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

Genomics|Update|Infectious Diseases

Volume 34  Number 25  June 25 - July 2, 2015

Advanced Molecular Detection in Action

• Antimicrobials/ Vaccines/ Interventions
• Detection/ Diagnosis
• Epidemiology/ Outbreaks/ Transmission
• Evolution/ Ecology/ Populations
• Host-Microbe Interactions

• Methods/ Tools
• Pathogenicity / Antimicrobial Resistance
• Policy
• Reviews/ News/ Commentaries

Antimicrobials/ Vaccines/ Interventions

It's all about those bases: The need for incorporating parasite genetic heterogeneity into the development of schistosome vaccines.
Gleichsner AM et al. PLoS Negl Trop Dis 2015 Jun (6) e0003805

Protection against Shiga toxigenic Escherichia coli by non-GMO receptor-mimic bacterial ghosts.
Paton AW et al. Infect. Immun. 2015 Jun 22.

Cost-effectiveness of HIV drug resistance testing to inform switching to second line antiretroviral therapy in low income settings.
Phillips A et al. PLoS ONE 2014 (10) e109148

Genomics reveals the worldwide distribution of multidrug-resistant serotype 6E pneumococci.
van Tonder AJ et al. J. Clin. Microbiol. 2015 Jul (7) 2271-85

Assessing the paradox between transmitted and acquired HIV type 1 drug resistance mutations in the Swiss HIV cohort study from 1998 to 2012.
Yang Wan-Lin et al. J. Infect. Dis. 2015 Jul 1. (1) 28-38

Top of Page

---

Detection/ Diagnosis

Evolutionary trajectories and diagnostic challenges of potentially zoonotic avian influenza viruses H5N1 and H9N2 co-circulating in Egypt.
Naguib MM et al. Infect. Genet. Evol. 2015 Jun 3.

Label-free identification of individual bacteria using Fourier transform light scattering 
Jo YJ, et al. Optics Express 2015; 23(12): 15792-15805. (2015)

Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing
Cao MD, et al. bioRxiv, May 15, 2015.

Efficient detection of pathogenic leptospires using 16S ribosomal RNA.
Backstedt BT et al. PLoS ONE 2015 (6) e0128913

Bank vole prion protein as an apparently universal substrate for RT-QuIC-based detection and discrimination of prion strains.
Orrú CD et al. PLoS Pathog. 2015 Jun (6) e1004983

Recombinase polymerase amplification assay for rapid diagnostics of dengue infection.
Abd El WA et al. PLoS ONE 2015 (6) e0129682

PCR melting profile as a tool for outbreak studies of Salmonella enterica in chickens.
Zaczek A et al. BMC Vet. Res. 2015 137

Evaluation of signature erosion in Ebola virus due to genomic drift and its impact on the performance of diagnostic assays.
Sozhamannan S et al. Viruses 2015 (6) 3130-54

Detection of Zika virus in saliva.
Musso D et al. J. Clin. Virol. 2015 Jul 53-5

Development of cross-priming amplification assays for rapid and sensitive detection of Aeromonas hydrophila.
Meng S et al. Lett. Appl. Microbiol. 2015 Jun 15.

Validation and clinical application of a nested PCR for paracoccidioidomycosis diagnosis in clinical samples from Colombian patients.
Gaviria M et al. Braz J Infect Dis 2015 Jun 19.

On-chip purification and detection of hepatitis C virus RNA from human plasma.
Vaghi V et al. Biophys. Chem. 2015 Jun 11.

Comparison of double-locus sequence typing (DLST) and multilocus sequence typing (MLST) for the investigation of Pseudomonas aeruginosa populations.
Cholley P et al. Diagn. Microbiol. Infect. Dis. 2015 Aug (4) 274-7

Comparison of sample preparation methods, instrumentation platforms, and contemporary commercial databases for identification of clinically relevant mycobacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry.
Wilen CB et al. J. Clin. Microbiol. 2015 Jul (7) 2308-15

Evaluation of unbiased next-generation sequencing of RNA (RNA-seq) as a diagnostic method in influenza virus-positive respiratory samples.
Fischer N et al. J. Clin. Microbiol. 2015 Jul (7) 2238-50

Simple real-time PCR and amplicon sequencing method for identification of plasmodium species in human whole blood.
Lefterova MI et al. J. Clin. Microbiol. 2015 Jul (7) 2251-7

Top of Page

---

Epidemiology/ Outbreaks/ Transmission

Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa.
Carroll MW et al. Nature 2015 Jun 17.

Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone.
Park DJ et al. Cell 2015 Jun 18. (7) 1516-26 (CDC Author)

Evidence of self-sustaining drug resistant HIV-1 lineages among untreated patients in the United Kingdom
Mbisa JL, et al. Clin Infect Dis, May 19, 2015.

Detection of livestock-associated meticillin-resistant Staphylococcus aureus CC398 in retail pork, United Kingdom, February 2015
Hadjirin NF, et al. Eurosurveillance 2015;20(24):pii=21156.

Diverse genotypes of Yersinia pestis caused plague in Madagascar in 2007.
Riehm JM et al. PLoS Negl Trop Dis 2015 Jun (6) e0003844

The role of human transportation networks in mediating the genetic structure of seasonal influenza in the United States.
Bozick BA et al. PLoS Pathog. 2015 Jun (6) e1004898

Investigating fungal outbreaks in the 21st century.
Litvintseva AP et al. PLoS Pathog. 2015 May (5) e1004804 (CDC Author)

Molecular epidemiology and characterization of an outbreak causing Klebsiella pneumoniae clone carrying chromosomally located bla CTX-M-15 at a German University-Hospital.
Mshana SE et al. BMC Microbiol. 2015 122

An outbreak of colistin-resistant Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae in the Netherlands (July to December 2013), with inter-institutional spread.
Weterings V et al. Eur. J. Clin. Microbiol. Infect. Dis. 2015 Jun 12.

Airborne transmission of melioidosis to humans from environmental aerosols contaminated with B. pseudomallei.
Chen Pei-S et al. PLoS Negl Trop Dis 2015 Jun (6) e0003834

First report of autochthonous transmission of Zika virus in Brazil.
Zanluca C et al. Mem. Inst. Oswaldo Cruz 2015 09/06 (4) 569-572

Assessment of Mycobacterium tuberculosis transmission in Oxfordshire, UK, 2007-12, with whole pathogen genome sequences: an observational study.
Walker TM et al. Lancet Respir Med 2014 Apr (4) 285-92

Outbreak of NDM-1-producing Klebsiella pneumoniae causing neonatal infection in a teaching hospital in mainland China.
Zhang XY et al. Antimicrob. Agents Chemother. 2015 Jul (7) 4349-51

Top of Page

---

Evolution/ Ecology/ Populations

Genetic heterogeneity and phylogeny of Trichuris spp. from captive non-human primates based on ribosomal DNA sequence data.
Cavallero S et al. Infect. Genet. Evol. 2015 Jun 9.

Population structure and genetic diversity of the parasite Trichomonas vaginalis in Bristol, UK.
Hawksworth J et al. Infect. Genet. Evol. 2015 Jun 5.

Genotyping of community-associated methicillin resistant Staphylococcus aureus (CA-MRSA) in a tertiary care centre in Mysore, South India: ST2371-SCCmec IV emerges as the major clone.
Rajan V et al. Infect. Genet. Evol. 2015 Jun 1.

Fine-scale genetic structure of Triatoma infestans in the Argentine Chaco.
Piccinali RV et al. Infect. Genet. Evol. 2015 May 29.

High recombinant frequency in extraintestinal pathogenic Escherichia coli strains.
Rodríguez-Beltrán J et al. Mol. Biol. Evol. 2015 Mar 24.

Rampant parasexuality evolves in a hospital pathogen during antibiotic selection.
Beabout Kathryn et al. Mol. Biol. Evol. 2015 Jun 9.

Unraveling the transmission ecology of polio.
Martinez-Bakker M et al. PLoS Biol. 2015 Jun (6) e1002172

Genetic and antigenic characterization of Bungowannah virus, a novel pestivirus.
Kirkland PD et al. Vet. Microbiol. 2015 Aug 5. (3-4) 252-9

Full-genome sequence of the first G8P[14] rotavirus strain detected in the United States.
Mijatovic-Rustempasic S et al. Genome Announc 2015 (3) (CDC Author)

Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana.
Chen Y et al. Mol. Ecol. 2015 Jun 6. (CDC Author)

Detection of Zika virus infection in Thailand, 2012-2014.
Buathong R et al. Am. J. Trop. Med. Hyg. 2015 Jun 22.

Molecular characterization of a new human echovirus 11 isolate associated with severe hand, foot and mouth disease in Yunnan, China, in 2010.
Su T et al. Arch. Virol. 2015 Jun 23.

Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese.
Luo T et al. Proc. Natl. Acad. Sci. U.S.A. 2015 Jun 15.

