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Thiriet-Rupert S, Josse J, Perez-Pascual D, Tasse J, Andre C, Abad L, Lebeaux D, Ghigo JM, Laurent F, Beloin C. Analysis of In-Patient Evolution of Escherichia coli Reveals Potential Links to Relapse of Bone and Joint Infections. J Infect Dis 2024; 229:1546-1556. [PMID: 38041851 DOI: 10.1093/infdis/jiad528] [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: 06/02/2023] [Revised: 11/03/2023] [Accepted: 11/29/2023] [Indexed: 12/04/2023] Open
Abstract
Bone and joint infections (BJIs) are difficult to treat and affect a growing number of patients, in which relapses are observed in 10-20% of case. These relapses, which call for prolonged antibiotic treatment and increase resistance emergence risk, may originate from ill-understood adaptation of the pathogen to the host. Here, we investigated 3 pairs of Escherichia coli strains from BJI cases and their relapses to unravel adaptations within patients. Whole-genome comparison presented evidence for positive selection and phenotypic characterization showed that biofilm formation remained unchanged, contrary to what is usually described in such cases. Although virulence was not modified, we identified the loss of 2 virulence factors contributing to immune system evasion in one of the studied strains. Other strategies, including global growth optimization and colicin production, likely allowed the strains to outcompete competitors. This work highlights the variety of strategies allowing in-patient adaptation in BJIs.
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Affiliation(s)
| | - Jérôme Josse
- Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - David Perez-Pascual
- Genetics of Biofilms Laboratory, Institut Pasteur, Université de Paris-Cité, Paris, France
| | - Jason Tasse
- Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Camille Andre
- Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Lélia Abad
- Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - David Lebeaux
- Genetics of Biofilms Laboratory, Institut Pasteur, Université de Paris-Cité, Paris, France
- Département de Maladies Infectieuses et Tropicales, AP-HP, Hôpital Saint-Louis, Lariboisière, Paris, France
- FHU PROTHEE (Prosthetic joint infections: innovative strategies to overcome a medico-surgical challenge) Group
| | - Jean-Marc Ghigo
- Genetics of Biofilms Laboratory, Institut Pasteur, Université de Paris-Cité, Paris, France
| | - Frédéric Laurent
- Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, Université de Paris-Cité, Paris, France
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Weinroth MD, Clawson ML, Harhay GP, Eppinger M, Harhay DM, Smith TPL, Bono JL. Escherichia coli O157:H7 tir 255 T > A allele strains differ in chromosomal and plasmid composition. Front Microbiol 2023; 14:1303387. [PMID: 38169669 PMCID: PMC10758439 DOI: 10.3389/fmicb.2023.1303387] [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: 09/27/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O157:H7 strains with the T allele in the translocated intimin receptor polymorphism (tir) 255 A > T gene associate with human disease more than strains with an A allele; however, the allele is not thought to be the direct cause of this difference. We sequenced a diverse set of STEC O157:H7 strains (26% A allele, 74% T allele) to identify linked differences that might underlie disease association. The average chromosome and pO157 plasmid size and gene content were significantly greater within the tir 255 A allele strains. Eighteen coding sequences were unique to tir 255 A allele chromosomes, and three were unique to tir 255 T allele chromosomes. There also were non-pO157 plasmids that were unique to each tir 255 allele variant. The overall average number of prophages did not differ between tir 255 allele strains; however, there were different types between the strains. Genomic and mobile element variation linked to the tir 255 polymorphism may account for the increased frequency of the T allele isolates in human disease.
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Affiliation(s)
- Margaret D. Weinroth
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Michael L. Clawson
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Gregory P. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Mark Eppinger
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
- South Texas Center for Emerging Infectious Diseases, San Antonio, TX, United States
| | - Dayna M. Harhay
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - Timothy P. L. Smith
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
| | - James L. Bono
- Department of Molecular Microbiology and Immunology, USDA ARS Meat Animal Research Center, Clay Center, NE, United States
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Zhou X, Kang X, Chen J, Song Y, Jia C, Teng L, Tang Y, Jiang Z, Peng X, Tao X, Xu Y, Huang L, Xu X, Xu Y, Zhang T, Yu S, Gong J, Wang S, Liu Y, Zhu G, Kehrenberg C, Weill FX, Barrow P, Li Y, Zhao G, Yue M. Genome degradation promotes Salmonella pathoadaptation by remodeling fimbriae-mediated proinflammatory response. Natl Sci Rev 2023; 10:nwad228. [PMID: 37965675 PMCID: PMC10642762 DOI: 10.1093/nsr/nwad228] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/07/2023] [Accepted: 08/08/2023] [Indexed: 11/16/2023] Open
Abstract
Understanding changes in pathogen behavior (e.g. increased virulence, a shift in transmission channel) is critical for the public health management of emerging infectious diseases. Genome degradation via gene depletion or inactivation is recognized as a pathoadaptive feature of the pathogen evolving with the host. However, little is known about the exact role of genome degradation in affecting pathogenic behavior, and the underlying molecular detail has yet to be examined. Using large-scale global avian-restricted Salmonella genomes spanning more than a century, we projected the genetic diversity of Salmonella Pullorum (bvSP) by showing increasingly antimicrobial-resistant ST92 prevalent in Chinese flocks. The phylogenomic analysis identified three lineages in bvSP, with an enhancement of virulence in the two recently emerged lineages (L2/L3), as evidenced in chicken and embryo infection assays. Notably, the ancestor L1 lineage resembles the Salmonella serovars with higher metabolic flexibilities and more robust environmental tolerance, indicating stepwise evolutionary trajectories towards avian-restricted lineages. Pan-genome analysis pinpointed fimbrial degradation from a virulent lineage. The later engineered fim-deletion mutant, and all other five fimbrial systems, revealed behavior switching that restricted horizontal fecal-oral transmission but boosted virulence in chicks. By depleting fimbrial appendages, bvSP established persistent replication with less proinflammation in chick macrophages and adopted vertical transovarial transmission, accompanied by ever-increasing intensification in the poultry industry. Together, we uncovered a previously unseen paradigm for remodeling bacterial surface appendages that supplements virulence-enhanced evolution with increased vertical transmission.
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Affiliation(s)
- Xiao Zhou
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Ningbo Academy of Agricultural Sciences, Ningbo 315040, China
| | - Xiamei Kang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Jiaqi Chen
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yan Song
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Chenghao Jia
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Lin Teng
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yanting Tang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Zhijie Jiang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Xianqi Peng
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Xiaoxi Tao
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Yiwei Xu
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Linlin Huang
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
| | - Xuebin Xu
- Department of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
| | - Yaohui Xu
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou 450053, China
| | - Tengfei Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Shenye Yu
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
| | - Shaohui Wang
- Department of Animal Public Health, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yuqing Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Corinna Kehrenberg
- Institute for Veterinary Food Science, Faculty of Veterinary Medicine, Justus-Liebig University Giessen, Giessen 35392, Germany
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des bactéries pathogènes entériques, Paris 75724, France
| | - Paul Barrow
- School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK
| | - Yan Li
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Guoping Zhao
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Min Yue
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Hainan Institute of Zhejiang University, Sanya 572025, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
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Noh S, Larson ER, Covitz RM, Chen A, Mazumder PR, Peck RF, Hamilton MC, Dettmann RA. Facultative symbiont virulence determines horizontal transmission rate without host strain specificity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528903. [PMID: 36824889 PMCID: PMC9949114 DOI: 10.1101/2023.02.16.528903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
In facultative symbioses, only a fraction of hosts are associated with a symbiont. Understanding why specific host and symbiont strains are associated can inform us of the evolutionary forces affecting facultative symbioses. Possibilities include ongoing host-symbiont coevolution driven by reciprocal selection, or priority effects that are neutral in respect to the host-symbiont interaction. We hypothesized that ongoing host-symbiont coevolution would lead to higher fitness estimates for naturally co-occurring (native) host and symbiont combinations compared to nonnative combinations. We used the Dictyostelium discoideum - Paraburkholderia bonniea system to test this hypothesis. P. bonniea features a reduced genome size relative to another Paraburkholderia symbiont of D. discoideum, indicating a significant history of coevolution with its host. Facultative symbionts may experience continued genome reduction if coevolution is ongoing, or their genome size may have reached a stable state if the symbiosis has also stabilized. Our work demonstrates that ongoing coevolution is unlikely for D. discoideum and P. bonniea. The system instead represents a stable facultative symbiosis. Specifically associated host and symbiont strains in this system are the result of priority effects, and presently unassociated hosts are simply uncolonized. We find evidence for a virulence-transmission trade-off without host strain specificity, and identify candidate virulence factors in the genomes of P. bonniea strains that may contribute to variation in benevolence.
