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Raghuram V, Petit RA, Karol Z, Mehta R, Weissman DB, Read TD. Average nucleotide identity-based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome. mSystems 2024; 9:e0014324. [PMID: 38934646 DOI: 10.1128/msystems.00143-24] [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: 01/29/2024] [Accepted: 04/16/2024] [Indexed: 06/28/2024] Open
Abstract
Staphylococcus aureus causes both hospital- and community-acquired infections in humans worldwide. Due to the high incidence of infection, S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole-genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of average nucleotide identity revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10%-95% of genomes) could be divided into those closely linked to strain background ("strain-concentrated") and those highly variable within strains ("strain-diffuse"). Non-core genes had different patterns of chromosome location. Notably, strain-diffuse genes were associated with prophages; strain-concentrated genes were associated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic resistance genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core, and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions. IMPORTANCE We analyzed the genomic diversity of Staphylococcus aureus, a globally prevalent bacterial species that causes serious infections in humans. Our goal was to build a genetic picture of the different strains of S. aureus and which genes may be associated with them. We reprocessed >84,000 genomes and subsampled to remove redundancy. We found that individual samples sharing >99.5% of their genome could be grouped into strains. We also showed that a portion of genes that are present in intermediate frequency in the species are strongly associated with some strains but completely absent from others, suggesting a role in strain specificity. This work lays the foundation for understanding individual gene histories of the S. aureus species and also outlines strategies for processing large bacterial genomic data sets.
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Affiliation(s)
- Vishnu Raghuram
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Robert A Petit
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Zach Karol
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | - Rohan Mehta
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | | | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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2
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Batisti Biffignandi G, Chindelevitch L, Corbella M, Feil EJ, Sassera D, Lees JA. Optimising machine learning prediction of minimum inhibitory concentrations in Klebsiella pneumoniae. Microb Genom 2024; 10:001222. [PMID: 38529944 PMCID: PMC10995625 DOI: 10.1099/mgen.0.001222] [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: 11/23/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
Minimum Inhibitory Concentrations (MICs) are the gold standard for quantitatively measuring antibiotic resistance. However, lab-based MIC determination can be time-consuming and suffers from low reproducibility, and interpretation as sensitive or resistant relies on guidelines which change over time. Genome sequencing and machine learning promise to allow in silico MIC prediction as an alternative approach which overcomes some of these difficulties, albeit the interpretation of MIC is still needed. Nevertheless, precisely how we should handle MIC data when dealing with predictive models remains unclear, since they are measured semi-quantitatively, with varying resolution, and are typically also left- and right-censored within varying ranges. We therefore investigated genome-based prediction of MICs in the pathogen Klebsiella pneumoniae using 4367 genomes with both simulated semi-quantitative traits and real MICs. As we were focused on clinical interpretation, we used interpretable rather than black-box machine learning models, namely, Elastic Net, Random Forests, and linear mixed models. Simulated traits were generated accounting for oligogenic, polygenic, and homoplastic genetic effects with different levels of heritability. Then we assessed how model prediction accuracy was affected when MICs were framed as regression and classification. Our results showed that treating the MICs differently depending on the number of concentration levels of antibiotic available was the most promising learning strategy. Specifically, to optimise both prediction accuracy and inference of the correct causal variants, we recommend considering the MICs as continuous and framing the learning problem as a regression when the number of observed antibiotic concentration levels is large, whereas with a smaller number of concentration levels they should be treated as a categorical variable and the learning problem should be framed as a classification. Our findings also underline how predictive models can be improved when prior biological knowledge is taken into account, due to the varying genetic architecture of each antibiotic resistance trait. Finally, we emphasise that incrementing the population database is pivotal for the future clinical implementation of these models to support routine machine-learning based diagnostics.
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Affiliation(s)
- Gherard Batisti Biffignandi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, England, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Leonid Chindelevitch
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, England, UK
| | - Marta Corbella
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - John A. Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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Raghuram V, Petit RA, Karol Z, Mehta R, Weissman DB, Read TD. Average Nucleotide Identity based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577756. [PMID: 38352482 PMCID: PMC10862745 DOI: 10.1101/2024.01.29.577756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Staphylococcus aureus causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of core gene Average Nucleotide Identity (ANI) revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10-95% of genomes) could be divided into those closely linked to strain background ("strain-concentrated") and those highly variable within strains ("strain-diffuse"). Non-core genes had different patterns of chromosome location; notably, strain-diffuse associated with prophages, strain-concentrated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions.
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Affiliation(s)
- Vishnu Raghuram
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Robert A Petit
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Zach Karol
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | - Rohan Mehta
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | | | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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Barilar I, Battaglia S, Borroni E, Brandao AP, Brankin A, Cabibbe AM, Carter J, Chetty D, Cirillo DM, Claxton P, Clifton DA, Cohen T, Coronel J, Crook DW, Dreyer V, Earle SG, Escuyer V, Ferrazoli L, Fowler PW, Gao GF, Gardy J, Gharbia S, Ghisi KT, Ghodousi A, Gibertoni Cruz AL, Grandjean L, Grazian C, Groenheit R, Guthrie JL, He W, Hoffmann H, Hoosdally SJ, Hunt M, Iqbal Z, Ismail NA, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle AS, Lalvani A, Lapierre SG, Laurenson IF, Letcher B, Lin WH, Liu C, Liu D, Malone KM, Mandal A, Mansjö M, Calisto Matias DVL, Meintjes G, de Freitas Mendes F, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser KA, Ngcamu D, Nhung HN, Niemann S, Nilgiriwala KS, Nimmo C, O’Donnell M, Okozi N, Oliveira RS, Omar SV, Paton N, Peto TEA, Pinhata JMW, Plesnik S, Puyen ZM, Rabodoarivelo MS, Rakotosamimanana N, Rancoita PMV, Rathod P, Robinson ER, Rodger G, Rodrigues C, Rodwell TC, Roohi A, Santos-Lazaro D, Shah S, Smith G, Kohl TA, Solano W, Spitaleri A, Steyn AJC, Supply P, Surve U, Tahseen S, Thuong NTT, Thwaites G, Todt K, Trovato A, Utpatel C, Van Rie A, Vijay S, Walker AS, Walker TM, Warren R, Werngren J, Wijkander M, Wilkinson RJ, Wilson DJ, Wintringer P, Xiao YX, Yang Y, Yanlin Z, Yao SY, Zhu B. Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach. Nat Commun 2024; 15:488. [PMID: 38216576 PMCID: PMC10786857 DOI: 10.1038/s41467-023-44325-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024] Open
Abstract
The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis. However, molecular diagnostics to date have focused largely on first-line drugs and predicting susceptibilities in a binary manner (classifying strains as either susceptible or resistant). Here, we used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration (MIC) in 15,211 Mycobacterium tuberculosis clinical isolates from 23 countries across five continents. We identified 492 unique MIC-elevating variants across 13 drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.
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Carter J. Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach. RESEARCH SQUARE 2023:rs.3.rs-3378915. [PMID: 37886522 PMCID: PMC10602118 DOI: 10.21203/rs.3.rs-3378915/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis; however, molecular diagnostics to date have focused largely on first-line drugs and predicting binary susceptibilities. We used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration in 15,211 Mycobacterium tuberculosis patient isolates from 23 countries across five continents. This identified 492 unique MIC-elevating variants across thirteen drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.
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Dekhil N, Mardassi H. Genomic changes underpinning the emergence of a successful Mycobacterium tuberculosis Latin American and Mediterranean clonal complex. Front Microbiol 2023; 14:1159994. [PMID: 37425998 PMCID: PMC10325029 DOI: 10.3389/fmicb.2023.1159994] [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: 02/06/2023] [Accepted: 05/26/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction The Latin American and Mediterranean sublineage (L4.3/LAM) is the most common generalist sublineage of Mycobacterium tuberculosis lineage 4 (L4), yet certain L4.3/LAM genotypes appear to be confined to particular geographic regions. This is typically the case of a L4.3/LAM clonal complex (CC), TUN4.3_CC1, which is the most preponderant in Tunisia (61.5% of L4.3/LAM). Methods Here, we used whole-genome sequencing data of 346 globally distributed L4 clinical strains, including 278 L4.3/LAM isolates, to reconstruct the evolutionary history of TUN4.3_CC1 and delineate critical genomic changes underpinning its success. Results and Discussion Phylogenomic coupled to phylogeographic analyses indicated that TUN4.3_CC1 has evolved locally, being confined mainly to North Africa. Maximum likelihood analyses using the site and branch-site models of the PAML package disclosed strong evidence of positive selection in the gene category "cell wall and cell processes" of TUN4.3_CC1. Collectively, the data indicate that TUN4.3_CC1 has inherited several mutations, which could have potentially contributed to its evolutionary success. Of particular interest are amino acid replacements at the esxK and eccC2 genes of the ESX/Type VII secretion system, which were found to be specific to TUN4.3_CC1, being common to almost all isolates. Because of its homoplastic nature, the esxK mutation could potentially have endowed TUN4.3_CC1 with a selective advantage. Moreover, we noticed the occurrence of additional, previously described homoplasic nonsense mutations in ponA1 and Rv0197. The mutation in the latter gene, a putative oxido-reductase, has previously been shown to be correlated with enhanced transmissibility in vivo. In sum, our findings unveiled several features underpinning the success of a locally evolved L4.3/LAM clonal complex, lending further support to the critical role of genes encoded by the ESX/type VII secretion system.
