Genomics|Update|Infectious Diseases ► Methods

Genomics|Update|Infectious Diseases

Volume 34  Number 7  February 19- March 5, 2015

Methods

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species.
Greenblum Sharon et al. Cell 2015 Feb 12. (4) 583-94

How to optimise the yield of forensic and clinical post-mortem microbiology with an adequate sampling: a proposal for standardisation.
Fernández-Rodríguez A et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Feb 14.

Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences.
Pérez-Losada Marcos et al. Infect. Genet. Evol. 2015 Mar 296-307

Building high-quality assay libraries for targeted analysis of SWATH MS data.
Schubert Olga T et al. Nat Protoc 2015 Mar (3) 426-41

Genomics|Update|Infectious Diseases ► Host-Pathogen Interactions

Genomics|Update|Infectious Diseases

Volume 34  Number 7  February 19- March 5, 2015

Host-Pathogen Interactions

Genetically Modifying the Insect Gut Microbiota to Control Chagas Disease Vectors through Systemic RNAi.
Taracena Mabel L et al. PLoS Negl Trop Dis 2015 Feb (2) e0003358

Patterns of genome evolution that have accompanied host adaptation in Salmonella.
Langridge Gemma C et al. Proc. Natl. Acad. Sci. U.S.A. 2015 Jan 20. (3) 863-8

Microbiota that affect risk for shigellosis in children in low-income countries.
Lindsay Brianna et al. Emerging Infect. Dis. 2015 Feb (2) 242-50

Toll-like receptor 1 and 10 polymorphisms, Helicobacter pylori susceptibility and risk of gastric lesions in a high-risk Chinese population.
Tang Fu-Bing et al. Infect. Genet. Evol. 2015 Feb 14.

Wound healing genes and susceptibility to cutaneous leishmaniasis in Brazil: Role of COL1A1.
Almeida Lucas et al. Infect. Genet. Evol. 2015 Mar 225-9

Influence of interleukin 10 polymorphisms -592 and -1082 to the HIV, HBV and HCV serostatus among intravenous drug users.
Kallas Eveli et al. Infect. Genet. Evol. 2015 Mar 175-80

Maternal human leukocyte antigen-G (HLA-G) genetic variants associate with in utero mother-to-child transmission of HIV-1 in Black South Africans.
Hong Heather A et al. Infect. Genet. Evol. 2015 Mar 147-58

Increased frequency of JC-polyomavirus detection in rheumatoid arthritis patients treated with multiple biologics.
Verheyen Jens et al. Med. Microbiol. Immunol. 2015 Feb 13.

Genomics|Update|Infectious Diseases ► Evolution, Ecology, Pathogenicity, Populations

Genomics|Update|Infectious Diseases

Volume 34  Number 7  February 19- March 5, 2015

Evolution, Ecology, Pathogenicity, Populations

CRF19_cpx is an evolutionary fit HIV-1 variant strongly associated with rapid progression to AIDS in Cuba
Kouri V, et al. eBioMedicine, Jan 28, 2015.

Genomic Analysis of the Evolution and Global Spread of Hyper-invasive Meningococcal Lineage 5
Harrison OB, et al. eBioMedicine, Jan 13, 2015.

Extent of Mycobacterium bovis transmission among animals of dairy and beef cattle and deer farms in South Korea determined by variable-number tandem repeats typing.
Je Sungmo et al. Vet. Microbiol. 2015 Jan 15.

Clonal distribution of multidrug-resistant Enterobacter cloacae.
Girlich Delphine et al. Diagn. Microbiol. Infect. Dis. 2015 Jan 16.

An overview of various typing methods for clinical epidemiology of the emerging pathogen Stenotrophomonas maltophilia.
Gherardi Giovanni et al. Diagn. Microbiol. Infect. Dis. 2014 Nov 15.

Comparison of Porcine Epidemic Diarrhea Viruses from Germany and the United States, 2014 
Hanke D, et al. Emerg Infect Dis, Mar 2015.

Reassortant Highly Pathogenic Influenza A(H5N6) Virus in Laos 
Wong FY, et al. Emerg Infect Dis, Mar 2015.

Molecular epidemiology of coxsackievirus A6 associated with outbreaks of hand, foot, and mouth disease in Tianjin, China, in 2013.
Tan Xiaojuan et al. Arch. Virol. 2015 Feb 15.

Molecular epidemiology of echoviruses 11 and 30 in Russia: Different properties of genotypes within an enterovirus serotype.
Yarmolskaya Maria S et al. Infect. Genet. Evol. 2015 Mar 244-8

Dynamics and evolution of highly pathogenic porcine reproductive and respiratory syndrome virus following its introduction into a herd concurrently infected with both types 1 and 2.
Chaikhumwang Puwich et al. Infect. Genet. Evol. 2015 Mar 164-74

Geographical segregation of Cryptosporidium parvum multilocus genotypes in Europe
Caccio SM, et al. Infect Genet Evol, Feb 13, 2015.

Detection and characterization of a novel human parechovirus genotype in Thailand
Chuchaona W, et al. Infect Genet Evol, Feb 11, 2015.

Mycobacterium tuberculosis lineage 7 strains are associated with prolonged patient delay in pulmonary tuberculosis patients in Amhara Region, Ethiopia.
Yimer Solomon A et al. J. Clin. Microbiol. 2015 Feb 11.