Monitoring of Ebola virus Makona evolution through establishment of advanced genomic capability in Liberia.
Kugelman JR et al. Emerging Infect. Dis. 2015 Jul (7) 1135-43

Complete genome sequence of Bordetella pertussis D420.
Boinett CJ et al. Genome Announc 2015 (3)

Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion.
Lamelas A et al. MBio 2014 (5) e01974-14

Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals.
Cavanagh JP et al. J. Antimicrob. Chemother. 2014 Nov (11) 2920-7

Detection of entebbe bat virus after 54 years.
Kading RC et al. Am. J. Trop. Med. Hyg. 2015 Jun 22. (CDC Author)

First genome sequence of St. Louis encephalitis virus (SLEV) isolated from a human in Brazil.
Vedovello D et al. Arch. Virol. 2015 May (5) 1189-95

Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic
Simon-Loriere E, et al. Nature, Jun 24, 2015.

Epidemiological and virological characteristics of influenza viruses circulating in Cambodia from 2009 to 2011.
Horm SV et al. PLoS ONE 2014 (10) e110713 (CDC Author)

Top of Page

---

Host-Microbe Interactions

Categorical complexities of Plasmodium falciparum malaria in individuals is associated with genetic variations in ADORA2A and GRK5 genes.
Gupta H et al. Infect. Genet. Evol. 2015 Jun 9.

Clostridium butyricum strains and dysbiosis linked to necrotizing enterocolitis in preterm neonates.
Cassir N et al. Clin. Infect. Dis. 2015 Jun 17.

Inherited DOCK2 deficiency in patients with early-onset invasive infections.
Dobbs K et al. N. Engl. J. Med. 2015 Jun 18. (25) 2409-22

Host transcriptional response to influenza and other acute respiratory viral infections - a prospective cohort study.
Zhai Y et al. PLoS Pathog. 2015 Jun (6) e1004869

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment
Burns MB, et al. Genome Medicine 2015, 7:55.

Apolipoprotein E and protection against hepatitis E virus infection in American, non-Hispanic blacks.
Zhang L et al. Hepatology 2015 Jun 11. (CDC Author)

Norovirus infection and disease in an Ecuadorian birth cohort: Association of certain norovirus genotypes with host FUT2 secretor status.
Lopman BA et al. J. Infect. Dis. 2015 Jun 1. (11) 1813-21 (CDC Author)

Topographic diversity of the respiratory tract mycobiome and alteration in HIV and lung disease.
Cui L et al. Am. J. Respir. Crit. Care Med. 2015 Apr 15. (8) 932-42

A naturally occurring variant of the human prion protein completely prevents prion disease.
Asante EA et al. Nature 2015 Jun 10.

Top of Page

---

Methods/Tools

Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data
Sahl JW, et al. Genome Med, Jun 9, 2015.

'SEEDY' (Simulation of Evolutionary and Epidemiological Dynamics): An R package to follow accumulation of within-host mutation in pathogens.
Worby CJ et al. PLoS ONE 2015 (6) e0129745

A complete bacterial genome assembled de novo using only nanopore sequencing data.
Loman NJ et al. Nat. Methods 2015 Jun 15.

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
Croucher NJ et al. Nucleic Acids Res. 2015 Feb 18. (3) e15

Sequence analysis of lip R: A good method for molecular epidemiology of clinical isolates of Mycobacterium tuberculosis.
Saedi S et al. Curr. Microbiol. 2015 Jun 11.

Ultra-large alignments using phylogeny-aware profiles.
Nguyen Nam-Phuong D et al. Genome Biol. 2015 Jun 16. (1) 124

Top of Page

---

Pathogenicity / Antimicrobial Resistance

Evaluation of the zoonotic potential of a novel reassortant H1N2 swine influenza virus with gene constellation derived from multiple viral sources.
Lee JH et al. Infect. Genet. Evol. 2015 Jun 4.

Towards new drug targets? Function prediction of putative proteins of Neisseria meningitidis MC58 and their virulence characterization.
Shahbaaz M et al. OMICS 2015 Jun 15.

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health 
Holt KE, et al. PNAS, Jun 22, 2015. doi: 10.1073/pnas.1501049112

Detection of virulence-associated genes characteristic of intestinal Escherichia coli pathotypes, including the Enterohemorrhagic / Enteroaggregative O104:H4 in bovines from Germany and Spain.
Cabal A et al. Microbiol. Immunol. 2015 Jun 18.

