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Liu GY, Yu D, Fan MM, Zhang X, Jin ZY, Tang C, Liu XF. Antimicrobial resistance crisis: could artificial intelligence be the solution? Mil Med Res 2024; 11:7. [PMID: 38254241 PMCID: PMC10804841 DOI: 10.1186/s40779-024-00510-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Antimicrobial resistance is a global public health threat, and the World Health Organization (WHO) has announced a priority list of the most threatening pathogens against which novel antibiotics need to be developed. The discovery and introduction of novel antibiotics are time-consuming and expensive. According to WHO's report of antibacterial agents in clinical development, only 18 novel antibiotics have been approved since 2014. Therefore, novel antibiotics are critically needed. Artificial intelligence (AI) has been rapidly applied to drug development since its recent technical breakthrough and has dramatically improved the efficiency of the discovery of novel antibiotics. Here, we first summarized recently marketed novel antibiotics, and antibiotic candidates in clinical development. In addition, we systematically reviewed the involvement of AI in antibacterial drug development and utilization, including small molecules, antimicrobial peptides, phage therapy, essential oils, as well as resistance mechanism prediction, and antibiotic stewardship.
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Affiliation(s)
- Guang-Yu Liu
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Key Laboratory of Inflammation and Immunoregulation of Hangzhou, Hangzhou Normal University, Hangzhou, 311121, China
| | - Dan Yu
- National Key Discipline of Pediatrics Key Laboratory of Major Diseases in Children Ministry of Education, Laboratory of Dermatology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Mei-Mei Fan
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Key Laboratory of Inflammation and Immunoregulation of Hangzhou, Hangzhou Normal University, Hangzhou, 311121, China
| | - Xu Zhang
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ze-Yu Jin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christoph Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
| | - Xiao-Fen Liu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Key Laboratory of Clinical Pharmacology of Antibiotics, National Health Commission of the People's Republic of China, National Clinical Research Centre for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
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2
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Camargo AP, Call L, Roux S, Nayfach S, Huntemann M, Palaniappan K, Ratner A, Chu K, Mukherjeep S, Reddy TBK, Chen IM, Ivanova N, Eloe-Fadrosh E, Woyke T, Baltrus D, Castañeda-Barba S, de la Cruz F, Funnell BE, Hall JJ, Mukhopadhyay A, Rocha EC, Stalder T, Top E, Kyrpides N. IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata. Nucleic Acids Res 2024; 52:D164-D173. [PMID: 37930866 PMCID: PMC10767988 DOI: 10.1093/nar/gkad964] [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: 08/29/2023] [Revised: 10/09/2023] [Accepted: 10/14/2023] [Indexed: 11/08/2023] Open
Abstract
Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.
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Affiliation(s)
- Antonio Pedro Camargo
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lee Call
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stephen Nayfach
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marcel Huntemann
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Anna Ratner
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ken Chu
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Supratim Mukherjeep
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - T B K Reddy
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - I-Min A Chen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Natalia N Ivanova
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David A Baltrus
- School of Plant Sciences, University of Arizona, Tucson AZ, USA
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson AZ, USA
| | | | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (Consejo Superior de Investigaciones Científicas – Universidad de Cantabria), Cantabria, Spain
| | - Barbara E Funnell
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - James P J Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Eva Top
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Nikos C Kyrpides
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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3
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Garcillán-Barcia MP, Redondo-Salvo S, de la Cruz F. Plasmid classifications. Plasmid 2023; 126:102684. [PMID: 37116631 DOI: 10.1016/j.plasmid.2023.102684] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/09/2023] [Accepted: 04/17/2023] [Indexed: 04/30/2023]
Abstract
Plasmids are universally present in bacteria and play key roles in the dissemination of genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive from the efforts to classify plasmids. Here, we review the main plasmid classification systems, starting by phenotype-based methods, such as fertility inhibition and incompatibility, followed by schemes based on a single gene (replicon type and MOB class), and finishing with recently developed approaches that use genetic distances between whole plasmid sequences. A comparison of the latter highlights significant differences between them. We further discuss the need for an operational definition of plasmid species that reveals their biological features, akin to plasmid taxonomic units (PTUs).
