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Torrillo PA, Lieberman TD. Reversions mask the contribution of adaptive evolution in microbiomes. eLife 2024; 13:e93146. [PMID: 39240756 PMCID: PMC11379459 DOI: 10.7554/elife.93146] [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: 09/29/2023] [Accepted: 07/30/2024] [Indexed: 09/08/2024] Open
Abstract
When examining bacterial genomes for evidence of past selection, the results depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by dN/dS, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with opposite implications for dynamical intuition and applications of dN/dS. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the dN/dS decay given only dozens of locally fluctuating selective pressures, which is realistic in the context of Bacteroides genomes. The success of the adaptive reversion model argues for interpreting low values of dN/dS obtained from long timescales with caution as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short timescales.
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Affiliation(s)
- Paul A Torrillo
- Institute for Medical Engineering and Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Tami D Lieberman
- Institute for Medical Engineering and Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
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Ali F. Patterns of Change in Nucleotide Diversity Over Gene Length. Genome Biol Evol 2024; 16:evae078. [PMID: 38608148 PMCID: PMC11040516 DOI: 10.1093/gbe/evae078] [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: 07/18/2023] [Revised: 03/26/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to estimate Effective population size based on the diversity of synonymous sites demand a better understanding of their selective constraints. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site of a gene. The degree of reduction in diversity at the translation initiation site and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of translation-associated traits such as the avoidance of mRNA secondary structure around translation initiation site, the number of rRNAs, and relative codon usage of ribosomal genes. Evolutionary simulations under purifying selection reproduce the observed patterns and diversity-length correlation and highlight that selective constraints on the 5'-region of a gene may be more extensive than previously believed. These results have implications for the estimation of effective population size, and relative mutation rates, and for genome scans of genes under positive selection based on "silent-site" diversity.
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Affiliation(s)
- Farhan Ali
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
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Ali F. Patterns of change in nucleotide diversity over gene length. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548940. [PMID: 37503020 PMCID: PMC10369989 DOI: 10.1101/2023.07.13.548940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to identify sites under positive selection require an understanding of the expected diversity in its absence. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site (TIS) of a gene. The degree of reduction in diversity at the TIS and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of fast-growth adaptations such as the avoidance of mRNA secondary structure around TIS, the number of rRNAs, and relative codon usage of ribosomal genes. Thus, the dependence of nucleotide diversity on gene length is governed by a combination of selective and non-selective processes. These results have implications for the estimation of effective population size and relative mutation rates based on "silent-site" diversity, and for pN/pS-based prediction of genes under selection.
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Affiliation(s)
- Farhan Ali
- Biodesign Institute, Arizona State University, Tempe, Arizona
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Mokrousov I, Slavchev I, Solovieva N, Dogonadze M, Vyazovaya A, Valcheva V, Masharsky A, Belopolskaya O, Dimitrov S, Zhuravlev V, Portugal I, Perdigão J, Dobrikov GM. Molecular Insight into Mycobacterium tuberculosis Resistance to Nitrofuranyl Amides Gained through Metagenomics-like Analysis of Spontaneous Mutants. Pharmaceuticals (Basel) 2022; 15:ph15091136. [PMID: 36145357 PMCID: PMC9504009 DOI: 10.3390/ph15091136] [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: 08/12/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
We performed synthesis of new nitrofuranyl amides and investigated their anti-TB activity and primary genetic response of mycobacteria through whole-genome sequencing (WGS) of spontaneous resistant mutants. The in vitro activity was assessed on reference strain Mycobacterium tuberculosis H37Rv. The most active compound 11 was used for in vitro selection of spontaneous resistant mutants. The same mutations in six genes were detected in bacterial cultures grown under increased concentrations of 11 (2×, 4×, 8× MIC). The mutant positions were presented as mixed wild type and mutant alleles while increasing the concentration of the compound led to the semi-proportional and significant increase in mutant alleles. The identified genes belong to different categories and pathways. Some of them were previously reported as mediating drug resistance or drug tolerance, and counteracting oxidative and nitrosative stress, in particular: Rv0224c, fbiC, iniA, and Rv1592c. Gene-set interaction analysis revealed a certain weak interaction for gene pairs Rv1592–Rv1639c and Rv1592–Rv0224c. To conclude, this study experimentally demonstrated a multifaceted primary genetic response of M. tuberculosis to the action of nitrofurans. All three 11-treated subcultures independently presented the same six SNPs, which suggests their non-random occurrence and likely causative relationship between compound action and possible resistance mechanism.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 197101 St. Petersburg, Russia
- Henan International Joint Laboratory of Children’s Infectious Diseases, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
- Correspondence: (I.M.); (G.M.D.)