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Hachani A, Giulieri SG, Guérillot R, Walsh CJ, Herisse M, Soe YM, Baines SL, Thomas DR, Cheung SD, Hayes AS, Cho E, Newton HJ, Pidot S, Massey RC, Howden BP, Stinear TP. A high-throughput cytotoxicity screening platform reveals agr-independent mutations in bacteraemia-associated Staphylococcus aureus that promote intracellular persistence. eLife 2023; 12:84778. [PMID: 37289634 DOI: 10.7554/elife.84778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Staphylococcus aureus infections are associated with high mortality rates. Often considered an extracellular pathogen, S. aureus can persist and replicate within host cells, evading immune responses, and causing host cell death. Classical methods for assessing S. aureus cytotoxicity are limited by testing culture supernatants and endpoint measurements that do not capture the phenotypic diversity of intracellular bacteria. Using a well-established epithelial cell line model, we have developed a platform called InToxSa (intracellular toxicity of S. aureus) to quantify intracellular cytotoxic S. aureus phenotypes. Studying a panel of 387 S. aureus bacteraemia isolates, and combined with comparative, statistical, and functional genomics, our platform identified mutations in S. aureus clinical isolates that reduced bacterial cytotoxicity and promoted intracellular persistence. In addition to numerous convergent mutations in the Agr quorum sensing system, our approach detected mutations in other loci that also impacted cytotoxicity and intracellular persistence. We discovered that clinical mutations in ausA, encoding the aureusimine non-ribosomal peptide synthetase, reduced S. aureus cytotoxicity, and increased intracellular persistence. InToxSa is a versatile, high-throughput cell-based phenomics platform and we showcase its utility by identifying clinically relevant S. aureus pathoadaptive mutations that promote intracellular residency.
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Affiliation(s)
- Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Stefano G Giulieri
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Calum J Walsh
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Marion Herisse
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ye Mon Soe
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - David R Thomas
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Infection and Immunity Program, Department of Microbiology and Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Shane Doris Cheung
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Australia
| | - Ashleigh S Hayes
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Australia
| | - Hayley J Newton
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Infection and Immunity Program, Department of Microbiology and Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Sacha Pidot
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Ruth C Massey
- School of Microbiology, University College Cork, Cork, Ireland
- School of Medicine, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute, University of Melbourne, Melbourne, Australia
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Zhou Z, Yi H, Zhou Q, Wang L, Zhu Y, Wang W, Liu Z, Xiong H. Evolution and epidemic success of Mycobacterium tuberculosis in eastern China: evidence from a prospective study. BMC Genomics 2023; 24:241. [PMID: 37147590 PMCID: PMC10161668 DOI: 10.1186/s12864-023-09312-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/14/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Lineage distribution of Mycobacterium tuberculosis (Mtb) isolates is strongly associated with geographically distinct human populations, and its transmission can be further impacted by the bacterial genome. However, the epidemic success of Mtb isolates at an individual level was unknown in eastern China. Knowledge regarding the emergence and transmission of Mtb isolates as well as relevant factors may offer a new solution to curb the spread of the disease. Thus, this study aims to reveal the evolution and epidemic success of Mtb isolates in eastern China. RESULTS Of initial 1040 isolates, 997 were retained after removing duplicates and those with insufficient sequencing depth. Of the final samples, 733 (73.52%) were from Zhejiang Province, and 264 (26.48%) were from Shanghai City. Lineage 2 and lineage 4 accounted for 80.44% and 19.56%, with common ancestors dating around 7017 years ago and 6882 years ago, respectively. Sub-lineage L2.2 (80.34%) contributed the majority of total isolates, followed by L4.4 (8.93%) and L4.5 (8.43%). Additionally, 51 (5.12%) isolates were identified to be multidrug-resistant (MDR), of which 21 (29.17%) were pre-extensively drug-resistant (pre-XDR). One clade harboring katG S315T mutation may date back to 65 years ago and subsequently acquired mutations conferring resistance to another five antibiotic drugs. The prevalence of compensatory mutation was the highest in pre-XDR isolates (76.19%), followed by MDR isolates (47.06%) and other drug-resistant isolates (20.60%). Time-scaled haplotypic density analyses suggested comparable success indices between lineage 2 and lineage 4 (P = 0.306), and drug resistance did not significantly promote the transmission of Mtb isolates (P = 0.340). But for pre-XDR isolates, we found a higher success index in those with compensatory mutations (P = 0.025). Mutations under positive selection were found in genes associated with resistance to second-line injectables (whiB6) and drug tolerance (prpR) in both lineage 2 and lineage 4. CONCLUSIONS Our study demonstrates the population expansion of lineage 2 and lineage 4 in eastern China, with comparable transmission capacity, while accumulation of resistance mutations does not necessarily facilitate the success of Mtb isolates. Compensatory mutations usually accompany drug resistance and significantly contribute to the epidemiological transmission of pre-XDR strains. Prospective molecular surveillance is required to further monitor the emergence and spread of pre-XDR/XDR strains in eastern China.
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Affiliation(s)
- Zonglei Zhou
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Huaiming Yi
- Center for Disease Control and Prevention of Changshan County, 324200, Zhejiang, China
| | - Qingrong Zhou
- Center for Disease Control and Prevention of Jiangshan City, 324100, Zhejiang, China
| | - Luqi Wang
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Yue Zhu
- School of Public Health, Fudan University, Shanghai, 200032, China
| | - Weibing Wang
- School of Public Health, Fudan University, Shanghai, 200032, China.
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, 200032, China.
| | - Zhengwe Liu
- Institute of Tuberculosis Control, Zhejiang Provincial Center for Disease Control and Prevention, 310051, Zhejiang, China.
| | - Haiyan Xiong
- School of Public Health, Fudan University, Shanghai, 200032, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, 200032, China
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White-tailed deer ( Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern. Proc Natl Acad Sci U S A 2023; 120:e2215067120. [PMID: 36719912 PMCID: PMC9963525 DOI: 10.1073/pnas.2215067120] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (WTD) and its ability to transmit from deer to deer raised concerns about the role of WTD in the epidemiology and ecology of the virus. Here, we present a comprehensive cross-sectional study assessing the prevalence, genetic diversity, and evolution of SARS-CoV-2 in WTD in the State of New York (NY). A total of 5,462 retropharyngeal lymph node samples collected from free-ranging hunter-harvested WTD during the hunting seasons of 2020 (Season 1, September to December 2020, n = 2,700) and 2021 (Season 2, September to December 2021, n = 2,762) were tested by SARS-CoV-2 real-time RT-PCR (rRT-PCR). SARS-CoV-2 RNA was detected in 17 samples (0.6%) from Season 1 and in 583 samples (21.1%) from Season 2. Hotspots of infection were identified in multiple confined geographic areas of NY. Sequence analysis of SARS-CoV-2 genomes from 164 samples demonstrated the presence of multiple SARS-CoV-2 lineages and the cocirculation of three major variants of concern (VOCs) (Alpha, Gamma, and Delta) in WTD. Our analysis suggests the occurrence of multiple spillover events (human to deer) of the Alpha and Delta lineages with subsequent deer-to-deer transmission and adaptation of the viruses. Detection of Alpha and Gamma variants in WTD long after their broad circulation in humans in NY suggests that WTD may serve as a wildlife reservoir for VOCs no longer circulating in humans. Thus, implementation of continuous surveillance programs to monitor SARS-CoV-2 dynamics in WTD is warranted, and measures to minimize virus transmission between humans and animals are urgently needed.
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Abdel-Glil MY, Hotzel H, Tomaso H, Didelot X, Brandt C, Seyboldt C, Linde J, Schwarz S, Neubauer H, El-Adawy H. Genomic epidemiology of Campylobacter fetus subsp. venerealis from Germany. Front Vet Sci 2023; 9:1069062. [PMID: 36744226 PMCID: PMC9893283 DOI: 10.3389/fvets.2022.1069062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
Campylobacter fetus subsp. venerealis (Cfv) causes bovine genital campylobacteriosis (BGC), a World Organization for Animal Health (WOAH)-listed trade-relevant disease characterized by severe reproductive losses, such as infertility, early embryonic death and abortion in cattle. BGC has significant economic implications that have prompted several countries to adopt stringent eradication and surveillance measures to contain the disease. In Germany, there has been a low incidence of BGC cases over the past 28 years. This study aimed to illustrate the genomic diversity of German Cfv strains isolated from different federal states in Germany. This study analyzed 63 Cfv strains, collected between 1985 and 2015, by whole-genome sequencing and compared them with genome data of 91 international Cfv isolates. The phylogenetic analysis showed that the Cfv population is genetically conserved and has geographic clusters. In Germany, one phylogenetic lineage comprising all strains was identified. This German lineage was part of a subclade that probably emerged in the nineteenth century and diversified over time. The results of this study point to a non-recurrent cross-border introduction of Cfv in Germany. The BGC control interventions in Germany can be considered successful as no outbreaks were reported since 2015.
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Affiliation(s)
- Mostafa Y. Abdel-Glil
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany,Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany,Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, Egypt,*Correspondence: Mostafa Y. Abdel-Glil ✉
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Christian Brandt
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Christian Seyboldt
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Jörg Linde
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany,Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Hosny El-Adawy
- Friedrich-Loeffler-Institut—Federal Research Institute for Animal Health (FLI), Institute of Bacterial Infections and Zoonoses, Jena, Germany,Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt,Hosny El-Adawy ✉
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11
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Bizarria R, Pietrobon TDC, Ferreira H, Rodrigues A. Polymorphisms of rDNA genes in Cyberlindnera yeast suggest birth-and-death evolution events. FEMS Yeast Res 2023; 23:foad032. [PMID: 37291697 DOI: 10.1093/femsyr/foad032] [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: 01/20/2023] [Revised: 04/28/2023] [Accepted: 06/07/2023] [Indexed: 06/10/2023] Open
Abstract
In eukaryotes, the ribosome machinery is encoded by repeats of the ribosomal RNA genes: 26/28S, 18S, 5.8S, and 5S, structured in tandem arrays and frequently homogenized within a genome. This homogenization is thought to be driven by concerted evolution, evolving as a unit, which contributes to its target as the species barcode in modern taxonomy. However, high heterogeneity of rDNA genes has been reported, including in Saccharomycotina yeasts. Here, we describe the polymorphisms and heterogeneity of D1/D2 domains (26S rRNA) and the intergenic transcribed spacer of a new yeast species with affinities to the genus Cyberlindnera and their evolution. Both regions are not homogenized, failing the prediction of concerted evolution. Phylogenetic network analysis of cloned sequences revealed that Cyberlindnera sp. rDNAs are diverse and evolved by reticulation rather than by bifurcating tree evolution model. Predicted rRNA secondary structures also confirmed structural differences, except for some conserved hairpin loops. We hypothesize that some rDNA is inactive within this species and evolves by birth-and-death rather than concerted evolution. Our findings propel further investigation into the evolution of rDNA genes in yeasts.
