Volume 34 Number 23 June 11-18, 2015
Antimicrobials/ Vaccines/ Interventions
Trends in use of genotypic resistance testing and frequency of major drug resistance among antiretroviral-naive persons in the HIV Outpatient Study, 1999-2011.
Buchacz K et al. J. Antimicrob. Chemother. 2015 May 15. (CDC Author)
Buchacz K et al. J. Antimicrob. Chemother. 2015 May 15. (CDC Author)
A global health diagnostic for personalized medicine in resource-constrained world settings: A simple PCR-RFLP method for genotyping CYP2B6 g.15582C>T and science and policy relevance for optimal use of antiretroviral drug efavirenz
Evans J, et al. OMICS, June 2015, 19(6): 332-338.
Evans J, et al. OMICS, June 2015, 19(6): 332-338.
Engineered phagemids for nonlytic, targeted antibacterial therapies.
Krom RJ et al. Nano Lett. 2015 Jun 8.
Krom RJ et al. Nano Lett. 2015 Jun 8.
A broad protection provided by matrix protein 2 (M2) of avian influenza virus.
Meng Q et al. Vaccine 2015 May 30.
Meng Q et al. Vaccine 2015 May 30.
Detection/ Diagnosis
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
Chiu CY, et al. bioRxiv, Jun 3, 2015.
Chiu CY, et al. bioRxiv, Jun 3, 2015.
Comprehensive serological profiling of human populations using a synthetic human virome
Xu GJ, et al. Science, Jun 5, 2015.
Xu GJ, et al. Science, Jun 5, 2015.
Detection of acute HIV-1 infection by RT-LAMP.
Rudolph DL et al. PLoS ONE 2015 (5) e0126609 (CDC Author)
Rudolph DL et al. PLoS ONE 2015 (5) e0126609 (CDC Author)
Borrelia miyamotoi disease in the northeastern United States: A case series.
Molloy PJ et al. Ann. Intern. Med. 2015 Jun 9.
Molloy PJ et al. Ann. Intern. Med. 2015 Jun 9.
Laboratory testing for Middle East respiratory syndrome coronavirus, California, USA, 2013-2014.
Shahkarami M, et al. Emerg Infect Dis, Sep 2015.
Shahkarami M, et al. Emerg Infect Dis, Sep 2015.
Genomic assays for identification of chikungunya virus in blood donors, Puerto Rico, 2014.
Chiu CY, et al. Emerg Infect Dis, Aug 2015.
Chiu CY, et al. Emerg Infect Dis, Aug 2015.
Three human gnathostomiasis cases in Thailand with molecular identification of causative parasite species.
Jongthawin J et al. Am. J. Trop. Med. Hyg. 2015 Jun 8.
Jongthawin J et al. Am. J. Trop. Med. Hyg. 2015 Jun 8.
Improved detection of Escherichia coli and coliform bacteria by multiplex PCR.
Molina F et al. BMC Biotechnol. 2015 (1) 48
Molina F et al. BMC Biotechnol. 2015 (1) 48
Improvements to a PCR-based serogrouping scheme for Salmonella enterica from dairy farm samples.
Karns JS et al. J. Food Prot. 2015 Jun (6) 1182-5
Karns JS et al. J. Food Prot. 2015 Jun (6) 1182-5
Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi.
Carpi Gi et al. BMC Genomics 2015 (1) 434
Carpi Gi et al. BMC Genomics 2015 (1) 434
Accurate genotyping of hepatitis C virus through nucleotide sequencing and identification of new HCV subtypes in China population.
Tong YQ et al. Clin. Microbiol. Infect. 2015 Jun 5.
Tong YQ et al. Clin. Microbiol. Infect. 2015 Jun 5.
Epidemiology/ Outbreaks/ Transmission
Hypothesis: Cryptosporidium genetic diversity mirrors national disease notification rate.
Takumi K et al. Parasit Vectors 2015 Jun 6. (1) 308 (CDC Author)
Takumi K et al. Parasit Vectors 2015 Jun 6. (1) 308 (CDC Author)
Molecular epidemiology of HIV-1 infection among men who have sex with men in Taiwan in 2012.
Huang Szu-W et al. PLoS ONE 2015 (6) e0128266
Huang Szu-W et al. PLoS ONE 2015 (6) e0128266
Enterovirus 71 infection in children with hand, foot, and mouth disease in Shanghai, China: epidemiology, clinical feature and diagnosis.
