1
|
Ribeiro S, Chaumet G, Alves K, Nourikyan J, Shi L, Lavergne JP, Mijakovic I, de Bernard S, Buffat L. BacSPaD: A Robust Bacterial Strains' Pathogenicity Resource Based on Integrated and Curated Genomic Metadata. Pathogens 2024; 13:672. [PMID: 39204272 PMCID: PMC11357117 DOI: 10.3390/pathogens13080672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
The vast array of omics data in microbiology presents significant opportunities for studying bacterial pathogenesis and creating computational tools for predicting pathogenic potential. However, the field lacks a comprehensive, curated resource that catalogs bacterial strains and their ability to cause human infections. Current methods for identifying pathogenicity determinants often introduce biases and miss critical aspects of bacterial pathogenesis. In response to this gap, we introduce BacSPaD (Bacterial Strains' Pathogenicity Database), a thoroughly curated database focusing on pathogenicity annotations for a wide range of high-quality, complete bacterial genomes. Our rule-based annotation workflow combines metadata from trusted sources with automated keyword matching, extensive manual curation, and detailed literature review. Our analysis classified 5502 genomes as pathogenic to humans (HP) and 490 as non-pathogenic to humans (NHP), encompassing 532 species, 193 genera, and 96 families. Statistical analysis demonstrated a significant but moderate correlation between virulence factors and HP classification, highlighting the complexity of bacterial pathogenicity and the need for ongoing research. This resource is poised to enhance our understanding of bacterial pathogenicity mechanisms and aid in the development of predictive models. To improve accessibility and provide key visualization statistics, we developed a user-friendly web interface.
Collapse
Affiliation(s)
- Sara Ribeiro
- AltraBio SAS, 69007 Lyon, France (L.B.)
- Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, Université Lyon 1, CNRS, UMR 5086, 69007 Lyon, France
| | | | | | | | - Lei Shi
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Göteborg, Sweden
| | - Jean-Pierre Lavergne
- Bases Moléculaires et Structurales des Systèmes Infectieux, IBCP, Université Lyon 1, CNRS, UMR 5086, 69007 Lyon, France
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Göteborg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | | | | |
Collapse
|
2
|
Uchuwittayakul A, Thangsunan P, Thangsunan P, Rodkhum C, Srisapoome P. Molecular structure and functional responses of IgM, IgT and IgD to Flavobacterium covae and Streptococcus iniae infection in Asian seabass (Lates calcarifer Bloch, 1790). FISH & SHELLFISH IMMUNOLOGY 2024; 153:109823. [PMID: 39122096 DOI: 10.1016/j.fsi.2024.109823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
The Asian seabass (Lates calcarifer) faces significant disease threats, which are exacerbated by intensive farming practices and environmental changes. Therefore, understanding its immune system is crucial. The current study presents a comprehensive analysis of immune-related genes in Asian seabass peripheral blood leukocytes (PBLs) using Iso-seq technology, identifying 16 key pathways associated with 7,857 immune-related genes, comprising 634 unique immune-related genes. The research marks the first comprehensive report on the entire immunoglobulin repertoire in Asian seabass, revealing specific characteristics of immunoglobulin heavy chain constant region transcripts, including IgM (Cμ, ighm), IgT (Cτ, ight), and IgD (Cδ, ighd). The study confirms the presence of membrane-bound form, ighmmb, ightmb, ighdmb of IgM, IgT and IgD and secreted form, ighmsc and ightsc of IgM and IgT, respectively, with similar structural patterns and conserved features in amino acids across immunoglobulin molecules, including cysteine residues crucial for structural integrity observed in other teleost species. In response to bacterial infections by Flavobacterium covae (formerly F. columnare genomovar II) and Streptococcus iniae, both secreted and membrane-bound forms of IgM (ighmmb and ighmsc) and IgT (ightmb and ightsc) show significant expression, indicating their roles in systemic and mucosal immunity. The expression of membrane-bound form IgD gene, ighdmb, predominantly exhibits targeted upregulation in PBLs, suggesting a regulatory role in B cell-mediated immunity. The findings underscore the dynamic and tissue-specific expression of immunoglobulin repertoires, ighmmb, ighmsc, ightmb, ightsc and ighdmb in Asian seabass, indicating a sophisticated immune response to bacterial pathogens. These findings have practical implications for fish aquaculture, and disease control strategies, serving as a valuable resource for advancing research in Asian seabass immunology.
Collapse
Affiliation(s)
- Anurak Uchuwittayakul
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand; Center of Excellence in Aquatic Animal Health Management (CE AAHM), Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand.
| | - Pattanapong Thangsunan
- Division of Biochemistry and Biochemical Innovation, Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence for Innovation in Chemistry, and Research Laboratory on Advanced Materials for Sensor and Biosensor Innovation, Material Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Patcharapong Thangsunan
- Division of Biochemistry and Biochemical Innovation, Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; Office of Research Administration, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Channarong Rodkhum
- Center of Excellence in Fish Infectious Diseases (CE FID), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Prapansak Srisapoome
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand; Center of Excellence in Aquatic Animal Health Management (CE AAHM), Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand.