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Affiliation(s)
- Suegene Noh
- Biology Department, Colby College, Waterville, Maine, USA
| | | | - Rachel M. Covitz
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Anna Chen
- Biology Department, Colby College, Waterville, Maine, USA
| | | | - Ron F. Peck
- Biology Department, Colby College, Waterville, Maine, USA
| | - Marisa C. Hamilton
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Robert A. Dettmann
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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Buzzanca D, Kerkhof PJ, Alessandria V, Rantsiou K, Houf K. Arcobacteraceae comparative genome analysis demonstrates genome heterogeneity and reduction in species isolated from animals and associated with human illness. Heliyon 2023; 9:e17652. [PMID: 37449094 PMCID: PMC10336517 DOI: 10.1016/j.heliyon.2023.e17652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/30/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
The Arcobacteraceae family groups Gram-negative bacterial species previously included in the family Campylobacteraceae. These species of which some are considered foodborne pathogens, have been isolated from different environmental niches and hosts. They have been isolated from various types of foods, though predominantly from food of animal origin, as well as from stool of humans with enteritis. Their different abilities to survive in different hosts and environments suggest an evolutionary pressure with consequent variation in their genome content. Moreover, their different physiological and genomic characteristics led to the recent proposal to create new genera within this family, which is however criticized due to the lack of discriminatory features and biological and clinical relevance. Aims of the present study were to assess the Arcobacteraceae pangenome, and to characterize existing similarities and differences in 20 validly described species. For this, analysis has been conducted on the genomes of the corresponding type strains obtained by Illumina sequencing, applying several bioinformatic tools. Results of the present study do not support the proposed division into different genera and revealed the presence of pangenome partitions with numbers comparable to other Gram-negative bacteria genera, such as Campylobacter. Different gene class compositions in animal and human-associated species are present, including a higher percentage of virulence-related gene classes such as cell motility genes. The adaptation to environmental and/or host conditions of some species was identified by the presence of specific genes. Furthermore, a division into pathogenic and non-pathogenic species is suggested, which can support future research on food safety and public health.
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Affiliation(s)
- Davide Buzzanca
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Pieter-Jan Kerkhof
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
| | - Valentina Alessandria
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Kurt Houf
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, Merelbeke, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Karel Lodewijk Ledeganckstraat 35, 9000 Ghent, Belgium
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Palmieri N, Apostolakos I, Paudel S, Hess M. The genetic network underlying the evolution of pathogenicity in avian Escherichia coli. Front Vet Sci 2023; 10:1195585. [PMID: 37415967 PMCID: PMC10321414 DOI: 10.3389/fvets.2023.1195585] [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: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction Colibacillosis is a worldwide prevalent disease in poultry production linked to Escherichia coli strains that belong to the avian pathogenic E. coli (APEC) pathotype. While many virulence factors have been linked to APEC isolates, no single gene or set of genes has been found to be exclusively associated with the pathotype. Moreover, a comprehensive description of the biological processes linked to APEC pathogenicity is currently lacking. Methods In this study, we compiled a dataset of 2015 high-quality avian E. coli genomes from pathogenic and commensal isolates, based on publications from 2000 to 2021. We then conducted a genome-wide association study (GWAS) and integrated candidate gene identification with available protein-protein interaction data to decipher the genetic network underlying the biological processes connected to APEC pathogenicity. Results Our GWAS identified variations in gene content for 13 genes and SNPs in 3 different genes associated with APEC isolates, suggesting both gene-level and SNP-level variations contribute to APEC pathogenicity. Integrating protein-protein interaction data, we found that 15 of these genes clustered in the same genetic network, suggesting the pathogenicity of APEC might be due to the interplay of different regulated pathways. We also found novel candidate genes including an uncharacterized multi-pass membrane protein (yciC) and the outer membrane porin (ompD) as linked to APEC isolates. Discussion Our findings suggest that convergent pathways related to nutrient uptake from host cells and defense from host immune system play a major role in APEC pathogenicity. In addition, the dataset curated in this study represents a comprehensive historical genomic collection of avian E. coli isolates and constitutes a valuable resource for their comparative genomics investigations.
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Affiliation(s)
- Nicola Palmieri
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | | | - Surya Paudel
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Michael Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
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Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates. mSphere 2023; 8:e0049522. [PMID: 36794931 PMCID: PMC10117131 DOI: 10.1128/msphere.00495-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering and mortality and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last 10 years from 16 French broiler farms. Comparative genomics, genome-wide association studies, and the measured susceptibility to serum, biofilm-forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate the origin of the isolates or the phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically, and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster into a few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole-genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first data set on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage that is probably also circulating elsewhere that should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum-related diseases.
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Sharma U, Rawat D, Mukherjee P, Farooqi F, Mishra V, Sharma RS. Ecological life strategies of microbes in response to antibiotics as a driving factor in soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158791. [PMID: 36108841 DOI: 10.1016/j.scitotenv.2022.158791] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/31/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.
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Affiliation(s)
- Udita Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Deepak Rawat
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Department of Environmental Studies, Janki Devi Memorial College, University of Delhi, Delhi 110060, India
| | - Paromita Mukherjee
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Furqan Farooqi
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India
| | - Vandana Mishra
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Centre for Interdisciplinary Studies on Mountain & Hill Environment (CISMHE), University of Delhi, Delhi 110007, India.
| | - Radhey Shyam Sharma
- Bioresources & Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi 110007, India; Delhi School of Climate Change & Sustainability, Institute of Eminence, University of Delhi, Delhi 110007, India.
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9
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Bohlin J. A simple stochastic model describing the evolution of genomic GC content in asexually reproducing organisms. Sci Rep 2022; 12:18569. [PMID: 36329129 PMCID: PMC9631610 DOI: 10.1038/s41598-022-21709-z] [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: 07/01/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
A genome's nucleotide composition can usually be summarized with (G)uanine + (C)ytosine (GC) or (A)denine + (T)hymine (AT) frequencies as GC% = 100% - AT%. Genomic AT/GC content has been linked to environment and selective processes in asexually reproducing organisms. A model is presented relating the evolution of genomic GC content over time to AT [Formula: see text] GC and GC [Formula: see text] AT mutation rates. By employing Itô calculus it is shown that if mutation rates are subject to random perturbations, that can vary over time, several implications follow. In particular, an extra Brownian motion term appears influencing genomic nucleotide variability; the greater the random perturbations the more genomic nucleotide variability. This can have several interpretations depending on the context. For instance, reducing the influence of the random perturbations on the AT/GC mutation rates and thus genomic nucleotide variability, to limit fitness decreasing and deleterious mutations, will likely suggest channeling of resources. On the other hand, increased genomic nucleotide diversity may be beneficial in variable environments. In asexually reproducing organisms, the Brownian motion term can be considered to be inversely reflective of the selective pressures an organism is subjected to at the molecular level. The presented model is a generalization of a previous model, limited to microbial symbionts, to all asexually reproducing, non-recombining organisms. Last, a connection between the presented model and the classical Luria-Delbrück mutation model is presented in an Itô calculus setting.
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Affiliation(s)
- Jon Bohlin
- grid.418193.60000 0001 1541 4204Division of Infection Control, Department of Methods Development and Analysis, Norwegian Institute of Public Health, Oslo, Norway ,grid.418193.60000 0001 1541 4204Centre for Fertility and Health, Norwegian Institute of Public Health, P.O. Box 4404, Lovisenberggata 8, 0403 Oslo, Norway
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10
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Kittiwan N, Calland JK, Mourkas E, Hitchings MD, Murray S, Tadee P, Tadee P, Duangsonk K, Meric G, Sheppard SK, Patchanee P, Pascoe B. Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs. Microb Genom 2022; 8:mgen000882. [PMID: 36326658 PMCID: PMC9836093 DOI: 10.1099/mgen.0.000882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Streptococcus suis is a leading cause of bacterial meningitis in South-East Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry, causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis. Gene flow between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome characterization identified extensive genetic diversity and frequent AMR carriage in isolates from healthy pigs. Multiple AMR genes were identified, conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptible to three or more different antimicrobial classes, and 75 % of non-serotype 2 isolates were non-susceptible to six or more classes (compared to 37.5 % of serotype 2 isolates). AMR genes were found on integrative and conjugative elements previously observed in other species, suggesting a mobile gene pool that can be accessed by invasive disease isolates. This article contains data hosted by Microreact.
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Affiliation(s)
- Nattinee Kittiwan
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Veterinary Research and Development Center (Upper Northern Region), Hang Chat, Lampang 52190, Thailand
| | - Jessica K. Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK
| | - Matthew D. Hitchings
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, UK
| | - Susan Murray
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, UK,Present address: Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
| | - Pakpoom Tadee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Phacharaporn Tadee
- Faculty of Animal Science and Technology, Maejo University, Chiang Mai 50290, Thailand
| | - Kwanjit Duangsonk
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Guillaume Meric
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK,Present address: Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Samuel K. Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK,Faculty of Allied Medical Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Prapas Patchanee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,*Correspondence: Prapas Patchanee,
| | - Ben Pascoe
- Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK,Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK,*Correspondence: Ben Pascoe,
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11
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Genomic evolution and adaptation of arthropod-associated Rickettsia. Sci Rep 2022; 12:3807. [PMID: 35264613 PMCID: PMC8907221 DOI: 10.1038/s41598-022-07725-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
Rickettsia species are endosymbionts hosted by arthropods and are known to cause mild to fatal diseases in humans. Here, we analyse the evolution and diversity of 34 Rickettsia species using a pangenomic meta-analysis (80 genomes/41 plasmids). Phylogenomic trees showed that Rickettsia spp. diverged into two Spotted Fever groups, a Typhus group, a Canadensis group and a Bellii group, and may have inherited their plasmids from an ancestral plasmid that persisted in some strains or may have been lost by others. The results suggested that the ancestors of Rickettsia spp. might have infected Acari and/or Insecta and probably diverged by persisting inside and/or switching hosts. Pangenomic analysis revealed that the Rickettsia genus evolved through a strong interplay between genome degradation/reduction and/or expansion leading to possible distinct adaptive trajectories. The genus mainly shared evolutionary relationships with α-proteobacteria, and also with γ/β/δ-proteobacteria, cytophagia, actinobacteria, cyanobacteria, chlamydiia and viruses, suggesting lateral exchanges of several critical genes. These evolutionary processes have probably been orchestrated by an abundance of mobile genetic elements, especially in the Spotted Fever and Bellii groups. In this study, we provided a global evolutionary genomic view of the intracellular Rickettsia that may help our understanding of their diversity, adaptation and fitness.