Wang Y et al. Virol. J. 2015 Jun 3. (1) 83
Wang Y et al. Virol. J. 2015 Jun 3. (1) 83
Small hospitals matter: insights from the emergence and spread of vancomycin-resistant enterococci in 2 public hospitals in inner Brazil.
Correa Adriana AF et al. Diagn. Microbiol. Infect. Dis. 2015 Jul (3) 227-33
Correa Adriana AF et al. Diagn. Microbiol. Infect. Dis. 2015 Jul (3) 227-33
Whole genome sequencing in real-time investigation and management of a Pseudomonas aeruginosa outbreak on a neonatal intensive care unit.
Davis RJ et al. Infect Control Hosp Epidemiol 2015 Jun 8. 1-7
Davis RJ et al. Infect Control Hosp Epidemiol 2015 Jun 8. 1-7
Reemergence and amplification of tuberculosis in the Canadian arctic.
Lee RS et al. J. Infect. Dis. 2015 Jun 15. (12) 1905-14
Lee RS et al. J. Infect. Dis. 2015 Jun 15. (12) 1905-14
Transmissibility of tuberculosis among school contacts: An outbreak investigation in a boarding middle school, China.
Ma Mai-Juan et al. Infect. Genet. Evol. 2015 Jun 148-55
Ma Mai-Juan et al. Infect. Genet. Evol. 2015 Jun 148-55
Evolution/ Ecology/ Populations
Bottlenecks in HIV-1 transmission: insights from the study of founder viruses
Joseph SB, et al. Nat Rev Microbiol, Jun 8, 2015.
Joseph SB, et al. Nat Rev Microbiol, Jun 8, 2015.
Global circulation patterns of seasonal influenza viruses vary with antigenic drift.
Bedford T et al. Nature 2015 Jun 8.
Bedford T et al. Nature 2015 Jun 8.
Draft whole-genome sequences of 10 enterotoxigenic Escherichia coli serogroup O6 strains.
Pattabiraman V et al. Genome Announc 2015 (3) (CDC Author)
Pattabiraman V et al. Genome Announc 2015 (3) (CDC Author)
Cryptosporidium genotypes and subtypes distribution in river water in Iran.
Mahmoudi MR et al. J Water Health 2015 Jun (2) 600-6 (CDC Author)
Mahmoudi MR et al. J Water Health 2015 Jun (2) 600-6 (CDC Author)
Locally confined clonal complexes of Mycobacterium ulcerans in two Buruli ulcer endemic regions of Cameroon.
Bolz M et al. PLoS Negl Trop Dis 2015 Jun (6) e0003802
Bolz M et al. PLoS Negl Trop Dis 2015 Jun (6) e0003802
Close genetic relationship between Salmonella enterica serovar Enteritidis isolated from patients with diarrhea and poultry in the Republic of Korea.
Lee Dong-Hun et al. Clin. Microbiol. Infect. 2015 Jun 5.
Lee Dong-Hun et al. Clin. Microbiol. Infect. 2015 Jun 5.
Parallel epidemics of community-associated methicillin-resistant Staphylococcus aureus USA300 in North and South America.
Planet PJ et al. J. Infect. Dis. 2015 Jun 5.
Planet PJ et al. J. Infect. Dis. 2015 Jun 5.
Molecular characterization of H9N2 avian influenza viruses isolated from vaccinated broiler chickens in northeast Iran.
Bahari P et al. Trop Anim Health Prod 2015 Jun 9.
Bahari P et al. Trop Anim Health Prod 2015 Jun 9.
Evolutionary dynamics of foot-and-mouth disease virus O/ME-SA/Ind2001 lineage.
Subramaniam S et al. Vet. Microbiol. 2015 May 27.
Subramaniam S et al. Vet. Microbiol. 2015 May 27.
First insights into circulating mycobacterium tuberculosis complex lineages and drug resistance in Guinea.
Ejo M et al. Infect. Genet. Evol. 2015 Jul 314-9
Ejo M et al. Infect. Genet. Evol. 2015 Jul 314-9
Genome-based discrimination between group I Clostridium botulinum and Clostridium sporogenes strains: implications for bacterial taxonomy.
