian agribusiness. However, biotic and abiotic factors are of great concern, causing huge grain yield and quality losses. Phosphorus (P) deficiency is important among the abiotic factors because most Brazilian soils have a highly P-fixing nature. Thus, large amounts of phosphate fertilizers are regularly applied to overcome the rapid precipitation of P. Searching for alternatives to improve the use of P by crops is essential to reduce the demand for P input. The use of multifunctional rhizobacteria can be considered one of these alternatives. In this sense, the objective of the present work was to select and validate bacterial strains with triple action (plant growth promoter, phosphate solubilizer, and biocontrol agent) in maize and soybean, aiming to develop a multifunctional microbial inoculant for Brazilian agriculture. Bacterial strains with high indole acetic acid (IAA) production, phosphate solubilization, and antifungal activity against soil pathogenic fungi (Rhizoctonia solani, Macrophomina phaseolina, and Fusarium solani) were selected from the maize rhizosphere. Then, they were evaluated as growth promoters in maize under greenhouse conditions. Based on this study, strain 03 (Ag75) was selected due to its high potential for increasing biomass (root and shoot) and shoot P content in maize. This strain was identified through genomic sequencing as Bacillus velezensis. In field experiments, the inoculation of this bacterium increased maize and soybean yields by 17.8 and 26.5%, respectively, compared to the control (25 kg P2O5). In addition, the inoculation results did not differ from the control with 84 kg P2O5, indicating that it is possible to reduce the application of phosphate in these crops. Thus, the Ag75 strain has great potential for developing a multifunctional microbial inoculant that combines the ability to solubilize phosphate, promote plant growth, and be a biocontrol agent for several phytopathogenic fungi.
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Characterization of the virulence of three novel clade 2 Clostridioides (Clostridium) difficile strains and a two-year screening in animals and humans in Brazil. PLoS One 2022; 17:e0273013. [PMID: 36026500 PMCID: PMC9416996 DOI: 10.1371/journal.pone.0273013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/29/2022] [Indexed: 11/19/2022] Open
Abstract
Clostridioides (Clostridium) difficile infection (CDI) is an evolving global healthcare problem, and owing to the diverse and dynamic molecular epidemiology of C. difficile, new strains continue to emerge. In Brazil, only two cases of CDI due to the so called hypervirulent PCR ribotype (RT) 027 belonging to clade 2 have ever been reported, whereas incidence of CDI due to another “hypervirulent” RT078 (clade 5) has not yet been reported. In contrast, novel clade 2 strains have been identified in different hospitals. To better understand the epidemiology of CDIs in Brazil, this study aimed to genotypically and phenotypically characterize three novel Brazilian clade 2 strains (RT883, 884, and 885) isolated from patients with confirmed CDI. In addition, to better understand the circulating RTs, a two-year sampling was conducted in patients from the same hospital and in several domestic and wild animal species. The three strains examined showed lower production of A/B toxins than the control RT027, although two of these strains harbored a truncated tcdC gene. All strains showed swimming motility similar to that of RT027, while RT883 showed higher spore production than the reference strain. In the in vivo hamster model, the lethality of all strains was found to be similar to that of RT027. Both cgMLST and cgMLSA analyses revealed a high genetic similarity among the three-novel clade 2 isolates. In the two-year survey in animals and humans, RT883, 884, and 885 were not detected; however, three new RTs (RT988, RT989, and RT990) were isolated, two of which were genetically related to the three previously reported clade 2 strains. RT106 and RT126 were most frequently detected in humans (47.9%) and animals (57.9%), respectively. Furthermore, RT027 and RT078 were not detected in humans. The results of this study suggest that these novel clade 2 strains have virulence potential and that new strains from clade 2 continue to emerge in our setting, indicating the need for long-term local surveillance.