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12
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Huang CT, Cho ST, Lin YC, Tan CM, Chiu YC, Yang JY, Kuo CH. Comparative Genome Analysis of ‘Candidatus Phytoplasma luffae’ Reveals the Influential Roles of Potential Mobile Units in Phytoplasma Evolution. Front Microbiol 2022; 13:773608. [PMID: 35300489 PMCID: PMC8923039 DOI: 10.3389/fmicb.2022.773608] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/07/2022] [Indexed: 12/23/2022] Open
Abstract
Phytoplasmas are insect-transmitted plant pathogens that cause substantial losses in agriculture. In addition to economic impact, phytoplasmas induce distinct disease symptoms in infected plants, thus attracting attention for research on molecular plant-microbe interactions and plant developmental processes. Due to the difficulty of establishing an axenic culture of these bacteria, culture-independent genome characterization is a crucial tool for phytoplasma research. However, phytoplasma genomes have strong nucleotide composition biases and are repetitive, which make it challenging to produce complete assemblies. In this study, we utilized Illumina and Oxford Nanopore sequencing technologies to obtain the complete genome sequence of ‘Candidatus Phytoplasma luffae’ strain NCHU2019 that is associated with witches’ broom disease of loofah (Luffa aegyptiaca) in Taiwan. The fully assembled circular chromosome is 769 kb in size and is the first representative genome sequence of group 16SrVIII phytoplasmas. Comparative analysis with other phytoplasmas revealed that NCHU2019 has a remarkably repetitive genome, possessing a pair of 75 kb repeats and at least 13 potential mobile units (PMUs) that account for ∼25% of its chromosome. This level of genome repetitiveness is exceptional for bacteria, particularly among obligate pathogens with reduced genomes. Our genus-level analysis of PMUs demonstrated that these phytoplasma-specific mobile genetic elements can be classified into three major types that differ in gene organization and phylogenetic distribution. Notably, PMU abundance explains nearly 80% of the variance in phytoplasma genome sizes, a finding that provides a quantitative estimate for the importance of PMUs in phytoplasma genome variability. Finally, our investigation found that in addition to horizontal gene transfer, PMUs also contribute to intra-genomic duplications of effector genes, which may provide redundancy for subfunctionalization or neofunctionalization. Taken together, this work improves the taxon sampling for phytoplasma genome research and provides novel information regarding the roles of mobile genetic elements in phytoplasma evolution.
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Affiliation(s)
- Ching-Ting Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Choon-Meng Tan
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Ching Chiu
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
| | - Jun-Yi Yang
- Institute of Biochemistry, National Chung Hsing University, Taichung, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- *Correspondence: Jun-Yi Yang,
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Chih-Horng Kuo,
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13
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Nicholson D, Salamina M, Panek J, Helena-Bueno K, Brown CR, Hirt RP, Ranson NA, Melnikov SV. Adaptation to genome decay in the structure of the smallest eukaryotic ribosome. Nat Commun 2022; 13:591. [PMID: 35105900 PMCID: PMC8807834 DOI: 10.1038/s41467-022-28281-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/14/2022] [Indexed: 12/18/2022] Open
Abstract
The evolution of microbial parasites involves the counterplay between natural selection forcing parasites to improve and genetic drifts forcing parasites to lose genes and accumulate deleterious mutations. Here, to understand how this counterplay occurs at the scale of individual macromolecules, we describe cryo-EM structure of ribosomes from Encephalitozoon cuniculi, a eukaryote with one of the smallest genomes in nature. The extreme rRNA reduction in E. cuniculi ribosomes is accompanied with unparalleled structural changes, such as the evolution of previously unknown molten rRNA linkers and bulgeless rRNA. Furthermore, E. cuniculi ribosomes withstand the loss of rRNA and protein segments by evolving an ability to use small molecules as structural mimics of degenerated rRNA and protein segments. Overall, we show that the molecular structures long viewed as reduced, degenerated, and suffering from debilitating mutations possess an array of compensatory mechanisms that allow them to remain active despite the extreme molecular reduction. Many parasitic organisms contain molecular structures that are drastically smaller than analogous structures in non-parasitic organisms. Here the authors describe a cryo-EM structure of the ribosome from E. cuniculi that reveals that it compensated rRNA truncations by evolving the ability to use small molecules as ribosomal building blocks.
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Affiliation(s)
- David Nicholson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Marco Salamina
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Johan Panek
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Karla Helena-Bueno
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Charlotte R Brown
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert P Hirt
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sergey V Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK. .,Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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14
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Pursey E, Dimitriu T, Paganelli FL, Westra ER, van Houte S. CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200464. [PMID: 34839714 PMCID: PMC8628084 DOI: 10.1098/rstb.2020.0464] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/21/2021] [Indexed: 01/19/2023] Open
Abstract
The acquisition of antibiotic resistance (ABR) genes via horizontal gene transfer (HGT) is a key driver of the rise in multidrug resistance amongst bacterial pathogens. Bacterial defence systems per definition restrict the influx of foreign genetic material, and may therefore limit the acquisition of ABR. CRISPR-Cas adaptive immune systems are one of the most prevalent defences in bacteria, found in roughly half of bacterial genomes, but it has remained unclear if and how much they contribute to restricting the spread of ABR. We analysed approximately 40 000 whole genomes comprising the full RefSeq dataset for 11 species of clinically important genera of human pathogens, including Enterococcus, Staphylococcus, Acinetobacter and Pseudomonas. We modelled the association between CRISPR-Cas and indicators of HGT, and found that pathogens with a CRISPR-Cas system were less likely to carry ABR genes than those lacking this defence system. Analysis of the mobile genetic elements (MGEs) targeted by CRISPR-Cas supports a model where this host defence system blocks important vectors of ABR. These results suggest a potential 'immunocompromised' state for multidrug-resistant strains that may be exploited in tailored interventions that rely on MGEs, such as phages or phagemids, to treat infections caused by bacterial pathogens. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
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Affiliation(s)
- Elizabeth Pursey
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Tatiana Dimitriu
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Fernanda L. Paganelli
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edze R. Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, Cornwall, UK
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15
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Dover LG, Thompson AR, Sutcliffe IC, Sangal V. Phylogenomic Reappraisal of Fatty Acid Biosynthesis, Mycolic Acid Biosynthesis and Clinical Relevance Among Members of the Genus Corynebacterium. Front Microbiol 2021; 12:802532. [PMID: 35003033 PMCID: PMC8733736 DOI: 10.3389/fmicb.2021.802532] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
The genus Corynebacterium encompasses many species of biotechnological, medical or veterinary significance. An important characteristic of this genus is the presence of mycolic acids in their cell envelopes, which form the basis of a protective outer membrane (mycomembrane). Mycolic acids in the cell envelope of Mycobacterium tuberculosis have been associated with virulence. In this study, we have analysed the genomes of 140 corynebacterial strains, including representatives of 126 different species. More than 50% of these strains were isolated from clinical material from humans or animals, highlighting the true scale of pathogenic potential within the genus. Phylogenomically, these species are very diverse and have been organised into 19 groups and 30 singleton strains. We find that a substantial number of corynebacteria lack FAS-I, i.e., have no capability for de novo fatty acid biosynthesis and must obtain fatty acids from their habitat; this appears to explain the well-known lipophilic phenotype of some species. In most species, key genes associated with the condensation and maturation of mycolic acids are present, consistent with the reports of mycolic acids in their species descriptions. Conversely, species reported to lack mycolic acids lacked these key genes. Interestingly, Corynebacterium ciconiae, which is reported to lack mycolic acids, appears to possess all genes required for mycolic acid biosynthesis. We suggest that although a mycolic acid-based mycomembrane is widely considered to be the target for interventions by the immune system and chemotherapeutics, the structure is not essential in corynebacteria and is not a prerequisite for pathogenicity or colonisation of animal hosts.
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16
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Bohr LL, Youngblom MA, Eldholm V, Pepperell CS. Genome reorganization during emergence of host-associated Mycobacterium abscessus. Microb Genom 2021; 7. [PMID: 34874249 PMCID: PMC8767326 DOI: 10.1099/mgen.0.000706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium abscessus is a rapid growing, free-living species of bacterium that also causes lung infections in humans. Human infections are usually acquired from the environment; however, dominant circulating clones (DCCs) have emerged recently in both M. abscessus subsp. massiliense and subsp. abscessus that appear to be transmitted among humans and are now globally distributed. These recently emerged clones are potentially informative about the ecological and evolutionary mechanisms of pathogen emergence and host adaptation. The geographical distribution of DCCs has been reported, but the genomic processes underlying their transition from environmental bacterium to human pathogen are not well characterized. To address this knowledge gap, we delineated the structure of M. abscessus subspecies abscessus and massiliense using genomic data from 200 clinical isolates of M. abscessus from seven geographical regions. We identified differences in overall patterns of lateral gene transfer (LGT) and barriers to LGT between subspecies and between environmental and host-adapted bacteria. We further characterized genome reorganization that accompanied bacterial host adaptation, inferring selection pressures acting at both genic and intergenic loci. We found that both subspecies encode an expansive pangenome with many genes at rare frequencies. Recombination appears more frequent in M. abscessus subsp. massiliense than in subsp. abscessus, consistent with prior reports. We found evidence suggesting that phage are exchanged between subspecies, despite genetic barriers evident elsewhere throughout the genome. Patterns of LGT differed according to niche, with less LGT observed among host-adapted DCCs versus environmental bacteria. We also found evidence suggesting that DCCs are under distinct selection pressures at both genic and intergenic sites. Our results indicate that host adaptation of M. abscessus was accompanied by major changes in genome evolution, including shifts in the apparent frequency of LGT and impacts of selection. Differences were evident among the DCCs as well, which varied in the degree of gene content remodelling, suggesting they were placed differently along the evolutionary trajectory toward host adaptation. These results provide insight into the evolutionary forces that reshape bacterial genomes as they emerge into the pathogenic niche.
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Affiliation(s)
- Lindsey L Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Madison A Youngblom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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17
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Real-time kinetic studies of Mycobacterium tuberculosis LexA-DNA interaction. Biosci Rep 2021; 41:230259. [PMID: 34792534 PMCID: PMC8607333 DOI: 10.1042/bsr20211419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional repressor, LexA, regulates the ‘SOS’ response, an indispensable bacterial DNA damage repair machinery. Compared with its Escherichia coli ortholog, LexA from Mycobacterium tuberculosis (Mtb) possesses a unique N-terminal extension of additional 24 amino acids in its DNA-binding domain (DBD) and 18 amino acids insertion at its hinge region that connects the DBD to the C-terminal dimerization/autoproteolysis domain. Despite the importance of LexA in ‘SOS’ regulation, Mtb LexA remains poorly characterized and the functional importance of its additional amino acids remained elusive. In addition, the lack of data on kinetic parameters of Mtb LexA–DNA interaction prompted us to perform kinetic analyses of Mtb LexA and its deletion variants using Bio-layer Interferometry (BLI). Mtb LexA is seen to bind to different ‘SOS’ boxes, DNA sequences present in the operator regions of damage-inducible genes, with comparable nanomolar affinity. Deletion of 18 amino acids from the linker region is found to affect DNA binding unlike the deletion of the N-terminal stretch of extra 24 amino acids. The conserved RKG motif has been found to be critical for DNA binding. Overall, the present study provides insights into the kinetics of the interaction between Mtb LexA and its target ‘SOS’ boxes. The kinetic parameters obtained for DNA binding of Mtb LexA would be instrumental to clearly understand the mechanism of ‘SOS’ regulation and activation in Mtb.
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18
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Murray GGR, Balmer AJ, Herbert J, Hadjirin NF, Kemp CL, Matuszewska M, Bruchmann S, Hossain ASMM, Gottschalk M, Tucker AW, Miller E, Weinert LA. Mutation rate dynamics reflect ecological change in an emerging zoonotic pathogen. PLoS Genet 2021; 17:e1009864. [PMID: 34748531 PMCID: PMC8601623 DOI: 10.1371/journal.pgen.1009864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/18/2021] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
Mutation rates vary both within and between bacterial species, and understanding what drives this variation is essential for understanding the evolutionary dynamics of bacterial populations. In this study, we investigate two factors that are predicted to influence the mutation rate: ecology and genome size. We conducted mutation accumulation experiments on eight strains of the emerging zoonotic pathogen Streptococcus suis. Natural variation within this species allows us to compare tonsil carriage and invasive disease isolates, from both more and less pathogenic populations, with a wide range of genome sizes. We find that invasive disease isolates have repeatedly evolved mutation rates that are higher than those of closely related carriage isolates, regardless of variation in genome size. Independent of this variation in overall rate, we also observe a stronger bias towards G/C to A/T mutations in isolates from more pathogenic populations, whose genomes tend to be smaller and more AT-rich. Our results suggest that ecology is a stronger correlate of mutation rate than genome size over these timescales, and that transitions to invasive disease are consistently accompanied by rapid increases in mutation rate. These results shed light on the impact that ecology can have on the adaptive potential of bacterial pathogens.
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Affiliation(s)
- Gemma G. R. Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Andrew J. Balmer
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Josephine Herbert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nazreen F. Hadjirin
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Caroline L. Kemp
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sebastian Bruchmann
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Marcelo Gottschalk
- Département de Pathologie et Microbiologie, Université de Montréal, Montréal, Canada
| | - Alexander W. Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Eric Miller
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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19
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Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen. PLoS Pathog 2021; 17:e1009606. [PMID: 34015034 PMCID: PMC8171923 DOI: 10.1371/journal.ppat.1009606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/02/2021] [Accepted: 05/03/2021] [Indexed: 11/19/2022] Open
Abstract
The emergence of new pathogens is a major threat to public and veterinary health. Changes in bacterial habitat such as a switch in host or disease tropism are typically accompanied by genetic diversification. Staphylococcus aureus is a multi-host bacterial species associated with human and livestock infections. A microaerophilic subspecies, Staphylococcus aureus subsp. anaerobius, is responsible for Morel’s disease, a lymphadenitis restricted to sheep and goats. However, the evolutionary history of S. aureus subsp. anaerobius and its relatedness to S. aureus are unknown. Population genomic analyses of clinical S. aureus subsp. anaerobius isolates revealed a highly conserved clone that descended from a S. aureus progenitor about 1000 years ago before differentiating into distinct lineages that contain African and European isolates. S. aureus subsp. anaerobius has undergone limited clonal expansion, with a restricted population size, and an evolutionary rate 10-fold slower than S. aureus. The transition to its current restricted ecological niche involved acquisition of a pathogenicity island encoding a ruminant host-specific effector of abscess formation, large chromosomal re-arrangements, and the accumulation of at least 205 pseudogenes, resulting in a highly fastidious metabolism. Importantly, expansion of ~87 insertion sequences (IS) located largely in intergenic regions provided distinct mechanisms for the control of expression of flanking genes, including a novel mechanism associated with IS-mediated anti-anti-sense decoupling of ancestral gene repression. Our findings reveal the remarkable evolutionary trajectory of a host-restricted bacterial pathogen that resulted from extensive remodelling of the S. aureus genome through an array of diverse mechanisms in parallel. The emergence of new pathogens is a major threat to public and veterinary health. Some bacteria such as Staphylococcus aureus, have the capacity to infect many different host species including humans and livestock while others such as the closely-related S. aureus subsp. anaerobius, associated with a single type of pathology called Morel’s disease in small ruminants, are highly niche-restricted. However, our understanding of the genetic basis for such differences in bacterial host-tropism is very limited. Here, we discovered that S. aureus subsp. anaerobius evolved from an S. aureus ancestor and underwent an array of extensive changes to its genome that accompanied the transition to its current restricted lifestyle. We observed genome decay involving loss of function of hundreds of genes, large intra-chromosomal rearrangements affecting most of the genome, acquisition of a pathogenicity island, and expansion of large numbers of insertion sequences that are inserted at intergenic sites around the genome. Importantly, we found that IS elements affect the expression of neighbouring genes in different ways including a novel mechanism of IS-enabled disruption of ancestral gene repression. Taken together, we provide a remarkable example of radical genomic changes associated with evolutionary transition from a multi-host to highly restricted host ecology.
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20
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Murray GGR, Charlesworth J, Miller EL, Casey MJ, Lloyd CT, Gottschalk M, Tucker AW(D, Welch JJ, Weinert LA. Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence. Mol Biol Evol 2021; 38:1570-1579. [PMID: 33313861 PMCID: PMC8042751 DOI: 10.1093/molbev/msaa323] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). Although genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, that is, host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of nonfunctional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a consistent correlate of pathogenicity in bacteria.