Weigand MR et al. Appl. Environ. Microbiol. 2015 Jun 5. (CDC Author)
Weigand MR et al. Appl. Environ. Microbiol. 2015 Jun 5. (CDC Author)
Host-Microbe Interactions
Staphylococcus aureus and the ecology of the nasal microbiome
Liu CM, et al. Science Adv, Jun 5, 2015.
Liu CM, et al. Science Adv, Jun 5, 2015.
Host susceptibility to non-tuberculous mycobacterial infections.
Wu Un-In et al. Lancet Infect Dis 2015 Jun 3.
Wu Un-In et al. Lancet Infect Dis 2015 Jun 3.
Differences in the epidemiology of human cases of avian influenza A(H7N9) and A(H5N1) viruses infection.
Qin Y et al. Clin. Infect. Dis. 2015 May 4.
Qin Y et al. Clin. Infect. Dis. 2015 May 4.
Mechanisms linking metabolism of Helicobacter pylori to (18)O and (13)C-isotopes of human breath CO2.
Som S et al. Sci Rep 2015 10936
Som S et al. Sci Rep 2015 10936
Integration of tumour and viral genomic characterizations in HBV-related hepatocellular carcinomas.
Amaddeo Gi et al. Gut 2015 May (5) 820-9
Amaddeo Gi et al. Gut 2015 May (5) 820-9
Additive effects of HLA alleles and innate immune genes determine viral outcome in HCV infection.
Fitzmaurice K et al. Gut 2015 May (5) 813-9
Fitzmaurice K et al. Gut 2015 May (5) 813-9
Salmonella manipulation of host signaling pathways provokes cellular transformation associated with gallbladder carcinoma.
Scanu T et al. Cell Host Microbe 2015 May 27.
Scanu T et al. Cell Host Microbe 2015 May 27.
Methods/Tools
Computational tools for parsimony phylogenetic analysis of omics data
Salazar J, et al. OMICS: A Journal of Integrative Biology. Jun 3, 2015. doi:10.1089/omi.2015.0018.
Salazar J, et al. OMICS: A Journal of Integrative Biology. Jun 3, 2015. doi:10.1089/omi.2015.0018.
Comparison of time-motion analysis of conventional stool culture and the BD MAX™ Enteric Bacterial Panel (EBP).
Mortensen JE et al. BMC Clin Pathol 2015 9
Mortensen JE et al. BMC Clin Pathol 2015 9
ProDeGe: a computational protocol for fully automated decontamination of genomes.
Tennessen K et al. ISME J 2015 Jun 9.
Tennessen K et al. ISME J 2015 Jun 9.
Resources for genetic and genomic analysis of emerging pathogen Acinetobacter baumannii.
Gallagher LA et al. J. Bacteriol. 2015 Jun 15. (12) 2027-35
Gallagher LA et al. J. Bacteriol. 2015 Jun 15. (12) 2027-35
Pathogenicity / Antimicrobial Resistance
Characterisation of a mobilisable plasmid conferring florfenicol and chloramphenicol resistance in Actinobacillus pleuropneumoniae.
Bossé JT et al. Vet. Microbiol. 2015 May 28.
Bossé JT et al. Vet. Microbiol. 2015 May 28.
Evaluation of the relationship between Chlamydia pecorum sequence types and disease using a species-specific multi-locus sequence typing scheme (MLST).
Jelocnik M et al. Vet. Microbiol. 2014 Nov 7. (1-2) 214-22
Jelocnik M et al. Vet. Microbiol. 2014 Nov 7. (1-2) 214-22
Molecular characterization of antimicrobial susceptibility of Salmonella isolates: First identification of a plasmid carrying qnrD or oqxAB in Taiwan.
Kao Cheng-Yen et al. J Microbiol Immunol Infect 2015 May 14.
Kao Cheng-Yen et al. J Microbiol Immunol Infect 2015 May 14.
The use of whole-genome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae.
Espedido BA et al. J. Clin. Pathol. 2015 Jun 8.
Espedido BA et al. J. Clin. Pathol. 2015 Jun 8.
Current perspectivesin pathogenesis and antimicrobial resistance of enteroaggregative Escherichia coli.
Kong H et al. Microb. Pathog. 2015 Jun 6.
Kong H et al. Microb. Pathog. 2015 Jun 6.