| |
Collapse
|
3
|
Sun Y, Zhao X, Fan X, Wang M, Li C, Liu Y, Wu P, Yan Q, Sun L. Assessing the impact of sequencing platforms and analytical pipelines on whole-exome sequencing. Front Genet 2024; 15:1334075. [PMID: 38818042 PMCID: PMC11137314 DOI: 10.3389/fgene.2024.1334075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/30/2024] [Indexed: 06/01/2024] Open
Affiliation(s)
- Yanping Sun
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xiaochao Zhao
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xue Fan
- Clinical Research Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Miao Wang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Chaoyang Li
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Ping Wu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Sun
- GeneMind Biosciences Company Limited, Shenzhen, China
| |
Collapse
|
4
|
Hoarau AOG, Mavingui P, Miltgen G. Comprehensive analysis of antimicrobial resistance in the Southwest Indian Ocean: focus on WHO critical and high priority pathogens. Front Public Health 2024; 12:1357345. [PMID: 38628847 PMCID: PMC11018943 DOI: 10.3389/fpubh.2024.1357345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
The spread of antimicrobial resistance (AMR) is a major global concern, and the islands of the Southwest Indian Ocean (SWIO) are not exempt from this phenomenon. As strategic crossroads between Southern Africa and the Indian subcontinent, these islands are constantly threatened by the importation of multidrug-resistant bacteria from these regions. In this systematic review, our aim was to assess the epidemiological situation of AMR in humans in the SWIO islands, focusing on bacterial species listed as priority by the World Health Organization. Specifically, we examined Enterobacterales, Acinetobacter spp., Pseudomonas spp. resistant to carbapenems, and Enterococcus spp. resistant to vancomycin. Our main objectives were to map the distribution of these resistant bacteria in the SWIO islands and identify the genes involved in their resistance mechanisms. We conducted literature review focusing on Comoros, Madagascar, Maldives, Mauritius, Mayotte, Reunion Island, Seychelles, Sri Lanka, and Zanzibar. Our findings revealed a growing interest in the investigation of these pathogens and provided evidence of their active circulation in many of the territories investigated. However, we also identified disparities in terms of data availability between the targeted bacteria and among the different territories, emphasizing the need to strengthen collaborative efforts to establish an efficient regional surveillance network.
Collapse
Affiliation(s)
- Axel O. G. Hoarau
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Patrick Mavingui
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Guillaume Miltgen
- Université de La Réunion, Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
- Laboratoire de Bactériologie, CHU Félix Guyon, Saint-Denis, La Réunion, France
- Centre Régional en Antibiothérapie (CRAtb) de La Réunion, Saint-Pierre, La Réunion, France
| |
Collapse
|
5
|
Nivedita S, Behera SS, Behera HT, Gouda SK, Panda AN, Ray L. Comparative genome-wide analysis of novel Streptomyces isolates RC1831 and RC1832: deciphering the role of functional carbohydrate (CAZy) active genes including chitinase for production of chitosan. 3 Biotech 2024; 14:114. [PMID: 38524236 PMCID: PMC10954598 DOI: 10.1007/s13205-024-03936-5] [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: 05/16/2023] [Accepted: 01/21/2024] [Indexed: 03/26/2024] Open
Abstract
This work compares two bacterial isolates Streptomyces barkulensis RC1831 and Streptomyces chitinovorans RC1832 isolated from Chilika Lake sediments in Odisha, India, using whole-genome sequence analysis. According to the results of the genome analysis, the RC1831 genome has a chromosome with 6,383,258 bp (72.9% GC) and 6145 coding sequences and 66 RNA, while the RC1832 genome has a chromosome with 6,055,792 bp (73.1% GC) and 5824 coding sequences and 63 RNA. Further analysis of the carbohydrate active enzyme (CAZyme) revealed that RC1831 contains 78 glycoside hydrolase family genes, whereas RC1832 includes 50 glycoside hydrolases that have the potential to regulate the chitin-degrading enzymes. KAAS (KEGG Automatic Annotation Server) and AntiSMASH online tool V3.0.5 were used to identify a biosynthetic gene cluster in the isolated strain's genome. The detailed comparative analysis of the genes between the strains will help to gain better insight of chitin and other carbohydrate polymer degradation and secondary metabolite production in both the strains as well as the evolutionary relationship and possibilities of industrial application of these strains. Chitosan production might be explained by genes for the chitin breakdown pathway found in the genome sequence, but genes for later-stage conversion were not found. One significant biomolecule with a wide range of industrial uses is chitosan. Therefore, using these microbes to produce chitosan offers a viable waste disposal solution. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03936-5.
Collapse
Affiliation(s)
- Suchismita Nivedita
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha India
| | | | | | - Sudhansu Kumar Gouda
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha India
| | | | - Lopamudra Ray
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha India
| |
Collapse
|
6
|
Kordi M, Talkhounche PG, Vahedi H, Farrokhi N, Tabarzad M. Heterologous Production of Antimicrobial Peptides: Notes to Consider. Protein J 2024; 43:129-158. [PMID: 38180586 DOI: 10.1007/s10930-023-10174-w] [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] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
Heavy and irresponsible use of antibiotics in the last century has put selection pressure on the microbes to evolve even faster and develop more resilient strains. In the confrontation with such sometimes called "superbugs", the search for new sources of biochemical antibiotics seems to have reached the limit. In the last two decades, bioactive antimicrobial peptides (AMPs), which are polypeptide chains with less than 100 amino acids, have attracted the attention of many in the control of microbial pathogens, more than the other types of antibiotics. AMPs are groups of components involved in the immune response of many living organisms, and have come to light as new frontiers in fighting with microbes. AMPs are generally produced in minute amounts within organisms; therefore, to address the market, they have to be either produced on a large scale through recombinant DNA technology or to be synthesized via chemical methods. Here, heterologous expression of AMPs within bacterial, fungal, yeast, plants, and insect cells, and points that need to be considered towards their industrialization will be reviewed.