| | - Ivaylo Slavchev
- Institute of Organic Chemistry with Centre of Phytochemistry, Acad. G. Bonchev Street, bl. 9, 1113 Sofia, Bulgaria
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - Marine Dogonadze
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 197101 St. Petersburg, Russia
| | - Violeta Valcheva
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, bl. 26, 1113 Sofia, Bulgaria
| | - Aleksey Masharsky
- Resource Center “Bio-bank Center”, Research Park of St. Petersburg State University, 198504 St. Petersburg, Russia
| | - Olesya Belopolskaya
- Resource Center “Bio-bank Center”, Research Park of St. Petersburg State University, 198504 St. Petersburg, Russia
| | - Simeon Dimitrov
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, bl. 26, 1113 Sofia, Bulgaria
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - Isabel Portugal
- iMed.ULisboa–Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, 1649004 Lisbon, Portugal
| | - João Perdigão
- iMed.ULisboa–Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, 1649004 Lisbon, Portugal
| | - Georgi M. Dobrikov
- Institute of Organic Chemistry with Centre of Phytochemistry, Acad. G. Bonchev Street, bl. 9, 1113 Sofia, Bulgaria
- Correspondence: (I.M.); (G.M.D.)
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Lázaro-Perona F, Dahdouh E, Sotillo A, Pérez-Blanco V, Villa J, Viedma E, Ruiz-Carrascoso G, Mingorance J. Dissemination of a single ST11 clone of OXA-48-producing Klebsiella pneumoniae within a large polyclonal hospital outbreak determined by genomic sequencing. Microb Genom 2022; 8. [PMID: 35394416 PMCID: PMC9453077 DOI: 10.1099/mgen.0.000808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The population structure of a set of OXA-48-producing Klebsiella pneumoniae isolates belonging to sequence type 11 (ST11 Kp-OXA) and obtained from two hospitals in Madrid in the period from 2012 to 2015 was studied by genome sequencing. Overall, 97 ST11 Kp-OXA isolates were sequenced and their population structure and demography were studied by Bayesian phylodynamic analysis using core-genome SNVs. In total, 92 isolates were from Hospital La Paz, 57 of them from two selected units. The remaining five isolates were from different units of Hospital Doce de Octubre. Altogether, 96 out of the 97 ST11 Kp-OXA isolates could be ascribed to a single lineage that evolved into three sublineages. Demographic inference showed an expansion of the ST11 Kp-OXA in the first half of 2013 in agreement with the registered incidences. Dated phylogeny showed transmission clusters within hospital wards, between wards and between hospitals. The ST11 Kp-OXA outbreak in Hospital La Paz was largely due to the expansion of a single clone that was transmitted between different units and to Hospital Doce de Octubre. This clone diverged into three sub-lineages and spread out following a mixed mode of neutral core-genome evolution with some features of antibiotic selection, frequent large deletions and plasmid loss and gain events.
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Affiliation(s)
- Fernando Lázaro-Perona
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| | - Elias Dahdouh
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| | - Alma Sotillo
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| | - Verónica Pérez-Blanco
- Servicio de Medicina Preventiva, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| | - Jennifer Villa
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Imas12, Avenida de Córdoba sn, Madrid 28041, Spain
| | - Esther Viedma
- Servicio de Microbiología, Hospital Universitario 12 de Octubre, Imas12, Avenida de Córdoba sn, Madrid 28041, Spain
| | - Guillermo Ruiz-Carrascoso
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
| | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana 261, 28046 Madrid, Spain
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