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Draft Genome Sequence of Geobacillus stearothermophilus Strain K4E3_SPR_NPP, Isolated from Kasol Hot Spring, Himachal Pradesh, India. Microbiol Resour Announc 2022; 11:e0019422. [PMID: 35587782 PMCID: PMC9202378 DOI: 10.1128/mra.00194-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Geobacillus stearothermophilus strain K4E3_SPR_NPP is a thermophilic bacterium growing optimally at 70°C. Here, we present the draft genome sequence of Geobacillus stearothermophilus strain K4E3_SPR_NPP, which was isolated from Kasol Hot Spring (72.3°C), Himachal Pradesh, India (32°0′46.35″N, 77°19′0.4908″E).
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Aldea I, Gibello A, Hernández M, Leekitcharoenphon P, Bortolaia V, Moreno MA. Clonal and plasmid-mediated flow of ESBL/AmpC genes in Escherichia coli in a commercial laying hen farm. Vet Microbiol 2022; 270:109453. [DOI: 10.1016/j.vetmic.2022.109453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 03/09/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022]
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Abstract
Root nodulating rhizobia are nearly ubiquitous in soils and provide the critical service of nitrogen fixation to thousands of legume species, including staple crops. However, the magnitude of fixed nitrogen provided to hosts varies markedly among rhizobia strains, despite host legumes having mechanisms to selectively reward beneficial strains and to punish ones that do not fix sufficient nitrogen. Variation in the services of microbial mutualists is considered paradoxical given host mechanisms to select beneficial genotypes. Moreover, the recurrent evolution of non-fixing symbiont genotypes is predicted to destabilize symbiosis, but breakdown has rarely been observed. Here, we deconstructed hundreds of genome sequences from genotypically and phenotypically diverse Bradyrhizobium strains and revealed mechanisms that generate variation in symbiotic nitrogen fixation. We show that this trait is conferred by a modular system consisting of many extremely large integrative conjugative elements and few conjugative plasmids. Their transmissibility and propensity to reshuffle genes generate new combinations that lead to uncooperative genotypes and make individual partnerships unstable. We also demonstrate that these same properties extend beneficial associations to diverse host species and transfer symbiotic capacity among diverse strains. Hence, symbiotic nitrogen fixation is underpinned by modularity, which engenders flexibility, a feature that reconciles evolutionary robustness and instability. These results provide new insights into mechanisms driving the evolution of mobile genetic elements. Moreover, they yield a new predictive model on the evolution of rhizobial symbioses, one that informs on the health of organisms and ecosystems that are hosts to symbionts and that helps resolve the long-standing paradox.
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Draft Genome Sequence of Brevibacillus brevis LABIM17, a Biotechnologically Important Antimicrobial-Producing Bacterium. Microbiol Resour Announc 2022; 11:e0000622. [PMID: 35191747 PMCID: PMC8928766 DOI: 10.1128/mra.00006-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Brevibacillus brevis LABIM17 is a bacterial isolate with biotechnological potential. Its draft genome sequence contains a chromosome of 5,950,202 bp, with 5,477 coding sequences, and exhibits 12 clusters involved in the production of secondary metabolites, which are likely responsible for its antimicrobial activity against several human and plant pathogens.
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Nabi N, Ben Hafsa A, Gaillard V, Nesme X, Chaouachi M, Vial L. Evolutionary classification of tumor- and root-inducing plasmids based on T-DNAs and virulence regions. Mol Phylogenet Evol 2022; 169:107388. [PMID: 35017066 DOI: 10.1016/j.ympev.2022.107388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 11/15/2020] [Accepted: 12/08/2021] [Indexed: 11/19/2022]
Abstract
Tumor-inducing (Ti) and root-inducing (Ri) plasmids of Agrobacterium that display a large diversity are involved in crown gall and hairy root plant diseases. Their phylogenetic relationships were inferred from an exhaustive set of Ti and Ri plasmids (including 36 new complete Ti plasmids) by focusing on T-DNA and virulence regions. The opine synthase gene content of T-DNAs revealed 13 opine types corresponding to former classifications based on opines detected in diseased plants, while the T-DNA gene content more finely separate opine types in 18 T-DNA organizations. This classification was supported by the phylogeny of T-DNA oncogenes of Ti plasmids. The five gene organizations found in Ti/Ri vir regions was supported by the phylogeny of common vir genes. The vir organization was found to be likely an ancestral plasmid trait separating "classic" Ti plasmids (with one or two T-DNAs) and "Ri and vine-Ti" plasmids. A scenario generally supported by the repABC phylogeny. T-DNAs likely evolved later with the acquisition of opine characteristics as last steps in the Ti/Ri plasmid evolution. This novel evolutionary classification of Ti/Ri plasmids was found to be relevant for accurate crown gall and hairy root epidemiology.