Shifts in the antibiotic susceptibility, serogroups, and clonal complexes of Neisseria meningitidis in Shanghai, China: A time trend analysis of the pre-quinolone and quinolone eras.
Chen M et al. PLoS Med. 2015 Jun (6) e1001838
Chen M et al. PLoS Med. 2015 Jun (6) e1001838
An outbreak of infections caused by extensively drug-resistant Klebsiella pneumoniae strains during a short period of time in a Chinese teaching hospital: epidemiology study and molecular characteristics.
Zhou T et al. Diagn. Microbiol. Infect. Dis. 2015 Jul (3) 240-4
Zhou T et al. Diagn. Microbiol. Infect. Dis. 2015 Jul (3) 240-4
Emergence of colistin resistance without loss of fitness and virulence after prolonged colistin administration in a patient with extensively drug-resistant Acinetobacter baumannii.
Durante-Mangoni E et al. Diagn. Microbiol. Infect. Dis. 2015 Jul (3) 222-6
Durante-Mangoni E et al. Diagn. Microbiol. Infect. Dis. 2015 Jul (3) 222-6
The genetics of Leishmania virulence.
Bifeld E et al. Med. Microbiol. Immunol. 2015 Jun 6.
Bifeld E et al. Med. Microbiol. Immunol. 2015 Jun 6.
Policy
All over the map: A 10-year review of state outbreak reporting 
(Report) Center for Science in the Public Interest, 2015.
(Report) Center for Science in the Public Interest, 2015.
Reviews/ News/ Commentaries
Startup molecular assemblies developing novel enzymatic DNA synthesis tech
Macron D. GenomeWeb, Jun 5, 2015.
Macron D. GenomeWeb, Jun 5, 2015.
Unregulated faecal transplants could squander gut-bug promise
New Scientist, Jun 4, 2015.
New Scientist, Jun 4, 2015.
Genomic sequencing technology advances make food poisoning outbreaks easier to control
Ockenden W. ABC News (Australia), Jun 1, 2015.
Ockenden W. ABC News (Australia), Jun 1, 2015.
Novel programs and discoveries aim to combat antibiotic resistance
Hampton T. JAMA, Jun 3, 2015.
Hampton T. JAMA, Jun 3, 2015.
Study shows impact of BD max enteric bacterial panel on lab workflow
Johnson M. GenomeWeb, Jun 8, 2015.
Johnson M. GenomeWeb, Jun 8, 2015.
As MERS outbreak surges, genetic tests show virus hasn't mutated
Doucleff M. NPR, June 8, 2015.
Doucleff M. NPR, June 8, 2015.
Recent CDC evaluation of commercial MERS MDx could be boon in light of new outbreak
Johnson M. GenomeWeb, Jun 9, 2015.
Johnson M. GenomeWeb, Jun 9, 2015.
Genetic mutation blocks prion disease
Deng B. Nature, Jun 10, 2015.
Deng B. Nature, Jun 10, 2015.
Expected and unexpected features of the newly discovered bat influenza A-like viruses.
Ma W et al. PLoS Pathog. 2015 Jun (6) e1004819
Ma W et al. PLoS Pathog. 2015 Jun (6) e1004819
What can we learn about the Ebola outbreak from tweets?
Odlum M et al. Am J Infect Control 2015 Jun 1. (6) 563-71
Odlum M et al. Am J Infect Control 2015 Jun 1. (6) 563-71
Target product profile (TPP) for Chagas disease point-of-care diagnosis and assessment of response to treatment.
Porrás AI et al. PLoS Negl Trop Dis 2015 Jun (6) e0003697
Porrás AI et al. PLoS Negl Trop Dis 2015 Jun (6) e0003697
The next 20 years of genome research
Schatz MC. bioRxiv, Jun 3, 2015.
Schatz MC. bioRxiv, Jun 3, 2015.
Funders must encourage scientists to share
Bobrow M. Nature, Jun 10, 2015.
Bobrow M. Nature, Jun 10, 2015.
South Korean MERS outbreak spotlights lack of research
Butler D. Nature, Jun 9, 2015.
Butler D. Nature, Jun 9, 2015.
An array of options: A guide for how and when to transition from the microarray to RNA-seq
Yandell K. The Scientist, Jun 10, 2015.
Yandell K. The Scientist, Jun 10, 2015.
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