Collapse
Affiliation(s)
- Masoumeh Kordi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Parnian Ghaedi Talkhounche
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Helia Vahedi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Naser Farrokhi
- Department of Cell & Molecular Biology, Faculty of Life Sciences & Biotechnology, Shahid Beheshti University, Tehran, Iran.
| | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
7
|
Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [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: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
Collapse
Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
| |
Collapse
|
8
|
Kuruwa S, Zade A, Shah S, Moidu R, Lad S, Chande C, Joshi A, Hirani N, Nikam C, Bhattacharya S, Poojary A, Kapoor M, Kondabagil K, Chatterjee A. An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi, and ARG. J Appl Microbiol 2024; 135:lxae037. [PMID: 38346849 DOI: 10.1093/jambio/lxae037] [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: 08/30/2023] [Revised: 01/26/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
AIMS The use of metagenomics for pathogen identification in clinical practice has been limited. Here we describe a workflow to encourage the clinical utility and potential of NGS for the screening of bacteria, fungi, and antimicrobial resistance genes (ARGs). METHODS AND RESULTS The method includes target enrichment, long-read sequencing, and automated bioinformatics. Evaluation of several tools and databases was undertaken across standard organisms (n = 12), clinical isolates (n = 114), and blood samples from patients with suspected bloodstream infections (n = 33). The strategy used could offset the presence of host background DNA, error rates of long-read sequencing, and provide accurate and reproducible detection of pathogens. Eleven targets could be successfully tested in a single assay. Organisms could be confidently identified considering ≥60% of best hits of a BLAST-based threshold of e-value 0.001 and a percent identity of >80%. For ARGs, reads with percent identity of >90% and >60% overlap of the complete gene could be confidently annotated. A kappa of 0.83 was observed compared to standard diagnostic methods. Thus, a workflow for the direct-from-sample, on-site sequencing combined with automated genomics was demonstrated to be reproducible. CONCLUSION NGS-based technologies overcome several limitations of current day diagnostics. Highly sensitive and comprehensive methods of pathogen screening are the need of the hour. We developed a framework for reliable, on-site, screening of pathogens.
Collapse
Affiliation(s)
- Sanjana Kuruwa
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Amrutraj Zade
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanchi Shah
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rameez Moidu
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shailesh Lad
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Chhaya Chande
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Ameeta Joshi
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Nilma Hirani
- Department of Microbiology, Sir J. J. Group of Hospitals, Mumbai 400008, India
| | - Chaitali Nikam
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
- Thyrocare Technologies Pvt. Ltd, Navi Mumbai 400703, India
| | - Sanjay Bhattacharya
- Department of Microbiology, Tata Medical Center, 14, MAR(E-W), DH Block (Newtown), Action Area I, Newtown, Kolkata, Chakpachuria 700160, India
| | - Aruna Poojary
- Department of Microbiology, Breach Candy Hospital and Research Center, Mumbai 400026, India
| | - Mahua Kapoor
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kiran Kondabagil
- Department of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anirvan Chatterjee
- HaystackAnalytics Pvt. Ltd, SINE, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
9
|
Henares D, Lo SW, Perez-Argüello A, Redin A, Ciruela P, Garcia-Garcia JJ, Brotons P, Yuste J, Sá-Leão R, Muñoz-Almagro C. Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae. J Clin Microbiol 2023; 61:e0074123. [PMID: 38092657 PMCID: PMC10729682 DOI: 10.1128/jcm.00741-23] [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: 06/12/2023] [Accepted: 10/01/2023] [Indexed: 12/20/2023] Open
Abstract
Whole genome sequencing (WGS)-based approaches for pneumococcal capsular typing have become an alternative to serological methods. In silico serotyping from WGS has not yet been applied to long-read sequences produced by third-generation technologies. The objective of the study was to determine the capsular types of pneumococci causing invasive disease in Catalonia (Spain) using serological typing and WGS and to compare the performance of different bioinformatics pipelines using short- and long-read data from WGS. All invasive pneumococcal pediatric isolates collected in Hospital Sant Joan de Déu (Barcelona) from 2013 to 2019 were included. Isolates were assigned a capsular type by serological testing based on anticapsular antisera and by different WGS-based pipelines: Illumina sequencing followed by serotyping with PneumoCaT, SeroBA, and Pathogenwatch vs MinION-ONT sequencing coupled with serotyping by Pathogenwatch from pneumococcal assembled genomes. A total of 119 out of 121 pneumococcal isolates were available for sequencing. Twenty-nine different serotypes were identified by serological typing, with 24F (n = 17; 14.3%), 14 (n = 10; 8.4%), and 15B/C (n = 8; 6.7%) being the most common serotypes. WGS-based pipelines showed initial concordance with serological typing (>91% of accuracy). The main discrepant results were found at the serotype level within a serogroup: 6A/B, 6C/D, 9A/V, 11A/D, and 18B/C. Only one discrepancy at the serogroup level was observed: serotype 29 by serological testing and serotype 35B/D by all WGS-based pipelines. Thus, bioinformatics WGS-based pipelines, including those using third-generation sequencing, are useful for pneumococcal capsular assignment. Possible discrepancies between serological typing and WGS-based approaches should be considered in pneumococcal capsular-type surveillance studies.
