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

Genomics|Update|Infectious Diseases

Volume 34  Number 1  January 8-15, 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

What is a resistance gene? Ranking risk in resistomes
Martinez JL, et al. Nat Rev Microbiol, Dec 15, 2014.

Genetic characterisation of drug resistance and clonal dynamics of Acinetobacter baumannii in a hospital setting in Mexico
Bocanenegra-Ibarias P, et al. Int J Antimicrob Agents, Dec 5, 2014.

Complete genome sequence of a Klebsiella pneumoniae isolate with chromosomally encoded carbapenem resistance and colibactin synthesis loci
Conlan S, et al. Genome Announc 2014;2(6): pii: e01332-14.

Yellow fever virus: Genetic and phenotypic diversity and implications for detection, prevention and therapy
Beasley DW, et al. Antiviral Res, Dec 26, 2014.

From genome screening to creation of vaccine against Trypanosoma cruzi by use of immunoinformatics
Teh-Poot C, et al. J Infect Dis 2015; 211(2): 258-266.

Comment:
Neglected tropical diseases, bioinformatics, and vaccines
Rodrigues MM, Ersching J. J Infect Dis 2015; 211(2): 175-177.

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Detection and Diagnosis

Comparison of species identification of endocarditis associated viridans streptococci using rnpB genotyping and two MALDI-TOF systems
Isaaksson J, et al. Diag Microbiol Infect Dis, Dec 26, 2014.

Heptaplex PCR melting curve analysis for rapid detection of plasmid-mediated AmpC β-lactamase genes
Liu Z, et al. J Microbiol Methods, Dec 27, 2014.

General and advanced diagnostic tools to detect Mycobacterium tuberculosis and their drug susceptibility: a review
Gazi MA, et al. Eur J Clin Microbiol Infect Dis, Jan 6, 2015.

Molecular genotyping and quantitation assay for rotavirus surveillance 
Liu J, et al. J Virol Methods 2015; 213: 157-163.

Recombinase polymerase amplification as a promising tool in hepatitis C virus diagnosis 
Zaghloul H, El-Shahat M. World J Hepatol 2014;6(12):916-22.

Universal single-probe RT-PCR assay for diagnosis of dengue virus infections
Alm E, et al. PLoS Negl Trop Dis 2014; 8(12): e3416.

Malaria detection using inertial microfluidics
Warkiani ME, et al. Lab Chip, Dec 24, 2014.

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Epidemiology, Outbreaks, Transmission

Klebsiella pneumoniae carbapenemase (KPC) producing K. pneumoniae at a single institution: insights into endemicity from whole genome sequencing
Mathers AJ, et al. Antimicrob Agents Chemother, Jan 5, 2015.

Dynamics of MDR Enterobacter cloacae outbreaks in a neonatal unit in Nepal: insights using wider sampling frames and next-generation sequencing
Stoesser N, et al. J Antimicrob Chemother, Jan 3, 2015.

Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread  characterized the onset of the epidemic 
Eppinger M, et al. mBio 2014; 5(6): e01721-14.

Pneumonic plague outbreak, northern Madagascar, 2011
Richard V, et al. Emerg Infect Dis 2015; 21(1): 8-15.

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, Dec 30, 2014.

Comment:
Emerging problems impeding the elimination of the last polioviruses: silent circulation of wild strains in a well-immunized population
Delpeyroux F, Colbère-Garapin F. Clin Infect Dis, Dec 30, 2014.

Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?
Dennis AM1, et al. J Acquir Immune Defic Syndr 2014;67(2):181-95.

Investigating the zoonotic origin of the West African Ebola epidemic
Saez AM, et al. EMBO Mol Med 2014; 7: 17-23.

A case of long‐term excretion and subclinical infection with MERS‐coronavirus in a health care worker
Al-Gethamy M, et al. Clin Infect Dis, Dec 16, 2014.

Epidemic and molecular evolution of human bocavirus in hospitalized children with acute respiratory tract infection
Lu QB, et al. Euro J Clin Microbiol Infect Dis 2015; 34(1): 75-81.

Pathological and molecular diagnosis of the 2013 African swine fever outbreak in Lusaka, Zambia
Yabe J, et al. Trop Anim Health Prod, Dec 23, 2014.

