Phylogenomics

Foundations, Methods, and Pathogen Analysis

1st Edition - May 17, 2024
Editors: Igor Mokrousov, Egor Shitikov
Language: English
Paperback ISBN:
9 7 8 - 0 - 3 2 3 - 9 9 8 8 6 - 4
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 9 1 3 0 9 - 6

Phylogenomics: Foundations, Methods, and Pathogen Analysis offers a deep overview of phylogenomics as a field, compelling recent developments, and detailed methods and approache… Read more

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Phylogenomics: Foundations, Methods, and Pathogen Analysis offers a deep overview of phylogenomics as a field, compelling recent developments, and detailed methods and approaches for conducting new research. Early chapters introduce phylogenomic analysis of viruses and bacteria, deciphering bacterial outbreaks, and evolution of drug resistance and virulence, with a second section on methods offering instruction in tools for SNP calling and dealing with big datasets, use of Bayesian approach in molecular epidemiology, bacterial evolution modeling and evolutionary reconstruction in the presence of mosaic sequences. Part 3 offers various examples of phylogenomic analysis across medically significant bacteria and viruses, including Yersinia pestis, Salmonella, Mycobacterium tuberculosis, HIV-1, measles virus as well as ancient pathogens research.

Cover image
Title page
Table of Contents
Copyright
List of contributors
Preface
Part I: General topics and foundations
Chapter 1. Phylogenomic analysis and the origin and early evolution of viruses
Abstract
1.1 Introduction
1.2 Retrodiction
1.3 The analytical basis of the phylogenetic framework
1.4 Rooting trees
1.5 Phylogenomic analysis
1.6 Deep evolutionary explorations with alignment-free methods
1.7 Untangling the origin and evolution of viruses with structural phylogenomics
1.8 Conclusions
Acknowledgments
References
Chapter 2. Application of next-generation sequencing for genetic and phenotypic studies of bacteria
Abstract
2.1 Introduction
2.2 Whole genome sequence data
2.3 Reference genomes
2.4 Pangenome, core genome, and accessory genome
2.5 Principles of genotypic classification
2.6 Species classification and identification using whole genome sequencing data
2.7 Genotyping based on whole genome sequencing data
2.8 Genotyping and control of infectious diseases
2.9 Genotyping and human genetics of infectious diseases
2.10 Conclusion
References
Chapter 3. Genomic insights into deciphering bacterial outbreaks
Abstract
3.1 Introduction
3.2 Genomes and variation
3.3 Sequencing whole genomes
3.4 Outbreak delimitation
3.5 Forensic analysis of outbreaks and transmissions
3.6 Conclusion
References
Chapter 4. Drug resistance in bacteria, molecular mechanisms, and evolution
Abstract
4.1 Introduction
4.2 What are antibiotics
4.3 Mechanisms of bacterial resistance to antibiotics
4.4 Evolution of antibiotic resistance
4.5 Classes of antibiotics, mechanisms of action and resistance
4.6 Disruptors of cell envelope
4.7 Other antibiotics
4.8 Origin and evolution of bacterial resistance
4.9 Newer approaches to deal with antimicrobial resistance
4.10 Conclusions
Acknowledgments
References
Chapter 5. Virulence evolution of bacterial species
Abstract
5.1 Introduction
5.2 What is virulence?
5.3 Models for the evolution of virulence
5.4 Molecular infection biology
5.5 Virulence factors and mechanisms in Gram-negative pathogens
5.6 Virulence factors and mechanisms in Gram-positive bacteria
5.7 Acid-fast bacteria
5.8 Final remarks
References
Part II: Methods in the phylogenomics
Chapter 6. Modeling evolutionary changes of k-mer patterns of bacterial genomes
Abstract
6.1 Introduction
6.2 Estimation of evolutionary distances by comparison of k-mer patterns
6.3 Driving forces on the k-mer pattern evolution
6.4 Using graph models in investigation of k-mer pattern evolution
6.5 Conclusion
References
Chapter 7. Clock rates and Bayesian evaluation of temporal signal
Abstract
7.1 Introduction
7.2 TMRCAs and mutation rate
7.3 Tip-dating and tip randomization
7.4 Population changes through time
7.5 Case study: Is there a molecular clock in Mycobacterium tuberculosis?
7.6 Models limits and sensitivity
7.7 Fluctuating mutation rates
7.8 The rise of fine-tuned phyloepidemiology models
7.9 Conclusion and perspectives
Acknowledgments
References
Chapter 8. Microbial evolutionary reconstruction in the presence of mosaic sequences
Abstract
8.1 Introduction
8.2 Biological processes giving rise to viral and bacterial mosaic sequences
8.3 Mosaic sequence and structure detection methods
8.4 Potential impacts of mixed evolutionary signals on traditional phylogenetic reconstruction
8.5 Tree-based approaches to dealing with mosaic sequences and mixed evolutionary signals
8.6 Network-based approaches to reconstructing an entangled evolutionary history
8.7 Final remarks
Acknowledgments
References
Chapter 9. Tools for short variant calling and the way to deal with big datasets
Abstract
9.1 Introduction
9.2 Types of whole genome sequencing data
9.3 Pretreatment of data
9.4 Calling of short variants
9.5 Postprocessing of variants
9.6 Large datasets and computational solutions to deal with them
9.7 All-in-one pipelines
9.8 Conclusion
Funding
Acknowledgments
References
Part III: Phylogenomics of specific pathogens
Chapter 10. Phylogenomics of Yersinia pestis
Abstract
10.1 Introduction
10.2 Phylogeny and geographic distribution of extant Yersinia pestis populations
10.3 Origin and transmission pattern of three historic pandemics
10.4 Characters of evolutionary dynamics