Collapse
Affiliation(s)
- Desiree Henares
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Stephanie W. Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Milner Center for Evolution, Life Sciences Department, University of Bath, Bath, United Kingdom
| | - Amaresh Perez-Argüello
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Alba Redin
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Pilar Ciruela
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Surveillance and Public Health Emergency Response, Public Health Agency of Catalonia (ASPCAT), Barcelona, Spain
| | - Juan Jose Garcia-Garcia
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- Pediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Department of Surgery and Medical-Surgical Specialties, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Pedro Brotons
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Jose Yuste
- Spanish Pneumococcal Reference Laboratory, National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER of Respiratory Diseases (CIBERES), Instituto de salud Carlos III, Madrid, Spain
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Carmen Muñoz-Almagro
- Department of RDI Microbiology, Hospital Sant Joan de Déu, Barcelona, Spain
- Infectious Diseases and Microbiome, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
- School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| |
Collapse
|
10
|
Wang C, Ahsan T, Ding A, Han D, Zang CQ, Huang YQ, Hussain K. Whole genome analysis of Bacillus amyloliquefaciens TA-1, a promising biocontrol agent against Cercospora arachidicola pathogen of early leaf spot in Arachis hypogaea L. BMC PLANT BIOLOGY 2023; 23:410. [PMID: 37667202 PMCID: PMC10478280 DOI: 10.1186/s12870-023-04423-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Early leaf spot disease, caused by Cercospora arachidicola, is a devastating peanut disease that has severely impacted peanut production and quality. Chemical fungicides pollute the environment; however, Bacillus bacteria can be used as an environmentally friendly alternative to chemical fungicides. To understand the novel bacterial strain and unravel its molecular mechanism, De novo whole-genome sequencing emerges as a rapid and efficient omics approach. RESULTS In the current study, we identified an antagonistic strain, Bacillus amyloliquefaciens TA-1. In-vitro assay showed that the TA-1 strain was a strong antagonist against C. arachidicola, with an inhibition zone of 88.9 mm. In a greenhouse assay, results showed that the TA-1 strain had a significant biocontrol effect of 95% on peanut early leaf spot disease. De novo whole-genome sequencing analysis, shows that strain TA-1 has a single circular chromosome with 4172 protein-coding genes and a 45.91% guanine and cytosine (GC) content. Gene function was annotated using non-redundant proteins from the National Center for Biotechnology Information (NCBI), Swiss-Prot, the Kyoto Encyclopedia of Genes and Genomes (KEGG), clusters of orthologous groups of proteins, gene ontology, pathogen-host interactions, and carbohydrate-active enZYmes. antiSMASH analysis predicted that strain TA-1 can produce the secondary metabolites siderophore, tailcyclized peptide, myxochelin, bacillibactin, paenibactin, myxochelin, griseobactin, benarthin, tailcyclized, and samylocyclicin. CONCLUSION The strain TA-1 had a significant biological control effect against peanut early leaf spot disease in-vitro and in greenhouse assays. Whole genome analysis revealed that, TA-1 strain belongs to B. amyloliquefaciens and could produce the antifungal secondary metabolites.
Collapse
Affiliation(s)
- Chen Wang
- Plant Protection College, Shenyang Agricultural University, Shenyang, 110866, China
| | - Taswar Ahsan
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, P.R. China
| | - Ao Ding
- Plant Protection College, Shenyang Agricultural University, Shenyang, 110866, China
| | - Di Han
- Plant Protection College, Shenyang Agricultural University, Shenyang, 110866, China
| | - Chao-Qun Zang
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, P.R. China
| | - Yu-Qian Huang
- Plant Protection College, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Khalid Hussain
- Department of Botany, University of Gujrat, 50700, Gujrat, Pakistan
| |
Collapse
|
11
|
Roberts SM, Aldis M, Wright ET, Gonzales CB, Lai Z, Weintraub ST, Hardies SC, Serwer P. Siphophage 0105phi7-2 of Bacillus thuringiensis: Novel Propagation, DNA, and Genome-Implied Assembly. Int J Mol Sci 2023; 24:ijms24108941. [PMID: 37240285 DOI: 10.3390/ijms24108941] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Diversity of phage propagation, physical properties, and assembly promotes the use of phages in ecological studies and biomedicine. However, observed phage diversity is incomplete. Bacillus thuringiensis siphophage, 0105phi-7-2, first described here, significantly expands known phage diversity, as seen via in-plaque propagation, electron microscopy, whole genome sequencing/annotation, protein mass spectrometry, and native gel electrophoresis (AGE). Average plaque diameter vs. plaque-supporting agarose gel concentration plots reveal unusually steep conversion to large plaques as agarose concentration decreases below 0.2%. These large plaques sometimes have small satellites and are made larger by orthovanadate, an ATPase inhibitor. Phage head-host-cell binding is observed by electron microscopy. We hypothesize that this binding causes plaque size-increase via biofilm evolved, ATP stimulated ride-hitching on motile host cells by temporarily inactive phages. Phage 0105phi7-2 does not propagate in liquid culture. Genomic sequencing/annotation reveals history as temperate phage and distant similarity, in a virion-assembly gene cluster, to prototypical siphophage SPP1 of Bacillus subtilis. Phage 0105phi7-2 is distinct in (1) absence of head-assembly scaffolding via either separate protein or classically sized, head protein-embedded peptide, (2) producing partially condensed, head-expelled DNA, and (3) having a surface relatively poor in AGE-detected net negative charges, which is possibly correlated with observed low murine blood persistence.
Collapse
Affiliation(s)
- Samantha M Roberts
- Department of Microbiology, Immunology and Molecular Genetics, UT Health, San Antonio, TX 78229, USA
| | - Miranda Aldis
- Department of Microbiology, Immunology and Molecular Genetics, UT Health, San Antonio, TX 78229, USA
| | - Elena T Wright
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
| | - Cara B Gonzales
- Department of Comprehensive Dentistry, UT Health, San Antonio, TX 78229, USA
| | - Zhao Lai
- Department of Molecular Medicine, UT Health, San Antonio, TX 78229, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
| | - Stephen C Hardies
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
| | - Philip Serwer
- Department of Biochemistry and Structural Biology, UT Health, San Antonio, TX 78229, USA
| |
Collapse
|
12
|
Krøvel AV, Hetland MAK, Bernhoff E, Bjørheim AS, Soma MA, Löhr IH. Long-read sequencing for reliably calling the mompS allele in Legionella pneumophila sequence-based typing. Front Cell Infect Microbiol 2023; 13:1176182. [PMID: 37256104 PMCID: PMC10226664 DOI: 10.3389/fcimb.2023.1176182] [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: 02/28/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023] Open
Abstract
Sequence-based typing (SBT) of Legionella pneumophila is a valuable tool in epidemiological studies and outbreak investigations of Legionnaires' disease. In the L. pneumophila SBT scheme, mompS2 is one of seven genes that determine the sequence type (ST). The Legionella genome typically contains two copies of mompS (mompS1 and mompS2). When they are non-identical it can be challenging to determine the mompS2 allele, and subsequently the ST, from Illumina short-reads. In our collection of 233 L. pneumophila genomes, there were 62 STs, 18 of which carried non-identical mompS copies. Using short-reads, the mompS2 allele was misassembled or untypeable in several STs. Genomes belonging to ST154 and ST574, which carried mompS1 allele 7 and mompS2 allele 15, were assigned an incorrect mompS2 allele and/or mompS gene copy number when short-read assembled. For other isolates, mainly those carrying non-identical mompS copies, short-read assemblers occasionally failed to resolve the structure of the mompS-region, also resulting in untypeability from the short-read data. In this study, we wanted to understand the challenges we observed with calling the mompS2 allele from short-reads, assess if other short-read methods were able to resolve the mompS-region, and investigate the possibility of using long-reads to obtain the mompS alleles, and thereby perform L. pneumophila SBT from long-reads only. We found that the choice of short-read assembler had a major impact on resolving the mompS-region and thus SBT from short-reads, but no method consistently solved the mompS2 allele. By using Oxford Nanopore Technology (ONT) sequencing together with Trycycler and Medaka for long-read assembly and polishing we were able to resolve the mompS copies and correctly identify the mompS2 allele, in accordance with Sanger sequencing/EQA results for all tested isolates (n=35). The remaining six genes of the SBT profile could also be determined from the ONT-only reads. The STs called from ONT-only assemblies were also consistent with hybrid-assemblies of Illumina and ONT reads. We therefore propose ONT sequencing as an alternative method to perform L. pneumophila SBT to overcome the mompS challenge observed with short-reads. To facilitate this, we have developed ONTmompS (https://github.com/marithetland/ONTmompS), an in silico approach to determine L. pneumophila ST from long-read or hybrid assemblies.
Collapse
Affiliation(s)
- Anne Vatland Krøvel
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- National Reference Laboratory for Legionella, Stavanger University Hospital, Stavanger, Norway
| | - Marit A. K. Hetland
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- Department of Biological Sciences, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- National Reference Laboratory for Legionella, Stavanger University Hospital, Stavanger, Norway
| | - Anna Steensen Bjørheim
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- National Reference Laboratory for Legionella, Stavanger University Hospital, Stavanger, Norway
| | - Markus André Soma
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Iren H. Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- National Reference Laboratory for Legionella, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| |
Collapse
|
13
|
Foster-Nyarko E, Cottingham H, Wick RR, Judd LM, Lam MMC, Wyres KL, Stanton TD, Tsang KK, David S, Aanensen DM, Brisse S, Holt KE. Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae. Microb Genom 2023; 9:mgen000936. [PMID: 36752781 PMCID: PMC9997738 DOI: 10.1099/mgen.0.000936] [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] [Indexed: 02/09/2023] Open
Abstract
Oxford Nanopore Technologies (ONT) sequencing has rich potential for genomic epidemiology and public health investigations of bacterial pathogens, particularly in low-resource settings and at the point of care, due to its portability and affordability. However, low base-call accuracy has limited the reliability of ONT data for critical tasks such as antimicrobial resistance (AMR) and virulence gene detection and typing, serotype prediction, and cluster identification. Thus, Illumina sequencing remains the standard for genomic surveillance despite higher capital and running costs. We tested the accuracy of ONT-only assemblies for common applied bacterial genomics tasks (genotyping and cluster detection, implemented via Kleborate, Kaptive and Pathogenwatch), using data from 54 unique Klebsiella pneumoniae isolates. ONT reads generated via MinION with R9.4.1 flowcells were basecalled using three alternative models [Fast, High-accuracy (HAC) and Super-accuracy (SUP), available within ONT's Guppy software], assembled with Flye and polished using Medaka. Accuracy of typing using ONT-only assemblies was compared with that of Illumina-only and hybrid ONT+Illumina assemblies, constructed from the same isolates as reference standards. The most resource-intensive ONT-assembly approach (SUP basecalling, with or without Medaka polishing) performed best, yielding reliable capsule (K) type calls for all strains (100 % exact or best matching locus), reliable multi-locus sequence type (MLST) assignment (98.3 % exact match or single-locus variants), and good detection of acquired AMR genes and mutations (88-100 % correct identification across the various drug classes). Distance-based trees generated from SUP+Medaka assemblies accurately reflected overall genetic relationships between isolates. The definition of outbreak clusters from ONT-only assemblies was problematic due to inflation of SNP counts by high base-call errors. However, ONT data could be reliably used to 'rule out' isolates of distinct lineages from suspected transmission clusters. HAC basecalling + Medaka polishing performed similarly to SUP basecalling without polishing. Therefore, we recommend investing compute resources into basecalling (SUP model), wherever compute resources and time allow, and note that polishing is also worthwhile for improved performance. Overall, our results show that MLST, K type and AMR determinants can be reliably identified with ONT-only R9.4.1 flowcell data. However, cluster detection remains challenging with this technology.
Collapse
Affiliation(s)
- Ebenezer Foster-Nyarko
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- *Correspondence: Ebenezer Foster-Nyarko,
| | - Hugh Cottingham
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Ryan R. Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Louise M. Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Margaret M. C. Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Thomas D. Stanton
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Kara K. Tsang
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Oxford University, Oxford OX3 7LF, UK
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, Oxford University, Oxford OX3 7LF, UK
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Kathryn E. Holt
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| |
Collapse
|
14
|
Alkatheri AH, Yap PSX, Abushelaibi A, Lai KS, Cheng WH, Erin Lim SH. Microbial Genomics: Innovative Targets and Mechanisms. Antibiotics (Basel) 2023; 12:antibiotics12020190. [PMID: 36830101 PMCID: PMC9951906 DOI: 10.3390/antibiotics12020190] [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: 10/18/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Multidrug resistance (MDR) has become an increasing threat to global health because bacteria can develop resistance to antibiotics over time. Scientists worldwide are searching for new approaches that go beyond traditional antibiotic discovery and development pipelines. Advances in genomics, however, opened up an unexplored therapeutic opportunity for the discovery of new antibacterial agents. Genomic approaches have been used to discover several novel antibiotics that target critical processes for bacterial growth and survival, including histidine kinases (HKs), LpxC, FabI, peptide deformylase (PDF), and aminoacyl-tRNA synthetases (AaRS). In this review, we will discuss the use of microbial genomics in the search for innovative and promising drug targets as well as the mechanisms of action for novel antimicrobial agents. We will also discuss future directions on how the utilization of the microbial genomics approach could improve the odds of antibiotic development having a more successful outcome.
Collapse
Affiliation(s)
- Asma Hussain Alkatheri
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Polly Soo-Xi Yap
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor 47500, Malaysia
| | - Aisha Abushelaibi
- Office of Campus Director, Abu Dhabi Colleges, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Wan-Hee Cheng
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana BBN, Nilai 71800, Malaysia
| | - Swee-Hua Erin Lim
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
- Correspondence:
| |
Collapse
|
15
|
Gerbig GR, Piontkivska H, Smith TC, White R, Mukherjee J, Benson H, Rosenbaum M, Leibler JH. Genetic characterization of Staphylococcus aureus isolated from Norway rats in Boston, Massachusetts. Vet Med Sci 2023; 9:272-281. [PMID: 36524786 PMCID: PMC9856981 DOI: 10.1002/vms3.1020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Despite the importance of domesticated animals in the generation and transmission of antibiotic-resistant Staphylococcus aureus, the role of wild animals, specifically rodents, in the ecology of S. aureus remains unclear. We recovered and genotyped S. aureus isolates from wild Norway rats (Rattus norvegicus) in Boston, Massachusetts to examine genetic relationships between common human and animal S. aureus isolates in a large US metropolitan area. METHODS We collected and necropsied 63 rats from June 2016 to June 2017. Nasal, foot pad, fur, and fecal swabs were collected. Staphylococcus aureus was isolated using culture-based methods and polymerase chain reaction confirmation. S. aureus isolates were spa typed, tested for antibiotic susceptibility, and whole genome sequenced. Assembled sequences were uploaded to the Comprehensive Antibiotic Resistance Database to identify antibiotic resistance elements. A phylogenetic tree was constructed using the neighbor-joining method with the maximum composite likelihood distance in MEGA7. RESULTS We recovered 164 Gram-positive bacterial isolates from Norway rats. Nineteen isolates from eight individual rats were confirmed as S. aureus (prevalence: 12.9% (8/63)). All S. aureus isolates were methicillin-susceptible S. aureus (MSSA), pvl-negative, and resistant to penicillin. Two isolates displayed resistance to erythromycin. Four different S. aureus spa types were detected (t933, t10751, t18202, and t189). Thirteen unique antibiotic resistance elements were identified, and all isolates shared genes mepR, mgrA, arlR, and S. aureus norA. Phylogenetic analysis if the 19 S. aureus isolates revealed they were genetically similar to four clades of S. aureus with similar resistance gene profiles isolated from both human- and animal-derived S. aureus, as well as formed a distinct phylogenetic cluster composed only of rat isolates. CONCLUSIONS Wild rodents may serve as a reservoir or vector of antibiotic resistance genes in the urban environment with relevance for human and animal health.
Collapse
Affiliation(s)
| | | | - Tara C. Smith
- College of Public HealthKent State UniversityKentOhioUSA
| | - Ruairi White
- Department of Infectious Disease and Global Health, Cummings School of Veterinary MedicineTufts UniversityNorth GraftonMassachussetsUSA
| | - Jean Mukherjee
- Department of Infectious Disease and Global Health, Cummings School of Veterinary MedicineTufts UniversityNorth GraftonMassachussetsUSA
| | - Hayley Benson
- Department of Infectious Disease and Global Health, Cummings School of Veterinary MedicineTufts UniversityNorth GraftonMassachussetsUSA
| | - Marieke Rosenbaum
- Department of Infectious Disease and Global Health, Cummings School of Veterinary MedicineTufts UniversityNorth GraftonMassachussetsUSA
| | - Jessica H. Leibler
- Department of Environmental HealthBoston University School of Public HealthBostonMassachusettsUSA
| |
Collapse
|
16
|
Yamaoka Y, Saruuljavkhlan B, Alfaray RI, Linz B. Pathogenomics of Helicobacter pylori. Curr Top Microbiol Immunol 2023; 444:117-155. [PMID: 38231217 DOI: 10.1007/978-3-031-47331-9_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The human stomach bacterium Helicobacter pylori, the causative agent of gastritis, ulcers and adenocarcinoma, possesses very high genetic diversity. H. pylori has been associated with anatomically modern humans since their origins over 100,000 years ago and has co-evolved with its human host ever since. Predominantly intrafamilial and local transmission, along with genetic isolation, genetic drift, and selection have facilitated the development of distinct bacterial populations that are characteristic for large geographical areas. H. pylori utilizes a large arsenal of virulence and colonization factors to mediate the interaction with its host. Those include various adhesins, the vacuolating cytotoxin VacA, urease, serine protease HtrA, the cytotoxin-associated genes pathogenicity island (cagPAI)-encoded type-IV secretion system and its effector protein CagA, all of which contribute to disease development. While many pathogenicity-related factors are present in all strains, some belong to the auxiliary genome and are associated with specific phylogeographic populations. H. pylori is naturally competent for DNA uptake and recombination, and its genome evolution is driven by extraordinarily high recombination and mutation rates that are by far exceeding those in other bacteria. Comparative genome analyses revealed that adaptation of H. pylori to individual hosts is associated with strong selection for particular protein variants that facilitate immune evasion, especially in surface-exposed and in secreted virulence factors. Recent studies identified single-nucleotide polymorphisms (SNPs) in H. pylori that are associated with the development of severe gastric disease, including gastric cancer. Here, we review the current knowledge about the pathogenomics of H. pylori.
Collapse
Affiliation(s)
- Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1, Idaigaoka, Hasama-machi, Yufu Oita, 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Universitas Airlangga, Surabaya, 60286, East Java, Indonesia
| | - Bodo Linz
- Division of Microbiology, Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.
| |
Collapse
|
17
|
Cai X, Peng Y, Li M, Qiu Y, Wang Y, Xu L, Hou Q. Comparative genomic analyses of the clinically-derived Winkia strain NY0527: the reassignment of W. neuii subsp. neuii and W. neuii subsp. antitratus into two separate species and insights into their virulence characteristics. Front Microbiol 2023; 14:1147469. [PMID: 37152761 PMCID: PMC10160630 DOI: 10.3389/fmicb.2023.1147469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Background Winkia neuii, previously known as Actinomyces neuii, is increasingly recognized as a causative agent of various human infections, while its taxonomy and genomic insights are still understudied. Methods A Winkia strain NY0527 was isolated from the hip abscess of a patient, and its antibiotic susceptibility was assessed. The genome was hybrid assembled from long-reads and short-reads sequencing. Whole-genome-based analyses on taxa assignment, strain diversity, and pathogenesis were conducted. Results The strain was found to be highly susceptible to beta-lactam antibiotics, but resistant to erythromycin, clindamycin, and amikacin. The complete genome sequences of this strain were assembled and found to consist of a circular chromosome and a circular plasmid. Sequence alignment to the NCBI-nt database revealed that the plasmid had high sequence identity (>90%) to four Corynebacterium plasmids, with 40-50% query sequence coverage. Furthermore, the plasmid was discovered to possibly originate from the sequence recombination events of two Corynebacterium plasmid families. Phylogenomic tree and genomic average nucleotide identity analyses indicated that many Winkia sp. strains were still erroneously assigned as Actinomyces sp. strains, and the documented subspecies within W. neuii should be reclassified as two separate species (i.e., W. neuii and W. anitratus). The core genome of each species carried a chromosome-coded beta-lactamase expression repressor gene, which may account for their broadly observed susceptibility to beta-lactam antibiotics in clinical settings. Additionally, an ermX gene that expresses fluoroquinolone resistance was shared by some W. neuii and W. anitratus strains, possibly acquired by IS6 transposase-directed gene transfer events. In contrast, tetracycline resistance genes were exclusively carried by W. neuii strains. In particular, W. neuii was found to be more pathogenic than W. anitratus by encoding more virulence factors (i.e., 35-38 in W. neuii vs 27-31 in W. anitratus). Moreover, both species encoded two core pathogenic virulence factors, namely hemolysin and sialidase, which may facilitate their infections by expressing poreformation, adhesion, and immunoglobulin deglycosylation activities. Conclusion This study highlights the underappreciated taxonomic diversity of Winkia spp. and provides populational genomic insights into their antibiotic susceptibility and pathogenesis for the first time, which could be helpful in the clinical diagnosis and treatment of Winkia spp. infections.
Collapse
Affiliation(s)
- Xunchao Cai
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Yao Peng
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Meng Li
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Yifeng Qiu
- Department of Urology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Yuhan Wang
- Department of Urology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Long Xu
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
- *Correspondence: Long Xu,
| | - Qi Hou
- Department of Urology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
- International Cancer Center, Shenzhen Key Laboratory, Hematology Institution of Shenzhen University, Shenzhen, China
- *Correspondence: Long Xu,
| |
Collapse
|
18
|
Huggins LG, Colella V, Atapattu U, Koehler AV, Traub RJ. Nanopore Sequencing Using the Full-Length 16S rRNA Gene for Detection of Blood-Borne Bacteria in Dogs Reveals a Novel Species of Hemotropic Mycoplasma. Microbiol Spectr 2022; 10:e0308822. [PMID: 36250862 PMCID: PMC9769565 DOI: 10.1128/spectrum.03088-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/26/2022] [Indexed: 01/09/2023] Open
Abstract
Dogs across the globe are afflicted by diverse blood- and vector-borne bacteria (VBB), many of which cause severe disease and can be fatal. Diagnosis of VBB infections can be challenging due to the low concentration of bacteria in the blood, the frequent occurrence of coinfections, and the wide range of known, emerging, and potentially novel VBB species encounterable. Therefore, there is a need for diagnostics that address these challenges by being both sensitive and capable of detecting all VBB simultaneously. We detail the first employment of a nanopore-based sequencing methodology conducted on the Oxford Nanopore Technologies (ONT) MinION device to accurately elucidate the "hemobacteriome" from canine blood through sequencing of the full-length 16S rRNA gene. We detected a diverse range of important canine VBB, including Ehrlichia canis, Anaplasma platys, Mycoplasma haemocanis, Bartonella clarridgeiae, "Candidatus Mycoplasma haematoparvum", a novel species of hemotropic mycoplasma, and Wolbachia endosymbionts of filarial worms, indicative of filariasis. Our nanopore-based protocol was equivalent in sensitivity to both quantitative PCR (qPCR) and Illumina sequencing when benchmarked against these methods, achieving high agreement as defined by the kappa statistics (k > 0.81) for three key VBB. Utilizing the ability of the ONT' MinION device to sequence long read lengths provides an excellent alternative diagnostic method by which the hemobacteriome can be accurately characterized to the species level in a way previously unachievable using short reads. We envision our method to be translatable to multiple contexts, such as the detection of VBB in other vertebrate hosts, including humans, while the small size of the MinION device is highly amenable to field use. IMPORTANCE Blood- and vector-borne bacteria (VBB) can cause severe pathology and even be lethal for dogs in many regions across the globe. Accurate characterization of all the bacterial pathogens infecting a canine host is critical, as coinfections are common and emerging and novel pathogens that may go undetected by traditional diagnostics frequently arise. Deep sequencing using devices from Oxford Nanopore Technologies (ONT) provides a solution, as the long read lengths achievable provide species-level taxonomic identification of pathogens that previous short-read technologies could not accomplish. We developed a protocol using ONT' MinION sequencer to accurately detect and classify a wide spectrum of VBB from canine blood at a sensitivity comparable to that of regularly used diagnostics, such as qPCR. This protocol demonstrates great potential for use in biosurveillance and biosecurity operations for the detection of VBB in a range of vertebrate hosts, while the MinION sequencer's portability allows this method to be used easily in the field.