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Affiliation(s)
- Nesrine Nabi
- Unité de Recherche UR17ES30 Génomique, Biotechnologie et Stratégies Antivirales, Institut Supérieur de Biotechnologie, Université de Monastir, Monastir, Tunisie.
| | - Ahmed Ben Hafsa
- Unité de Recherche UR17ES30 Génomique, Biotechnologie et Stratégies Antivirales, Institut Supérieur de Biotechnologie, Université de Monastir, Monastir, Tunisie
| | - Vincent Gaillard
- Laboratoire d'Ecologie Microbienne (LEM), UCBL, CNRS, INRAE, VetAgro Sup, Univ Lyon, F-69622 Villeurbanne Cedex, France
| | - Xavier Nesme
- Laboratoire d'Ecologie Microbienne (LEM), UCBL, CNRS, INRAE, VetAgro Sup, Univ Lyon, F-69622 Villeurbanne Cedex, France
| | - Maher Chaouachi
- Unité de Recherche UR17ES30 Génomique, Biotechnologie et Stratégies Antivirales, Institut Supérieur de Biotechnologie, Université de Monastir, Monastir, Tunisie
| | - Ludovic Vial
- Laboratoire d'Ecologie Microbienne (LEM), UCBL, CNRS, INRAE, VetAgro Sup, Univ Lyon, F-69622 Villeurbanne Cedex, France.
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Stevens DM, Tang A, Coaker G. A Genetic Toolkit for Investigating Clavibacter Species: Markerless Deletion, Permissive Site Identification, and an Integrative Plasmid. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1336-1345. [PMID: 34890250 DOI: 10.1094/mpmi-07-21-0171-ta] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The development of knockout mutants and expression variants are critical for understanding genotype-phenotype relationships. However, advances in these techniques in gram-positive actinobacteria have stagnated over the last decade. Actinobacteria in the Clavibacter genus are composed of diverse crop pathogens that cause a variety of wilt and cankering diseases. Here, we present a suite of tools for genetic manipulation in the tomato pathogen Clavibacter michiganensis including a markerless deletion system, an integrative plasmid, and an R package for identification of permissive sites for plasmid integration. The vector pSelAct-KO is a recombination-based, markerless knockout system that uses dual selection to engineer seamless deletions of a region of interest, providing opportunities for repeated higher-order genetic knockouts. The efficacy of pSelAct-KO was demonstrated in C. michiganensis and was confirmed using whole-genome sequencing. We developed permissR, an R package to identify permissive sites for chromosomal integration, which can be used in conjunction with pSelAct-Express, a nonreplicating integrative plasmid that enables recombination into a permissive genomic location. Expression of enhanced green fluorescent protein by pSelAct-Express was verified in two candidate permissive regions predicted by permissR in C. michiganensis. These molecular tools are essential advances for investigating gram-positive actinobacteria, particularly for important pathogens in the Clavibacter genus.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Danielle M Stevens
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, Davis, CA 95616, U.S.A
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, U.S.A
| | - Andrea Tang
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, U.S.A
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616, U.S.A
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Neubert K, Zuchantke E, Leidenfrost RM, Wünschiers R, Grützke J, Malorny B, Brendebach H, Al Dahouk S, Homeier T, Hotzel H, Reinert K, Tomaso H, Busch A. Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures. BMC Genomics 2021; 22:822. [PMID: 34773979 PMCID: PMC8590783 DOI: 10.1186/s12864-021-08115-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/12/2021] [Indexed: 02/08/2023] Open
Abstract
