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

Genomics|Update|Infectious Diseases

Volume 34  Number 20  May 21-28, 2015

Advanced Molecular Detection in Action

Antimicrobials, Vaccines, Interventions

A high throughput protein microarray approach to classify HIV monoclonal antibodies and variant antigens.
Dotsey EY et al. PLoS ONE 2015 (5) e0125581

Naturally occurring deletion/insertion mutations within HBV whole genome sequences in HBeAg-positive chronic hepatitis B patients are correlated with baseline serum HBsAg and HBeAg levels and might predict a shorter interval to HBeAg loss and seroconversion during antiviral treatment.
Hao R et al. Infect. Genet. Evol. 2015 May 12.

Silencing the buzz: a new approach to population suppression of mosquitoes by feeding larvae double-stranded RNAs.
Whyard S et al. Parasit Vectors 2015 96

Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria
Yosef I, et al. PNAS, May 18, 2014.

Polymorphic variation in susceptibility and metabolism of triclosan-resistant mutants of Escherichia coli and Klebsiella pneumoniae clinical strains obtained after exposure to biocides and antibiotics.
Curiao T et al. Antimicrob. Agents Chemother. 2015 Jun (6) 3413-23

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Detection and Diagnosis

Comparison of diagnostic techniques for the detection of Cryptosporidium oocysts in animal samples.
Ezzaty MM et al. Exp. Parasitol. 2015 Apr-May 14-20

Rapid whole genome sequencing of M. tuberculosis directly from clinical samples.
Brown Amanda C et al. J. Clin. Microbiol. 2015 May 13.

Sensitive detection of norovirus using phage nanoparticle reporters in lateral-flow assay.
Hagström AEV et al. PLoS ONE 2015 (5) e0126571

Detection of low-level mixed-population drug resistance in mycobacterium tuberculosis using high fidelity amplicon sequencing.
Colman RE et al. PLoS ONE 2015 (5) e0126626

Multiplex gastrointestinal pathogen panels: implications for infection control.
Rand KH et al. Diagn. Microbiol. Infect. Dis. 2015 Jun (2) 154-7

Multiplex real-time PCR assay using TaqMan probes for the identification of Trypanosoma cruzi DTUs in biological and clinical samples. 
Cura CI et al. PLoS Negl Trop Dis 2015 May (5) e0003765

International external quality assessment study for molecular detection of Lassa virus 
Nikisins S, et al. PLoS Negl Trop Dis 2015; 9(5): e0003793.

Direct detection of influenza A/B in less than twenty minutes using a commercially-available rapid PCR assay. 
Binnicker MJ et al. J. Clin. Microbiol. 2015 Apr 29.

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Epidemiology, Outbreaks, Transmission

Genotypic and spatial analysis of Mycobacterium tuberculosis transmission in a high-incidence urban setting.
Ribeiro FK et al. Clin. Infect. Dis. 2015 May 5.

What caused the outbreak of ESBL-producing Klebsiella pneumoniae in a neonatal intensive care unit, Germany 2009 to 2012? Reconstructing transmission with epidemiological analysis and whole-genome sequencing.
Haller S et al. BMJ Open 2015 (5) e007397

An unidentified cluster of infection in the Peruvian Amazon region.
Cornejo A et al. J Infect Dev Ctries 2015 (5) 524-529

Investigating fungal outbreaks in the 21st century 
Litvintseva AP, et al. PLoS Pathog 11(5): e1004804. (CDC Author)

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Evolution, Ecology, Pathogenicity, Populations

Deep sequencing analysis of the Ixodes ricinus haemocytome.
Kotsyfakis M et al. PLoS Negl Trop Dis 2015 May (5) e0003754

Genetic diversity and host associations in Campylobacter jejuni from human cases and broilers in 2000 and 2008.
Griekspoor P et al. Vet. Microbiol. 2015 May 5.

Characterisation of Chlamydia pneumoniae and other novel chlamydial infections in captive snakes.
Taylor-Brown A et al. Vet. Microbiol. 2015 Apr 28.

Antimicrobial resistance and population structure of Staphylococcus epidermidis recovered from animals and humans.
Argudín MA et al. Vet. Microbiol. 2015 Apr 27.

Identification and characterization of expressed retrotransposons in the genome of the Paracoccidioides species complex.
Soares MA et al. BMC Genomics 2015 376

Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity.
Li Y et al. BMC Genomics 2015 369

A novel multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) method for Propionibacterium acnes.
Hauck Y et al. Infect. Genet. Evol. 2015 May 9.

