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

Genomics|Update|Infectious Diseases

Volume 34  Number 11  March 19-26, 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

DNA sequencing for the confirmation of rifampin resistance detected by Cepheid Xpert® MTB/RIF Assay. 
McAlister AJ et al. J. Clin. Microbiol. 2015 Mar 4. (CDC Author)

In vivo horizontal gene transfer of the carbapenemase OXA-48 during a nosocomial outbreak. 
Göttig S et al. Clin. Infect. Dis. 2015 Mar 10.

Circulation of a multiresistant, conjugative, IncA/C plasmid within the nosocomial Providencia stuartii population in the Athens area. 
Giakkoupi P et al. Diagn. Microbiol. Infect. Dis. 2015 Feb 23.

Acinetobacter calcoaceticus from a fatal case of pneumonia harboring bla NDM-1 on a widely distributed plasmid. 
Li P et al. BMC Infect. Dis. 2015 Dec (1) 870

Molecular analysis of the integrons of metallo-ß-lactamase-producing Pseudomonas aeruginosa isolates collected by nationwide surveillance programs across Japan. 
Mano Y et al. BMC Microbiol. 2015 Dec (1) 378

Assessment of multidrug resistance, clonality and virulence in non-PCV-13 Streptococcus pneumoniae serotypes in Canada, 2011-13. 
Golden AR et al. J. Antimicrob. Chemother. 2015 Mar 11.

Presence and new genetic environment of pleuromutilin-lincosamide-streptogramin A resistance gene lsa(E) in Erysipelothrix rhusiopathiae of swine origin. 
Zhang A et al. Vet. Microbiol. 2015 Feb 25.

Drug-resistance mechanisms and tuberculosis drugs. 
Köser CU et al. Lancet 2015 Jan 24. (9965) 305-7

Search for novel candidate mutations for metronidazole resistance in helicobacter pylori using next-generation sequencing. 
Binh TT et al. Antimicrob. Agents Chemother. 2015 Apr (4) 2343-8

Evolution and SNPs in Methicillin-resistant Staphylococcus aureus strains with reduced susceptibility to vancomycin and daptomycin, based on determination of the complete genome.
Yamaguchi T et al. Antimicrob. Agents Chemother. 2015 Mar 16.

Integrated sentinel surveillance linking genetic, antigenic and epidemiologic monitoring of influenza vaccine-virus relatedness and effectiveness, 2013-14 season.
Skowronski DM et al. J. Infect. Dis. 2015 Mar 17.

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Detection and Diagnosis

Multi-center evaluation of the BD MAX? Enteric Bacterial Panel PCR assay for the rapid detection of Salmonella spp., Shigella spp., Campylobacter spp. (C. jejuni and C. coli), and Shiga toxin 1 and 2 genes. 
Harrington SM et al. J. Clin. Microbiol. 2015 Mar 4.

Salmonella serotype determination utilizing high-throughput genome sequencing data. 
Zhang S et al. J. Clin. Microbiol. 2015 Mar 11. (CDC Author)

Development of a metabolic biosignature for detection of early Lyme disease. 
Molins CR et al. Clin. Infect. Dis. 2015 Mar 11. (CDC Author)

Development of a single nucleotide polymorphism barcode to genotype plasmodium vivax infections.
Baniecki ML et al. PLoS Negl Trop Dis 2015 Mar (3) e0003539

Urine sample preparation in 96-well filter plates to characterize inflammatory and infectious diseases of the urinary tract. 
Yu Y et al. Adv. Exp. Med. Biol. 2015 77-87

Use of MALDI-TOF mass spectrometry fingerprinting to characterize Enterococcus spp. and Escherichia coli isolates. 
Santos T et al. J Proteomics 2015 Mar 6.

Advances in molecular diagnosis of parasitic enteropathogens. 
Byrne S et al. Pathology 2015 Apr (3) 234-42

Evaluation of conjunctival swab as a mass-screening tool for molecular diagnosis of canine visceral leishmaniasis. 
Leite RS et al. Parasitol. Res. 2015 Mar 19.

Combined stool-based multiplex PCR and microscopy for enhanced pathogen detection in patients with persistent diarrhoea and asymptomatic controls from Côte d'Ivoire. 
Becker SL et al. Clin. Microbiol. Infect. 2015 Mar 3.

Application of a seven-target pyrosequencing assay to improve the detection of neuraminidase inhibitor-resistant influenza A(H3N2) viruses. 
Tamura D et al. Antimicrob. Agents Chemother. 2015 Apr (4) 2374-9 (CDC Author)

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Epidemiology, Outbreaks, Transmission

Epidemiological and viral genomic sequence analysis of the 2014 Ebola outbreak reveals clustered transmission. 
Scarpino SV et al. Clin. Infect. Dis. 2015 Apr 1. (7) 1079-82

Whole-genome sequencing and epidemiological analysis do not provide evidence for cross-transmission of mycobacterium abscessus in a cohort of pediatric cystic fibrosis patients. 
Harris KA et al. Clin. Infect. Dis. 2015 Apr 1. (7) 1007-16

Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area. 
Guerra-Assunção J et al. Elife 2015

MALDI-TOF and comparative genomic analysis of M-18 GAS strains associated with acute rheumatic fever outbreak in Northeast Italy, 2012-2013. 
Gaibani P et al. J. Clin. Microbiol. 2015 Mar 4.