Background We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation “short-read” and third-generation “long-read” sequencing methods. Results We focused on short-read assemblers, hybrid assemblers, and analysis of the genomic structure with particular emphasis on insertion sequences and the Francisella pathogenicity island. The A5-miseq pipeline performed best for MiSeq data, Mira for Ion Torrent data, and ABySS for HiSeq data from eight short-read assembly methods. Two approaches were applied to benchmark long-read and hybrid assembly strategies: long-read-first assembly followed by correction with short reads (Canu/Pilon, Flye/Pilon) and short-read-first assembly along with scaffolding based on long reads (Unicyler, SPAdes). Hybrid assembly can resolve large repetitive regions best with a “long-read first” approach. Conclusions Genomic structures of the Francisella pathogenicity islands frequently showed misassembly. Insertion sequences (IS) could be used to perform an evolutionary conservation analysis. A phylogenetic structure of insertion sequences and the evolution within the clades elucidated the clade structure of the highly conservative F. tularensis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08115-x.
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Affiliation(s)
- Kerstin Neubert
- Department of Mathematics and Computer Science, Algorithmic Bioinformatics, Freie Universität Berlin, Institute of Computer Science, Takustr. 9, 14195, Berlin, Germany.,German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Eric Zuchantke
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany
| | - Robert Maximilian Leidenfrost
- Department of Biotechnology and Chemistry, Mittweida University of Applied Sciences, Technikumplatz 17a, 09648, Mittweida, Germany
| | - Röbbe Wünschiers
- Department of Biotechnology and Chemistry, Mittweida University of Applied Sciences, Technikumplatz 17a, 09648, Mittweida, Germany
| | - Josephine Grützke
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Burkhard Malorny
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Holger Brendebach
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Sascha Al Dahouk
- German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277, Berlin, Germany
| | - Timo Homeier
- Friedrich-Loeffler-Institut, Institute of Epidemiology, Südufer, 10 17493, Greifswald, Insel Riems, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany
| | - Knut Reinert
- Department of Mathematics and Computer Science, Algorithmic Bioinformatics, Freie Universität Berlin, Institute of Computer Science, Takustr. 9, 14195, Berlin, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany
| | - Anne Busch
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07749, Jena, Germany. .,Department of Anaesthesiology and Intensive Care Medicine, University Hospital Jena, Jena, Germany.
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Burkholderia perseverans sp. nov., a bacterium isolated from the Restinga ecosystem, is a producer of volatile and diffusible compounds that inhibit plant pathogens. Braz J Microbiol 2021; 52:2145-2152. [PMID: 34287810 DOI: 10.1007/s42770-021-00560-w] [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: 04/16/2021] [Accepted: 06/28/2021] [Indexed: 10/20/2022] Open
Abstract
Gram-negative, aerobic, rod-shaped, non-spore-forming, motile bacteria, designated CBAS 719 T, CBAS 732 and CBAS 720 were isolated from leaf litter samples, collected in Espírito Santo State, Brazil, in 2008. Sequences of the 16S rRNA, gyrB, lepA and recA genes showed that these strains grouped with Burkholderia plantarii LMG 9035 T, Burkholderia gladioli LMG 2216 T and Burkholderia glumae LMG 2196 T in a clade of phytopathogenic Burkholderia species. Digital DNA-DNA hybridization experiments and ANI analyses demonstrated that strain CBAS 719 T represents a novel species in this lineage that is very closely related with B. plantarii. The genome sequence of the type strain is 7.57 Mbp and its G + C content is 69.01 mol%. The absence of growth on TSA medium supplemented with 3% (w/v) NaCl, citrate assimilation, β-galactosidase (PNPG) activity, and of lipase C14 activity differentiated strain CBAS 719 T from B. plantarii LMG 9035 T, its nearest phylogenetic neighbor. Its predominant fatty acid components were C16:0, C18:1 ω7c, cyclo-C17:0 and summed feature 3 (C16:1 ω7c and/or C15:0 iso 2-OH). Based on these genotypic and phenotypic characteristics, the strains CBAS 719 T, CBAS 732 and CBAS 720 are classified in a novel Burkholderia species, for which the name Burkholderia perseverans sp. nov. is proposed. The type strain is CBAS 719 T (= LMG 31557 T = INN12T).