Episodic Nucleotide Substitutions in Seasonal Influenza Virus H3N2 Can Be Explained by Stochastic Genealogical Process without Positive Selection.
Kim Kangchon et al. Mol. Biol. Evol. 2015 Mar (3) 704-10

Genomics|Update|Infectious Diseases ► Epidemiology, Outbreaks, Transmission

Genomics|Update|Infectious Diseases

Volume 34  Number 7  February 19- March 5, 2015

Epidemiology, Outbreaks, Transmission

Antiretroviral Treatment Failure, Drug resistance and Subtype Diversity in the only Pediatric HIV Clinic in Rhode Island.
Rogo Tanya et al. Clin. Infect. Dis. 2015 Jan 30.

Tuberculosis Microepidemics among Dispersed Migrants, Birmingham, UK, 2004-2013 
Munang ML, et al. Emerg Infect Dis, Mar 2015.

Spillover of Mycobacterium bovis from Wildlife to Livestock, South Africa 
Musoke J, et al. Emerg Infect Dis, Mar 2015.

Mycobacterium bovis Infection in Humans and Cats in Same Household, Texas, USA, 2012 
Ramdas KE, et al. Emerg Infect Dis, Mar 2015.

Genomics|Update|Infectious Diseases ► Detection and Diagnosis

Genomics|Update|Infectious Diseases

Volume 34  Number 7  February 19- March 5, 2015

Detection and Diagnosis

Nanomicroarray and Multiplex Next-Generation Sequencing for Simultaneous Identification and Characterization of Influenza Viruses 
Zhao J, et al. Emerg Infect Dis, Mar 2015.

Microbial diagnosis of bloodstream infection: Towards molecular diagnosis directly from blood.
Opota Onya et al. Clin. Microbiol. Infect. 2015 Feb 13.

Multilocus sequence typing approach for a broader range of species of Leishmania genus: Describing parasite diversity in Argentina.
Marco Jorge D et al. Infect. Genet. Evol. 2015 Mar 308-17

Development of a Multilocus Sequence Typing scheme for the study of Anaplasma marginale population structure over space and time.
Guillemi Eliana C et al. Infect. Genet. Evol. 2015 Mar 186-94

Whole genome detection of rotavirus mixed infections in human, porcine and bovine samples co-infected with various rotavirus strains collected from sub-Saharan Africa
Nyaga MM, et al. Infect Genet Evol, Feb 17, 2015.

Clinical application of whole genome sequencing to inform treatment for multi-drug resistant tuberculosis cases.
Witney Adam A et al. J. Clin. Microbiol. 2015 Feb 11.

Variola virus specific diagnostic assays: characterization, sensitivity, and specificity.
Kondas Ashley V et al. J. Clin. Microbiol. 2015 Feb 11.

Genomics|Update|Infectious Diseases ► Antimicrobials, Vaccines, Interventions

Genomics|Update|Infectious Diseases

Volume 34  Number 7  February 19- March 5, 2015

Antimicrobials, Vaccines, Interventions

Intrachromosomal Amplification, Locus Deletion and Point Mutation in the Aquaglyceroporin AQP1 Gene in Antimony Resistant Leishmania (Viannia) guyanensis.
Monte-Neto Rubens et al. PLoS Negl Trop Dis 2015 Feb (2) e0003476

Pre-Treatment HIV Drug Resistance and HIV-1 Subtype C are Independently Associated with Virologic Failure: Results from the Multi-national PEARLS (ACTG A5175) Clinical Trial.
Kantor R et al. Clin. Infect. Dis. 2015 Feb 13.

The Clinical Significance of HIV Subtype Variability in Regard to Treatment Outcome.
Wainberg Mark A et al. Clin. Infect. Dis. 2015 Feb 13.

A Single Phosphorodiamidate Morpholino Oligomer Targeting VP24 Protects Rhesus Monkeys against Lethal Ebola Virus Infection.
Warren Travis K et al. MBio 2015 (1)

G1P[8] species A rotavirus over 27years - Pre- and post-vaccination eras - in Brazil: Full genomic constellation analysis and no evidence for selection pressure by Rotarix® vaccine.
da Silva Marcelle Figueira Marques et al. Infect. Genet. Evol. 2015 Mar 206-18

Absence of Putative Artemisinin Resistance Mutations Among Plasmodium falciparum in Sub-Saharan Africa: A Molecular Epidemiologic Study.
Taylor Steve M et al. J. Infect. Dis. 2015 Mar 1. (5) 680-8

Oral multicomponent DNA vaccine delivered by attenuated Salmonella elicited immunoprotection against American trypanosomiasis.
Cazorla Silvia I et al. J. Infect. Dis. 2015 Mar 1. (5) 698-707

Safety and immunogenicity of DNA vaccines encoding Ebolavirus and Marburgvirus wild-type glycoproteins in a phase I clinical trial.
Sarwar Uzma N et al. J. Infect. Dis. 2015 Feb 15. (4) 549-57

Rapid and profound shifts in the vaginal microbiota following antibiotic treatment for bacterial vaginosis.
Mayer Bryan T et al. J. Infect. Dis. 2015 Feb 12.