Recurrence due to relapse or reinfection with Mycobacterium tuberculosis: A whole-genome sequencing approach in a large, population-based cohort with a high HIV infection prevalence and active follow-up.
Guerra-Assunção JA et al. J. Infect. Dis. 2015 Apr 1. (7) 1154-63

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Evolution, Ecology, Pathogenicity, Populations

Genetic analysis and characterization of wild poliovirus type 1 during sustained transmission in a population with >95% vaccine coverage, Israel 2013. 
Shulman LM et al. Clin. Infect. Dis. 2015 Apr 1. (7) 1057-64

Dissemination, divergence and establishment of H7N9 influenza viruses in China. 
Lam TTY et al. Nature 2015 Mar 11.

Discovery of novel rhabdoviruses in the blood of healthy individuals from West Africa. 
Stremlau MH et al. PLoS Negl Trop Dis 2015 Mar (3) e0003631

Prevalence and diversity of small mammal-associated bartonella species in rural and urban kenya. 
Halliday JEB et al. PLoS Negl Trop Dis 2015 Mar (3) e0003608 (CDC Author)

Comparative analysis of field-isolate and monkey-adapted plasmodium vivax genomes. 
Chan Ernest R et al. PLoS Negl Trop Dis 2015 Mar (3) e0003566 (CDC Author)

Complete genomic sequence for an avian group g rotavirus from South Africa. 
Stucker KM et al. Genome Announc 2015 (2) (CDC Author)

Subtyping novel zoonotic pathogen cryptosporidium chipmunk genotype I. 
Guo Y et al. J. Clin. Microbiol. 2015 Mar 11. (CDC Author)

Molecular characterization of echinococcus granulosus sensu lato from farm animals in Egypt. 
Amer S et al. PLoS ONE 2015 (3) e0118509 (CDC Author)

Draft genome sequence of a New Delhi Metallo-ß-Lactamase-5 (NDM-5)-producing multidrug-resistant Escherichia coli isolate. 
de Man TJB et al. Genome Announc 2015 (2) (CDC Author)

Delineation of Culicoides species by morphology and barcode exemplified by three new species of the subgenus Culicoides (Diptera: Ceratopogonidae) from Scandinavia. 
Nielsen SA et al. Parasit Vectors 2015 Dec (1) 750

Evolutionary analysis of Tembusu virus: Evidence for the emergence of a dominant genotype. 
Dai L et al. Infect. Genet. Evol. 2015 Mar 11.

Emergence in Taiwan of novel norovirus GII.4 variants causing acute gastroenteritis and intestinal hemorrhage in children. 
Chen SY et al. J. Med. Microbiol. 2015 Mar 9.

Epidemiological and etiological characteristics of hand, foot, and mouth disease in Wuhan, China from 2012 to 2013: Outbreaks of Coxsackieviruses A10. 
Yang Q et al. J. Med. Virol. 2015 Mar 9.

Evolution and population genomics of the Lyme borreliosis pathogen, Borrelia burgdorferi. 
Seifert SN et al. Trends Genet. 2015 Mar 9.

Molecular epidemiology of adenovirus type 21 respiratory strains isolated from US military trainees (1996-2014). 
Kajon AE et al. J. Infect. Dis. 2015 Mar 6.

Emergence of infectious malignant thrombocytopenia in Japanese macaques (Macaca fuscata) by SRV-4 after transmission to a novel host. 
Okamoto M et al. Sci Rep 2015 8850

Identifying the pattern of molecular evolution for Zaire Ebolavirus in the 2014 outbreak in West Africa. 
Liu SQ et al. Infect. Genet. Evol. 2015 Mar 4. 51-59

Similarity of currently circulating H1N1 virus with the 2009 pandemic clone: Viability of an imminent pandemic. 
Banerjee R et al. Infect. Genet. Evol. 2015 Feb 28.

Molecular epidemiology study of swine influenza virus revealing a reassorted virus H1N1 in swine farms in Cuba. 
Pérez LJ et al. Prev. Vet. Med. 2015 Feb 23.

Genetic lineages and antimicrobial resistance in Pseudomonas spp. isolates recovered from food samples. 
Estepa V et al. Foodborne Pathog. Dis. 2015 Mar 16.

Group C Streptococcus dysgalactiae subsp. equisimilis in south-east Brazil: Genetic diversity, resistance profile, and the first report of human and equine isolates belonging to the same MLST lineage. 
Silva LG et al. J. Med. Microbiol. 2015 Mar 9.

Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus. 
Baines SL et al. MBio 2015 (2)

Characterization of Staphylococcus aureus strains isolated from faeces of healthy neonates and potential mother-to-infant microbial transmission through breastfeeding. 
Benito D et al. FEMS Microbiol. Ecol. 2015 Mar (3)

Common isolation of New Delhi metallo-beta-lactamase 1-producing Enterobacteriaceae in a large surgical hospital in Vietnam.
Tran HH et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Mar 3.

Genetic diversity and population structure in the Leishmania guyanensis vector Lutzomyia anduzei (Diptera, Psychodidae) from the Brazilian Amazon.
Scarpassa VM et al. Infect. Genet. Evol. 2015 Apr 312-20

Geographical segregation of Cryptosporidium parvum multilocus genotypes in Europe.
Cacciò SM et al. Infect. Genet. Evol. 2015 Apr 245-9

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Host-Pathogen Interactions

Susceptibility to tuberculosis is associated with variants in the ASAP1 gene encoding a regulator of dendritic cell migration. 
Curtis J et al. Nat. Genet. 2015 Mar 16.

Evolutionary insights into host-pathogen interactions from mammalian sequence data 
Sironi M, et al. Nat Rev Genet 2015;16:224?236.

Innate susceptibility to norovirus infections influenced by FUT2 genotype in a United States pediatric population. 
Currier RL et al. Clin. Infect. Dis. 2015 Mar 5. (CDC Author)

G6PD gene variants and its association with malaria in a Sri Lankan population. 
Dewasurendra RL et al. Malar. J. 2015 Dec (1) 603

Higher proportion of viral basal core promoter mutant increases the risk of liver cirrhosis in hepatitis B carriers. 
Tseng TC et al. Gut 2015 Feb (2) 292-302

Viral factors and predicting disease outcomes in chronic hepatitis B. 
Revill P et al. Gut 2015 Feb (2) 191-3

Characterization and genotyping of the DRB1 gene of the major histocompatibility complex (MHC) in the Marmota monax, animal model of hepatitis B. 
Moreno-Cugnon L et al. Mol. Immunol. 2015 Feb (2) 505-12

Prevalence of human papillomavirus in penile malignant tumors: viral genotyping and clinical aspects. 
de Sousa IDB et al. BMC Urol 2015 Dec (1) 7

A single natural nucleotide mutation alters bacterial pathogen host tropism.
Viana D et al. Nat. Genet. 2015 Feb 16.

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Methods

Punch card programmable microfluidics. 
Korir G et al. PLoS ONE 2015 (3) e0115993

Xenosurveillance: a novel mosquito-based approach for examining the human-pathogen landscape. 
Grubaugh ND et al. PLoS Negl Trop Dis 2015 Mar (3) e0003628

Metacommunity and phylogenetic structure determine wildlife and zoonotic infectious disease patterns in time and space. 
Suzán G et al. Ecol Evol 2015 Feb (4) 865-73

Integration of published information into a resistance-associated mutation database for Mycobacterium tuberculosis.
Salamon H et al. J. Infect. Dis. 2015 Apr 1. (suppl 2) S50-S57

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Policy

FDA issues draft guidance on use of electronic informed consent (eIC) 
Rethinking Clinical Trials, Mar 10, 2015.

Enduring and emerging challenges of informed consent. 
Grady C et al. N. Engl. J. Med. 2015 Feb 26. (9) 855-62

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Reviews, News and Commentaries

Horizontal gene transfer a hallmark of animal genomes? 
Madhusoodanan J. The Scientist, Mar 12, 2015.

Flu genomes trace H7N9 evolution. 
Butler D et al. Nature 2015 Mar 12. (7542) 137

PANGEA-HIV: phylogenetics for generalised epidemics in Africa. 
Pillay D et al. Lancet Infect Dis 2015 Mar (3) 259-61

Identification of new respiratory viruses in the new millennium. 
Berry M et al. Viruses 2015 (3) 996-1019

Pre-symptomatic diagnosis and treatment of filovirus diseases. 
Shurtleff AC et al. Front Microbiol 2015 108

Tuberculosis diagnostics in 2015: Landscape, priorities, needs, and prospects. 
Pai M et al. J. Infect. Dis. 2015 Apr 1. (suppl 2) S21-S28

Microbiome editing with CRISPR/Cas9 has research, diagnostic potential 
Han AP. GenomeWeb, Mar 16, 2015.

PGT, Case Western to develop NGS-based tests for HIV drug resistance 
GenomeWeb, Mar 12, 2015.

FDA clears Quidel's trichomonas assay 
GenomeWeb, Mar 17, 2015.

Tute Genomics shares genetic variants database on Google genomics 
Proffitt A. Bio-IT World, Mar 12, 2015.

BioFire respiratory panel less sensitive for pertussis than standard PCR; has specificity edge 
Johnson M. Genome Web, Mar 13, 2015.

PacBio at AGBT 
Bio-IT World, Mar 3, 2015.

Protection without a vaccine 
Zimmer C. New York Times, Mar 9, 2015.