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Jha V, Dafale NA, Hathi Z, Purohit H. Genomic and functional potential of the immobilized microbial consortium MCSt-1 for wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:146110. [PMID: 33684742 DOI: 10.1016/j.scitotenv.2021.146110] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
Treatment of wastewater prior to release in water bodies is an imperative need of the current time to address the global water crises. Thus, consortium MCSt-1 was designed for an effective wastewater treatment based on its cellulolytic, proteolytic, lipolytic, phenol and sodium dodecyl sulfate degrading activities along with effective nutrient removal capacity. Performance of the designed consortium was assayed using two differently configured lab-scale bioreactors as subjected to immobilization on two different matrices (pebbles and nylon mesh). Consortium MCSt-1 proficiently removes soluble chemical oxygen demand, nitrate, ammonia and phosphorus with 83%, 67%, 76%, and 62% removal efficiency, respectively. The immobilization on a mesh is recommended as it exhibited better biofilm formation, hence results in significant organic load and nutrient removal. The functional potential of the consortium MCSt-1 explored through genome characterization and reveal the presence of genes responsible for phosphorus metabolism and removal (pst operon and ppk), ammonia assimilation (amt), and nitrate; nitrite reductase (nar, nir, nor). Additionally, consortium members also annotated with the phenol, catechol and benzoate degradation, stress response, heavy metal and antibiotics resistance genes. Hence, the designed consortium MCSt-1 can withstand the harsh condition of treatment plants and serves as the best solution for enhancing wastewater treatment efficiency.
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Affiliation(s)
- Varsha Jha
- Environmental Biotechnology and Genomics Division, CSIR - National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR - National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Zubeen Hathi
- City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong Special Administrative Region
| | - Hemant Purohit
- Environmental Biotechnology and Genomics Division, CSIR - National Environmental Engineering Research Institute (NEERI), Nagpur 440020, India
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Marti H, Bommana S, Read TD, Pesch T, Prähauser B, Dean D, Borel N. Generation of Tetracycline and Rifamycin Resistant Chlamydia Suis Recombinants. Front Microbiol 2021; 12:630293. [PMID: 34276577 PMCID: PMC8278220 DOI: 10.3389/fmicb.2021.630293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/03/2021] [Indexed: 01/01/2023] Open
Abstract
The Chlamydiaceae are a family of obligate intracellular, gram-negative bacteria known to readily exchange DNA by homologous recombination upon co-culture in vitro, allowing the transfer of antibiotic resistance residing on the chlamydial chromosome. Among all the obligate intracellular bacteria, only Chlamydia (C.) suis naturally integrated a tetracycline resistance gene into its chromosome. Therefore, in order to further investigate the readiness of Chlamydia to exchange DNA and especially antibiotic resistance, C. suis is an excellent model to advance existing co-culture protocols allowing the identification of factors crucial to promote homologous recombination in vitro. With this strategy, we co-cultured tetracycline-resistant with rifamycin group-resistant C. suis, which resulted in an allover recombination efficiency of 28%. We found that simultaneous selection is crucial to increase the number of recombinants, that sub-inhibitory concentrations of tetracycline inhibit rather than promote the selection of double-resistant recombinants, and identified a recombination-deficient C. suis field isolate, strain SWA-110 (1-28b). While tetracycline resistance was detected in field isolates, rifampicin/rifamycin resistance (RifR) had to be induced in vitro. Here, we describe the protocol with which RifR C. suis strains were generated and confirmed. Subsequent whole-genome sequencing then revealed that G530E and D461A mutations in rpoB, a gene encoding for the β-subunit of the bacterial RNA polymerase (RNAP), was likely responsible for rifampicin and rifamycin resistance, respectively. Finally, whole-genome sequencing of recombinants obtained by co-culture revealed that recombinants picked from the same plate may be sibling clones and confirmed C. suis genome plasticity by revealing variable, apparently non-specific areas of recombination.