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Evolution, Ecology, Pathogenicity, Populations

Bacterial evolution. The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer.
Borgeaud S, et al. Science 2015; 347: 63-67.

Comment:
RNA-seq study of cholera pathogen connects bacteria-killing mechanism to horizontal gene transfer
Han AP. GenomeWeb, Jan 2, 2015. [by free subscription only]

Phylodynamic analysis of clinical and environmental Vibrio cholerae isolates from Haiti reveals diversification driven by positive selection
Azarian T, et al. mBio  2014; 5(6): e01824-14.

Draft whole-genome sequences of 10 serogroup O6 enterotoxigenic Escherichia coli strains
Pattabiraman V, Bopp CA. Genome Announc 2014;2(6): pii: e01274-14.

Evolution of invasion in a diverse set of Fusobacterium species
McGuire AM, et al. mBio 2014; 5(6): e01864-14.

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, Dec 27, 2014.

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis
Howell KJ, et al. BMC Genomics 2014; 15:1179.

Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and   highlight the survival attributes of Mycobacterium tuberculosis
Rahman SA, et al. mBio 2014; 5(6): e02020-14.

Multiple sampling and discriminatory fingerprinting reveals clonally complex and compartmentalized infections by M. bovis in cattle 
Navarro Y, et al. Vet Microbiol 2015; 175(1): 99–104.

Within-host nucleotide diversity of virus populations: Insights from next-generation sequencing
Nelson CW, Hughes AL. Infect Genet Evol 2015; 30: 1–7.

Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus
Pu J, et al. Proc Natl Acad Sci USA, Dec 29, 2014.

Identification of the source of A (H10N8) virus causing human infection
Xu Y, et al. Infect Genet Evol, Dec 27, 2014.

Contemporary avian influenza A virus subtype H1, H6, H7, H10, and H15 hemagglutinin genes encode a mammalian virulence factor similar to the 1918 pandemic virus H1 hemagglutinin
Qi L, et al. mBio 2014; 5(6): e02116-14.

Multilocus sequence typing approach for a broader range of species of Leishmania genus: describing parasite diversity in Argentina
Marco JD. Infect Genet Evol, Dec 31, 2014.

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.
Neafsey DE, et al. Science 2015; 347: 1258522.

Comment:
Evolutionary genomics. Conundrum of jumbled mosquito genomes.
Clark AG, Messer PW. Science 2015; 347: 27-28. 

Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics.
Fontaine MC, et al. Science 2015; 347: 1258524.

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Host-Pathogen Interactions

Potential of fecal microbiota for early‐stage detection of colorectal cancer 
Zeller G, et al. Mol Syst Biol 2014; 10:766.

The Bacteroides fragilis toxin gene is prevalent in the colon mucosa of colorectal cancer patients 
Boleij A, et al. Clin Infect Dis 2015; 60(2): 208-215.

Patterns of genome evolution that have accompanied host adaptation in Salmonella 
Langridge GC, Proc Natl Acad Sci USA, Dec 22, 2014.

Pseudomonas aeruginosa adaptation to human hosts 
Snitkin ES, Segre JA. Nat Genet 2015; 47: 2–3.

Reverse zoonosis of influenza to swine: new perspectives on the human–animal interface 
Nelson MI, Vincent AL. Trends Microbiol, Jan 4, 2015.

Influence of interleukin 10 polymorphisms -592 and -1082 to the HIV, HBV and HCV serostatus among intravenous drug users
Kailas E, et al. Infect Genet Evol, Dec 24, 2014.

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution 
Hayward A, et al. Proc Nat Acad Sci, Dec 22, 2014.

Comment: 
New study reveals extensive retroviral activity across vertebrates 
Macron D. GenomeWeb, Dec 22, 2014. [by free subscription only]

Diet dominates host genotype in shaping the murine gut microbiota 
Carmody RM, et al. Cell Host Microbe, Dec 18, 2014.

Host demise as a beneficial function of indigenous microbiota in human hosts 
Blaser MJ, Webb GF. mBio 2014; 5(6): e02262-14.