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Affiliation(s)
- M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (Consejo Superior de Investigaciones Científicas - Universidad de Cantabria), Cantabria, Spain.
| | - Santiago Redondo-Salvo
- Instituto de Biomedicina y Biotecnología de Cantabria (Consejo Superior de Investigaciones Científicas - Universidad de Cantabria), Cantabria, Spain; Biomar Microbial Technologies, León, Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (Consejo Superior de Investigaciones Científicas - Universidad de Cantabria), Cantabria, Spain.
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4
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Figueroa W, Cazares A, Cazares D, Wu Y, de la Cruz A, Welch M, Kameyama L, Nobrega FL, Guarneros G. Distribution and molecular evolution of the anti-CRISPR family AcrIF7. PLoS Biol 2023; 21:e3002072. [PMID: 37083687 PMCID: PMC10155984 DOI: 10.1371/journal.pbio.3002072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/03/2023] [Accepted: 03/10/2023] [Indexed: 04/22/2023] Open
Abstract
Anti-clustered regularly interspaced short palindromic repeats (CRISPRs) are proteins capable of blocking CRISPR-Cas systems and typically their genes are located on mobile genetic elements. Since their discovery, numerous anti-CRISPR families have been identified. However, little is known about the distribution and sequence diversity of members within a family, nor how these traits influence the anti-CRISPR's function and evolution. Here, we use AcrIF7 to explore the dissemination and molecular evolution of an anti-CRISPR family. We uncovered 5 subclusters and prevalent anti-CRISPR variants within the group. Remarkably, AcrIF7 homologs display high similarity despite their broad geographical, ecological, and temporal distribution. Although mainly associated with Pseudomonas aeruginosa, AcrIF7 was identified in distinct genetic backgrounds indicating horizontal dissemination, primarily by phages. Using mutagenesis, we recreated variation observed in databases but also extended the sequence diversity of the group. Characterisation of the variants identified residues key for the anti-CRISPR function and other contributing to its mutational tolerance. Moreover, molecular docking revealed that variants with affected function lose key interactions with its CRISPR-Cas target. Analysis of publicly available data and the generated variants suggests that the dominant AcrIF7 variant corresponds to the minimal and optimal anti-CRISPR selected in the family. Our study provides a blueprint to investigate the molecular evolution of anti-CRISPR families.
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Affiliation(s)
- Wendy Figueroa
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Adrian Cazares
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Yi Wu
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Ana de la Cruz
- Department of Genetics and Molecular Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Luis Kameyama
- Department of Genetics and Molecular Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico
| | - Franklin L Nobrega
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Gabriel Guarneros
- Department of Genetics and Molecular Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico
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5
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Jukič M, Bren U. Machine Learning in Antibacterial Drug Design. Front Pharmacol 2022; 13:864412. [PMID: 35592425 PMCID: PMC9110924 DOI: 10.3389/fphar.2022.864412] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 12/17/2022] Open
Abstract
Advances in computer hardware and the availability of high-performance supercomputing platforms and parallel computing, along with artificial intelligence methods are successfully complementing traditional approaches in medicinal chemistry. In particular, machine learning is gaining importance with the growth of the available data collections. One of the critical areas where this methodology can be successfully applied is in the development of new antibacterial agents. The latter is essential because of the high attrition rates in new drug discovery, both in industry and in academic research programs. Scientific involvement in this area is even more urgent as antibacterial drug resistance becomes a public health concern worldwide and pushes us increasingly into the post-antibiotic era. In this review, we focus on the latest machine learning approaches used in the discovery of new antibacterial agents and targets, covering both small molecules and antibacterial peptides. For the benefit of the reader, we summarize all applied machine learning approaches and available databases useful for the design of new antibacterial agents and address the current shortcomings.