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Affiliation(s)
- Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jane Charlesworth
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Eric L Miller
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Haverford College, Haverford, PA, USA
| | - Michael J Casey
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- School of Mathematical Sciences, University of Southampton, Southampton, United Kingdom
| | - Catrin T Lloyd
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Marcelo Gottschalk
- Département de Pathologie et Microbiologie, Université de Montréal, Montréal, QC, Canada
| | | | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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21
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McGinn J, Lamason RL. The enigmatic biology of rickettsiae: recent advances, open questions and outlook. Pathog Dis 2021; 79:ftab019. [PMID: 33784388 PMCID: PMC8035066 DOI: 10.1093/femspd/ftab019] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/26/2021] [Indexed: 02/05/2023] Open
Abstract
Rickettsiae are obligate intracellular bacteria that can cause life-threatening illnesses and are among the oldest known vector-borne pathogens. Members of this genus are extraordinarily diverse and exhibit a broad host range. To establish intracellular infection, Rickettsia species undergo complex, multistep life cycles that are encoded by heavily streamlined genomes. As a result of reductive genome evolution, rickettsiae are exquisitely tailored to their host cell environment but cannot survive extracellularly. This host-cell dependence makes for a compelling system to uncover novel host-pathogen biology, but it has also hindered experimental progress. Consequently, the molecular details of rickettsial biology and pathogenesis remain poorly understood. With recent advances in molecular biology and genetics, the field is poised to start unraveling the molecular mechanisms of these host-pathogen interactions. Here, we review recent discoveries that have shed light on key aspects of rickettsial biology. These studies have revealed that rickettsiae subvert host cells using mechanisms that are distinct from other better-studied pathogens, underscoring the great potential of the Rickettsia genus for revealing novel biology. We also highlight several open questions as promising areas for future study and discuss the path toward solving the fundamental mysteries of this neglected and emerging human pathogen.
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Affiliation(s)
- Jon McGinn
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Rebecca L Lamason
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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22
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Palau M, Piqué N, Ramírez-Lázaro MJ, Lario S, Calvet X, Miñana-Galbis D. Whole-Genome Sequencing and Comparative Genomics of Three Helicobacter pylori Strains Isolated from the Stomach of a Patient with Adenocarcinoma. Pathogens 2021; 10:331. [PMID: 33809022 PMCID: PMC7998635 DOI: 10.3390/pathogens10030331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 12/28/2022] Open
Abstract
Helicobacter pylori is a common pathogen associated with several severe digestive diseases. Although multiple virulence factors have been described, it is still unclear the role of virulence factors on H. pylori pathogenesis and disease progression. Whole genome sequencing could help to find genetic markers of virulence strains. In this work, we analyzed three complete genomes from isolates obtained at the same point in time from a stomach of a patient with adenocarcinoma, using multiple available bioinformatics tools. The genome analysis of the strains B508A-S1, B508A-T2A and B508A-T4 revealed that they were cagA, babA and sabB/hopO negative. The differences among the three genomes were mainly related to outer membrane proteins, methylases, restriction modification systems and flagellar biosynthesis proteins. The strain B508A-T2A was the only one presenting the genotype vacA s1, and had the most distinct genome as it exhibited fewer shared genes, higher number of unique genes, and more polymorphisms were found in this genome. With all the accumulated information, no significant differences were found among the isolates regarding virulence and origin of the isolates. Nevertheless, some B508A-T2A genome characteristics could be linked to the pathogenicity of H. pylori.
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Affiliation(s)
- Montserrat Palau
- Secció de Microbiologia, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Catalonia, Spain; (M.P.); (N.P.)
| | - Núria Piqué
- Secció de Microbiologia, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Catalonia, Spain; (M.P.); (N.P.)
| | - M. José Ramírez-Lázaro
- Digestive Diseases Service, Hospital de Sabadell, Institut Universitari Parc Taulí-UAB, Parc Tauli 1, 08208 Sabadell, Catalonia, Spain; (M.J.R.-L.); (S.L.); (X.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Monforte de Lemos 3–5, 28029 Madrid, Community of Madrid, Spain
| | - Sergio Lario
- Digestive Diseases Service, Hospital de Sabadell, Institut Universitari Parc Taulí-UAB, Parc Tauli 1, 08208 Sabadell, Catalonia, Spain; (M.J.R.-L.); (S.L.); (X.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Monforte de Lemos 3–5, 28029 Madrid, Community of Madrid, Spain
| | - Xavier Calvet
- Digestive Diseases Service, Hospital de Sabadell, Institut Universitari Parc Taulí-UAB, Parc Tauli 1, 08208 Sabadell, Catalonia, Spain; (M.J.R.-L.); (S.L.); (X.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Monforte de Lemos 3–5, 28029 Madrid, Community of Madrid, Spain
| | - David Miñana-Galbis
- Secció de Microbiologia, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Catalonia, Spain; (M.P.); (N.P.)
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23
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Abram K, Udaondo Z, Bleker C, Wanchai V, Wassenaar TM, Robeson MS, Ussery DW. Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups. Commun Biol 2021; 4:117. [PMID: 33500552 PMCID: PMC7838162 DOI: 10.1038/s42003-020-01626-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023] Open
Abstract
In this study, more than one hundred thousand Escherichia coli and Shigella genomes were examined and classified. This is, to our knowledge, the largest E. coli genome dataset analyzed to date. A Mash-based analysis of a cleaned set of 10,667 E. coli genomes from GenBank revealed 14 distinct phylogroups. A representative genome or medoid identified for each phylogroup was used as a proxy to classify 95,525 unassembled genomes from the Sequence Read Archive (SRA). We find that most of the sequenced E. coli genomes belong to four phylogroups (A, C, B1 and E2(O157)). Authenticity of the 14 phylogroups is supported by several different lines of evidence: phylogroup-specific core genes, a phylogenetic tree constructed with 2613 single copy core genes, and differences in the rates of gene gain/loss/duplication. The methodology used in this work is able to reproduce known phylogroups, as well as to identify previously uncharacterized phylogroups in E. coli species.
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Affiliation(s)
- Kaleb Abram
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | - Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | - Carissa Bleker
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, 37996, USA
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Visanu Wanchai
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | - Trudy M Wassenaar
- Molecular Microbiology and Genomics Consultants, 55576, Zotzenheim, Germany
| | - Michael S Robeson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | - David W Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA.
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24
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Metabolic Fate of Human Immunoactive Sterols in Mycobacterium tuberculosis. J Mol Biol 2020; 433:166763. [PMID: 33359098 DOI: 10.1016/j.jmb.2020.166763] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/05/2020] [Accepted: 12/12/2020] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis (Mtb) infection is among top ten causes of death worldwide, and the number of drug-resistant strains is increasing. The direct interception of human immune signaling molecules by Mtb remains elusive, limiting drug discovery. Oxysterols and secosteroids regulate both innate and adaptive immune responses. Here we report a functional, structural, and bioinformatics study of Mtb enzymes initiating cholesterol catabolism and demonstrated their interrelation with human immunity. We show that these enzymes metabolize human immune oxysterol messengers. Rv2266 - the most potent among them - can also metabolize vitamin D3 (VD3) derivatives. High-resolution structures show common patterns of sterols binding and reveal a site for oxidative attack during catalysis. Finally, we designed a compound that binds and inhibits three studied proteins. The compound shows activity against Mtb H37Rv residing in macrophages. Our findings contribute to molecular understanding of suppression of immunity and suggest that Mtb has its own transformation system resembling the human phase I drug-metabolizing system.
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25
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Sher AA, Jerome JP, Bell JA, Yu J, Kim HY, Barrick JE, Mansfield LS. Experimental Evolution of Campylobacter jejuni Leads to Loss of Motility, rpoN (σ54) Deletion and Genome Reduction. Front Microbiol 2020; 11:579989. [PMID: 33240235 PMCID: PMC7677240 DOI: 10.3389/fmicb.2020.579989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/14/2020] [Indexed: 12/18/2022] Open
Abstract
Evolution experiments in the laboratory have focused heavily on model organisms, often to the exclusion of clinically relevant pathogens. The foodborne bacterial pathogen Campylobacter jejuni belongs to a genus whose genomes are small compared to those of its closest genomic relative, the free-living genus Sulfurospirillum, suggesting genome reduction during the course of evolution to host association. In an in vitro experiment, C. jejuni serially passaged in rich medium in the laboratory exhibited loss of flagellar motility-an essential function for host colonization. At early time points the motility defect was often reversible, but after 35 days of serial culture, motility was irreversibly lost in most cells in 5 independently evolved populations. Population re-sequencing revealed disruptive mutations to genes in the flagellar transcriptional cascade, rpoN (σ54)-therefore disrupting the expression of the genes σ54 regulates-coupled with deletion of rpoN in all evolved lines. Additional mutations were detected in virulence-related loci. In separate in vivo experiments, we demonstrate that a phase variable (reversible) motility mutant carrying an adenine deletion within a homopolymeric tract resulting in truncation of the flagellar biosynthesis gene fliR was deficient for colonization in a C57BL/6 IL-10-/- mouse disease model. Re-insertion of an adenine residue partially restored motility and ability to colonize mice. Thus, a pathogenic C. jejuni strain was rapidly attenuated by experimental laboratory evolution and demonstrated genomic instability during this evolutionary process. The changes observed suggest C. jejuni is able to evolve in a novel environment through genome reduction as well as transition, transversion, and slip-strand mutations.