Whole genome sequencing investigation of a tuberculosis outbreak in Port-au-Prince, Haiti caused by a strain with a "low-level" rpoB mutation L511P - insights into a mechanism of resistance escalation.
Ocheretina O et al. PLoS ONE 2015 (6) e0129207

A proteomic characterization of Bordetella pertussis clinical isolates associated with a California state pertussis outbreak.
Williamson YM et al. Int J Proteomics 2015 536537 (CDC Author)

A novel botulinum toxin, previously reported as serotype H, has a hybrid structure of known serotypes A and F that is neutralized with serotype A antitoxin.
Maslanka SE et al. J. Infect. Dis. 2015 Jun 10. (CDC Author)

Emergence of decreased susceptibility and resistance to extended-spectrum cephalosporins in Neisseria gonorrhoeae in Korea.
Lee H et al. J. Antimicrob. Chemother. 2015 Jun 17.

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study
Walker TM, et al. Lancet Infect Dis, Jun 24, 2015.

Escherichia coli O104:H4 pathogenesis: an enteroaggregative E. coli/Shiga toxin-producing E. coli explosive cocktail of high virulence.
Navarro-Garcia F et al. Microbiol Spectr 2014 Dec (6)

Top of Page

---

Policy

The case for improved diagnostic tools to control Ebola virus disease in West Africa and how to get there.
Chua AC et al. PLoS Negl Trop Dis 2015 Jun (6) e0003734

Seeking broader support, House Committee moves Dx regulatory proposal into draft legislation
Ray T. GenomeWeb, Jun 17, 2015.

Top of Page

---

Reviews/ News/ Commentaries

Towards a body-on-a-chip
Economist, Jun 13, 2015.

ETH Zurich team uses MALDI for single-cell analysis of microorganisms
Bonislawski A. GenomeWeb, Jun 12, 2015.

Novel holographic microscopy technique rapidly identifies bacteria
Healio Infectious Disease, Jun 18, 2015.

MERS research outpaced by outbreaks
Keener AB. The Scientist, Jun 18, 2015.

US, European research teams track evolution, transmission of Ebola virus in West African outbreak
Karow J. GenomeWeb, Jun 18, 2015.

DARPA grants Wyss Institute researchers up to $4.7M for gut microbiome research
GenomeWeb, Jun 17, 2015.

Broad Institute gets $20M gift to battle tuberculosis with genomic technology
GenomeWeb, Jun 22, 2015.

NIH earmarks $1.5M to fund human microbiome research projects
GenomeWeb, Jun 22, 2015.

Ebola drug trial terminated
Keener AB. The Scientist, Jun 23, 2015.

Despite retraction, researchers still concerned that sequencing study data was fabricated
Heger M. GenomeWeb, Jun 23, 2015.

FDA clears Quidel's Solana MDx platform, group A strep assay
GenomeWeb, Jun 23, 2015.

Great basin, BYU using $5M NIH grant to develop rapid CRE MDx
GenomeWeb, Jun 24, 2015.

Urban microbes come out of the shadows: Genomic sequences reveal cities' teeming masses of bacteria and viruses. 
Ehrenberg R. Nature, Jun 22, 2015.

Safe food, healthy business
Tauxe R. CDC Foundation, Jun 17, 2015.

Can the bacteria in your gut explain your mood?
Smith PA. New York Times Magazine, Jun 23, 2015.

Mining the microbial dark matter Microbiologists are finding new ways to explore the vast universe of unknown microbes in the hunt for antibiotics. 
Lok C. Nature, Jun 16, 2015.

Korean MERS virus is not a mutation, say experts
Sachan D. BMJ 2015;350:h3243. 

Amid panic, a chance to learn about MERS
Kupferschmidt K. Science, Jun 12, 2015.

HIV family trees reveal viral spread
Cohen J. Science, Jun 10, 2015.

Biological warfare: Microorganisms as drivers of host-parasite interactions.
Dheilly NM et al. Infect. Genet. Evol. 2015 May 27.

Flow cytometry on-a-chip
Perkel JM. The Scientist, Jun 1, 2015.

Novel programs and discoveries aim to combat antibiotic resistance.
Hampton T et al. JAMA 2015 Jun 3.

Neonatal necrotizing enterocolitis, a clostridial disease?
Butel MJ, et al. Clin Infect Dis, Jun 17, 2015.

The irreversibility of HIV drug resistance
Kouyos RD, Gunthard HF. Clin Infect Dis, May 19, 2015.

Neurodegeneration: Evolved protection against human prions
Telling G. Nature, Jun 24, 2015.