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Affiliation(s)
- Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia.,Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia.,Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Koper, Slovenia
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6
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Algarni S, Ricke SC, Foley SL, Han J. The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria. Front Microbiol 2022; 13:859854. [PMID: 35432284 PMCID: PMC9008345 DOI: 10.3389/fmicb.2022.859854] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Steven L. Foley
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- *Correspondence: Jing Han,
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7
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Kim YJ, Seo KH, Kim S, Bae S. Phylogenetic Comparison and Characterization of an mcr-1-Harboring Complete Plasmid Genome Isolated from Enterobacteriaceae. Microb Drug Resist 2022; 28:492-497. [PMID: 35180355 PMCID: PMC9058865 DOI: 10.1089/mdr.2021.0164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Global dissemination of mobilized colistin resistance (mcr)-1-carrying plasmids has been reported. This study aimed to investigate the global dissemination of these plasmids using whole genome sequencing to provide better understanding on genetic characteristics. Sixty-seven complete plasmid genomes harboring mcr-1 were obtained. Phylogeny was built against full plasmid genomes. Different replicon types of plasmid were compared in terms of antimicrobial resistance genes (ARGs), insertion sequence, and other functional genes. Five different replicon types of plasmid (IncX4, IncI2, IncP1, IncHIA, and IncFIB) were found to harbor mcr-1. IncX4 and IncI2 types of plasmid were well clustered in accordance with the country where they were isolated (and not as IncHIA and IncFIB). Three insertion sequences (ISApl1, ISKpn26, and IS1294) were identified in up- and/or downstream of mcr-1. Plasmids IncX4 and IncI2 were observed across the sample origin. Plasmids IncX4 showed high uniformity regardless of the origin of isolates and harbored H–NS coding genes, a facilitator for successful plasmid transfer. All three insertion sequences were observed in IncI2 plasmids. IncHI2 plasmids harbored various ARGs in addition to mcr-1. Our results elucidate the characteristics and phylogenetic relationships of complete mcr-1-harboring plasmids, indicating that global dissemination of mcr-1 is primarily owing to plasmid transfer rather than clonal spread.
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Affiliation(s)
- Young-Ji Kim
- Division of Antimicrobial Resistance Research, Center for Infectious Disease Research, National Institute of Infectious Diseases, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Kun-Ho Seo
- Center for One Health, College of Veterinary Medicine, Konkuk University, Gwangjin-gu, Seoul, Republic of Korea
| | - Seolhui Kim
- Division of Antimicrobial Resistance Research, Center for Infectious Disease Research, National Institute of Infectious Diseases, Korea National Institute of Health, Cheongju, Republic of Korea
| | - Songmee Bae
- Division of Antimicrobial Resistance Research, Center for Infectious Disease Research, National Institute of Infectious Diseases, Korea National Institute of Health, Cheongju, Republic of Korea
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8
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Gushgari-Doyle S, Schicklberger M, Li YV, Walker R, Chakraborty R. Plant Growth Promotion Diversity in Switchgrass-Colonizing, Diazotrophic Endophytes. Front Microbiol 2021; 12:730440. [PMID: 34867848 PMCID: PMC8633415 DOI: 10.3389/fmicb.2021.730440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022] Open
Abstract
Endophytic nitrogen-fixing (diazotrophic) bacteria are essential members of the microbiome of switchgrass (Panicum virgatum), considered to be an important commodity crop in bioenergy production. While endophytic diazotrophs are known to provide fixed atmospheric nitrogen to their host plant, there are many other plant growth-promoting (PGP) capabilities of these organisms to be demonstrated. The diversity of PGP traits across different taxa of switchgrass-colonizing endophytes is understudied, yet critical for understanding endophytic function and improving cultivation methods of important commodity crops. Here, we present the isolation and characterization of three diazotrophic endophytes: Azospirillum agricola R1C, Klebsiella variicola F10Cl, and Raoultella terrigena R1Gly. Strains R1C and F10Cl were isolated from switchgrass and strain R1Gly, while isolated from tobacco, is demonstrated herein to colonize switchgrass. Each strain exhibited highly diverse genomic and phenotypic PGP capabilities. Strain F10Cl and R1Gly demonstrated the highest functional similarity, suggesting that, while endophyte community structure may vary widely based on host species, differences in functional diversity are not a clearly delineated. The results of this study advance our understanding of diazotrophic endophyte diversity, which will allow us to design robust strategies to improve cultivation methods of many economically important commodity crops.
