Genomics|Update|Infectious Diseases ► Advanced Molecular Detection in Action

Genomics|Update|Infectious Diseases

Volume 34  Number 6  February 12-19, 2015

Advanced Molecular Detection in Action

• Antimicrobials, Vaccines, Interventions
• Detection & Diagnosis
• Epidemiology, Outbreaks, Transmission
• Evolution, Ecology, Pathogenicity, Populations

• Host-Pathogen Interactions
• Methods
• Policy
• Reviews, News & Commentaries

Antimicrobials, Vaccines, Interventions

Search for novel candidate mutations for metronidazole resistance in Helicobacter pylori using next-generation sequencing

Binh TT, et al. Antimicrob Agents Chemother. 2015 Feb 2.

Evolution of carbapenem-resistant Acinetobacter baumannii revealed through whole-genome sequencing and comparative genomic analysis.

Li H, et al. Antimicrob Agents Chemother. 2015 Feb;59(2):1168-76.

Characterization of plasmids in extensively drug-resistant Acinetobacter strains isolated in India and Pakistan.

Jones LS, et al. Antimicrob Agents Chemother. 2015 Feb;59(2):923-9.

Genomic insights into intrinsic and acquired drug resistance mechanisms in Achromobacter xylosoxidans.

Hu Y, et al. Antimicrob Agents Chemother. 2015 Feb;59(2):1152-61.

Complete nucleotide sequence of the IncN plasmid encoding IMP-6 and CTX-M-2 from emerging carbapenem-resistant Enterobacteriaceae in Japan.

Kayama S, et al. Antimicrob Agents Chemother. 2015 Feb;59(2):1356-9.

Dissemination of NDM metallo-β-lactamase genes among clinical isolates of Enterobacteriaceae collected during the SMART Global Surveillance Study from 2008 to 2012.

Biedenbach D, et al. Antimicrob Agents Chemother. 2015 Feb;59(2):826-30.

Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase.

Arat S, et al. Antimicrob Agents Chemother. 2015 Feb;59(2):1182-92.

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 MF, et al. Infect Genet Evol. 2015 Mar;30:206-18.

Safety and immunogenicity of DNA vaccines encoding Ebolavirus and Marburgvirus wild-type glycoproteins in a phase I clinical trial.

Sarwar UN, et al. J Infect Dis. 2015 Feb 15;211(4):549-57.

Application of a 7-target pyrosequencing assay to improve the detection of neuraminidase inhibitor resistant influenza A(H3N2) viruses

Tamura D, et al. Antimicrob Agents Chemother. 2015 Feb 2.

Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia.

Takala-Harrison S, et al. J Infect Dis. 2015 Mar 1;211(5):670-9.

Absence of putative artemisinin resistance mutations among Plasmodium falciparum in Sub-Saharan Africa: A molecular epidemiologic study.

Taylor SM, et al. J Infect Dis. 2015 Mar 1;211(5):680-8.

The emergence of resistance to the benzimidazole anthlemintics in parasitic nematodes of livestock is characterised by multiple independent hard and soft selective sweeps.

Redman E, et al. PLoS Negl Trop Dis. 2015 Feb 6;9(2):e0003494.

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Detection and Diagnosis

Molecular analysis and antimicrobial susceptibility of enterotoxigenic Escherichia coli from diarrheal patients.

Pan H, et al. Diagn Microbiol Infect Dis. 2015 Feb;81(2):126-31.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry identifies Pseudomonas aeruginosa high-risk clones.

Cabrolier N, et al. J Clin Microbiol. 2015 Feb 4.

Fusobacterium nucleatum subspecies identification by matrix-assisted laser desorption/ionization time of flight mass spectrometry.

Nie S, et al. J Clin Microbiol. 2015 Feb 4.

Fluorescent immunochromatography for rapid and sensitive typing of seasonal influenza viruses

Sakurai A, et al. PLoS One 2015 Feb 4;10(2):e0116715.

The cryptococcal antigen lateral flow assay: A point-of-care diagnostic at an opportune time.

Tang MW, et al. Crit Rev Microbiol. 2015 Jan 23:1-9.

Detection of Rickettsia spp in Ticks by MALDI-TOF MS.

Yssouf A, et al. PLoS Negl Trop Dis. 2015 Feb 6;9(2):e0003473.

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Epidemiology, Outbreaks, Transmission

Differential single nucleotide polymorphism analysis of an outbreak caused by Salmonella enterica serovar Manhattan reveals epidemiological details missed by standard pulsed-field gel electrophoresis.

Scaltriti E, et al. J Clin Microbiol. 2015 Feb 4.

Emergence of an outbreak-associated Clostridium difficile variant with increased virulence.

Quesada-Gómez C, et al. J Clin Microbiol. 2015 Feb 4.

Whole-genome sequencing in hierarchy with pulsed-field gel electrophoresis: the utility of this approach to establish possible sources of MRSA cross-transmission

Moore G, et al. J Hosp Infect. 2015 Jan 13.

Tuberculous spondylitis in Russia and prominent role of multidrug-resistant clone Mycobacterium tuberculosis Beijing B0/W148

Vyazovaya A, et al. Antimicrob Agents Chemother. 2015 Feb 2.

Evolution and transmission patterns of extensively drug-resistant tuberculosis in China.

Wang F, et al. Antimicrob Agents Chemother. 2015 Feb;59(2):818-25.

Molecular characterization of HIV-1 infection in Northwest Spain (2009-2013): Investigation of the subtype F outbreak.

Paraskevis D, et al. Infect Genet Evol. 2015 Mar;30:96-101.

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Evolution, Ecology, Pathogenicity, Populations

Geospatial resolution of human and bacterial diversity with city-scale metagenomics  [PDF 5.56 MB]

Afshinnekoo E, et al. Cell Systems 2015; 1:1-15.

Comment:

Metagenomic study offers glimpse of NYC subway system microbes

GenomeWeb, Feb 5, 2015.

Geographically distinct Escherichia coli O157 isolates differ by lineage, shiga toxin genotype, and total shiga toxin production.

Mellor GE, et al. J Clin Microbiol. 2015 Feb;53(2):579-86.

Comparative analysis of super-shedder strains of Escherichia coli O157:H7 reveals distinctive genomic features and a strongly aggregative adherent phenotype on bovine rectoanal junction squamous epithelial cells

Cote R, et al. PLoS One 2015 Feb 9;10(2):e0116743.

Genomic sequences of six botulinum neurotoxin-producing strains representing three clostridial species illustrate the mobility and diversity of botulinum neurotoxin genes.

Smith TJ, et al. Infect Genet Evol. 2015 Mar;30:102-13.

Identification and characterization of regions of difference between the Salmonella Gallinarum biovar Gallinarum and the Salmonella Gallinarum biovar Pullorum genomes.

Batista DF, et al. Infect Genet Evol. 2015 Mar;30:74-81.

Phylogenetic analysis of environmental Legionella pneumophila isolates from an endemic area (Alcoy, Spain).

Sánchez-Busó L, et al. Infect Genet Evol. 2015 Mar;30:45-54.

Finer characterization of Mycobacterium tuberculosis using spoligotyping and 15-loci MIRU-VNTRs reveals phylogeographical specificities of isolates circulating in Guyana and Suriname.

Streit E, et al. Infect Genet Evol. 2015 Mar;30:114-9

Genome sequence of enterovirus D68 and clinical disease, Thailand.

Vongpunsawad S, et al. Emerg Infect Dis. 2015 Feb;21(2):384.

Genome characterization of a GII.6 norovirus strain identified in China.

Xue L, et al. Infect Genet Evol. 2015 Feb 4.

Molecular epidemiology of echoviruses 11 and 30 in Russia: Different properties of genotypes within an enterovirus serotype.

Yarmolskaya MS, et al. Infect Genet Evol. 2015 Mar;30:244-8.

Genetic and antigenic analysis of foot-and-mouth disease virus serotype O responsible for outbreaks in India during 2013.

Subramaniam S, et al. Infect Genet Evol. 2015 Mar;30:59-64.

Homologous recombination in pestiviruses: Identification of three putative novel events between different subtypes/genogroups.

Weber MN, et al.  Infect Genet Evol. 2015 Mar;30:219-24.

Molecular characterization of a new mosaic simian immunodeficiency virus in a naturally infected tantalus monkey (Chlorocebus tantalus) from Cameroon: A challenge to the virus-host co-evolution of SIVagm in African green monkeys.

Ayouba A, et al. Infect Genet Evol. 2015 Mar;30:65-73.

A new member of the pteropine orthoreovirus species isolated from fruit bats imported to Italy.

Lorusso A, et al. Infect Genet Evol. 2015 Mar;30:55-8.

Plasmodium falciparum field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype.

Brown TS, et al. Infect Genet Evol. 2015 Mar;30:318-22.

Multilocus typing and population structure of Cryptosporidium from children in Zaragoza, Spain.

Ramo A, et al. Infect Genet Evol. 2015 Feb 6.

Multilocus sequence typing approach for a broader range of species of Leishmania genus: Describing parasite diversity in Argentina.

Marco JD, et al. Infect Genet Evol. 2015 Mar;30:308-17.

Development of a multilocus sequence typing scheme for the study of Anaplasma marginale population structure over space and time.

Guillemi EC, et al. Infect Genet Evol. 2015 Mar;30:186-94.

Genetic blueprint of the zoonotic pathogen Toxocara canis.

Zhu XQ, et al. Nat Commun, Feb 4, 2015.

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Host-Pathogen Interactions

The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes

Kostic AD, et al. Cell Host Microbe, Feb 5, 2015.

Association between Helicobacter spp. infections and hepatobiliary malignancies: A review

Segura-López FK, et al. World J Gastroenterol. 2015 Feb 7;21(5):1414-1423.

Influence of IL10 gene polymorphisms on the severity of liver fibrosis and susceptibility to liver cirrhosis in HBV/HCV-infected patients.

Guo PF, et al. Infect Genet Evol. 2015 Mar;30:89-95.

Wound healing genes and susceptibility to cutaneous leishmaniasis in Brazil: Role of COL1A1.

Almeida L, et al. Infect Genet Evol. 2015 Mar;30:225-9.

Multi-locus analysis of Giardia duodenalis from nonhuman primates kept in zoos in China: Geographical segregation and host-adaptation of assemblage B isolates.

Karim MR, et al. Infect Genet Evol. 2015 Mar;30:82-8.

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Methods

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.

Sharon I, et al. Genome Res. 2015 Feb 9.

Comment:

Metagenomic sequencing with synthetic long reads illustrates vast microbial diversity

Heger M. GenomeWeb, Feb 10, 2015.

Reconstructing (super)trees from data sets with missing distances: Not all is lost.

Kettleborough G, et al. Mol Biol Evol. 2015 Feb 4.

Bayesian inference of infectious disease transmission from whole-genome sequence data

Didelot X, et al. Mol Biol Evol. 2014;31(7):1869-79.

Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences.

Pérez-Losada M, et al. Infect Genet Evol. 2015 Mar;30C:296-307.

Within-host nucleotide diversity of virus populations: Insights from next-generation sequencing.

Nelson CW, Hughes AL. Infect Genet Evol. 2015 Mar;30C:1-7.

Accurate quantification of episomal HIV-1 two-long terminal repeat circles by use of optimized DNA isolation and droplet digital PCR.

Malatinkova E, et al. J Clin Microbiol. 2015 Feb;53(2):699-701.

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Policy

Horizontal gene transfer in human pathogens.

Juhas M. Crit Rev Microbiol. 2015 Feb;41(1):101-8.

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Reviews, News and Commentaries

Startup One Codex building platform to ID pathogens from NGS data

Fong T. GenomeWeb, Feb 10, 2015.

Quick DNA scans could ensure food is safe to eat

Neimark J. Sci Am, Feb 4, 2015.

Google to reshape how it provides health information, Mayo Clinic joins as a partner

Verel D. MedCity News, Feb 10, 2015.

As Ebola epidemic begins to slow, trials of drugs and vaccines speed up

Kuehn BM. JAMA, Feb 11, 2015.

New York’s Chief Medical Examiner seeks to lead in DNA research

Goodman JD. New York Times, Feb 9, 2015.

GenomeWeb updates on molecular diagnostics:

T2 Biosystems inks $8.5M Lyme disease Dx deal with Canon US Life Sciences

Rheonix gets $1.5M NIH grant to commercialize POC HIV/AIDS test

Biocartis, Janssen Diagnostic developing PCR-based Ebola test