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Methods

Cost-effective pooling of DNA from nasopharyngeal swab samples for large-scale detection of bacteria by real-time PCR
Edouard S, et al. Clin Chem, Dec 31, 2014.

Comment:
Pooling and concentrating DNA from nasopharyngeal swabs prior to RT-PCR saves money
GenomeWeb, Jan 5, 2015. [by free subscription only]

A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes
Bratcher HB, et al. BMC Genomics. 2014; 15: 1138.

Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not 
Hedge J, Wilson DJ. mBio 2014; 5(6):e02158-14.

Flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks
Kang Y, et al. mBio 2014; 5(6): e01867-14.

Chromosomal transfers in mycoplasmas: when minimal genomes go mobile
Dordet-Frisoni E, et al. mBio 2014; 5(6): e01958-14.

Global avian influenza surveillance in wild birds: a strategy to capture viral diversity
Machalaba C, et al. Emerg Infect Dis, April 2015.

Recombination in viruses: Mechanisms, methods of study, and evolutionary consequences
Pérez-Losada M, et al. Infect Genet Evol, Dec 23, 2014. 

Isolation and enrichment of Cryptosporidium DNA and verification of DNA purity for whole genome sequencing
Guo Y, et al. J Clin Microbiol, Dec 17,2014.

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Policy

The President's national security agenda: curtailing Ebola, safeguarding the future
Gostin LO, et al. JAMA 2015;313(1):27-28.

Communicating uncertainty — Ebola, public health, and the scientific process
Rosenbaum L. N Engl J Med 2015; 372:7-9.

FDA regulation of laboratory-developed diagnostic tests: Protect the public, advance the science
Sharfstein J. JAMA, Jan 5, 2015.

Genetic testing and FDA regulation: Overregulation threatens the emergence of genomic medicine
Evans JP, Watson MS. JAMA, Jan 5, 2015.

Q&A: FDA's Alberto Gutierrez fields questions on evolving LDT, CDx regulations
Ray T. GenomeWeb, Dec 30, 2014. [by free subscription only]

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Reviews, News and Commentaries

The year in pathogens
Sharlach M. The Scientist, Dec 29, 2014.

Infectious disease MDx 2014: qPCR for Ebola; disease panels; isothermal amplification
Johnson M, Genome Web Jan 5, 2015 [by free subscription only]

New clues to where the Ebola epidemic started
Maron DF. Nature, Dec 31, 2014.

FDA grants first CLIA waiver for nucleic acid-based flu diagnostic test
FDA, Jan 6, 2015.

Get your flu shot anyway, despite genetic "drift"
Kroll D. Forbes.com, Dec 31, 2014.

Science scores major victory in fight against antibiotic resistance
Maron DF. Salon, Jan 1, 2015.

Mistaken identities
Researchers are working to automate the arduous task of identifying—and amending—mislabeled sequences in genetic databases
Grens K. The Scientist, Jan 1, 2015.

The arXiv preprint server hits 1 million articles
Van Noorden R. Nature, Dec 30, 2014.

The next big step for Wikidata—forming a hub for researchers
Eissfeldt J, Tony1. Wikipedia Signpost, Dec 31, 2014.

Illumina plans to tap consumer market for its smartphone-ready DNA chip
DarkDaily, Dec 29, 2014.

Breakdown + Breakdown runners-up. Breakdown of the year: Ebola
Cohen J. Science, 2014; 346: 1450-1451.

Microbiology. Persisters unmasked.
Holden DW. Science 2015; 347: 30-32.

A movable defense 
Koonin EV, Krupovich M. The Scientist, Jan 1, 2015.

Nanopore sequencing is here to stay 
Krol A. Bio-IT World, Dec 22, 2014.

Mathematical models for emerging disease
Dobson A. Science 2014; 346: 1294-1295. 

The two cultures of mathematics and biology
Pachter L. Bits of DNA (blog), Dec 30, 2014.

GenomeWeb updates on molecular diagnostics [by free subscription only]:

FDA issues EUA for Roche Ebola MDx test

Cepheid's HIV MDx assay gains CE-IVD mark 

Roche's Cobas CMV viral load assay gets CE mark 

SpeeDx preps to launch meningitis MDx test in 2015