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Affiliation(s)
- Sara Gushgari-Doyle
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcus Schicklberger
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yifan V Li
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Robert Walker
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Climate and Ecosystem Sciences, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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9
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Uddin TM, Chakraborty AJ, Khusro A, Zidan BRM, Mitra S, Emran TB, Dhama K, Ripon MKH, Gajdács M, Sahibzada MUK, Hossain MJ, Koirala N. Antibiotic resistance in microbes: History, mechanisms, therapeutic strategies and future prospects. J Infect Public Health 2021; 14:1750-1766. [PMID: 34756812 DOI: 10.1016/j.jiph.2021.10.020] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/04/2021] [Accepted: 10/14/2021] [Indexed: 12/22/2022] Open
Abstract
Antibiotics have been used to cure bacterial infections for more than 70 years, and these low-molecular-weight bioactive agents have also been used for a variety of other medicinal applications. In the battle against microbes, antibiotics have certainly been a blessing to human civilization by saving millions of lives. Globally, infections caused by multidrug-resistant (MDR) bacteria are on the rise. Antibiotics are being used to combat diversified bacterial infections. Synthetic biology techniques, in combination with molecular, functional genomic, and metagenomic studies of bacteria, plants, and even marine invertebrates are aimed at unlocking the world's natural products faster than previous methods of antibiotic discovery. There are currently only few viable remedies, potential preventive techniques, and a limited number of antibiotics, thereby necessitating the discovery of innovative medicinal approaches and antimicrobial therapies. MDR is also facilitated by biofilms, which makes infection control more complex. In this review, we have spotlighted comprehensively various aspects of antibiotics viz. overview of antibiotics era, mode of actions of antibiotics, development and mechanisms of antibiotic resistance in bacteria, and future strategies to fight the emerging antimicrobial resistant threat.
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Affiliation(s)
- Tanvir Mahtab Uddin
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh.
| | - Arka Jyoti Chakraborty
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh.
| | - Ameer Khusro
- Research Department of Plant Biology and Biotechnology, Loyola College, Nungambakkam, Chennai, Tamil Nadu, India.
| | - Bm Redwan Matin Zidan
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh.
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh.
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh.
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, Uttar Pradesh, India.
| | - Md Kamal Hossain Ripon
- Department of Pharmacy, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh.
| | - Márió Gajdács
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, 6720 Szeged, Hungary.
| | | | - Md Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, 77 Satmasjid Road, Dhanmondi, Dhaka 1205, Bangladesh.
| | - Niranjan Koirala
- Department of Natural Products Research, Dr. Koirala Research Institute for Biotechnology and Biodiversity, Kathmandu 44600, Nepal.
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10
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Bhatt P, Bhandari G, Bhatt K, Maithani D, Mishra S, Gangola S, Bhatt R, Huang Y, Chen S. Plasmid-mediated catabolism for the removal of xenobiotics from the environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126618. [PMID: 34329102 DOI: 10.1016/j.jhazmat.2021.126618] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/27/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.
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Affiliation(s)
- Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Geeta Bhandari
- Department of Biochemistry and Biotechnology, Sardar Bhagwan Singh University, Dehradun 248161, Uttarakhand, India
| | - Kalpana Bhatt
- Department of Botany and Microbiology, Gurukul Kangri University, Haridwar 249404, Uttarakhand, India
| | - Damini Maithani
- Department of Microbiology, G.B Pant University of Agriculture and Technology Pantnagar, U.S Nagar, Uttarakhand, India
| | - Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Saurabh Gangola
- School of Agriculture, Graphic Era Hill University, Bhimtal Campus, 263136, Uttarakhand, India
| | - Rakesh Bhatt
- Department of Civil Engineering, Indian Institute of Technology, Kanpur 208016, Uttar Pradesh, India
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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11
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Matlock W, Chau KK, AbuOun M, Stubberfield E, Barker L, Kavanagh J, Pickford H, Gilson D, Smith RP, Gweon HS, Hoosdally SJ, Swann J, Sebra R, Bailey MJ, Peto TEA, Crook DW, Anjum MF, Read DS, Walker AS, Stoesser N, Shaw LP. Genomic network analysis of environmental and livestock F-type plasmid populations. THE ISME JOURNAL 2021; 15:2322-2335. [PMID: 33649550 PMCID: PMC8319146 DOI: 10.1038/s41396-021-00926-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/08/2021] [Accepted: 02/03/2021] [Indexed: 12/02/2022]
Abstract
F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.