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Affiliation(s)
- Hanna Marti
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Sankhya Bommana
- Division of Infectious Diseases, Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, United States
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States.,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Theresa Pesch
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Barbara Prähauser
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Deborah Dean
- Division of Infectious Diseases, Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, United States.,Joint Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, CA, United States.,Joint Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Nicole Borel
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
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Gharbi R, Khanna V, Frigui W, Mhenni B, Brosch R, Mardassi H. Phenotypic and genomic hallmarks of a novel, potentially pathogenic rapidly growing Mycobacterium species related to the Mycobacterium fortuitum complex. Sci Rep 2021; 11:13011. [PMID: 34155223 PMCID: PMC8217490 DOI: 10.1038/s41598-021-91737-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
Previously, we have identified a putative novel rapidly growing Mycobacterium species, referred to as TNTM28, recovered from the sputum of an apparently immunocompetent young man with an underlying pulmonary disease. Here we provide a thorough characterization of TNTM28 genome sequence, which consists of one chromosome of 5,526,191 bp with a 67.3% G + C content, and a total of 5193 predicted coding sequences. Phylogenomic analyses revealed a deep-rooting relationship to the Mycobacterium fortuitum complex, thus suggesting a new taxonomic entity. TNTM28 was predicted to be a human pathogen with a probability of 0.804, reflecting the identification of several virulence factors, including export systems (Sec, Tat, and ESX), a nearly complete set of Mce proteins, toxin-antitoxins systems, and an extended range of other genes involved in intramacrophage replication and persistence (hspX, ahpC, sodA, sodC, katG, mgtC, ClpR, virS, etc.), some of which had likely been acquired through horizontal gene transfer. Such an arsenal of potential virulence factors, along with an almost intact ESX-1 locus, might have significantly contributed to TNTM28 pathogenicity, as witnessed by its ability to replicate efficiently in macrophages. Overall, the identification of this new species as a potential human pathogen will help to broaden our understanding of mycobacterial pathogenesis.
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Affiliation(s)
- Reem Gharbi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Varun Khanna
- Institut Pasteur, Hub Bioinformatique et Biostatistique, C3BI, Unité de Services et de Recherche, USR 3756, Institut Pasteur CNRS, Paris, France
| | - Wafa Frigui
- Institut Pasteur (IP), Unit for Integrated Mycobacterial Pathogenomics, 75015, Paris, France
| | - Besma Mhenni
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Roland Brosch
- Institut Pasteur (IP), Unit for Integrated Mycobacterial Pathogenomics, 75015, Paris, France
| | - Helmi Mardassi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.