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Affiliation(s)
- Azam A. Sher
- Comparative Enteric Diseases Laboratory, East Lansing, MI, United States
- Comparative Medicine and Integrative Biology, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States
| | - John P. Jerome
- Comparative Enteric Diseases Laboratory, East Lansing, MI, United States
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Julia A. Bell
- Comparative Enteric Diseases Laboratory, East Lansing, MI, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Julian Yu
- Comparative Enteric Diseases Laboratory, East Lansing, MI, United States
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Hahyung Y. Kim
- Comparative Enteric Diseases Laboratory, East Lansing, MI, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Jeffrey E. Barrick
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
| | - Linda S. Mansfield
- Comparative Enteric Diseases Laboratory, East Lansing, MI, United States
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, United States
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States
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26
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Teelucksingh T, Thompson LK, Cox G. The Evolutionary Conservation of Escherichia coli Drug Efflux Pumps Supports Physiological Functions. J Bacteriol 2020; 202:e00367-20. [PMID: 32839176 PMCID: PMC7585057 DOI: 10.1128/jb.00367-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bacteria harness an impressive repertoire of resistance mechanisms to evade the inhibitory action of antibiotics. One such mechanism involves efflux pump-mediated extrusion of drugs from the bacterial cell, which significantly contributes to multidrug resistance. Intriguingly, most drug efflux pumps are chromosomally encoded components of the intrinsic antibiotic resistome. In addition, in terms of xenobiotic detoxification, bacterial efflux systems often exhibit significant levels of functional redundancy. Efflux pumps are also considered to be highly conserved; however, the extent of conservation in many bacterial species has not been reported and the majority of genes that encode efflux pumps appear to be dispensable for growth. These observations, in combination with an increasing body of experimental evidence, imply alternative roles in bacterial physiology. Indeed, the ability of efflux pumps to facilitate antibiotic resistance could be a fortuitous by-product of ancient physiological functions. Using Escherichia coli as a model organism, we here evaluated the evolutionary conservation of drug efflux pumps and we provide phylogenetic analysis of the major efflux families. We show the E. coli drug efflux system has remained relatively stable and the majority (∼80%) of pumps are encoded in the core genome. This analysis further supports the importance of drug efflux pumps in E. coli physiology. In this review, we also provide an update on the roles of drug efflux pumps in the detoxification of endogenously synthesized substrates and pH homeostasis. Overall, gaining insight into drug efflux pump conservation, common evolutionary ancestors, and physiological functions could enable strategies to combat these intrinsic and ancient elements.
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Affiliation(s)
- Tanisha Teelucksingh
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Laura K Thompson
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Georgina Cox
- College of Biological Sciences, Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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27
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Bukhdruker S, Varaksa T, Grabovec I, Marin E, Shabunya P, Kadukova M, Grudinin S, Kavaleuski A, Gusach A, Gilep A, Borshchevskiy V, Strushkevich N. Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450. Int J Mol Sci 2020; 21:E7683. [PMID: 33081390 PMCID: PMC7589583 DOI: 10.3390/ijms21207683] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/04/2023] Open
Abstract
Spreading of the multidrug-resistant (MDR) strains of the one of the most harmful pathogen Mycobacterium tuberculosis (Mtb) generates the need for new effective drugs. SQ109 showed activity against resistant Mtb and already advanced to Phase II/III clinical trials. Fast SQ109 degradation is attributed to the human liver Cytochrome P450s (CYPs). However, no information is available about interactions of the drug with Mtb CYPs. Here, we show that Mtb CYP124, previously assigned as a methyl-branched lipid monooxygenase, binds and hydroxylates SQ109 in vitro. A 1.25 Å-resolution crystal structure of the CYP124-SQ109 complex unambiguously shows two conformations of the drug, both positioned for hydroxylation of the ω-methyl group in the trans position. The hydroxylated SQ109 presumably forms stabilizing H-bonds with its target, Mycobacterial membrane protein Large 3 (MmpL3). We anticipate that Mtb CYPs could function as analogs of drug-metabolizing human CYPs affecting pharmacokinetics and pharmacodynamics of antitubercular (anti-TB) drugs.
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Affiliation(s)
- Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (S.B.); (E.M.); (M.K.); (A.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Research Center Jülich, 52428 Jülich, Germany
| | - Tatsiana Varaksa
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.V.); (I.G.); (P.S.); (A.K.); (A.G.)
| | - Irina Grabovec
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.V.); (I.G.); (P.S.); (A.K.); (A.G.)
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (S.B.); (E.M.); (M.K.); (A.G.)
| | - Polina Shabunya
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.V.); (I.G.); (P.S.); (A.K.); (A.G.)
| | - Maria Kadukova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (S.B.); (E.M.); (M.K.); (A.G.)
- Grenoble Alpes University, CNRS, Inria, Grenoble INP, LJK, 38000 Grenoble, France;
| | - Sergei Grudinin
- Grenoble Alpes University, CNRS, Inria, Grenoble INP, LJK, 38000 Grenoble, France;
| | - Anton Kavaleuski
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.V.); (I.G.); (P.S.); (A.K.); (A.G.)
| | - Anastasiia Gusach
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (S.B.); (E.M.); (M.K.); (A.G.)
| | - Andrei Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.V.); (I.G.); (P.S.); (A.K.); (A.G.)
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry, 119435 Moscow, Russia
- R&D Department, MT-Medicals LLC, 121205 Moscow, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia; (S.B.); (E.M.); (M.K.); (A.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Research Center Jülich, 52428 Jülich, Germany
| | - Natallia Strushkevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.V.); (I.G.); (P.S.); (A.K.); (A.G.)
- Center for Computational and Data-Intensive Science and Engineering (CDISE), Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
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28
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Bohlin J, Rose B, Brynildsrud O, Birgitte Freiesleben De Blasio. A simple stochastic model describing genomic evolution over time of GC content in microbial symbionts. J Theor Biol 2020; 503:110389. [PMID: 32634385 DOI: 10.1016/j.jtbi.2020.110389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/21/2020] [Accepted: 06/24/2020] [Indexed: 11/29/2022]
Abstract
An organism's genomic base composition is usually summarized by its AT or GC content due to Chargaff's parity laws. Variation in prokaryotic GC content can be substantial between taxa but is generally small within microbial genomes. This variation has been found to correlate with both phylogeny and environmental factors. Since novel single-nucleotide polymorphisms (SNPs) within genomes are at least partially linked to the environment through natural selection, SNP GC content can be considered a compound measure of an organism's environmental influences, lifestyle, phylogeny as well as other more or less random processes. While there are several models describing genomic GC content few, if any, consider AT/GC mutation rates subjected to random perturbations. We present a mathematical model that describes how GC content in microbial genomes evolves over time as a function of the AT → GC and GC → AT mutation rates with Gaussian white noise disturbances. The model, which is suited specifically to non-recombining vertically transmitted prokaryotic symbionts, suggests that small differences in the AT/GC mutation rates can lead to profound differences in outcome due to the ensuing stochastic process. In other words, the model indicates that time to extinction could be a consequence of the mutation rate trajectory on which the symbiont embarked early on in its evolutionary history.
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Affiliation(s)
- Jon Bohlin
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Production Animals, Faculty of Veterinary Medicine, Norwegian University of Life Science, Oslo, Norway
| | - Brittany Rose
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ola Brynildsrud
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Production Animals, Faculty of Veterinary Medicine, Norwegian University of Life Science, Oslo, Norway
| | - Birgitte Freiesleben De Blasio
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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29
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Shaw LP, Wang AD, Dylus D, Meier M, Pogacnik G, Dessimoz C, Balloux F. The phylogenetic range of bacterial and viral pathogens of vertebrates. Mol Ecol 2020; 29:3361-3379. [PMID: 32390272 DOI: 10.1111/mec.15463] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 03/20/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022]
Abstract
Many major human pathogens are multihost pathogens, able to infect other vertebrate species. Describing the general patterns of host-pathogen associations across pathogen taxa is therefore important to understand risk factors for human disease emergence. However, there is a lack of comprehensive curated databases for this purpose, with most previous efforts focusing on viruses. Here, we report the largest manually compiled host-pathogen association database, covering 2,595 bacteria and viruses infecting 2,656 vertebrate hosts. We also build a tree for host species using nine mitochondrial genes, giving a quantitative measure of the phylogenetic similarity of hosts. We find that the majority of bacteria and viruses are specialists infecting only a single host species, with bacteria having a significantly higher proportion of specialists compared to viruses. Conversely, multihost viruses have a more restricted host range than multihost bacteria. We perform multiple analyses of factors associated with pathogen richness per host species and the pathogen traits associated with greater host range and zoonotic potential. We show that factors previously identified as important for zoonotic potential in viruses-such as phylogenetic range, research effort, and being vector-borne-are also predictive in bacteria. We find that the fraction of pathogens shared between two hosts decreases with the phylogenetic distance between them. Our results suggest that host phylogenetic similarity is the primary factor for host-switching in pathogens.