Genome sequences of 11 Shiga toxin-producing Escherichia coli strains.
Gabrielsen C et al. Genome Announc 2015 (3)

Molecular characterization of resistance, virulence and clonality in vancomycin-resistant Enterococcus faecium and Enterococcus faecalis: A hospital-based study in Beijing, China.
Yang Jing-Xian et al. Infect. Genet. Evol. 2015 May 12.

Characterization of multiple NDM-1-producing enterobacteriaceae isolates from the same patient.
Tijet N et al. Antimicrob. Agents Chemother. 2015 Jun (6) 3648-51

Clinical epidemiology and molecular analysis of extended-spectrum-ß-lactamase-producing Escherichia coli in Nepal: Characteristics of sequence types 131 and 648.
Sherchan JB et al. Antimicrob. Agents Chemother. 2015 Jun (6) 3424-32

High prevalence of mupirocin resistance in Staphylococcus aureus isolates from a pediatric population.
Antonov NK et al. Antimicrob. Agents Chemother. 2015 Jun (6) 3350-6

Evolution and dissemination of OqxAB-like efflux pumps, an emerging quinolone resistance determinant among members of Enterobacteriaceae.
Wong MHY et al. Antimicrob. Agents Chemother. 2015 Jun (6) 3290-7

High prevalence of blaNDM-1 carbapenemase-encoding gene and 16S rRNA armA methyltransferase gene among Acinetobacter baumannii clinical isolates in Egypt.
El-Sayed-Ahmed M et al. Antimicrob. Agents Chemother. 2015 Jun (6) 3602-5

Longitudinal study of extended-spectrum-ß-lactamase- and ampC-producing enterobacteriaceae in household dogs.
Baede VO et al. Antimicrob. Agents Chemother. 2015 Jun (6) 3117-24

Complete nucleotide sequences of blaCTX-M-harboring IncF plasmids from community-associated Escherichia coli strains in the United States.
Li Jun-J et al. Antimicrob. Agents Chemother. 2015 Jun (6) 3002-7

Emergence of Escherichia coli producing OXA-48 ß-lactamase in the community in Switzerland.
Zurfluh K et al. Antimicrob Resist Infect Control 2015 9

KPC and NDM-1 genes in related Enterobacteriaceae strains and plasmids from Pakistan and the United States 
Pesesky MW, et al. Emerg Infect Dis, Jun 2015.

Sequence type 4821 clonal complex serogroup B Neisseria meningitidis in China, 1978?2013 
Zhu B, et al. Emerg Infect Dis, Jun 2015.

Viral genetic diversity and polymorphisms in a cohort of HIV-1-infected patients eligible for initiation of antiretroviral therapy in Abuja, Nigeria.
Diallo K et al. AIDS Res. Hum. Retroviruses 2015 May (5) 564-75 (CDC Author)

Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus.
Steinig EJ et al. BMC Genomics 2015 (1) 388

Bacterial factors associated with lethal outcome of Enteropathogenic Escherichia coli infection: Genomic case-control studies. 
Donnenberg MS et al. PLoS Negl Trop Dis 2015 May (5) e0003791

Molecular typing of pathogenic leptospira serogroup Icterohaemorrhagiae strains circulating in China during the Past 50 Years. 
Zhang C et al. PLoS Negl Trop Dis 2015 May (5) e0003762

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Host-Microbe Interactions

Dynamics and stabilization of the human gut microbiome during the first year of life.
Bäckhed F et al. Cell Host Microbe 2015 May 13. (5) 690-703

The quest for balance.
Goyal L et al. Cell Host Microbe 2015 May 13. (5) 537. (Introduction to a special issue on host-microbiota balance)

An integrative view of microbiome-host interactions in inflammatory bowel diseases.
Wlodarska M et al. Cell Host Microbe 2015 May 13. (5) 577-591

A new frontier: Oral microbes without borders (Intro to special issue on oral microbiome) 
Yilmaz O, Ojcius DM. Microbes Infect, May 20, 2015.

Experimental evolution of an RNA virus in wild birds: evidence for host-dependent impacts on population structure and competitive fitness. 
Grubaugh ND et al. PLoS Pathog. 2015 May (5) e1004874

Widespread recombination, reassortment, and transmission of unbalanced compound viral genotypes in natural arenavirus infections. 
Stenglein MD et al. PLoS Pathog. 2015 May (5) e1004900

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Methods

Machine learning applications in genetics and genomics.
Libbrecht MW et al. Nat. Rev. Genet. 2015 May 7.

