Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review

The PRISMA 2020 statement: an updated guideline for reporting systematic reviews

(2021) Matthew J Page et al.   BMJ-British Medical Journal

TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread

(2021) Saurav Dhar et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Whole-Genome-Sequence-Based Characterization of Extensively Drug-Resistant Acinetobacter baumannii Hospital Outbreak

(2020) Ghiwa Makke et al.   mSphere

Modeling Missing Cases and Transmission Links in Networks of Extensively Drug-Resistant Tuberculosis in KwaZulu-Natal, South Africa

(2020) Kristin N Nelson et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Nosocomial Outbreak of 2019 Novel Coronavirus Pneumonia in Wuhan, China

(2020) Xiaorong Wang et al.   EUROPEAN RESPIRATORY JOURNAL

Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda

(2020) Nicholas Bbosa et al.   Viruses-Basel

Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants

(2020) Benjamin Sobkowiak et al.   Microbial Genomics

Sampling and summarizing transmission trees with multi-strain infections

(2020) Palash Sashittal et al.   BIOINFORMATICS

Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates

(2020) Simon M. Firestone et al.   PLoS One

The emergence of SARS-CoV-2 in Europe and North America

(2020) Michael Worobey et al.   SCIENCE

Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times

(2020) Hesam Montazeri et al.   Statistical Applications in Genetics and Molecular Biology

Phylogenetic and phylodynamic analyses of SARS-CoV-2

(2020) Qing Nie et al.   VIRUS RESEARCH

What Should Health Departments Do with HIV Sequence Data?

(2020) Ethan Romero-Severson et al.   Viruses-Basel

Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase

(2020) Liang Wang et al.   Nature Communications

Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data

(2019) Finlay Campbell et al.   PLoS Computational Biology

Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

(2019) Oliver Ratmann et al.   Nature Communications

Transmission trees on a known pathogen phylogeny: enumeration and sampling

(2019) Matthew Hall et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimating Epidemic Incidence and Prevalence from Genomic Data

(2019) Timothy G Vaughan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstructing a transmission network and identifying risk factors of secondary transmissions in the 2010 foot‐and‐mouth disease outbreak in Japan

(2019) Yoko Hayama et al.   Transboundary and Emerging Diseases

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

(2019) Remco Bouckaert et al.   PLoS Computational Biology

Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases

(2019) M. Alamil et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Investigation of field intradermal tuberculosis test practices performed by veterinarians in France and factors that influence testing

(2019) Guillaume Crozet et al.   RESEARCH IN VETERINARY SCIENCE

Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains

(2019) Lucy van Dorp et al.   Microbial Genomics

StrainHub: a phylogenetic tool to construct pathogen transmission networks

(2019) Adriano de Bernardi Schneider et al.   BIOINFORMATICS

Tracing local and regional clusters of carbapenemase-producing Klebsiella pneumoniae ST512 with whole genome sequencing, Finland, 2013 to 2018

(2019) Janko van Beek et al.   Eurosurveillance

Nosocomial transmission of influenza: A retrospective cross‐sectional study using next generation sequencing at a hospital in England (2012‐2014)

(2019) Ruth M. Blackburn et al.   Influenza and Other Respiratory Viruses

Evaluating the use of whole genome sequencing for the investigation of a large mumps outbreak in Ontario, Canada

(2019) P. J. Stapleton et al.   Scientific Reports

High-resolution mapping of tuberculosis transmission: Whole genome sequencing and phylogenetic modelling of a cohort from Valencia Region, Spain

(2019) Yuanwei Xu et al.   PLOS MEDICINE

Improved characterisation of MRSA transmission using within-host bacterial sequence diversity

(2019) Matthew D Hall et al.   eLife

Genomic Investigation of a Mycobacterium tuberculosis Outbreak Involving Prison and Community Cases in Florida, United States

(2018) Marie Nancy Séraphin et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Estimating Transmission from Genetic and Epidemiological Data: A Metric to Compare Transmission Trees

(2018) Michelle Kendall et al.   STATISTICAL SCIENCE

Bayesian reconstruction of transmission within outbreaks using genomic variants

(2018) Nicola De Maio et al.   PLoS Computational Biology

When are pathogen genome sequences informative of transmission events?