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Affiliation(s)
- Liam P Shaw
- UCL Genetics Institute, University College London, London, UK.,Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Alethea D Wang
- UCL Genetics Institute, University College London, London, UK.,Canadian University Dubai, Dubai, United Arab Emirates
| | - David Dylus
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Magda Meier
- UCL Genetics Institute, University College London, London, UK.,Genetics and Genomic Medicine, University College London Institute of Child Health, London, UK
| | - Grega Pogacnik
- UCL Genetics Institute, University College London, London, UK
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Genetics Evolution and Environment, Centre for Life's Origins and Evolution, University College London, London, UK.,Department of Computer Science, University College London, London, UK
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30
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Gallant J, Mouton J, Ummels R, Ten Hagen-Jongman C, Kriel N, Pain A, Warren RM, Bitter W, Heunis T, Sampson SL. Identification of gene fusion events in Mycobacterium tuberculosis that encode chimeric proteins. NAR Genom Bioinform 2020; 2:lqaa033. [PMID: 33575588 PMCID: PMC7671302 DOI: 10.1093/nargab/lqaa033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/16/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis is a facultative intracellular pathogen responsible for causing tuberculosis. The harsh environment in which M. tuberculosis survives requires this pathogen to continuously adapt in order to maintain an evolutionary advantage. However, the apparent absence of horizontal gene transfer in M. tuberculosis imposes restrictions in the ways by which evolution can occur. Large-scale changes in the genome can be introduced through genome reduction, recombination events and structural variation. Here, we identify a functional chimeric protein in the ppe38-71 locus, the absence of which is known to have an impact on protein secretion and virulence. To examine whether this approach was used more often by this pathogen, we further develop software that detects potential gene fusion events from multigene deletions using whole genome sequencing data. With this software we could identify a number of other putative gene fusion events within the genomes of M. tuberculosis isolates. We were able to demonstrate the expression of one of these gene fusions at the protein level using mass spectrometry. Therefore, gene fusions may provide an additional means of evolution for M. tuberculosis in its natural environment whereby novel chimeric proteins and functions can arise.
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Affiliation(s)
- James Gallant
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa.,Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Jomien Mouton
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
| | - Roy Ummels
- Medical Microbiology and Infection Control, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
| | - Corinne Ten Hagen-Jongman
- Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands
| | - Nastassja Kriel
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.,Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, 001-0020, N20 W10 Kita-ku, Sapporo, Japan
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
| | - Wilbert Bitter
- Section of Molecular Microbiology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, The Netherlands.,Medical Microbiology and Infection Control, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HZ Amsterdam, The Netherlands
| | - Tiaan Heunis
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa.,Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Samantha L Sampson
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Medicine and Health Science, Stellenbosch University, Tygerberg, Cape Town 7505, South Africa
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Genetic diversity and population structure of Tenacibaculum maritimum, a serious bacterial pathogen of marine fish: from genome comparisons to high throughput MALDI-TOF typing. Vet Res 2020; 51:60. [PMID: 32381115 PMCID: PMC7204230 DOI: 10.1186/s13567-020-00782-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/08/2020] [Indexed: 01/08/2023] Open
Abstract
Tenacibaculum maritimum is responsible for tenacibaculosis, a devastating marine fish disease. This filamentous bacterium displays a very broad host range and a worldwide geographical distribution. We analyzed and compared the genomes of 25 T. maritimum strains, including 22 newly draft-sequenced genomes from isolates selected based on available MLST data, geographical origin and host fish. The genome size (~3.356 Mb in average) of all strains is very similar. The core genome is composed of 2116 protein-coding genes accounting for ~75% of the genes in each genome. These conserved regions harbor a moderate level of nucleotide diversity (~0.0071 bp-1) whose analysis reveals an important contribution of recombination (r/m ≥ 7) in the evolutionary process of this cohesive species that appears subdivided into several subgroups. Association trends between these subgroups and specific geographical origin or ecological niche remains to be clarified. We also evaluated the potential of MALDI-TOF-MS to assess the variability between T. maritimum isolates. Using genome sequence data, several detected mass peaks were assigned to ribosomal proteins. Additionally, variations corresponding to single or multiple amino acid changes in several ribosomal proteins explaining the detected mass shifts were identified. By combining nine polymorphic biomarker ions, we identified combinations referred to as MALDI-Types (MTs). By investigating 131 bacterial isolates retrieved from a variety of isolation sources, we identified twenty MALDI-Types as well as four MALDI-Groups (MGs). We propose this MALDI-TOF-MS Multi Peak Shift Typing scheme as a cheap, fast and an accurate method for screening T. maritimum isolates for large-scale epidemiological surveys.
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Montero DA, Canto FD, Velasco J, Colello R, Padola NL, Salazar JC, Martin CS, Oñate A, Blanco J, Rasko DA, Contreras C, Puente JL, Scheutz F, Franz E, Vidal RM. Cumulative acquisition of pathogenicity islands has shaped virulence potential and contributed to the emergence of LEE-negative Shiga toxin-producing Escherichia coli strains. Emerg Microbes Infect 2019; 8:486-502. [PMID: 30924410 PMCID: PMC6455142 DOI: 10.1080/22221751.2019.1595985] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens causing severe gastroenteritis, which may lead to hemolytic uremic syndrome. The Locus of Enterocyte Effacement (LEE), a Pathogenicity Island (PAI), is a major determinant of intestinal epithelium attachment of a group of STEC strains; however, the virulence repertoire of STEC strains lacking LEE, has not been fully characterized. The incidence of LEE-negative STEC strains has increased in several countries, highlighting the relevance of their study. In order to gain insights into the basis for the emergence of LEE-negative STEC strains, we performed a large-scale genomic analysis of 367 strains isolated worldwide from humans, animals, food and the environment. We identified uncharacterized genomic islands, including two PAIs and one Integrative Conjugative Element. Additionally, the Locus of Adhesion and Autoaggregation (LAA) was the most prevalent PAI among LEE-negative strains and we found that it contributes to colonization of the mice intestine. Our comprehensive and rigorous comparative genomic and phylogenetic analyses suggest that the accumulative acquisition of PAIs has played an important, but currently unappreciated role, in the evolution of virulence in these strains. This study provides new knowledge on the pathogenicity of LEE-negative STEC strains and identifies molecular markers for their epidemiological surveillance.
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Affiliation(s)
- David Arturo Montero
- a Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile , Santiago , Chile
| | - Felipe Del Canto
- a Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile , Santiago , Chile
| | - Juliana Velasco
- b Servicio de Urgencia Infantil, Hospital Clínico de la Universidad de Chile "Dr. José Joaquín Aguirre" , Santiago , Chile
| | - Rocío Colello
- c Centro de Investigación Veterinaria Tandil, CONICET-CIC, Facultad de Ciencias Veterinarias, UNCPBA , Tandil , Argentina
| | - Nora Lia Padola
- c Centro de Investigación Veterinaria Tandil, CONICET-CIC, Facultad de Ciencias Veterinarias, UNCPBA , Tandil , Argentina
| | - Juan Carlos Salazar
- a Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile , Santiago , Chile
| | - Carla San Martin
- d Departamento de Microbiología, Facultad de Ciencias Biológicas , Universidad de Concepción , Concepción , Chile
| | - Angel Oñate
- d Departamento de Microbiología, Facultad de Ciencias Biológicas , Universidad de Concepción , Concepción , Chile
| | - Jorge Blanco
- e Laboratorio de Referencia de E. coli, Facultad de Veterinaria , Universidad de Santiago de Compostela , Lugo , España
| | - David A Rasko
- f Department of Microbiology and Immunology , University of Maryland School of Medicine , Baltimore , MD , USA
| | - Carmen Contreras
- g Departamento de Microbiología Molecular , Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca , México
| | - Jose Luis Puente
- g Departamento de Microbiología Molecular , Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca , México
| | - Flemming Scheutz
- h Department of Bacteria, Parasites and Fungi , The International Collaborating Centre for Reference and Research on Escherichia and Klebsiella, Statens Serum Institut , Copenhagen , Denmark
| | - Eelco Franz
- i National Institute for Public Health, Centre for Infectious Disease Control , Bilthoven , The Netherlands
| | - Roberto M Vidal
- a Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile , Santiago , Chile.,j Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile , Santiago , Chile
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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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Botelho J, Grosso F, Peixe L. WITHDRAWN: Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution. Drug Resist Updat 2019. [DOI: 10.1016/j.drup.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Formylated N-terminal methionine is absent from the Mycoplasma hyopneumoniae proteome: Implications for translation initiation. Int J Med Microbiol 2019; 309:288-298. [PMID: 31126750 DOI: 10.1016/j.ijmm.2019.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/28/2019] [Accepted: 03/17/2019] [Indexed: 12/31/2022] Open
Abstract
N-terminal methionine excision (NME) is a proteolytic pathway that cleaves the N-termini of proteins, a process that influences where proteins localise in the cell and their turnover rates. In bacteria, protein biosynthesis is initiated by formylated methionine start tRNA (fMet-tRNAfMet). The formyl group is attached by formyltransferase (FMT) and is subsequently removed by peptide deformylase (PDF) in most but not all proteins. Methionine aminopeptidase then cleaves deformylated methionine to complete the process. Components of NME, particularly PDF, are promising therapeutic targets for bacterial pathogens. In Mycoplasma hyopneumoniae, a genome-reduced, major respiratory pathogen of swine, pdf and fmt are absent from its genome. Our bioinformatic analysis uncovered additional enzymes involved in formylated N-terminal methionine (fnMet) processing missing in fourteen mycoplasma species, including M. hyopneumoniae but not in Mycoplasma pneumoniae, a major respiratory pathogen of humans. Consistent with our bioinformatic studies, an analysis of in-house tryptic peptide libraries confirmed the absence of fnMet in M. hyopneumoniae proteins but, as expected fnMet peptides were detected in the proteome of M. pneumoniae. Additionally, computational molecular modelling of M. hyopneumoniae translation initiation factors reveal structural and sequence differences in areas known to interact with fMet-tRNAfMet. Our data suggests that some mycoplasmas have evolved a translation process that does not require fnMet.