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Melo RT, Galvão NN, Guidotti-Takeuchi M, Peres PABM, Fonseca BB, Profeta R, Azevedo VAC, Monteiro GP, Brenig B, Rossi DA. Molecular Characterization and Survive Abilities of Salmonella Heidelberg Strains of Poultry Origin in Brazil. Front Microbiol 2021; 12:674147. [PMID: 34220757 PMCID: PMC8253257 DOI: 10.3389/fmicb.2021.674147] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/12/2021] [Indexed: 12/02/2022] Open
Abstract
The aim of the study was to evaluate the genotypic and phenotypic characteristics of 20 strains of S. Heidelberg (SH) isolated from broilers produced in southern Brazil. The similarity and presence of genetic determinants linked to virulence, antimicrobial resistance, biofilm formation, and in silico-predicted metabolic interactions revealed this serovar as a threat to public health. The presence of the ompC, invA, sodC, avrA, lpfA, and agfA genes was detected in 100% of the strains and the luxS gene in 70% of them. None of the strains carries the blaSHV, mcr-1, qnrA, qnrB, and qnrS genes. All strains showed a multidrug-resistant profile to at least three non-β-lactam drugs, which include colistin, sulfamethoxazole, and tetracycline. Resistance to penicillin, ceftriaxone (90%), meropenem (25%), and cefoxitin (25%) were associated with the presence of blaCTX–M and blaCMY–2 genes. Biofilm formation reached a mature stage at 25 and 37°C, especially with chicken juice (CJ) addition. The sodium hypochlorite 1% was the least efficient in controlling the sessile cells. Genomic analysis of two strains identified more than 100 virulence genes and the presence of resistance to 24 classes of antibiotics correlated to phenotypic tests. Protein-protein interaction (PPI) prediction shows two metabolic pathways correlation with biofilm formation. Virulence, resistance, and biofilm determinants must be constant monitoring in SH, due to the possibility of occurring infections extremely difficult to cure and due risk of the maintenance of the bacterium in production environments.
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Affiliation(s)
- Roberta T Melo
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Newton N Galvão
- Ministry of Agriculture, Livestock and Supply, Rio de Janeiro, Brazil
| | | | - Phelipe A B M Peres
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Belchiolina B Fonseca
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Rodrigo Profeta
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco A C Azevedo
- Department of Genetics, Ecology and Evolution (GEE), Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme P Monteiro
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Daise A Rossi
- Faculty of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Brazil
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Melnikova DI, Nijland R, Magarlamov TY. The First Data on the Complete Genome of a Tetrodotoxin-Producing Bacterium. Toxins (Basel) 2021; 13:toxins13060410. [PMID: 34207879 PMCID: PMC8228330 DOI: 10.3390/toxins13060410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 11/17/2022] Open
Abstract
Tetrodotoxin (TTX)-producing bacteria have attracted great interest as a model system for study of the TTX biosynthetic route. Here, we report the complete genome of the TTX-producing bacterium Bacillus sp. 1839. The genome of the strain Bacillus sp. 1839, previously isolated from the TTX-bearing marine ribbon worm Cephalothrix cf. simula, was obtained using second generation Illumina and third generation nanopore sequencing technologies. Phylogenetic analysis has classified this strain as Cytobacillus gottheilii.
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Affiliation(s)
- Daria I. Melnikova
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia;
| | - Reindert Nijland
- Marine Animal Ecology Group, Department of Animal Sciences, Wageningen University and Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands;
| | - Timur Yu. Magarlamov
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, 690041 Vladivostok, Russia;
- Correspondence: ; Tel.: +7-914-661-7949
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Sillo F, Garbelotto M, Giordano L, Gonthier P. Genic introgression from an invasive exotic fungal forest pathogen increases the establishment potential of a sibling native pathogen. NEOBIOTA 2021. [DOI: 10.3897/neobiota.65.64031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Significant hybridization between the invasive North American fungal plant pathogen Heterobasidion irregulare and its Eurasian sister species H. annosum is ongoing in Italy. Whole genomes of nine natural hybrids were sequenced, assembled and compared with those of three genotypes each of the two parental species. Genetic relationships among hybrids and their level of admixture were determined. A multi-approach pipeline was used to assign introgressed genomic blocks to each of the two species. Alleles that introgressed from H. irregulare to H. annosum were associated with pathways putatively related to saprobic processes, while alleles that introgressed from the native to the invasive species were mainly linked to gene regulation. There was no overlap of allele categories introgressed in the two directions. Phenotypic experiments documented a fitness increase in H. annosum genotypes characterized by introgression of alleles from the invasive species, supporting the hypothesis that hybridization results in putatively adaptive introgression. Conversely, introgression from the native into the exotic species appeared to be driven by selection on genes favoring genome stability. Since the introgression of specific alleles from the exotic H. irregulare into the native H. annosum increased the invasiveness of the latter species, we propose that two invasions may be co-occurring: the first one by genotypes of the exotic species, and the second one by alleles belonging to the exotic species. Given that H. irregulare represents a threat to European forests, monitoring programs need to track not only exotic genotypes in native forest stands, but also exotic alleles introgressed in native genotypes.