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Affiliation(s)
- William Matlock
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Kevin K Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manal AbuOun
- Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | | | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hayleah Pickford
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Gilson
- Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | | | - H Soon Gweon
- UK Centre for Ecology & Hydrology, Wallingford, UK
- University of Reading, Reading, UK
| | | | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert Sebra
- Icahn Institute of Data Science and Genomic Technology, Mt Sinai, NY, USA
| | | | - Timothy E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU in Healthcare-Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU in Healthcare-Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Muna F Anjum
- Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | | | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR HPRU in Healthcare-Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- NIHR HPRU in Healthcare-Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Liam P Shaw
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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12
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Paganini JA, Plantinga NL, Arredondo-Alonso S, Willems RJL, Schürch AC. Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data. Microorganisms 2021; 9:1613. [PMID: 34442692 PMCID: PMC8400445 DOI: 10.3390/microorganisms9081613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
The incidence of infections caused by multidrug-resistant E. coli strains has risen in the past years. Antibiotic resistance in E. coli is often mediated by acquisition and maintenance of plasmids. The study of E. coli plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (n = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (n = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (n = 317, 50.23%), and performed best at reconstructing large plasmids (n = 166, 46.37%) and ARG-plasmids (n = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (n = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into E. coli plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on E. coli plasmids in the absence of long-read sequencing data.
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Affiliation(s)
- Julian A. Paganini
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
| | - Nienke L. Plantinga
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway;
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
| | - Anita C. Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (J.A.P.); (N.L.P.); (R.J.L.W.)
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13
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Pan-Genome Portrait of Bacillus mycoides Provides Insights into the Species Ecology and Evolution. Microbiol Spectr 2021; 9:e0031121. [PMID: 34287030 PMCID: PMC8552610 DOI: 10.1128/spectrum.00311-21] [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] [Indexed: 11/23/2022] Open
Abstract
Bacillus mycoides is poorly known despite its frequent occurrence in a wide variety of environments. To provide direct insight into its ecology and evolutionary history, a comparative investigation of the species pan-genome and the functional gene categorization of 35 isolates obtained from soil samples from northeastern Poland was performed. The pan-genome of these isolates is composed of 20,175 genes and is characterized by a strong predominance of adaptive genes (∼83%), a significant amount of plasmid genes (∼37%), and a great contribution of prophages and insertion sequences. The pan-genome structure and phylodynamic studies had suggested a wide genomic diversity among the isolates, but no correlation between lineages and the bacillus origin was found. Nevertheless, the two B. mycoides populations, one from Białowieża National Park, the last European natural primeval forest with soil classified as organic, and the second from mineral soil samples taken in a farm in Jasienówka, a place with strong anthropogenic pressure, differ significantly in the frequency of genes encoding proteins enabling bacillus adaptation to specific stress conditions and production of a set of compounds, thus facilitating their colonization of various ecological niches. Furthermore, differences in the prevalence of essential stress sigma factors might be an important trail of this process. Due to these numerous adaptive genes, B. mycoides is able to quickly adapt to changing environmental conditions. IMPORTANCE This research allows deeper understanding of the genetic organization of natural bacterial populations, specifically, Bacillus mycoides, a psychrotrophic member of the Bacillus cereus group that is widely distributed worldwide, especially in areas with continental cold climates. These thorough analyses made it possible to describe, for the first time, the B. mycoides pan-genome, phylogenetic relationship within this species, and the mechanisms behind the species ecology and evolutionary history. Our study indicates a set of functional properties and adaptive genes, in particular, those encoding sigma factors, associated with B. mycoides acclimatization to specific ecological niches and changing environmental conditions.