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36
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Transcriptional noise and exaptation as sources for bacterial sRNAs. Biochem Soc Trans 2019; 47:527-539. [PMID: 30837318 DOI: 10.1042/bst20180171] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Abstract
Understanding how new genes originate and integrate into cellular networks is key to understanding evolution. Bacteria present unique opportunities for both the natural history and experimental study of gene origins, due to their large effective population sizes, rapid generation times, and ease of genetic manipulation. Bacterial small non-coding RNAs (sRNAs), in particular, many of which operate through a simple antisense regulatory logic, may serve as tractable models for exploring processes of gene origin and adaptation. Understanding how and on what timescales these regulatory molecules arise has important implications for understanding the evolution of bacterial regulatory networks, in particular, for the design of comparative studies of sRNA function. Here, we introduce relevant concepts from evolutionary biology and review recent work that has begun to shed light on the timescales and processes through which non-functional transcriptional noise is co-opted to provide regulatory functions. We explore possible scenarios for sRNA origin, focusing on the co-option, or exaptation, of existing genomic structures which may provide protected spaces for sRNA evolution.
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Bridel S, Olsen AB, Nilsen H, Bernardet JF, Achaz G, Avendaño-Herrera R, Duchaud E. Comparative Genomics of Tenacibaculum dicentrarchi and "Tenacibaculum finnmarkense" Highlights Intricate Evolution of Fish-Pathogenic Species. Genome Biol Evol 2018; 10:452-457. [PMID: 29360975 PMCID: PMC5793721 DOI: 10.1093/gbe/evy020] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2018] [Indexed: 01/03/2023] Open
Abstract
The genus Tenacibaculum encompasses several species pathogenic for marine fish. Tenacibaculum dicentrarchi and "Tenacibaculum finnmarkense" (Quotation marks denote species that have not been validly named.) were retrieved from skin lesions of farmed fish such as European sea bass or Atlantic salmon. They cause a condition referred to as tenacibaculosis and severe outbreaks and important fish losses have been reported in Spanish, Norwegian, and Chilean marine farms. We report here the draft genomes of the T. dicentrarchi and "T. finnmarkense" type strains. These genomes were compared with draft genomes from field isolates retrieved from Chile and Norway and with previously published Tenacibaculum genomes. We used Average Nucleotide Identity and core genome-based phylogeny as a proxy index for species boundary delineation. This work highlights evolution of closely related fish-pathogenic species and suggests that homologous recombination likely contributes to genome evolution. It also corrects the species affiliation of strain AYD7486TD claimed by Grothusen et al. (2016).
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Affiliation(s)
- Sébastien Bridel
- VIM, INRA, Université Paris-Saclay, Jouy-en-Josas, France.,Labofarm, Finalab, Loudéac, France.,Université de Versailles Saint-Quentin-En-Yvelines, Montigny-Le-Bretonneux, France
| | | | | | | | - Guillaume Achaz
- Atelier de Bioinformatique, UMR 7205 ISyEB, MNHN-UPMC-CNRS-EPHE, Muséum National d'Histoire Naturelle, Paris, France
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Viña del Mar, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
| | - Eric Duchaud
- VIM, INRA, Université Paris-Saclay, Jouy-en-Josas, France
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Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli. mSphere 2018; 3:3/5/e00405-18. [PMID: 30282756 PMCID: PMC6170788 DOI: 10.1128/msphere.00405-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nodular thelitis is a chronic enzootic infection affecting dairy cows and goats. The causative agent was recently shown to be related to the leprosy-causing bacilli Mycobacterium leprae and Mycobacterium lepromatosis In this study, the genome of this pathogen was sequenced and analyzed. Phylogenomic analyses confirmed that the pathogen present in nodular thelitis and tuberculoid scrotitis is a distinct species related to the leprosy bacilli and Mycobacterium haemophilum Because the pathogen was originally isolated from a bovine udder, it was named "Mycobacterium uberis" The genome of "M. uberis" is only 3.12 Mb in length, which represents the smallest mycobacterial genome identified so far but which is close to that of leprosy bacilli in size. The genome contains 1,759 protein-coding genes and 1,081 pseudogenes, indicative of extensive reductive evolution and likely the reason that M. uberis cannot be grown axenically. The pseudogenization and genome reduction in M. uberis seem to have been to some extent independent from the results determined for the genomes of the leprosy bacilli.IMPORTANCE M. uberis is an emerging skin pathogen in dairy animals. Its genome underwent massive reduction and gene decay, leading to a minimal set of genes required for an obligatory intracellular lifestyle, which highly resembles the evolution of the leprosy agents M. leprae and M. lepromatosis The genomic similarity between M. uberis and the leprosy bacilli can help in identifying key virulence factors of these closely related species or in identifying genes responsible for the distinct differences between thelitis or scrotitis and leprosy with respect to clinical manifestations. Specific DNA markers can now be developed for quick detection of this pathogen.
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Kristensen TN, Ketola T, Kronholm I. Adaptation to environmental stress at different timescales. Ann N Y Acad Sci 2018; 1476:5-22. [PMID: 30259990 DOI: 10.1111/nyas.13974] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 08/24/2018] [Accepted: 09/08/2018] [Indexed: 12/21/2022]
Abstract
Environments are changing rapidly, and to cope with these changes, organisms have to adapt. Adaptation can take many shapes and occur at different speeds, depending on the type of response, the trait, the population, and the environmental conditions. The biodiversity crisis that we are currently facing illustrates that numerous species and populations are not capable of adapting with sufficient speed to ongoing environmental changes. Here, we discuss current knowledge on the ability of animals and plants to adapt to environmental stress on different timescales, mainly focusing on thermal stress and ectotherms. We discuss within-generation responses that can be fast and induced within minutes or hours, evolutionary adaptations that are often slow and take several generations, and mechanisms that lay somewhere in between and that include epigenetic transgenerational effects. To understand and predict the impacts of environmental change and stress on biodiversity, we suggest that future studies should (1) have an increased focus on understanding the type and speed of responses to fast environmental changes; (2) focus on the importance of environmental fluctuations and the predictability of environmental conditions on adaptive capabilities, preferably in field studies encompassing several fitness components; and (3) look at ecosystem responses to environmental stress and their resilience when disturbed.
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Affiliation(s)
- Torsten Nygaard Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department of Bioscience, University of Aarhus, Aarhus, Denmark
| | - Tarmo Ketola
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Ilkka Kronholm
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
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40
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Lo WS, Gasparich GE, Kuo CH. Convergent Evolution among Ruminant-Pathogenic Mycoplasma Involved Extensive Gene Content Changes. Genome Biol Evol 2018; 10:2130-2139. [PMID: 30102350 PMCID: PMC6117150 DOI: 10.1093/gbe/evy172] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2018] [Indexed: 01/21/2023] Open
Abstract
Convergent evolution, a process by which organisms evolved independently to have similar traits, provides opportunities to understand adaptation. The bacterial genus Mycoplasma contains multiple species that evolved independently to become ruminant pathogens, which represents an interesting study system for investigating the process. In this work, we determined the genome sequences of 11 Entomoplasma/Mesoplasma species. This new data set, together with the other available Mollicutes genomes, provided comprehensive taxon sampling for inferring the gene content evolution that led to the emergence of Mycoplasma Mycoides cluster. Our results indicated that the most recent common ancestor (MRCA) of the Mycoides-Entomoplasmataceae clade lost ∼15% of the core genes when it diverged from the Spiroplasma Apis clade. After this initial wave of genome reduction, relatively few gene gains or losses were inferred until the emergence of the Mycoides cluster. Compared with those Entomoplasmataceae lineages that maintained the association with insects, the MRCA of the Mycoides cluster experienced a second wave of gene losses, as well as acquiring >100 novel genes through horizontal gene transfer. These gene acquisitions involved many with the Mycoplasma Hominis/Pneumoniae lineages as the putative donors, suggesting that gene exchanges among these vertebrate symbionts with distinct phylogenetic affiliations may be important in the emergence of the Mycoides cluster. These findings demonstrated that the gene content of bacterial genomes could be exceedingly dynamic, even for those symbionts with highly reduced genomes. Moreover, the emergence of novel pathogens may involve extensive remodeling of gene content, rather than acquisition of few virulence genes.
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Affiliation(s)
- Wen-Sui Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department for Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tuebingen, Germany
| | | | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Saha MS, Pal S, Sarkar I, Roy A, Das Mohapatra PK, Sen A. Comparative genomics of Mycobacterium reveals evolutionary trends of M. avium complex. Genomics 2018; 111:426-435. [PMID: 29501678 DOI: 10.1016/j.ygeno.2018.02.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/01/2017] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic species, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done. Further the evolutionary features of M. avium complex also have been revealed. Mycobacterial genes are moderately GC rich showed higher expression level in PPs and significant negative correlation with biosynthetic cost of proteins. Translational selection pressure was observed in mycobacterial genes. MAC showed close relationship with NPs and higher evolutionary rate in MAC revealed their constant evolving nature.
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Affiliation(s)
- Mousumi Sarkar Saha
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India
| | - Shilpee Pal
- Department of Microbiology, Vidyasagar University, Midnapore 721102, India
| | - Indrani Sarkar
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India
| | - Ayan Roy
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India
| | | | - Arnab Sen
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India.
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