10.5 Conclusions
References
Chapter 11. Salmonella phylogenomics
Abstract
11.1 Introduction
11.2 Materials and methods
11.3 Results
11.4 Discussion
References
Chapter 12. The phylogenomics of Shigella spp.
Abstract
12.1 Shigella and shigellosis
12.2 The evolution of Shigella from Escherichia coli
12.3 The phylogenomics of individual Shigella spp
12.4 Interactions with the accessory genome
12.5 Outlook for Shigella phylogenomics
References
Chapter 13. Phylogenomic diversity within Corynebacterium diphtheriae, a reemerging threat to global public health
Abstract
13.1 Introduction
13.2 Biochemical characteristics
13.3 Global epidemiology
13.4 Phylogenomic diversity
13.5 Corynephages and tox gene diversity
13.6 Other virulence genes
13.7 Antibiotic resistance
13.8 Conclusion
References
Chapter 14. Phylogenomics of the East Asian lineage of Mycobacterium tuberculosis
Abstract
14.1 Introduction
14.2 An overview of L2 genotyping methods
14.3 Single nucleotide polymorphism-based L2 population structure
14.4 Genomic features of L2 at the level of regions of differences and IS6110
14.5 Concluding considerations
Acknowledgments
References
Chapter 15. Population genomics of Mycobacterium kansasii
Abstract
15.1 Background
15.2 Taxonomy and genomic diversity of Mycobacterium kansasii complex
15.3 Recombination driving speciation and diversification of the Mycobacterium kansasii complex
15.4 Genetic evidence of environmental source of clinical infections
15.5 Genes potentially contributing to the success of Mycobacterium kansasii
15.6 Within host adaptive evolution of Mycobacterium kansasii
15.7 Summary
References
Chapter 16. Taxonomy and phylogenomics of Leptospira
Abstract
16.1 Taxonomy/phylogeny
16.2 Genome architecture and gene repertoire
16.3 General features
16.4 Gene repertoire across Leptospira species
16.5 Concluding remarks
References
Chapter 17. Phylogenomics and evolution of measles virus
Abstract
17.1 Measles virus as a reemerging threat
17.2 Current status
17.3 Genome organization
17.4 Understanding phylogenomic diversity and evolution of MeV: data-led approach
17.5 Data sources for MeV: MeaNS, GenBank, UniProt, genome, PDB, IEDB
17.6 Analytical approaches: data to knowledge
17.7 Data curation and binning
17.8 Multiple sequence alignment
17.9 Named strain mapping
17.10 Recombination detection
17.11 Phylogenetic inference
17.12 Estimation of nucleotide substitution rate
17.13 Population stratification
17.14 Selection pressure
17.15 Genotype–phenotype correlation
17.16 Knowledge to translation
Acknowledgments
References
Chapter 18. Phylogenomics of human immunodeficiency virus type 1 (HIV-1)
Abstract
18.1 Introduction
18.2 Laboratory and analytical methods for genotyping human immunodeficiency virus type 1
18.3 Application of human immunodeficiency virus type 1 genotyping to clinical and phylogenomic investigations
18.4 Conclusions
References
Chapter 19. Respiratory syncytial viruses
Abstract
Abbreviations
19.1 Introduction
19.2 Respiratory syncytial virus phylogeny
19.3 Phylodynamics of the respiratory syncytial virus fusion protein
19.4 Selective pressure in the respiratory syncytial virus F gene/protein
19.5 Relationships among antigen, conformational epitope, and reinfection in the respiratory syncytial virus F protein
19.6 Perspective
Acknowledgments
Data availability statement
Conflicts of interest
References
Chapter 20. The phylogenomics of flaviviruses
Abstract
20.1 Introduction
20.2 Dengue virus
20.3 Zika virus
20.4 West Nile virus
20.5 Japanese encephalitis virus
20.6 Yellow fever virus
20.7 Tick-borne encephalitis virus
References
Chapter 21. How clonal is Staphylococcus aureus?
Abstract
21.1 Introduction
21.2 Why is the concept of clonality so relevant?
21.3 What are the specificities of the predominant clonal evolution* model?
21.4 Staphylococcus aureus and the predominant clonal evolution model
21.5 Concluding remarks
Acknowledgments
Glossary of specialized terms and abbreviations
References
Chapter 22. Genomic research of ancient pathogens in Central Asia
Abstract
22.1 Introduction
22.2 Methodological aspects of ancient DNA studies
22.3 Studies of ancient pathogens circulating in Central Asia
22.4 Studies of ancient pathogens circulating in Central Asia
22.5 Conclusions
Acknowledgments
References
Chapter 23. Subspecific nomenclature of the Cryptococcus neoformans/gattii complex and the predominant clonal evolution model
Abstract
23.1 Introduction
23.2 Clonality and population structure in the Cryptococcus neoformans/gattii complex
23.3 Cryptococcus neoformans/gattii complex and the predominant clonal evolution model
23.4 Widespread multilocus genotypes
23.5 Linkage disequilibrium
23.6 Widespread genetic clustering (near-clades*)
23.7 Russian doll patterns
23.8 Species concept, nomenclature, and the Cryptococcus neoformans/gattii complex near-clades
23.9 Conclusion: the Cryptococcus neoformans/gattii complex: a paradigmatic predominant clonal evolution case
23.10 “Evolutionary twins” can artefactually appear as different merely due to different scientific traditions
Glossary of specialized terms and abbreviations
References
Chapter 24. Phylogenomics of Mycobacterium leprae
Abstract
24.1 Introduction
24.2 Application of whole-genome sequencing for bacterial phylogeny
24.3 Genomics of Mycobacterium leprae
24.4 Phylogenomics and strain diversity of Mycobacterium leprae
24.5 Mycobacterium lepromatosis: newly discovered leprosy pathogen
24.6 Reservoirs of Mycobacterium leprae and Mycobacterium lepromatosis
24.7 Conclusion
Acknowledgments
References
Index