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14
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Lai S, Jia L, Subramanian B, Pan S, Zhang J, Dong Y, Chen WH, Zhao XM. mMGE: a database for human metagenomic extrachromosomal mobile genetic elements. Nucleic Acids Res 2021; 49:D783-D791. [PMID: 33074335 PMCID: PMC7778953 DOI: 10.1093/nar/gkaa869] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022] Open
Abstract
Extrachromosomal mobile genetic elements (eMGEs), including phages and plasmids, that can move across different microbes, play important roles in genome evolution and shaping the structure of microbial communities. However, we still know very little about eMGEs, especially their abundances, distributions and putative functions in microbiomes. Thus, a comprehensive description of eMGEs is of great utility. Here we present mMGE, a comprehensive catalog of 517 251 non-redundant eMGEs, including 92 492 plasmids and 424 759 phages, derived from diverse body sites of 66 425 human metagenomic samples. About half the eMGEs could be further grouped into 70 074 clusters using relaxed criteria (referred as to eMGE clusters below). We provide extensive annotations of the identified eMGEs including sequence characteristics, taxonomy affiliation, gene contents and their prokaryotic hosts. We also calculate the prevalence, both within and across samples for each eMGE and eMGE cluster, enabling users to see putative associations of eMGEs with human phenotypes or their distribution preferences. All eMGE records can be browsed or queried in multiple ways, such as eMGE clusters, metagenomic samples and associated hosts. The mMGE is equipped with a user-friendly interface and a BLAST server, facilitating easy access/queries to all its contents easily. mMGE is freely available for academic use at: https://mgedb.comp-sysbio.org.
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Affiliation(s)
- Senying Lai
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Longhao Jia
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Balakrishnan Subramanian
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaojun Pan
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Jinglong Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Yanqi Dong
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- College of Life Science, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Shanghai 200433, China
- Research Institute of Intelligent Complex System, Fudan University, Shanghai 200433, China
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15
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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16
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Hailemariam S, Zhao S, Wang J. Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen. Front Microbiol 2020; 11:1826. [PMID: 33013723 PMCID: PMC7507024 DOI: 10.3389/fmicb.2020.01826] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/10/2020] [Indexed: 02/02/2023] Open
Abstract
The unclassified Succinivibrionaceae lineages are abundant in high yielding multiparous cows, and their presence is positively correlated with milk yield and fat percentage and reduces methane emissions. However, it is still unclear which species are associated with the most efficient feed nutrient utilization and productivity. Here, we used integrated whole genome sequencing and matrix-assisted laser desorption/ionization mass spectrometry, coupled with phenotypic and chemotaxonomic analysis, to characterize S. dextrinosolvens Z6, a species in Succinivibrionaceae isolated from the rumen. To assess the role of S. dextrinosolvens Z6 in nitrogen metabolism, cells grown in different nitrogen sources were analyzed by RNA sequencing. The whole genome sequence result revealed a genome size of 3.47 Mbp with 38.9% of G + C content. A total of 2993 encoding sequences account for 98%. The genes for regulating carbohydrate (10.6%) and amino acid (9%) transport and metabolism were the most abundant. ANI (Average nucleotide identity) showed that SD-Z6 was most closely related to SD-22B (99.96%). The whole genome alignment of SD-Z6 with SD-22B showed a more than 0.34 Mb nucleotide difference. Growth of SD-Z6 occurred at a temperature 36–42°C with an optimum at 39.7°C, pH 6–8; the optimum pH was 6.9 and with 0–1% (w/v) NaCl. The maximum growth (OD600 0.825 ± 0.12) and microbial crude protein (MCP) (178.2 μg/ml) were observed in cells grown in amino acid. The maximum concentration of ammonia (3.96 ± 1.2) was observed in urea containing media and 1.06 mM (26.7% of the produced) remained after 24 h incubation. Activities of urease and glutamine synthase (P < 0.01) and glutamate dehydrogenase (P < 0.05) were significantly different in nitrogen and growth phase. Glutamate synthetase (P < 0.01) was significantly different only at different growth phases. In total, 1246 differentially expressed genes (DEGs) were identified in all nitrogen. Among DEGs, 33 were related to nitrogen metabolism. Their expression correlated with nitrogen sources and the intensity of enzyme activity. This result enhances our understanding of the roles of Succinivibrionaceae in the efficient nitrogen utilization and on environmental protection.