Detecting DNA viruses in oral fluids: evaluation of collection and storage methods.
Speicher DJ et al. Diagn. Microbiol. Infect. Dis. 2015 Jun (2) 120-7

Inexpensive, rapid prototyping of microfluidic devices using overhead transparencies and a laser print, cut and laminate fabrication method.
Thompson BL et al. Nat Protoc 2015 Jun (6) 875-86

Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.
Skums Pl et al. Bioinformatics 2015 Mar 1. (5) 682-90 (CDC Author)

Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing
Cao MD, et al. bioRxiv, May 20, 2015.

An evaluation of the accuracy and speed of metagenome analysis tools
Lindgreen S, et al. bioRxiv, May 15, 2015.

A de novo DNA Sequencing and Variant Calling Algorithm for Nanopores
Szalay T, Golovchenko JA. bioRxiv, May 19, 2015.

ReproPhylo: An Environment for Reproducible Phylogenomics
Szitenberg A, et al. bioRxiv, May 18, 2015.

Using the taxon-specific genes for the taxonomic classification of bacterial genomes. 
Gupta Ankit et al. BMC Genomics 2015 (1) 396

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Policy

Competency guidelines for public health laboratory professionals: CDC and the Association of Public Health Laboratories.
Ned-Sykes R et al. MMWR Surveill Summ 2015 May 15. 1-81 (CDC Author)

Buzzkill: regulatory uncertainty plagues rollout of genetically modified mosquitoes.
Chakradhar S et al. Nat. Med. 2015 May 7. (5) 416-8

Awareness and support of release of genetically modified "sterile" mosquitoes, Key West, Florida, USA.
Ernst KC et al. Emerging Infect. Dis. 2015 Feb (2) 320-4

Global health security: the wider lessons from the west African Ebola virus disease epidemic.
Heymann DL et al. Lancet 2015 May 9. (9980) 1884-901

What's next for the microbiome? 
Handelsman J, Stulberg ER. White House Office of Science and Technology Policy, May 21, 2015.

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Reviews, News and Commentaries

Oxford nanopore outlines specs for new sequencers, automated sample prep system, pay-as-go pricing
Karow J. GenomeWeb,May14,2015.

U.S. introduces new DNA standard for ensuring accuracy of genetic tests
Pear R. New York Times, May 14, 2015.

Weak oversight allows lab failures to put patients at risk
Gabler E. Milwaukee Journal Sentinel, May 17, 2015.

Stemming the tide of fake medicines
Editorial, New York Times, May 18, 2015.

Infectious diseases. Ebola survivors fight back in plasma studies.
Enserink Martin et al. Science 2015 May 15. (6236) 742-3

The cat microbiome
GenomeWeb, May 15, 2015.

Targeting antibiotic-resistant bacteria with CRISPR and phages
Azvolinsky A. The Scientist, May 19, 2015.

An unknown enemy: Drugs sought against EV-68 as paralysis link is explored.
Willyard Cassandra et al. Nat. Med. 2015 May (5) 419-21

FDA grants CLIA waiver for Roche strep A assay
GenomeWeb, May 19, 2015.

Stanford team employs Illumina long reads for transcriptome sequencing
Heger M. GenomeWeb, May 18, 2015.

Diagnostic errors linked to high incidence of incorrect antibiotic use
EurekAlert! May 18, 2015.

How a small backpack for fast genomic sequencing is helping combat Ebola
Loman N. The Conversation, May 15, 2015.

Of mice and mouse clicks: AI may predict which animal species carry diseases dangerous to people
Economist, May 23, 2015.

Gene sequencing helps track food pathogens: linking cases can guide investigators to sources of outbreaks 
Newman J. Wall Street Journal, May 21, 2015.

Rabies strain, never before identified, detected in New Mexico fox 
Outbreak News Today, May 20, 2015.

Systems biology for biologists.
Hillmer Rachel A et al. PLoS Pathog. 2015 May (5) e1004786

Defining the needs for next generation assays for tuberculosis.
Denkinger Claudia M et al. J. Infect. Dis. 2015 Apr 1. S29-38 (CDC Author)

No more hidden solutions in bioinformatics
Vihinen M. Nature, May 20, 2015.

How a small backpack for fast genomic sequencing is helping combat Ebola 
Loman N. The Conversation, May 15, 2015.