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Affiliation(s)
- Rodolfo Bizarria
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
| | - Tatiane de Castro Pietrobon
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
| | - Henrique Ferreira
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
| | - Andre Rodrigues
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, SP 13.506-900, Brazil
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12
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Genetic Features of Mycobacterium avium subsp. paratuberculosis Strains Circulating in the West of France Deciphered by Whole-Genome Sequencing. Microbiol Spectr 2022; 10:e0339222. [PMID: 36445077 PMCID: PMC9769990 DOI: 10.1128/spectrum.03392-22] [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] [Indexed: 12/03/2022] Open
Abstract
Paratuberculosis is a chronic infection of the intestine, mainly the ileum, caused by Mycobacterium avium subsp. paratuberculosis in cattle and other ruminants. This enzootic disease is present worldwide and has a negative impact on the dairy cattle industry. For this subspecies, the current genotyping tools do not provide the needed resolution to investigate the genetic diversity of closely related strains. These limitations can be overcome by the application of whole-genome sequencing (WGS), particularly for clonal populations such as M. avium subsp. paratuberculosis. The purpose of the present study was to undertake a WGS analysis with a panel of 200 animal field M. avium subsp. paratuberculosis strains selected based on a previous large-scale longitudinal study of Prim'Holstein and Normande dairy breeds naturally infected with M. avium subsp. paratuberculosis in the West of France. The pangenome analysis revealed that M. avium subsp. paratuberculosis has a closed pangenome. The phylogeny, based on alignment of 2,786 nonhomoplasic single nucleotide polymorphisms (SNPs), showed that the strain population is structured into three clades independently of the cattle breed or geographic distribution. The increased resolution of phylogeny obtained by WGS confirmed the homoplasic nature of the markers variable-number tandem repeat (VNTR) and short sequence repeat (SSR) used for M. avium subsp. paratuberculosis genotyping. These phylogenetic data also revealed independent introductions of the different genotypes in two main waves since at least 2003. WGS applied to this sampling demonstrated the presence of mixed infections in herds and at the individual animal level. Collectively, the phylogeny results inferred with French isolates compared to M. avium subsp. paratuberculosis isolates from around the world suggest introductions of M. avium subsp. paratuberculosis genotypes through the animal trade. Relationships between genetic traits and epidemiological data can now be investigated to better understand transmission dynamics of the disease. IMPORTANCE Mycobacterium avium subsp. paratuberculosis causes Johne's disease in ruminants, which is present worldwide and has significant negative impacts on the dairy cattle industry and animal welfare. Prevention and control of M. avium subsp. paratuberculosis infection are hampered by knowledge gaps in strain virulence, genotype distribution, and transmission dynamics. This work has revealed new insights into M. avium subsp. paratuberculosis strains currently circulating in western France and how they are related to strains circulating globally. We applied whole-genome sequencing (WGS) to obtain comprehensive information on genome evolution and discrimination of closely related strains. This approach revealed the history of M. avium subsp. paratuberculosis infection in France, refined the pangenomic characteristics of M. avium subsp. paratuberculosis, and demonstrated the existence of mixed infection in animals. Finally, this study identified predominant genotypes, which allow a better understanding of disease transmission dynamics. This information will facilitate tracking of this pathogen on farms and across agricultural regions, thus informing transmission pathways and disease control points.
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Merker M, Rasigade JP, Barbier M, Cox H, Feuerriegel S, Kohl TA, Shitikov E, Klaos K, Gaudin C, Antoine R, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Crudu V, Supply P, Niemann S, Wirth T. Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis. Nat Commun 2022; 13:5105. [PMID: 36042200 PMCID: PMC9426364 DOI: 10.1038/s41467-022-32455-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 08/01/2022] [Indexed: 11/09/2022] Open
Abstract
Transmission-driven multi-/extensively drug resistant (M/XDR) tuberculosis (TB) is the largest single contributor to human mortality due to antimicrobial resistance. A few major clades of the Mycobacterium tuberculosis complex belonging to lineage 2, responsible for high prevalence of MDR-TB in Eurasia, show outstanding transnational distributions. Here, we determined factors underlying the emergence and epidemic spread of the W148 clade by genome sequencing and Bayesian demogenetic analyses of 720 isolates from 23 countries. We dated a common ancestor around 1963 and identified two successive epidemic expansions in the late 1980s and late 1990s, coinciding with major socio-economic changes in the post-Soviet Era. These population expansions favored accumulation of resistance mutations to up to 11 anti-TB drugs, with MDR evolving toward additional resistances to fluoroquinolones and second-line injectable drugs within 20 years on average. Timescaled haplotypic density analysis revealed that widespread acquisition of compensatory mutations was associated with transmission success of XDR strains. Virtually all W148 strains harbored a hypervirulence-associated ppe38 gene locus, and incipient recurrent emergence of prpR mutation-mediated drug tolerance was detected. The outstanding genetic arsenal of this geographically widespread M/XDR strain clade represents a “perfect storm” that jeopardizes the successful introduction of new anti-M/XDR-TB antibiotic regimens. An outbreak of the multidrug-resistant Mycobacterium tuberculosis lineage W148 has spread widely across Russia, Central Asia and Europe. Here, the authors use whole genome sequences of ~700 isolates of this lineage collected over ~20 years to analyze its spread, evolution of drug resistance, and impact of compensatory mutations.
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Affiliation(s)
- Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | - Jean-Philippe Rasigade
- EPHE, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Université Lyon 1, ENS de Lyon, Lyon, France
| | - Maxime Barbier
- EPHE, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Helen Cox
- Division of Medical Microbiology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Kadri Klaos
- SA TUH United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany.,Lung Clinic Grosshansdorf, German Center for Lung Research (DZL), Airway Research Center North (ARCN), 22927, Großhansdorf, Germany
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Valeriu Crudu
- National TB Reference Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France.
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
| | - Thierry Wirth
- EPHE, PSL University, Paris, France. .,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
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14
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Dreyer V, Mandal A, Dev P, Merker M, Barilar I, Utpatel C, Nilgiriwala K, Rodrigues C, Crook DW, Crook DW, Peto TEA, Walker AS, Hoosdally SJ, Gibertoni Cruz AL, Carter J, Earle S, Kouchaki S, Yang Y, Walker TM, Fowler PW, Wilson D, Clifton DA, Iqbal Z, Hunt M, Knaggs J, Cirillo DM, Borroni E, Battaglia S, Ghodousi A, Spitaleri A, Cabibbe A, Tahseen S, Nilgiriwala K, Shah S, Rodrigues C, Kambli P, Surve U, Khot R, Niemann S, Kohl T, Merker M, Hoffmann H, Todt K, Plesnik S, Ismail N, Omar SV, Ngcamu LJD, Okozi N, Yao SY, Thwaites G, Thuong TNT, Ngoc NH, Srinivasan V, Moore D, Coronel J, Solano W, Gao GF, He G, Zhao Y, Ma A, Liu C, Zhu B, Laurenson I, Claxton P, Wilkinson RJ, Koch A, Lalvani A, Posey J, Gardy J, Werngren J, Paton N, Jou R, Wu MH, Xiao YX, Ferrazoli L, de Oliveira RS, Millard J, Warren R, Van Rie A, Lapierre SG, Rabodoarivelo MS, Rakotosamimanana N, Nimmo C, Musser K, Escuyer V, Cohen T, Rasigade JP, Wirth T, Mistry N, Niemann S. High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region. Genome Med 2022; 14:95. [PMID: 35989319 PMCID: PMC9394022 DOI: 10.1186/s13073-022-01076-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/20/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a serious health problem in India, also contributing to one-fourth of the global MDR tuberculosis (TB) burden. About 36% of the MDR MTBC strains are reported fluoroquinolone (FQ) resistant leading to high pre-extensively drug-resistant (pre-XDR) and XDR-TB (further resistance against bedaquiline and/or linezolid) rates. Still, factors driving the MDR/pre-XDR epidemic in India are not well defined.
Methods
In a retrospective study, we analyzed 1852 consecutive MTBC strains obtained from patients from a tertiary care hospital laboratory in Mumbai by whole genome sequencing (WGS). Univariate and multivariate statistics was used to investigate factors associated with pre-XDR. Core genome multi locus sequence typing, time scaled haplotypic density (THD) method and homoplasy analysis were used to analyze epidemiological success, and positive selection in different strain groups, respectively.
Results
In total, 1016 MTBC strains were MDR, out of which 703 (69.2%) were pre-XDR and 45 (4.4%) were XDR. Cluster rates were high among MDR (57.8%) and pre-XDR/XDR (79%) strains with three dominant L2 (Beijing) strain clusters (Cl 1–3) representing half of the pre-XDR and 40% of the XDR-TB cases. L2 strains were associated with pre-XDR/XDR-TB (P < 0.001) and, particularly Cl 1–3 strains, had high first-line and FQ resistance rates (81.6–90.6%). Epidemic success analysis using THD showed that L2 strains outperformed L1, L3, and L4 strains in short- and long-term time scales. More importantly, L2 MDR and MDR + strains had higher THD success indices than their not-MDR counterparts. Overall, compensatory mutation rates were highest in L2 strains and positive selection was detected in genes of L2 strains associated with drug tolerance (prpB and ppsA) and virulence (Rv2828c). Compensatory mutations in L2 strains were associated with a threefold increase of THD indices, suggesting improved transmissibility.
Conclusions
Our data indicate a drastic increase of FQ resistance, as well as emerging bedaquiline resistance which endangers the success of newly endorsed MDR-TB treatment regimens. Rapid changes in treatment and control strategies are required to contain transmission of highly successful pre-XDR L2 strains in the Mumbai Metropolitan region but presumably also India-wide.
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15
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Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches. mSystems 2022; 7:e0037822. [PMID: 35862809 PMCID: PMC9426533 DOI: 10.1128/msystems.00378-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human and animal pathogen, colonizing diverse ecological niches within its hosts. Predicting whether an isolate will infect a specific host and its subsequent clinical fate remains unknown. In this study, we investigated the S. aureus pangenome using a curated set of 356 strains, spanning a wide range of hosts, origins, and clinical display and antibiotic resistance profiles. We used genome-wide association study (GWAS) and random forest (RF) algorithms to discriminate strains based on their origins and clinical sources. Here, we show that the presence of sak and scn can discriminate strains based on their host specificity, while other genes such as mecA are often associated with virulent outcomes. Both GWAS and RF indicated the importance of intergenic regions (IGRs) and coding DNA sequence (CDS) but not sRNAs in forecasting an outcome. Additional transcriptomic analyses performed on the most prevalent clonal complex 8 (CC8) clonal types, in media mimicking nasal colonization or bacteremia, indicated three RNAs as potential RNA markers to forecast infection, followed by 30 others that could serve as infection severity predictors. Our report shows that genetic association and transcriptomics are complementary approaches that will be combined in a single analytical framework to improve our understanding of bacterial pathogenesis and ultimately identify potential predictive molecular markers. IMPORTANCE Predicting the outcome of bacterial colonization and infections, based on extensive genomic and transcriptomic data from a given pathogen, would be of substantial help for clinicians in treating and curing patients. In this report, genome-wide association studies and random forest algorithms have defined gene combinations that differentiate human from animal strains, colonization from diseases, and nonsevere from severe diseases, while it revealed the importance of IGRs and CDS, but not small RNAs (sRNAs), in anticipating an outcome. In addition, transcriptomic analyses performed on the most prevalent clonal types, in media mimicking either nasal colonization or bacteremia, revealed significant differences and therefore potent RNA markers. Overall, the use of both genomic and transcriptomic data in a single analytical framework can enhance our understanding of bacterial pathogenesis.
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16
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Le CT, Price EP, Sarovich DS, Nguyen TTA, Powell D, Vu-Khac H, Kurtböke Dİ, Knibb W, Chen SC, Katouli M. Comparative genomics of Nocardia seriolae reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam. Microb Genom 2022; 8. [PMID: 35786440 PMCID: PMC9455698 DOI: 10.1099/mgen.0.000845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between 2010 and 2015, nocardiosis outbreaks caused by Nocardia seriolae affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 N. seriolae strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics. PFGE identified a single cluster amongst all Vietnamese strains that was distinct from the Taiwanese strains. Like the PFGE findings, phylogenomic and SNP genotyping analyses revealed that all Vietnamese N. seriolae strains belonged to a single, unique clade. Strains fell into two subclades that differed by 103 SNPs, with almost no diversity within clades (0–5 SNPs). There was no association between geographical origin and subclade placement, suggesting frequent N. seriolae transmission between Vietnamese mariculture facilities during the outbreaks. The Vietnamese strains shared a common ancestor with strains from Japan and China, with the closest strain, UTF1 from Japan, differing by just 220 SNPs from the Vietnamese ancestral node. Draft Vietnamese genomes range from 7.55 to 7.96 Mbp in size, have an average G+C content of 68.2 % and encode 7 602–7958 predicted genes. Several putative virulence factors were identified, including genes associated with host cell adhesion, invasion, intracellular survival, antibiotic and toxic compound resistance, and haemolysin biosynthesis. Our findings provide important new insights into the epidemiology and pathogenicity of N. seriolae and will aid future vaccine development and disease management strategies, with the ultimate goal of nocardiosis-free aquaculture.
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Affiliation(s)
- Cuong T. Le
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Institute for Aquaculture, Nha Trang University, Nha Trang, Vietnam
| | - Erin P. Price
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Derek S. Sarovich
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Thu T. A. Nguyen
- Institute for Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
| | - Daniel Powell
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Hung Vu-Khac
- Central Vietnam Veterinary Institute, Nha Trang, Vietnam
| | - D. İpek Kurtböke
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Wayne Knibb
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan, ROC
| | - Mohammad Katouli
- Centre for Bioinnovation, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- *Correspondence: Mohammad Katouli,
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Alisoltani A, Jaroszewski L, Iyer M, Iranzadeh A, Godzik A. Increased Frequency of Indels in Hypervariable Regions of SARS-CoV-2 Proteins—A Possible Signature of Adaptive Selection. Front Genet 2022; 13:875406. [PMID: 35719386 PMCID: PMC9201826 DOI: 10.3389/fgene.2022.875406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Most attention in the surveillance of evolving SARS-CoV-2 genome has been centered on nucleotide substitutions in the spike glycoprotein. We show that, as the pandemic extends into its second year, the numbers and ratio of genomes with in-frame insertions and deletions (indels) increases significantly, especially among the variants of concern (VOCs). Monitoring of the SARS-CoV-2 genome evolution shows that co-occurrence (i.e., highly correlated presence) of indels, especially deletions on spike N-terminal domain and non-structural protein 6 (NSP6) is a shared feature in several VOCs such as Alpha, Beta, Delta, and Omicron. Indels distribution is correlated with spike mutations associated with immune escape and growth in the number of genomes with indels coincides with the increasing population resistance due to vaccination and previous infections. Indels occur most frequently in the spike, but also in other proteins, especially those involved in interactions with the host immune system. We also showed that indels concentrate in regions of individual SARS-CoV-2 proteins known as hypervariable regions (HVRs) that are mostly located in specific loop regions. Structural analysis suggests that indels remodel viral proteins’ surfaces at common epitopes and interaction interfaces, affecting the virus’ interactions with host proteins. We hypothesize that the increased frequency of indels, the non-random distribution of them and their independent co-occurrence in several VOCs is another mechanism of response to elevated global population immunity.
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Affiliation(s)
- Arghavan Alisoltani
- Biosciences Division, School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Lukasz Jaroszewski
- Biosciences Division, School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Mallika Iyer
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Adam Godzik
- Biosciences Division, School of Medicine, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Adam Godzik,
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On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy. Viruses 2022; 14:v14030580. [PMID: 35336987 PMCID: PMC8951735 DOI: 10.3390/v14030580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Trentino is an Italian province with a tourism-based economy, bordering the regions of Lombardy and Veneto, where the two earliest and largest outbreaks of COVID-19 occurred in Italy. The earliest cases in Trentino were reported in the first week of March 2020, with most of the cases occurring in the winter sport areas in the Dolomites mountain range. The number of reported cases decreased over the summer months and was followed by a second wave in the autumn and winter of 2020. Methods: we performed high-coverage Oxford Nanopore sequencing of 253 positive SARS-CoV-2 swabs collected in Trentino between March and December 2020. Results: in this work, we analyzed genome sequences to trace the routes through which the virus entered the area, and assessed whether the autumnal resurgence could be attributed to lineages persisting undetected during summer, or as a consequence of new introductions. Conclusions: Comparing the draft genomes analyzed with a large selection of European sequences retrieved from GISAID we found that multiple introductions of the virus occurred at the early stage of the epidemics; the two epidemic waves were unrelated; the second wave was due to reintroductions of the virus in summer when traveling restrictions were uplifted.
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Raghuram V, Alexander AM, Loo HQ, Petit RA, Goldberg JB, Read TD. Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations. Microbiol Spectr 2022; 10:e0133421. [PMID: 35044202 PMCID: PMC8768832 DOI: 10.1128/spectrum.01334-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/03/2022] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a prominent nosocomial pathogen that causes several life-threatening diseases, such as pneumonia and bacteremia. S. aureus modulates the expression of its arsenal of virulence factors through sensing and integrating responses to environmental signals. The agr (accessory gene regulator) quorum sensing (QS) system is a major regulator of virulence phenotypes in S. aureus. There are four agr specificity groups each with a different autoinducer peptide sequence encoded by the agrD gene. Although agr is critical for the expression of many toxins, paradoxically, S. aureus strains often have nonfunctional agr activity due to loss-of-function mutations in the four-gene agr operon. To understand patterns in agr variability across S. aureus, we undertook a species-wide genomic investigation. We developed a software tool (AgrVATE; https://github.com/VishnuRaghuram94/AgrVATE) for typing and detecting frameshift mutations in the agr operon. In an analysis of over 40,000 S. aureus genomes, we showed a close association between agr type and S. aureus clonal complex. We also found a strong linkage between agrBDC alleles (encoding the peptidase, autoinducing peptide itself, and peptide sensor, respectively) but not agrA (encoding the response regulator). More than 5% of the genomes were found to have frameshift mutations in the agr operon. While 52% of these frameshifts occurred only once in the entire species, we observed cases where the recurring mutations evolved convergently across different clonal lineages with no evidence of long-term phylogenetic transmission, suggesting that strains with agr frameshifts were evolutionarily short-lived. Overall, genomic analysis of agr operon suggests evolution through multiple processes with functional consequences that are not fully understood. IMPORTANCE Staphylococcus aureus is a globally pervasive pathogen that produces a plethora of toxic molecules that can harm host immune cells. Production of these toxins is mainly controlled by an active agr quorum-sensing system, which senses and responds to bacterial cell density. However, there are many reports of S. aureus strains with genetic changes leading to impaired agr activity that are often found during chronic bloodstream infections and may be associated with increased disease severity. We developed an open-source software called AgrVATE to type agr systems and identify mutations. We used AgrVATE for a species-wide genomic survey of S. aureus, finding that more than 5% of strains in the public database had nonfunctional agr systems. We also provided new insights into the evolution of these genetic mutations in the agr system. Overall, this study contributes to our understanding of a common but relatively understudied means of virulence regulation in S. aureus.
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Affiliation(s)
- Vishnu Raghuram
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Ashley M. Alexander
- Population Biology, Ecology, and Evolution Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Hui Qi Loo
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Robert A. Petit
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Joanna B. Goldberg
- Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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Species-Scale Genomic Analysis of Staphylococcus aureus Genes Influencing Phage Host Range and Their Relationships to Virulence and Antibiotic Resistance Genes. mSystems 2022; 7:e0108321. [PMID: 35040700 PMCID: PMC8765062 DOI: 10.1128/msystems.01083-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Phage therapy has been proposed as a possible alternative treatment for infections caused by the ubiquitous bacterial pathogen Staphylococcus aureus. However, successful therapy requires understanding the genetic basis of host range—the subset of strains in a species that could be killed by a particular phage. We searched diverse sets of S. aureus public genome sequences against a database of genes suggested from prior studies to influence host range to look for patterns of variation across the species. We found that genes encoding biosynthesis of molecules that were targets of S. aureus phage adsorption to the outer surface of the cell were the most conserved in the pangenome. Putative phage resistance genes that were core components of the pangenome genes had similar nucleotide diversity, ratio of nonsynonymous to synonymous substitutions, and functionality (measured by delta-bitscore) to other core genes. However, phage resistance genes that were not part of the core genome were significantly less consistent with the core genome phylogeny than all noncore genes in this set, suggesting more frequent movement between strains by horizontal gene transfer. Only superinfection immunity genes encoded by temperate phages inserted in the genome correlated with experimentally determined temperate phage resistance. Taken together, these results suggested that, while phage adsorption genes are heavily conserved in the S. aureus species, HGT may play a significant role in strain-specific evolution of host range patterns. IMPORTANCEStaphylococcus aureus is a widespread, hospital- and community-acquired pathogen that is commonly antibiotic resistant. It causes diverse diseases affecting both the skin and internal organs. Its ubiquity, antibiotic resistance, and disease burden make new therapies urgent, such as phage therapy, in which viruses specific to infecting bacteria clear infection. S. aureus phage host range not only determines whether phage therapy will be successful by killing bacteria but also horizontal gene transfer through transduction of host genetic material by phages. In this work, we comprehensively reviewed existing literature to build a list of S. aureus phage resistance genes and searched our database of almost 43,000 S. aureus genomes for these genes to understand their patterns of evolution, finding that prophages’ superinfection immunity correlates best with phage resistance and HGT. These findings improved our understanding of the relationship between known phage resistance genes and phage host range in the species.
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21
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Castelán-Sánchez HG, Martínez-Castilla LP, Sganzerla-Martínez G, Torres-Flores J, López-Leal G. Genome Evolution and Early Introductions of the SARS-CoV-2 Omicron Variant in Mexico. Virus Evol 2022; 8:veac109. [PMID: 36582501 PMCID: PMC9793848 DOI: 10.1093/ve/veac109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/15/2022] [Accepted: 11/30/2022] [Indexed: 12/04/2022] Open
Abstract
A new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), named Omicron (Pango lineage designation B.1.1.529), was first reported to the World Health Organization by South African health authorities on 24 November 2021. The Omicron variant possesses numerous mutations associated with increased transmissibility and immune escape properties. In November 2021, Mexican authorities reported Omicron's presence in the country. In this study, we infer the first introductory events of Omicron and the impact that human mobility has had on the spread of the virus. We also evaluated the adaptive evolutionary processes in Mexican SARS-CoV-2 genomes during the first month of the circulation of Omicron. We inferred 160 introduction events of Omicron in Mexico since its first detection in South Africa; subsequently, after the first introductions there was an evident increase in the prevalence of SARS-CoV-2 during January. This higher prevalence of the novel variant resulted in a peak of reported cases; on average 6 weeks after, a higher mobility trend was reported. During the peak of cases in the country from January to February 2022, the Omicron BA.1.1 sub-lineage dominated, followed by the BA.1 and BA.15 sub-lineages. Additionally, we identified the presence of diversifying natural selection in the genomes of Omicron and found six non-synonymous mutations in the receptor binding domain of the spike protein, all of them related to evasion of the immune response. In contrast, the other proteins in the genome are highly conserved; however, we identified homoplasic mutations in non-structural proteins, indicating a parallel evolution.
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Affiliation(s)
| | - León P Martínez-Castilla
- Programa de Investigadoras e Investigadores por México, Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Ciudad de México C.P. 03940, México
| | - Gustavo Sganzerla-Martínez
- Laboratory of Immunity, Shantou University Medical College, Shantou, People’s Republic of China, No. 22 Xinling Road Shantou, Guangdong Province 515041, China
- Department of Microbiology and Immunology, Dalhousie University, Halifax, 5850 College street, Halifax, NS B3H 4R2, Canada
| | - Jesús Torres-Flores
- Programa de Investigadoras e Investigadores por México, Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Ciudad de México C.P. 03940, México
- Laboratorio Nacional de Vacunología y Virus Tropicales, Escuela Nacional de Ciencias Biológicas-IPN, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tómas, Alcaldía Miguel Hidalgo CDMX C.P. 11340, México
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22
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Lorente-Leal V, Farrell D, Romero B, Álvarez J, de Juan L, Gordon SV. Performance and Agreement Between WGS Variant Calling Pipelines Used for Bovine Tuberculosis Control: Toward International Standardization. Front Vet Sci 2022; 8:780018. [PMID: 34970617 PMCID: PMC8712436 DOI: 10.3389/fvets.2021.780018] [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: 09/20/2021] [Accepted: 11/25/2021] [Indexed: 11/29/2022] Open
Abstract
Whole genome sequencing (WGS) and allied variant calling pipelines are a valuable tool for the control and eradication of infectious diseases, since they allow the assessment of the genetic relatedness of strains of animal pathogens. In the context of the control of tuberculosis (TB) in livestock, mainly caused by Mycobacterium bovis, these tools offer a high-resolution alternative to traditional molecular methods in the study of herd breakdown events. However, despite the increased use and efforts in the standardization of WGS methods in human tuberculosis around the world, the application of these WGS-enabled approaches to control TB in livestock is still in early development. Our study pursued an initial evaluation of the performance and agreement of four publicly available pipelines for the analysis of M. bovis WGS data (vSNP, SNiPgenie, BovTB, and MTBseq) on a set of simulated Illumina reads generated from a real-world setting with high TB prevalence in cattle and wildlife in the Republic of Ireland. The overall performance of the evaluated pipelines was high, with recall and precision rates above 99% once repeat-rich and problematic regions were removed from the analyses. In addition, when the same filters were applied, distances between inferred phylogenetic trees were similar and pairwise comparison revealed that most of the differences were due to the positioning of polytomies. Hence, under the studied conditions, all pipelines offer similar performance for variant calling to underpin real-world studies of M. bovis transmission dynamics.
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Affiliation(s)
- Víctor Lorente-Leal
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain.,Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Beatriz Romero
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain.,Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Julio Álvarez
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain.,Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Lucía de Juan
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain.,Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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23
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White AE, de-Dios T, Carrión P, Bonora GL, Llovera L, Cilli E, Lizano E, Khabdulina MK, Tleugabulov DT, Olalde I, Marquès-Bonet T, Balloux F, Pettener D, van Dorp L, Luiselli D, Lalueza-Fox C. Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome. BIOLOGY 2021; 10:biology10121324. [PMID: 34943238 PMCID: PMC8698332 DOI: 10.3390/biology10121324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 11/16/2022]
Abstract
The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.
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Affiliation(s)
- Anna E. White
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Toni de-Dios
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Pablo Carrión
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Gian Luca Bonora
- ISMEO—International Association for Mediterranean and East Studies, 00186 Rome, Italy;
| | - Laia Llovera
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy;
| | - Esther Lizano
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Maral K. Khabdulina
- K.A. Akishev Institute of Archaeology, L.N. Gumilev Eurasian National University, Nur-Sultan 010000, Kazakhstan; (M.K.K.); (D.T.T.)
| | - Daniyar T. Tleugabulov
- K.A. Akishev Institute of Archaeology, L.N. Gumilev Eurasian National University, Nur-Sultan 010000, Kazakhstan; (M.K.K.); (D.T.T.)
| | - Iñigo Olalde
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Centro de Investigación “Lascaray” Ikergunea, BIOMICs Research Group, Universidad del País Vasco, 01006 Vitoria-Gasteiz, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, Department of Genetics Evolution & Environment, University College London, London WC1E 6BT, UK;
| | - Davide Pettener
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
| | - Lucy van Dorp
- UCL Genetics Institute, Department of Genetics Evolution & Environment, University College London, London WC1E 6BT, UK;
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy;
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.E.W.); (T.d.-D.); (P.C.); (L.L.); (E.L.); (I.O.); (T.M.-B.)
- Correspondence: (L.v.D.); (D.L.); (C.L.-F.); Tel.: +34-617-277-935 (C.L.-F.)
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24
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Edwards DJ, Duchene S, Pope B, Holt KE. SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments. Microb Genom 2021; 7:000694. [PMID: 34874243 PMCID: PMC8767352 DOI: 10.1099/mgen.0.000694] [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: 01/18/2023] Open
Abstract
Homoplasic SNPs are considered important signatures of strong (positive) selective pressure, and hence of adaptive evolution for clinically relevant traits such as antibiotic resistance and virulence. Here we present a new tool, SNPPar, for efficient detection and analysis of homoplasic SNPs from large whole genome sequencing datasets (>1000 isolates and/or >100 000 SNPs). SNPPar takes as input an SNP alignment, tree and annotated reference genome, and uses a combination of simple monophyly tests and ancestral state reconstruction (ASR, via TreeTime) to assign mutation events to branches and identify homoplasies. Mutations are annotated at the level of codon and gene, to facilitate analysis of convergent evolution. Testing on simulated data (120 Mycobacterium tuberculosis alignments representing local and global samples) showed SNPPar can detect homoplasic SNPs with very high specificity (zero false-positives in all tests) and high sensitivity (zero false-negatives in 89 % of tests). SNPPar analysis of three empirically sampled datasets (Elizabethkingia anophelis, Burkholderia dolosa and M. tuberculosis) produced results that were in concordance with previous studies, in terms of both individual homoplasies and evidence of convergence at the codon and gene levels. SNPPar analysis of a simulated alignment of ~64 000 genome-wide SNPs from 2000 M. tuberculosis genomes took ~23 min and ~2.6 GB of RAM to generate complete annotated results on a laptop. This analysis required ASR be conducted for only 1.25 % of SNPs, and the ASR step took ~23 s and 0.4 GB of RAM. SNPPar automates the detection and annotation of homoplasic SNPs efficiently and accurately from large SNP alignments. As demonstrated by the examples included here, this information can be readily used to explore the role of homoplasy in parallel and/or convergent evolution at the level of nucleotide, codon and/or gene.
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Affiliation(s)
- David J. Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Sebastián Duchene
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria, Australia
| | - Bernard Pope
- Melbourne Bioinformatics, The University of Melbourne, 187 Grattan Street, Carlton, Victoria, Australia,Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, Victoria, Australia,Department of Medicine, Central Clinical School, Monash University, Clayton, Victoria, Australia,Department of Surgery (Royal Melbourne Hospital), Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Victoria, Australia
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia,Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK,*Correspondence: Kathryn E. Holt,
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25
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Wan Y, Mills E, Leung RC, Vieira A, Zhi X, Croucher NJ, Woodford N, Jauneikaite E, Ellington MJ, Sriskandan S. Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom. Microb Genom 2021; 7:000702. [PMID: 34860151 PMCID: PMC8767348 DOI: 10.1099/mgen.0.000702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance in enteric or urinary Escherichia coli is a risk factor for invasive E. coli infections. Due to widespread trimethoprim resistance amongst urinary E. coli and increased bacteraemia incidence, a national recommendation to prescribe nitrofurantoin for uncomplicated urinary tract infection was made in 2014. Nitrofurantoin resistance is reported in <6% urinary E. coli isolates in the UK, however, mechanisms underpinning nitrofurantoin resistance in these isolates remain unknown. This study aimed to identify the genetic basis of nitrofurantoin resistance in urinary E. coli isolates collected from north west London and then elucidate resistance-associated genetic alterations in available UK E. coli genomes. As a result, an algorithm was developed to predict nitrofurantoin susceptibility. Deleterious mutations and gene-inactivating insertion sequences in chromosomal nitroreductase genes nfsA and/or nfsB were identified in genomes of nine confirmed nitrofurantoin-resistant urinary E. coli isolates and additional 11 E. coli isolates that were highlighted by the prediction algorithm and subsequently validated to be nitrofurantoin-resistant. Eight categories of allelic changes in nfsA, nfsB, and the associated gene ribE were detected in 12412 E. coli genomes from the UK. Evolutionary analysis of these three genes revealed homoplasic mutations and explained the previously reported order of stepwise mutations. The mobile gene complex oqxAB, which is associated with reduced nitrofurantoin susceptibility, was identified in only one of the 12412 genomes. In conclusion, mutations and insertion sequences in nfsA and nfsB were leading causes of nitrofurantoin resistance in UK E. coli. As nitrofurantoin exposure increases in human populations, the prevalence of nitrofurantoin resistance in carriage E. coli isolates and those from urinary and bloodstream infections should be monitored.
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Affiliation(s)
- Yu Wan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ewurabena Mills
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Rhoda C.Y. Leung
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Present address: Department of Microbiology, Queen Mary Hospital, Hong Kong S.A.R., PR China
| | - Ana Vieira
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Xiangyun Zhi
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Nicholas J. Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Matthew J. Ellington
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, Colindale, London, United Kingdom
| | - Shiranee Sriskandan
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
- *Correspondence: Shiranee Sriskandan,
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26
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de-Dios T, Carrión P, Olalde I, Llovera Nadal L, Lizano E, Pàmies D, Marques-Bonet T, Balloux F, van Dorp L, Lalueza-Fox C. Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts. iScience 2021; 24:103021. [PMID: 34527890 PMCID: PMC8430385 DOI: 10.1016/j.isci.2021.103021] [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: 02/26/2021] [Revised: 05/14/2021] [Accepted: 08/19/2021] [Indexed: 12/04/2022] Open
Abstract
Ancient pathogen genomics is an emerging field allowing reconstruction of past epidemics. The demise of post-contact American populations may, at least in part, have been caused by paratyphoid fever brought by Europeans. We retrieved genome-wide data from two Spanish soldiers who were besieging the city of Barcelona in 1652, during the Reapers' War. Their ancestry derived from the Basque region and Sardinia, respectively, (at that time, this island belonged to the Spanish kingdom). Despite the proposed plague epidemic, we could not find solid evidence for the presence of the causative plague agent in these individuals. However, we retrieved from one individual a substantial fraction of the Salmonella enterica serovar Paratyphi C lineage linked to paratyphoid fever in colonial period Mexico. Our results support a growing body of evidence that Paratyphi C enteric fever was more prevalent in Europe and the Americas in the past than it is today.
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Affiliation(s)
- Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Pablo Carrión
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | | | - Esther Lizano
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
| | - Dídac Pàmies
- Antequem. Arqueologia-Patrimoni Cultural, 08301 Mataró, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), 08003 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
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In vivo evolution of an emerging zoonotic bacterial pathogen in an immunocompromised human host. Nat Commun 2021; 12:4495. [PMID: 34301946 PMCID: PMC8302680 DOI: 10.1038/s41467-021-24668-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 06/24/2021] [Indexed: 11/08/2022] Open
Abstract
Zoonotic transfer of animal pathogens to human hosts can generate novel agents, but the genetic events following such host jumps are not well studied. Here we characterize the mechanisms driving adaptive evolution of the emerging zoonotic pathogen Bordetella hinzii in a patient with interleukin-12 receptor β1 deficiency. Genomic sequencing of 24 B. hinzii isolates cultured from blood and stool over 45 months revealed a clonal lineage that had undergone extensive within-host genetic and phenotypic diversification. Twenty of 24 isolates shared an E9G substitution in the DNA polymerase III ε-subunit active site, resulting in a proofreading deficiency. Within this proofreading-deficient clade, multiple lineages with mutations in DNA repair genes and altered mutational spectra emerged and dominated clinical cultures for more than 12 months. Multiple enzymes of the tricarboxylic acid cycle and gluconeogenesis pathways were repeatedly mutated, suggesting rapid metabolic adaptation to the human environment. Furthermore, an excess of G:C > T:A transversions suggested that oxidative stress shaped genetic diversification during adaptation. We propose that inactivation of DNA proofreading activity in combination with prolonged, but sub-lethal, oxidative attack resulting from the underlying host immunodeficiency facilitated rapid genomic adaptation. These findings suggest a fundamental role for host immune phenotype in shaping pathogen evolution following zoonotic infection. Bordetella hinzii is an emerging pathogen with zoonotic risk to humans, known to be able to cause respiratory tract infection, bacteremia and endocarditis. Here, applying whole genome sequencing to bacterial isolates, the authors characterize the mechanisms driving adaptive evolution in B. hinzii in a patient with interleukin-12 receptor β1 deficiency, suggesting a role for host immune phenotype in shaping within-host pathogen evolution following zoonotic infection.
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Akkiz H. Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development. Front Med (Lausanne) 2021; 8:636532. [PMID: 34026780 PMCID: PMC8137987 DOI: 10.3389/fmed.2021.636532] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/25/2021] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of the coronavirus disease 2019 (COVID-19), has been identified in China in late December 2019. SARS-CoV-2 is an enveloped, positive-sense, single-stranded RNA betacoronavirus of the Coronaviridae family. Coronaviruses have genetic proofreading mechanism that corrects copying mistakes and thus SARS-CoV-2 genetic diversity is extremely low. Despite lower mutation rate of the virus, researchers have detected a total of 12,706 mutations in the SARS-CoV-2 genome, the majority of which were single nucleotide polymorphisms. Sequencing data revealed that the SARS-CoV-2 accumulates two-single nucleotide mutations per month in its genome. Recently, an amino acid aspartate (D) to glycine (G) (D614G) mutation due to an adenine to guanine nucleotide change at position 23,403 at the 614th amino-acid position of the spike protein in the original reference genotype has been identified. The SARS-CoV-2 viruses that carry the spike protein D614G mutation have become dominant variant around the world. The D614G mutation has been found to be associated with 3 other mutations in the spike protein. Clinical and pseudovirus experimental studies have demonstrated that the spike protein D614G mutation alters the virus phenotype. However, the impact of the mutation on the rate of transmission between people, disease severity and the vaccine and therapeutic development remains unclear. Three variants of SARS-CoV-2 have recently been identified. They are B.1.1.7 (UK) variant, B.1.351 (N501Y.V2, South African) variant and B.1.1.28 (Brazilian) variant. Epidemiological data suggest that they have a higher transmissibility than the original variant. There are reports that some vaccines are less efficacious against the B.1.351 variant. This review article discusses the effects of novel mutations in the SARS-CoV-2 genome on transmission, clinical outcomes and vaccine development.
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Affiliation(s)
- Hikmet Akkiz
- Department of Gastroenterology and Hepatology, The University of Çukurova, Adana, Turkey
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Coolen JPM, den Drijver EPM, Verweij JJ, Schildkraut JA, Neveling K, Melchers WJG, Kolwijck E, Wertheim HFL, Kluytmans JAJW, Huynen MA. Genome-wide analysis in Escherichia coli unravels a high level of genetic homoplasy associated with cefotaxime resistance. Microb Genom 2021; 7:000556. [PMID: 33843573 PMCID: PMC8208684 DOI: 10.1099/mgen.0.000556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 03/11/2021] [Indexed: 11/18/2022] Open
Abstract
Cefotaxime (CTX) is a third-generation cephalosporin (3GC) commonly used to treat infections caused by Escherichia coli. Two genetic mechanisms have been associated with 3GC resistance in E. coli. The first is the conjugative transfer of a plasmid harbouring antibiotic-resistance genes. The second is the introduction of mutations in the promoter region of the ampC β-lactamase gene that cause chromosome-encoded β-lactamase hyperproduction. A wide variety of promoter mutations related to AmpC hyperproduction have been described. However, their link to CTX resistance has not been reported. We recultured 172 cefoxitin-resistant E. coli isolates with known CTX minimum inhibitory concentrations and performed genome-wide analysis of homoplastic mutations associated with CTX resistance by comparing Illumina whole-genome sequencing data of all isolates to a PacBio sequenced reference chromosome. We mapped the mutations on the reference chromosome and determined their occurrence in the phylogeny, revealing extreme homoplasy at the -42 position of the ampC promoter. The 24 occurrences of a T at the -42 position rather than the wild-type C, resulted from 18 independent C>T mutations in five phylogroups. The -42 C>T mutation was only observed in E. coli lacking a plasmid-encoded ampC gene. The association of the -42 C>T mutation with CTX resistance was confirmed to be significant (false discovery rate <0.05). To conclude, genome-wide analysis of homoplasy in combination with CTX resistance identifies the -42 C>T mutation of the ampC promotor as significantly associated with CTX resistance and underlines the role of recurrent mutations in the spread of antibiotic resistance.
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Affiliation(s)
- Jordy P. M. Coolen
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evert P. M. den Drijver
- Department of Infection Control, Amphia Ziekenhuis, Breda, The Netherlands
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Jaco J. Verweij
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - Jodie A. Schildkraut
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eva Kolwijck
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heiman F. L. Wertheim
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan A. J. W. Kluytmans
- Department of Infection Control, Amphia Ziekenhuis, Breda, The Netherlands
- Laboratory for Microbiology, Microvida, Breda, The Netherlands
- Julius Center for Health Sciences and Primary Care, UMCU, Utrecht, The Netherlands
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
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Abstract
B. pseudomallei causes significant morbidity and mortality, but its geographic prevalence and genetic diversity are not well characterized, especially in the Western Hemisphere. A better understanding of the genetic relationships among clinical and environmental isolates will improve knowledge of the population structure of this bacterium as well as the ability to conduct epidemiological investigations of cases of melioidosis. Burkholderia pseudomallei is a Gram-negative bacterium that causes the sapronotic disease melioidosis. An outbreak in 2003 in the state of Ceara, Brazil, resulted in subsequent surveillance and environmental sampling which led to the recognition of B. pseudomallei as an endemic pathogen in that area. From 2003 to 2015, 24 clinical and 12 environmental isolates were collected across Ceara along with one from the state of Alagoas. Using next-generation sequencing, multilocus sequence typing, and single nucleotide polymorphism analysis, we characterized the genomic diversity of this collection to better understand the population structure of B. pseudomallei associated with Ceara. We found that the isolates in this collection form a distinct subclade compared to other examples from the Western Hemisphere. Substantial genetic diversity among the clinical and environmental isolates was observed, with 14 sequence types (STs) identified among the 37 isolates. Of the 31,594 core single-nucleotide polymorphisms (SNPs) identified, a high proportion (59%) were due to recombination. Because recombination events do not follow a molecular clock, the observation of high occurrence underscores the importance of identifying and removing recombination SNPs prior to evolutionary reconstructions and inferences in public health responses to B. pseudomallei outbreaks. Our results suggest long-term B. pseudomallei prevalence in this recently recognized region of melioidosis endemicity. IMPORTANCEB. pseudomallei causes significant morbidity and mortality, but its geographic prevalence and genetic diversity are not well characterized, especially in the Western Hemisphere. A better understanding of the genetic relationships among clinical and environmental isolates will improve knowledge of the population structure of this bacterium as well as the ability to conduct epidemiological investigations of cases of melioidosis.
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Alteri C, Cento V, Piralla A, Costabile V, Tallarita M, Colagrossi L, Renica S, Giardina F, Novazzi F, Gaiarsa S, Matarazzo E, Antonello M, Vismara C, Fumagalli R, Epis OM, Puoti M, Perno CF, Baldanti F. Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy. Nat Commun 2021; 12:434. [PMID: 33469026 PMCID: PMC7815831 DOI: 10.1038/s41467-020-20688-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/10/2020] [Indexed: 12/21/2022] Open
Abstract
From February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide. By analyzing 346 whole SARS-CoV-2 genomes, we demonstrate the presence of seven viral lineages in Lombardy, frequently sustained by local transmission chains and at least two likely to have originated in Italy. Six single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. The seven lineages, and the presence of local transmission clusters within three of them, revealed that sustained community transmission was underway before the first COVID-19 case had been detected in Lombardy. The Lombardy region of Italy was heavily affected early in the SARS-CoV-2 pandemic. Here, the authors use whole genome sequencing and show that there were multiple introductions into the region, with transmission occurring before the first case was detected.
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Affiliation(s)
- Claudia Alteri
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Valeria Cento
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Valentino Costabile
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Monica Tallarita
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Luna Colagrossi
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Renica
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Federica Giardina
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Federica Novazzi
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stefano Gaiarsa
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Elisa Matarazzo
- Residency in Microbiology and Virology, University of Milan, Milan, Italy
| | - Maria Antonello
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Chiara Vismara
- Chemico-clinical and Microbiological Analyses, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Roberto Fumagalli
- Department of Anesthesiology, Critical Care and Pain Medicine, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | | | - Massimo Puoti
- Infectious Diseases Unit, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia, Italy
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Rice AM, Castillo Morales A, Ho AT, Mordstein C, Mühlhausen S, Watson S, Cano L, Young B, Kudla G, Hurst LD. Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design. Mol Biol Evol 2021; 38:67-83. [PMID: 32687176 PMCID: PMC7454790 DOI: 10.1093/molbev/msaa188] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Large-scale re-engineering of synonymous sites is a promising strategy to generate vaccines either through synthesis of attenuated viruses or via codon-optimized genes in DNA vaccines. Attenuation typically relies on deoptimization of codon pairs and maximization of CpG dinucleotide frequencies. So as to formulate evolutionarily informed attenuation strategies that aim to force nucleotide usage against the direction favored by selection, here, we examine available whole-genome sequences of SARS-CoV-2 to infer patterns of mutation and selection on synonymous sites. Analysis of mutational profiles indicates a strong mutation bias toward U. In turn, analysis of observed synonymous site composition implicates selection against U. Accounting for dinucleotide effects reinforces this conclusion, observed UU content being a quarter of that expected under neutrality. Possible mechanisms of selection against U mutations include selection for higher expression, for high mRNA stability or lower immunogenicity of viral genes. Consistent with gene-specific selection against CpG dinucleotides, we observe systematic differences of CpG content between SARS-CoV-2 genes. We propose an evolutionarily informed approach to attenuation that, unusually, seeks to increase usage of the already most common synonymous codons. Comparable analysis of H1N1 and Ebola finds that GC3 deviated from neutral equilibrium is not a universal feature, cautioning against generalization of results.
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Affiliation(s)
- Alan M Rice
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Atahualpa Castillo Morales
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Alexander T Ho
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Christine Mordstein
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stefanie Mühlhausen
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Samir Watson
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Laura Cano
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Bethan Young
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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Comprehensive Genomic Investigation of Adaptive Mutations Driving the Low-Level Oxacillin Resistance Phenotype in Staphylococcus aureus. mBio 2020; 11:mBio.02882-20. [PMID: 33293382 PMCID: PMC7733948 DOI: 10.1128/mbio.02882-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antistaphylococcal penicillins such as oxacillin are the key antibiotics in the treatment of invasive methicillin-susceptible Staphylococcus aureus (MSSA) infections; however, mec gene-independent resistance adaptation can cause treatment failure. Despite its clinical relevance, the basis of this phenomenon remains poorly understood. Here, we investigated the genomic adaptation to oxacillin at an unprecedented scale using a large collection of 503 clinical mec-negative isolates and 30 in vitro-adapted isolates from independent oxacillin exposures. By combining comparative genomics, evolutionary convergence, and genome-wide association analysis, we found 21 genetic loci associated with low-level oxacillin resistance, underscoring the polygenic nature of this phenotype. Evidence of adaptation was particularly strong for the c-di-AMP signal transduction pathways (gdpP and dacA) and in the clpXP chaperone-protease complex. The role of mutations in gdpP in conferring low-level oxacillin resistance was confirmed by allele-swapping experiments. We found that resistance to oxacillin emerges at high frequency in vitro (median, 2.9 × 10-6; interquartile range [IQR], 1.9 × 10-6 to 3.9 × 10-6), which is consistent with a recurrent minimum inhibitory concentration (MIC) increase across the global phylogeny of clinical isolates. Nevertheless, adaptation in clinical isolates appears sporadically, with no stably adapted lineages, suggesting a high fitness cost of resistance, confirmed by growth assessment of mutants in rich media. Our data provide a broader understanding of the emergence and dynamics of oxacillin resistance adaptation in S. aureus and a framework for future surveillance of this clinically important phenomenon.IMPORTANCE The majority of Staphylococcus aureus strains causing human disease are methicillin-susceptible (MSSA) and can be treated with antistaphylococcal penicillins (such as oxacillin). While acquisition of the mec gene represents the main resistance mechanism to oxacillin, S. aureus can acquire low-level resistance through adaptive mutations in other genes. In this study, we used genomic approaches to understand the basis of S. aureus adaption to oxacillin and its dynamic at the population level. By combining a genome analysis of clinical isolates from persistent MSSA infections, in vitro selection of oxacillin resistance, and genome-wide association analysis on a large collection of isolates, we identified 21 genes linked to secondary oxacillin resistance. Adaptive mutations in these genes were easy to select when S. aureus was exposed to oxacillin, but they also came at a substantial cost in terms of bacterial fitness, suggesting that this phenotype emerges preferentially in the setting of sustained antibiotic exposure.
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van Dorp L, Richard D, Tan CCS, Shaw LP, Acman M, Balloux F. No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. Nat Commun 2020; 11:5986. [PMID: 33239633 PMCID: PMC7688939 DOI: 10.1038/s41467-020-19818-2] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023] Open
Abstract
COVID-19 is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any homoplasies observed in SARS-CoV-2 to date are significantly associated with increased viral transmission. To do so, we develop a phylogenetic index to quantify the relative number of descendants in sister clades with and without a specific allele. We apply this index to a curated set of recurrent mutations identified within a dataset of 46,723 SARS-CoV-2 genomes isolated from patients worldwide. We do not identify a single recurrent mutation in this set convincingly associated with increased viral transmission. Instead, recurrent mutations currently in circulation appear to be evolutionary neutral and primarily induced by the human immune system via RNA editing, rather than being signatures of adaptation. At this stage we find no evidence for significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Damien Richard
- Cirad, UMR PVBMT, F-97410 St Pierre, Réunion, France
- Université de la Réunion, UMR PVBMT, F-97490 St Denis, Réunion, France
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Liam P Shaw
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - François Balloux
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
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van Dorp L, Acman M, Richard D, Shaw LP, Ford CE, Ormond L, Owen CJ, Pang J, Tan CCS, Boshier FAT, Ortiz AT, Balloux F. Emergence of genomic diversity and recurrent mutations in SARS-CoV-2. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 83:104351. [PMID: 32387564 PMCID: PMC7199730 DOI: 10.1016/j.meegid.2020.104351] [Citation(s) in RCA: 510] [Impact Index Per Article: 127.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 is a SARS-like coronavirus of likely zoonotic origin first identified in December 2019 in Wuhan, the capital of China's Hubei province. The virus has since spread globally, resulting in the currently ongoing COVID-19 pandemic. The first whole genome sequence was published on January 5 2020, and thousands of genomes have been sequenced since this date. This resource allows unprecedented insights into the past demography of SARS-CoV-2 but also monitoring of how the virus is adapting to its novel human host, providing information to direct drug and vaccine design. We curated a dataset of 7666 public genome assemblies and analysed the emergence of genomic diversity over time. Our results are in line with previous estimates and point to all sequences sharing a common ancestor towards the end of 2019, supporting this as the period when SARS-CoV-2 jumped into its human host. Due to extensive transmission, the genetic diversity of the virus in several countries recapitulates a large fraction of its worldwide genetic diversity. We identify regions of the SARS-CoV-2 genome that have remained largely invariant to date, and others that have already accumulated diversity. By focusing on mutations which have emerged independently multiple times (homoplasies), we identify 198 filtered recurrent mutations in the SARS-CoV-2 genome. Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2. Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. We additionally provide an interactive user-friendly web-application to query the alignment of the 7666 SARS-CoV-2 genomes.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London WC1E 6BT, UK.
| | - Mislav Acman
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Damien Richard
- Cirad, UMR PVBMT, F-97410, St Pierre, Réunion, France; Université de la Réunion, UMR PVBMT, F-97490, St Denis, Réunion, France
| | - Liam P Shaw
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Charlotte E Ford
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Louise Ormond
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Juanita Pang
- UCL Genetics Institute, University College London, London WC1E 6BT, UK; Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, London WC1E 6BT, UK; Department of Infectious Disease, Imperial College, London W2 1NY, UK
| | - François Balloux
- UCL Genetics Institute, University College London, London WC1E 6BT, UK.
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020. [PMID: 32697968 DOI: 10.1016/j.cell.2020.06.043s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020; 182:812-827.e19. [PMID: 32697968 PMCID: PMC7332439 DOI: 10.1016/j.cell.2020.06.043] [Citation(s) in RCA: 2779] [Impact Index Per Article: 694.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 02/08/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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38
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020. [PMID: 32697968 DOI: 10.1016/j.cell.2020.06.043%0asummary] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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39
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Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni. Proc Natl Acad Sci U S A 2020; 117:11018-11028. [PMID: 32366649 PMCID: PMC7245135 DOI: 10.1073/pnas.1917168117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen (Campylobacter jejuni) in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist C. jejuni lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems.
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40
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Extensive survey of the ycf4 plastid gene throughout the IRLC legumes: Robust evidence of its locus and lineage specific accelerated rate of evolution, pseudogenization and gene loss in the tribe Fabeae. PLoS One 2020; 15:e0229846. [PMID: 32134967 PMCID: PMC7058334 DOI: 10.1371/journal.pone.0229846] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 02/15/2020] [Indexed: 12/12/2022] Open
Abstract
The genome organization and gene content of plastome (plastid genome) are highly conserved among most flowering plant species. Plastome variation (in size and gene order) is rare in photosynthetic species but size variation, rearrangements and gene/intron losses is attributed to groups of seed plants. Fabaceae (legume family), in particular the subfamily Papilionoideae and the inverted repeat lacking clade (IRLC), a largest legume lineage, display the most dramatic and structural change which providing an excellent model for understanding of mechanisms of genomic evolution. The IRLC comprises 52 genera and ca 4000 species divided into seven tribes. In present study, we have sampled several representatives from each tribe across the IRLC from various herbaria and field. The ycf4 gene, which plays a role in regulating and assembly of photosystem I, is more variable in the tribe Fabeae than in other tribes. In certain species of Lathyrus, Pisum and Vavilovia, all belonging to Fabeae, the gene is either absent or a pseudogene. Our study suggests that ycf4 gene has undergone positive selection. Furthermore, the rapid evolution of the gene is locus and lineage specific and is not a shared character of the IRLC in legumes.
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41
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van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Mol Biol Evol 2020; 37:773-785. [PMID: 31697387 PMCID: PMC7038659 DOI: 10.1093/molbev/msz264] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Adrien Rieux
- CIRAD, UMR PVBMT, St. Pierre de la Réunion, France
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rosa Fregel
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Spain
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Population Health and Immunity Division, Walter & Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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42
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Crispell J, Benton CH, Balaz D, De Maio N, Ahkmetova A, Allen A, Biek R, Presho EL, Dale J, Hewinson G, Lycett SJ, Nunez-Garcia J, Skuce RA, Trewby H, Wilson DJ, Zadoks RN, Delahay RJ, Kao RR. Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system. eLife 2019; 8:e45833. [PMID: 31843054 PMCID: PMC6917503 DOI: 10.7554/elife.45833] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/15/2019] [Indexed: 01/02/2023] Open
Abstract
Quantifying pathogen transmission in multi-host systems is difficult, as exemplified in bovine tuberculosis (bTB) systems, but is crucial for control. The agent of bTB, Mycobacterium bovis, persists in cattle populations worldwide, often where potential wildlife reservoirs exist. However, the relative contribution of different host species to bTB persistence is generally unknown. In Britain, the role of badgers in infection persistence in cattle is highly contentious, despite decades of research and control efforts. We applied Bayesian phylogenetic and machine-learning approaches to bacterial genome data to quantify the roles of badgers and cattle in M. bovis infection dynamics in the presence of data biases. Our results suggest that transmission occurs more frequently from badgers to cattle than vice versa (10.4x in the most likely model) and that within-species transmission occurs at higher rates than between-species transmission for both. If representative, our results suggest that control operations should target both cattle and badgers.
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Affiliation(s)
- Joseph Crispell
- School of Veterinary Medicine, Veterinary Sciences CentreUniversity College DublinDublinIreland
| | - Clare H Benton
- National Wildlife Management CentreAnimal & Plant Health Agency (APHA)LondonUnited Kingdom
| | - Daniel Balaz
- Roslin InstituteUniversity of EdinburghEdinburghUnited Kingdom
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)CambridgeUnited Kingdom
| | - Assel Ahkmetova
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUnited Kingdom
| | - Adrian Allen
- Agri-Food & Biosciences Institute Northern Ireland (AFBNI)BelfastUnited Kingdom
| | - Roman Biek
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUnited Kingdom
| | - Eleanor L Presho
- Agri-Food & Biosciences Institute Northern Ireland (AFBNI)BelfastUnited Kingdom
| | - James Dale
- Animal & Plant Health Agency (APHA)LondonUnited Kingdom
| | - Glyn Hewinson
- Centre for Bovine Tuberculosis, Institute of Biological, Environmental and Rural SciencesUniversity of AberystwythAberystwythUnited Kingdom
| | | | | | - Robin A Skuce
- Agri-Food & Biosciences Institute Northern Ireland (AFBNI)BelfastUnited Kingdom
| | | | - Daniel J Wilson
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population HealthUniversity of OxfordOxfordUnited Kingdom
| | - Ruth N Zadoks
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life SciencesUniversity of GlasgowGlasgowUnited Kingdom
| | - Richard J Delahay
- National Wildlife Management CentreAnimal & Plant Health Agency (APHA)LondonUnited Kingdom
| | - Rowland Raymond Kao
- Roslin InstituteUniversity of EdinburghEdinburghUnited Kingdom
- Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUnited Kingdom
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