Collapse
Affiliation(s)
- Lucas G. Huggins
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Vito Colella
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Ushani Atapattu
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Anson V. Koehler
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
19
|
Matthewman C, Narin A, Huston H, Hopkins CE. Systems to model the personalized aspects of microbiome health and gut dysbiosis. Mol Aspects Med 2022; 91:101115. [PMID: 36104261 DOI: 10.1016/j.mam.2022.101115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/03/2022] [Indexed: 01/17/2023]
Abstract
The human gut microbiome is a complex and dynamic microbial entity that interacts with the environment and other parts of the body including the brain, heart, liver, and immune system. These multisystem interactions are highly conserved from invertebrates to humans, however the complexity and diversity of human microbiota compositions often yield a context that is unique to each individual. Yet commonalities remain across species, where a healthy gut microbiome will be rich in symbiotic commensal biota while an unhealthy gut microbiota will be experiencing abnormal blooms of pathobiont bacteria. In this review we discuss how omics technologies can be applied in a personalized approach to understand the microbial crosstalk and microbial-host interactions that affect the delicate balance between eubiosis and dysbiosis in an individual gut microbiome. We further highlight the strengths of model organisms in identifying and characterizing these conserved synergistic and/or pathogenic host-microbe interactions. And finally, we touch upon the growing area of personalized therapeutic interventions targeting gut microbiome.
Collapse
|
20
|
Vasudeva G, Singh H, Paliwal S, Pinnaka AK. Metagenomics: An Approach for Unraveling the Community Structure and Functional Potential of Activated Sludge of a Common Effluent Treatment Plant. Front Microbiol 2022; 13:933373. [PMID: 35958153 PMCID: PMC9358654 DOI: 10.3389/fmicb.2022.933373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/17/2022] [Indexed: 11/23/2022] Open
Abstract
The common effluent treatment plant (CETP) located at Baddi treats the industrial effluent from various industries, leading to the pooling of a diverse range of substrates and metabolites. The nutrient loading and its availability decide the balance of the microbial community and its diversity. The samples thus collected from the activated sludge (BS14) of CETP and Sirsa river (SR1) from the vicinity of CETP effluent discharge were processed for the whole metagenome analysis to reveal the microbial community and its functional potential. The taxonomic classification of the BS14 sample showed the dominance of the bacterial community with 96% of abundance, whereas the SR1 was populated by eukaryotes representing 50.4% of the community of SR1. The bacterial community of SR1 was constituted of 47.2%. The functional analysis of BS14 and SR1 with GhostKOALA against the KEGG database assigned 43.7% and 27.8% of the open reading frames (ORFs) with functions. It revealed the xenobiotic degradation modules with complete pathways along with resistance against the beta-lactams. The analysis with the comprehensive antibiotic resistance database (CARD) revealed 33 and 32 unique types of antimicrobial resistance in BS14 and SR1, respectively. Both the samples were dominated by the beta-lactam resistance genes. The carbohydrate-active enzyme (CAZy) database assigned a total of 6,611 and 2,941 active enzymes to BS14 and SR1, respectively. In contrast, the glycosyl hydrolases (GH) and glycosyltransferases (GT) class of enzymes were found to be abundant in both the samples as compared with polysaccharide lyases (PL), auxiliary activities (AA), carbohydrate esterases (CE), and carbohydrate-binding module (CBM).
Collapse
|
21
|
Tanaya Behera H, Mojumdar A, Kumari K, Kumar Gouda S, Das S, Ray L. Exploration of genomic and functional features of chitinolytic bacterium Streptomyces chilikensis RC1830, isolated from Chilika Lake, India. 3 Biotech 2022; 12:120. [PMID: 35547016 PMCID: PMC9035197 DOI: 10.1007/s13205-022-03184-5] [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: 10/30/2021] [Accepted: 04/04/2022] [Indexed: 11/01/2022] Open
Abstract
Streptomyces chilikensis RC1830 was previously isolated as a novel chitinolytic streptomycete from Chilika Lake, Odisha, India. The strain RC1830 is a representative member of the soil-dwelling, filamentous Streptomyces group that produces the majority of natural antibiotics and secondary metabolites. The objective of this work was to assess the chitin degradation ability and whole-genome sequence of Streptomyces chilikensis RC1830. TLC analysis of the fermentation product revealed that strain RC1830 can convert shrimp shell colloidal chitin to N-acetylated chitooligosaccharides (N-AcCOS). A genome-wide investigation of RC1830 was also carried out to investigate the genetic basis for chitin breakdown. The result showed that the RC1830 genome possesses a chromosome with 7,121,774 bp (73.2% GC). The genome consists of 6807 coding sequences, 69 tRNA, and 3 rRNA genes. Furthermore, carbohydrate-active enzyme (CAZyme) analysis revealed that RC1830 has 89 glycoside hydrolase family genes, which could modulate the enzymes involved in the degradation of chitin ultimately producing industrially important COS. The whole-genome information of RC1830 could emphasize the mechanism involved in the RC1830's chitin breakdown activity, endowing RC1830 with a promising alternative for COS production. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03184-5.
Collapse
|