Literature DB >> 26878934

Bacterial genomic epidemiology, from local outbreak characterization to species-history reconstruction.

Stefano Gaiarsa1, Leone De Marco, Francesco Comandatore, Piero Marone, Claudio Bandi, Davide Sassera.   

Abstract

Bacteriology has embraced the next-generation sequencing revolution, swiftly moving from the time of single genome sequencing to the age of genomic epidemiology. Hundreds and now even thousands of genomes are being sequenced for single bacterial species, allowing unprecedented levels of resolution and insight in the evolution and epidemic diffusion of the main bacterial pathogens. Here, we present a review of some of the most recent and groundbreaking studies in this field.

Keywords:  Bacteria; Carbapenem-resistant Enterobacteriaceae; Genomic epidemiology; Mycobacterium tuberculosis; Next-generation sequencing; Salmonella Typhi; Staphylococcus aureus; Streptococcus pneumoniae

Mesh：

Year:  2015        PMID： 26878934      PMCID： PMC4768628          DOI： 10.1080/20477724.2015.1103503

Source DB:  PubMed          Journal:  Pathog Glob Health        ISSN： 2047-7724            Impact factor:   2.894


  72 in total

1.  Recent transmission of W-Beijing family Mycobacterium tuberculosis in rural eastern China.

Authors:  W Wang; Y Hu; B Mathema; W Jiang; B Kreiswirth; B Xu
Journal:  Int J Tuberc Lung Dis       Date:  2012       Impact factor: 2.373

2.  Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.

Authors:  H Tettelin; K E Nelson; I T Paulsen; J A Eisen; T D Read; S Peterson; J Heidelberg; R T DeBoy; D H Haft; R J Dodson; A S Durkin; M Gwinn; J F Kolonay; W C Nelson; J D Peterson; L A Umayam; O White; S L Salzberg; M R Lewis; D Radune; E Holtzapple; H Khouri; A M Wolf; T R Utterback; C L Hansen; L A McDonald; T V Feldblyum; S Angiuoli; T Dickinson; E K Hickey; I E Holt; B J Loftus; F Yang; H O Smith; J C Venter; B A Dougherty; D A Morrison; S K Hollingshead; C M Fraser
Journal:  Science       Date:  2001-07-20       Impact factor: 47.728

3.  Population-based surveillance for childhood invasive pneumococcal disease in the era of conjugate vaccine.

Authors:  Katherine Hsu; Stephen Pelton; Sudharani Karumuri; Dawn Heisey-Grove; Jerome Klein
Journal:  Pediatr Infect Dis J       Date:  2005-01       Impact factor: 2.129

4.  Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set.

Authors:  Ingrid Filliol; Alifiya S Motiwala; Magali Cavatore; Weihong Qi; Manzour Hernando Hazbón; Miriam Bobadilla del Valle; Janet Fyfe; Lourdes García-García; Nalin Rastogi; Christophe Sola; Thierry Zozio; Marta Inírida Guerrero; Clara Inés León; Jonathan Crabtree; Sam Angiuoli; Kathleen D Eisenach; Riza Durmaz; Moses L Joloba; Adrian Rendón; José Sifuentes-Osornio; Alfredo Ponce de León; M Donald Cave; Robert Fleischmann; Thomas S Whittam; David Alland
Journal:  J Bacteriol       Date:  2006-01       Impact factor: 3.490

5.  High prevalence of multi-drug resistant Streptococcus pneumoniae among healthy children in Thailand.

Authors:  Rapee Thummeepak; Nontapat Leerach; Duangkamol Kunthalert; Udomsak Tangchaisuriya; Aunchalee Thanwisai; Sutthirat Sitthisak
Journal:  J Infect Public Health       Date:  2014-12-23       Impact factor: 3.718

6.  Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans.

Authors:  Iñaki Comas; Mireia Coscolla; Tao Luo; Sonia Borrell; Kathryn E Holt; Midori Kato-Maeda; Julian Parkhill; Bijaya Malla; Stefan Berg; Guy Thwaites; Dorothy Yeboah-Manu; Graham Bothamley; Jian Mei; Lanhai Wei; Stephen Bentley; Simon R Harris; Stefan Niemann; Roland Diel; Abraham Aseffa; Qian Gao; Douglas Young; Sebastien Gagneux
Journal:  Nat Genet       Date:  2013-09-01       Impact factor: 38.330

7.  Clinical detection and characterization of bacterial pathogens in the genomics era.

Authors:  Pierre-Edouard Fournier; Gregory Dubourg; Didier Raoult
Journal:  Genome Med       Date:  2014-11-29       Impact factor: 11.117

8.  Quality scores for 32,000 genomes.

Authors:  Miriam L Land; Doug Hyatt; Se-Ran Jun; Guruprasad H Kora; Loren J Hauser; Oksana Lukjancenko; David W Ussery
Journal:  Stand Genomic Sci       Date:  2014-12-08

9.  Typhoid fever and paratyphoid fever: Systematic review to estimate global morbidity and mortality for 2010.

Authors:  Geoffrey C Buckle; Christa L Fischer Walker; Robert E Black
Journal:  J Glob Health       Date:  2012-06       Impact factor: 4.413

10.  Origin and evolution of European community-acquired methicillin-resistant Staphylococcus aureus.

Authors:  Marc Stegger; Thierry Wirth; Paal S Andersen; Robert L Skov; Anna De Grassi; Patricia Martins Simões; Anne Tristan; Andreas Petersen; Maliha Aziz; Kristoffer Kiil; Ivana Cirković; Edet E Udo; Rosa del Campo; Jaana Vuopio-Varkila; Norazah Ahmad; Sima Tokajian; Georg Peters; Frieder Schaumburg; Barbro Olsson-Liljequist; Michael Givskov; Elizabeth E Driebe; Henrik E Vigh; Adebayo Shittu; Nadjia Ramdani-Bougessa; Jean-Philippe Rasigade; Lance B Price; Francois Vandenesch; Anders R Larsen; Frederic Laurent
Journal:  MBio       Date:  2014-08-26       Impact factor: 7.867
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  4 in total

Review 1.  Tracing New Clinical Manifestations in Patients with COVID-19 in Chile and Its Potential Relationship with the SARS-CoV-2 Divergence.

Authors:  Alfonso J Rodriguez-Morales; Andrea Gabriela Rodriguez-Morales; Claudio A Méndez; Sebastián Hernández-Botero
Journal:  Curr Trop Med Rep       Date:  2020-04-18

2.  Genomic Epidemiology and Evolution of Diverse Lineages of Clinical Campylobacter jejuni Cocirculating in New Hampshire, USA, 2017.

Authors:  Cooper J Park; Jinfeng Li; Xinglu Zhang; Fengxiang Gao; Christopher S Benton; Cheryl P Andam
Journal:  J Clin Microbiol       Date:  2020-05-26       Impact factor: 5.948

3.  Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle.

Authors:  Isaiah Paolo A Lee; Cheryl P Andam
Journal:  BMC Microbiol       Date:  2019-12-27       Impact factor: 3.605

Review 4.  Spatial and Temporal Patterns of Typhoid and Paratyphoid Fever Outbreaks: A Worldwide Review, 1990-2018.

Authors:  Samuel Kim; Kang Sung Lee; Gi Deok Pak; Jean-Louis Excler; Sushant Sahastrabuddhe; Florian Marks; Jerome H Kim; Vittal Mogasale
Journal:  Clin Infect Dis       Date:  2019-10-30       Impact factor: 9.079
  4 in total

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