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Affiliation(s)
- Samson Hailemariam
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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17
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Acman M, van Dorp L, Santini JM, Balloux F. Large-scale network analysis captures biological features of bacterial plasmids. Nat Commun 2020; 11:2452. [PMID: 32415210 PMCID: PMC7229196 DOI: 10.1038/s41467-020-16282-w] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/23/2020] [Indexed: 11/30/2022] Open
Abstract
Many bacteria can exchange genetic material through horizontal gene transfer (HGT) mediated by plasmids and plasmid-borne transposable elements. Here, we study the population structure and dynamics of over 10,000 bacterial plasmids, by quantifying their genetic similarities and reconstructing a network based on their shared k-mer content. We use a community detection algorithm to assign plasmids into cliques, which correlate with plasmid gene content, bacterial host range, GC content, and existing classifications based on replicon and mobility (MOB) types. Further analysis of plasmid population structure allows us to uncover candidates for yet undescribed replicon genes, and to identify transposable elements as the main drivers of HGT at broad phylogenetic scales. Our work illustrates the potential of network-based analyses of the bacterial 'mobilome' and opens up the prospect of a natural, exhaustive classification framework for bacterial plasmids.
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Affiliation(s)
- Mislav Acman
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK.
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18
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Douarre PE, Mallet L, Radomski N, Felten A, Mistou MY. Analysis of COMPASS, a New Comprehensive Plasmid Database Revealed Prevalence of Multireplicon and Extensive Diversity of IncF Plasmids. Front Microbiol 2020; 11:483. [PMID: 32265894 PMCID: PMC7105883 DOI: 10.3389/fmicb.2020.00483] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/05/2020] [Indexed: 12/20/2022] Open
Abstract
Plasmids are genetic elements that enable rapid adaptation and evolution by transferring genes conferring selective advantages to their hosts. Conjugative plasmids are predominantly responsible for the global dissemination of antimicrobial resistance, representing an important threat to global health. As the number of plasmid sequences grows exponentially, it becomes critical to depict the global diversity and decipher the distribution of circulating plasmids in the bacterial community. To this end, we created COMPASS, a novel and comprehensive database compiling 12,084 complete plasmids with associated metadata from 1571 distinct species isolated worldwide over more than 100 years. The curation of the database allowed us to identify identical plasmids across different bacteria revealing mainly intraspecies dissemination and rare cases of horizontal transmission. We outlined and analyzed all relevant features, plasmid properties, host range and characterized their replication and mobilization systems. After an exhaustive comparison of PlasmidFinder and MOB-typer, the MOB-typer-based analysis revealed that the current knowledge embedded in the current typing schemes fails to classify all the plasmid sequences collected in COMPASS. We were able to categorize 6828 and 5229 plasmids by replicon and MOB typing, respectively, mostly associated with Proteobacteria and Firmicutes. We then searched for the presence of multiple core genes involved in replication and propagation. Our results showed that 2403 plasmids carried multiple replicons that were distributed in 206 bacterial species. The co-integration of replicon types from different incompatibility (Inc) groups is an adaptive mechanism, which plays an important role in plasmid survival and dissemination by extending their host range. Our results highlight the crucial role of IncF alleles (present in 56% of all multireplicons) and revealed that IncH, IncR, and IncU replicons were also frequently carried in multireplicons. Here, we provided a comprehensive picture of the different IncF subtypes by identifying 20 different profiles in 849 IncF multireplicons, which were mostly associated with Enterobacteriaceae. These results could provide the basis for a novel IncF plasmid nomenclature based on different allelic profiles.
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Affiliation(s)
- Pierre-Emmanuel Douarre
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
| | - Ludovic Mallet
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
| | - Nicolas Radomski
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
| | - Arnaud Felten
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Laboratory for Food Safety, Paris, France
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19
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Ndagi U, Falaki AA, Abdullahi M, Lawal MM, Soliman ME. Antibiotic resistance: bioinformatics-based understanding as a functional strategy for drug design. RSC Adv 2020; 10:18451-18468. [PMID: 35685616 PMCID: PMC9122625 DOI: 10.1039/d0ra01484b] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022] Open
Abstract
The use of antibiotics to manage infectious diseases dates back to ancient civilization, but the lack of a clear distinction between the therapeutic and toxic dose has been a major challenge. This precipitates the notion that antibiotic resistance was from time immemorial, principally because of a lack of adequate knowledge of therapeutic doses and continuous exposure of these bacteria to suboptimal plasma concentration of antibiotics. With the discovery of penicillin by Alexander Fleming in 1924, a milestone in bacterial infections' treatment was achieved. This forms the foundation for the modern era of antibiotic drugs. Antibiotics such as penicillins, cephalosporins, quinolones, tetracycline, macrolides, sulphonamides, aminoglycosides and glycopeptides are the mainstay in managing severe bacterial infections, but resistant strains of bacteria have emerged and hampered the progress of research in this field. Recently, new approaches to research involving bacteria resistance to antibiotics have appeared; these involve combining the molecular understanding of bacteria systems with the knowledge of bioinformatics. Consequently, many molecules have been developed to curb resistance associated with different bacterial infections. However, because of increased emphasis on the clinical relevance of antibiotics, the synergy between in silico study and in vivo study is well cemented and this facilitates the discovery of potent antibiotics. In this review, we seek to give an overview of earlier reviews and molecular and structural understanding of bacteria resistance to antibiotics, while focusing on the recent bioinformatics approach to antibacterial drug discovery. Understanding the evolution of antibiotic resistance at the molecular level as a functional tool for bioinformatic-based drug design.![]()
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Affiliation(s)
- Umar Ndagi
- Centre for Trans-Sahara Disease, Vaccine and Drug Research
- Ibrahim Badamasi Babangida University
- Lapai
- Nigeria
| | - Abubakar A. Falaki
- Department of Microbiology
- School of Agriculture and Applied Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Maryam Abdullahi
- Faculty of Pharmaceutical Sciences
- Ahmadu Bello University Zaria
- Nigeria
| | - Monsurat M. Lawal
- School of Laboratory Medicine and Medical Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Mahmoud E. Soliman
- Molecular Modeling and Drug Design Research Group
- School of Health Sciences
- University of KwaZulu Natal
- Durban 4001
- South Africa
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20
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Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution. Drug Resist Updat 2019; 44:100640. [PMID: 31492517 DOI: 10.1016/j.drup.2019.07.002] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.
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21
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Rigden DJ, Fernández X. The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. Nucleic Acids Res 2019; 47:D1-D7. [PMID: 30626175 PMCID: PMC6323895 DOI: 10.1093/nar/gky1267] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The 2019 Nucleic Acids Research (NAR) Database Issue contains 168 papers spanning molecular biology. Among them, 64 are new and another 92 are updates describing resources that appeared in the Issue previously. The remaining 12 are updates on databases most recently published elsewhere. This Issue contains two Breakthrough articles, on the Virtual Metabolic Human (VMH) database which links human and gut microbiota metabolism with diet and disease, and Vibrism DB, a database of mouse brain anatomy and gene (co-)expression with sophisticated visualization and session sharing. Major returning nucleic acid databases include RNAcentral, miRBase and LncRNA2Target. Protein sequence databases include UniProtKB, InterPro and Pfam, while wwPDB and RCSB cover protein structure. STRING and KEGG update in the section on metabolism and pathways. Microbial genomes are covered by IMG/M and resources for human and model organism genomics include Ensembl, UCSC Genome Browser, GENCODE and Flybase. Genomic variation and disease are well-covered by GWAS Catalog, PopHumanScan, OMIM and COSMIC, CADD being another major newcomer. Major new proteomics resources reporting here include iProX and jPOSTdb. The entire database issue is freely available online on the NAR website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 506 entries, adding 66 new resources and eliminating 147 discontinued URLs, bringing the current total to 1613 databases. It is available at http://www.oxfordjournals.org/nar/database/c.
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Affiliation(s)
- Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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Yano H, Shintani M, Tomita M, Suzuki H, Oshima T. Reconsidering plasmid maintenance factors for computational plasmid design. Comput Struct Biotechnol J 2018; 17:70-81. [PMID: 30619542 PMCID: PMC6312765 DOI: 10.1016/j.csbj.2018.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/08/2018] [Accepted: 12/09/2018] [Indexed: 12/18/2022] Open
Abstract
Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.
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Affiliation(s)
- Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1, Hamamatsu 432-8561, Japan
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 3-5-1, Hamamatsu 432-8561, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka, Yamagata 997-0035, Japan
- Faculty of Environment and Information Studies, Keio University, 5322, Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, 14-1, Baba-cho, Tsuruoka, Yamagata 997-0035, Japan
- Faculty of Environment and Information Studies, Keio University, 5322, Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Taku Oshima
- Department of Biotechnology, Toyama Prefectural University, 5180, Kurokawa, Imizu, Toyama 939-0398, Japan
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