(2018) Finlay Campbell et al.   PLoS Pathogens

Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak

(2018) Jason C. Kwong et al.   PeerJ

Multihospital Outbreak of a Middle East Respiratory Syndrome Coronavirus Deletion Variant, Jordan: A Molecular, Serologic, and Epidemiologic Investigation

(2018) Daniel C Payne et al.   Open Forum Infectious Diseases

Phylogenetic patterns recover known HIV epidemiological relationships and reveal common transmission of multiple variants

(2018) Thomas Leitner et al.   Nature Microbiology

outbreaker2: a modular platform for outbreak reconstruction

(2018) Finlay Campbell et al.   BMC BIOINFORMATICS

Whole Genome Sequencing detects Inter-Facility Transmission of Carbapenem-resistant Klebsiella pneumoniae

(2018) Melanie D. Spencer et al.   JOURNAL OF INFECTION

Tracking a serial killer: Integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks

(2018) Ifeoma Ezeoke et al.   PLoS One

The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology

(2018) Conor J. Meehan et al.   EBioMedicine

Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks

(2017) Xavier Didelot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Variable spontaneous mutation rate in clinical strains of multidrug-resistant Acinetobacter baumannii and differentially expressed proteins in a hypermutator strain

(2017) Morteza Karami-Zarandi et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Integrated genomic and interfacility patient-transfer data reveal the transmission pathways of multidrug-resistant Klebsiella pneumoniae in a regional outbreak

(2017) Evan S. Snitkin et al.   Science Translational Medicine

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

(2017) Don Klinkenberg et al.   PLoS Computational Biology

Reconstructing transmission trees for communicable diseases using densely sampled genetic data

(2016) Colin J. Worby et al.   Annals of Applied Statistics

Infectious Disease Dynamics in Heterogeneous Landscapes

(2016) Steven R. Parratt et al.   Annual Review of Ecology Evolution and Systematics

Phylogeography, phylodynamics and transmission chains of bovine viral diarrhea virus subtype 1f in Northern Italy

(2016) Francesco Cerutti et al.   INFECTION GENETICS AND EVOLUTION

Network inference from multimodal data: A review of approaches from infectious disease transmission

(2016) Bisakha Ray et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Ebola Virus Epidemiology and Evolution in Nigeria

(2016) Onikepe A. Folarin et al.   JOURNAL OF INFECTIOUS DISEASES

Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit

(2016) Taj Azarian et al.   PLoS One

Using genomics data to reconstruct transmission trees during disease outbreaks

(2016) M.D. HALL et al.   REVUE SCIENTIFIQUE ET TECHNIQUE-OFFICE INTERNATIONAL DES EPIZOOTIES

Emerging Concepts of Data Integration in Pathogen Phylodynamics

(2016) Guy Baele et al.   SYSTEMATIC BIOLOGY

Epidemiological and Evolutionary Inference of the Transmission Network of the 2014 Highly Pathogenic Avian Influenza H5N2 Outbreak in British Columbia, Canada

(2016) Wanhong Xu et al.   Scientific Reports

Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees

(2016) Eben Kenah et al.   PLoS Computational Biology

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

(2016) Nicola De Maio et al.   PLoS Computational Biology

Impact of HIV co-infection on the evolution and transmission of multidrug-resistant tuberculosis

(2016) Vegard Eldholm et al.   eLife

Genomic Analysis of Viral Outbreaks

(2016) Shirlee Wohl et al.   Annual Review of Virology

Ecological dynamics of influenza A viruses: cross-species transmission and global migration

(2016) Hongguang Ren et al.   Scientific Reports

Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center

(2015) Hajime Kanamori et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Phylogenetic visualization of the spread of H7 influenza A viruses

(2015) Daniel A. Janies et al.   CLADISTICS

The application of genomics to tracing bacterial pathogen transmission

(2015) Nicholas J Croucher et al.   CURRENT OPINION IN MICROBIOLOGY

The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus

(2015) Begoña Valdazo-González et al.   INFECTION GENETICS AND EVOLUTION

Tracing Origins of theSalmonellaBareilly Strain Causing a Food-borne Outbreak in the United States