Igor Mokrousov

Igor Mokrousov, 53 years old, PhD, DSc, is the Head of Laboratory of Molecular Epidemiology and Evolutionary Genetics at St. Petersburg Pasteur Institute, Russia. His research interests include study of evolution, phylogenomics, and molecular epidemiology of tuberculosis; phylogeography of Mycobacterium tuberculosis and co-evolution with humans; molecular mechanisms and genotypic detection of drug resistance. His current projects focus on the application of next-generation sequencing for genome-wide analysis to understand the pathogenetic characteristics and evolutionary trajectory of various M. tuberculosis lineages and emerging clones. Dr Mokrousov made a recognized contribution to the study of human-M. tuberculosis coevolution and put forward a hypothesis that evolutionary histories of H. sapiens and human pathogens are comirrored and coshaped. He proposed a new simple measure of genetic distance between geographic populations within a microbial species based on the observed difference in the frequencies of its genotypes.

Affiliations and expertise

Head of the Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, Russia

Egor Shitikov

Egor Shitikov, PhD, is the Head of Laboratory of Molecular Genetics of Microorganisms at Federal Research and Clinical Center of Physical-Chemical Medicine, Russia. His research interests are closely related to the systematic analysis of Mycobacterium tuberculosis: phylogenetic relationship of various strains, their definition and classification; the search for new drug-resistance determinants, virulence factors, and pathogenicity; development of rapid screening systems for certain pathogen groups; experiments on model organisms. The current topic focuses on the deep machine learning methods in Mycobacterium tuberculosis genomics for the building of an open platform for the analysis of the pathogen’s evolutionary signatures.

Affiliations and expertise

Head of the Laboratory of Molecular Genetics of Microorganisms, Federal Research and Clinical Center of Physical-Chemical Medicine, Russia

Life Sciences

Physical Sciences & Engineering

Social Sciences & Humanities

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