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Brinkrolf K, Shukla SP, Griep S, Rupp O, Heise P, Goesmann A, Heckel DG, Vogel H, Vilcinskas A. Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. BMC Genomics 2021; 22:323. [PMID: 33941076 PMCID: PMC8091737 DOI: 10.1186/s12864-021-07597-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/11/2021] [Indexed: 11/23/2022] Open
Abstract
Background Mutualistic interactions with microbes can help insects adapt to extreme environments and unusual diets. An intriguing example is the burying beetle Nicrophorus vespilloides, which feeds and reproduces on small vertebrate carcasses. Its fungal microbiome is dominated by yeasts that potentially facilitate carcass utilization by producing digestive enzymes, eliminating cadaver-associated toxic volatiles (that would otherwise attract competitors), and releasing antimicrobials to sanitize the microenvironment. Some of these yeasts are closely related to the biotechnologically important species Yarrowia lipolytica. Results To investigate the roles of these Yarrowia-like yeast (YLY) strains in more detail, we selected five strains from two different phylogenetic clades for third-generation sequencing and genome analysis. The first clade, represented by strain B02, has a 20-Mb genome containing ~ 6400 predicted protein-coding genes. The second clade, represented by strain C11, has a 25-Mb genome containing ~ 6300 predicted protein-coding genes, and extensive intraspecific variability within the ITS–D1/D2 rDNA region commonly used for species assignments. Phenotypic microarray analysis revealed that both YLY strains were able to utilize a diverse range of carbon and nitrogen sources (including microbial metabolites associated with putrefaction), and can grow in environments with extreme pH and salt concentrations. Conclusions The genomic characterization of five yeast strains isolated from N. vespilloides resulted in the identification of strains potentially representing new YLY species. Given their abundance in the beetle hindgut, and dominant growth on beetle-prepared carcasses, the analysis of these strains has revealed the genetic basis of a potential symbiotic relationship between yeasts and burying beetles that facilitates carcass digestion and preservation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07597-z.
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Affiliation(s)
- Karina Brinkrolf
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392, Giessen, Germany. .,Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35302, Giessen, Germany.
| | - Shantanu P Shukla
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Sven Griep
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35302, Giessen, Germany
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35302, Giessen, Germany
| | - Philipp Heise
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35302, Giessen, Germany
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392, Giessen, Germany.,Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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Draft Genome Sequence of Limnospira sp. Strain BM01, Isolated from a Hypersaline Lake of the Momela Ecosystem in Tanzania. Microbiol Resour Announc 2021; 10:10/16/e00132-21. [PMID: 33888498 PMCID: PMC8063641 DOI: 10.1128/mra.00132-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Limnospira includes cyanobacterial species used for industrial production of dietary supplements and nutraceutical agents. The metagenome-assembled genome of Limnospira sp. strain BM01 from Big Momela Lake (BM), Tanzania, was 6,228,312 bp long with a GC content of 44.8% and carried 4,921 proteins and 52 RNA genes, including 6 rRNA genes. The genus Limnospira includes cyanobacterial species used for industrial production of dietary supplements and nutraceutical agents. The metagenome-assembled genome of Limnospira sp. strain BM01 from Big Momela Lake, Tanzania, was 6,228,312 bp long with a GC content of 44.8% and carried 4,921 proteins and 52 RNA genes, including 6 rRNA genes.
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