(2015) Maria Hoffmann et al.   JOURNAL OF INFECTIOUS DISEASES

Chains of transmission and control of Ebola virus disease in Conakry, Guinea, in 2014: an observational study

(2015) Ousmane Faye et al.   LANCET INFECTIOUS DISEASES

Extracting transmission networks from phylogeographic data for epidemic and endemic diseases: Ebola virus in Sierra Leone, 2009 H1N1 pandemic influenza and polio in Nigeria

(2015) Michael Famulare et al.   International Health

A Systematic Bayesian Integration of Epidemiological and Genetic Data

(2015) Max S. Y. Lau et al.   PLoS Computational Biology

Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set

(2015) Matthew Hall et al.   PLoS Computational Biology

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

(2015) Nicola De Maio et al.   PLoS Genetics

Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area

(2015) JA Guerra-Assunção et al.   eLife

Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting

(2014) N. Stoesser et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Distribution of Pairwise Genetic Distances: A Tool for Investigating Disease Transmission

(2014) Colin J. Worby et al.   GENETICS

Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data

(2014) Xavier Didelot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Marked Microevolution of a Unique Mycobacterium tuberculosis Strain in 17 Years of Ongoing Transmission in a High Risk Population

(2014) Carolina Mehaffy et al.   PLoS One

Two-phase importance sampling for inference about transmission trees

(2014) E. Numminen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data

(2014) N. Mollentze et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates

(2014) Bram Vrancken et al.   PLoS Computational Biology

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data

(2014) Colin J. Worby et al.   PLoS Computational Biology

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

(2014) Thibaut Jombart et al.   PLoS Computational Biology

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

(2014) Alexandra Gavryushkina et al.   PLoS Computational Biology

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

(2013) Rolf J. F. Ypma et al.   GENETICS

Multiple Independent Emergences of Type 2 Vaccine-Derived Polioviruses during a Large Outbreak in Northern Nigeria

(2013) C. C. Burns et al.   JOURNAL OF VIROLOGY

Transmission of Equine Influenza Virus during an Outbreak Is Characterized by Frequent Mixed Infections and Loose Transmission Bottlenecks

(2013) Joseph Hughes et al.   PLoS Pathogens

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

(2012) Alexandre P Francisco et al.   BMC BIOINFORMATICS

Genetic Data Provide Evidence for Wind-Mediated Transmission of Highly Pathogenic Avian Influenza

(2012) Rolf J.F. Ypma et al.   JOURNAL OF INFECTIOUS DISEASES

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Combining Epidemiological and Genetic Networks Signifies the Importance of Early Treatment in HIV-1 Transmission

(2012) Narges Zarrabi et al.   PLoS One

Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation

(2012) J. C. Stack et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Detectable signals of episodic risk effects on acute HIV transmission: Strategies for analyzing transmission systems using genetic data

(2012) Shah Jamal Alam et al.   Epidemics

A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data

(2012) Marco J. Morelli et al.   PLoS Computational Biology

Phylodynamic analysis of a viral infection network

(2012) Teiichiro Shiino   Frontiers in Microbiology

Modelling the spread of infectious salmon anaemia among salmon farms based on seaway distances between farms and genetic relationships between infectious salmon anaemia virus isolates

(2011) M. Aldrin et al.   Journal of the Royal Society Interface

Genome-Scale Evolution and Phylodynamics of Equine H3N8 Influenza A Virus

(2011) P. R. Murcia et al.   JOURNAL OF VIROLOGY

Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data

(2011) R. J. F. Ypma et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian Influenza Epidemic

(2011) Arnaud Bataille et al.   PLoS Pathogens

Reconstructing disease outbreaks from genetic data: a graph approach

(2010) T Jombart et al.   HEREDITY

High-Resolution Typing by Integration of Genome Sequencing Data in a Large Tuberculosis Cluster

(2010) A. C. Schurch et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

(2010) D. I. Scaduto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Phylodynamics of Infectious Disease Epidemics

(2009) Erik M. Volz et al.   GENETICS

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

(2009) Gavin J. D. Smith et al.   NATURE

Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus

(2008) E. M Cottam et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES