Archive for February 21, 2017

Untargeted Metabolomics To Ascertain Antibiotic Modes of Action

Antimicrobial Agents and Chemotherapy April 2016 V.60 N.4 P.2281-2291

Isabel M. Vincent, David E. Ehmann, Scott D. Mills, Manos Perros, and Michael P. Barrett

Untargeted Metabolomics To Ascertain Antibiotic Modes of Action

Isabel M. Vincent, David E. Ehmann, Scott D. Mills, Manos Perros, and Michael P. Barrett

Deciphering the mode of action (MOA) of new antibiotics discovered through phenotypic screening is of increasing importance. Metabolomics offers a potentially rapid and cost-effective means of identifying modes of action of drugs whose effects are mediated through changes in metabolism.

Metabolomics techniques also collect data on off-target effects and drug modifications.

Here, we present data from an untargeted liquid chromatography-mass spectrometry approach to identify the modes of action of eight compounds: 1-[3-fluoro-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)phenyl]-3-[2-(trifluoromethyl)phenyl]urea (AZ1), 2-(cyclobutylmethoxy)-5′-deoxyadenosine, triclosan, fosmidomycin, CHIR-090, carbonyl cyanide m-chlorophenylhydrazone (CCCP), 5-chloro-2-(methylsulfonyl)-N-(1,3-thiazol-2-yl)-4-pyrimidinecarboxamide (AZ7), and ceftazidime.

Data analysts were blind to the compound identities but managed to identify the target as thymidylate kinase for AZ1, isoprenoid biosynthesis for fosmidomycin, acyl-transferase for CHIR-090, and DNA metabolism for 2-(cyclobutylmethoxy)-5′-deoxyadenosine.

Changes to cell wall metabolites were seen in ceftazidime treatments, although other changes, presumably relating to off-target effects, dominated spectral outputs in the untargeted approach.

Drugs which do not work through metabolic pathways, such as the proton carrier CCCP, have no discernible impact on the metabolome.

The untargeted metabolomics approach also revealed modifications to two compounds, namely, fosmidomycin and AZ7.

An untreated control was also analyzed, and changes to the metabolome were seen over 4 h, highlighting the necessity for careful controls in these types of studies.

Metabolomics is a useful tool in the analysis of drug modes of action and can complement other technologies already in use.

PDF

http://aac.asm.org/content/60/4/2281.full.pdf

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February 21, 2017 at 3:31 pm

Comparison of Phenotypic and Genotypic Approaches to Capsule Typing of Neisseria meningitidis by Use of Invasive and Carriage Isolate Collections

Journal of Clinical Microbiology January 2016 V.54 N.1 P.25-34

Epidemiology

Hal Jones, Naglaa Mohamed, Eduardo Rojas, Lubomira Andrew, Johanna Hoyos, Julio C. Hawkins, Lisa K. McNeil, Qin Jiang, Leonard W. Mayer, Xin Wang, Rodica Gilca, Philippe De Wals, Louise Pedneault, Joseph Eiden, Kathrin U. Jansen, and Annaliesa S. Anderson

aPfizer Vaccine Research and Development, Pearl River, New York, USA

bMeningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

cInstitut National de Santé Publique du Québec, Quebec City, Canada

dLaval University, Quebec City, Canada

eCHU de Québec, Quebec City, Canada

aPfizer Vaccine Research and Development, Pearl River, New York, USA

bMeningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

cInstitut National de Santé Publique du Québec, Quebec City, Canada

dLaval University, Quebec City, Canada

eCHU de Québec, Quebec City, Canada

Neisseria meningitidis serogroup B (MnB) is a leading cause of bacterial meningitis; however, MnB is most commonly associated with asymptomatic carriage in the nasopharyngeal cavity, as opposed to the disease state.

Two vaccines are now licensed for the prevention of MnB disease; a possible additional benefit of these vaccines could be to protect against disease indirectly by disrupting nasopharyngeal carriage (e.g., herd protection).

To investigate this possibility, accurate diagnostic approaches to characterize MnB carriage isolates are required. In contrast to invasive meningococcal disease (IMD) isolates, which can be readily serogrouped, carriage isolates often lack capsule expression, making standard phenotypic assays unsuitable for strain characterization.

Several antibody-based methods were evaluated for their abilities to serogroup isolates and were compared with two genotyping methods (real-time PCR [rt-PCR] and whole-genome sequencing [WGS]) to identify which approach would most accurately ascertain the polysaccharide groups associated with carriage isolates.

WGS and rt-PCR were in agreement for 99% of IMD isolates, including those with coding sequences for MnB, MnC, MnW, and MnY, and the phenotypic methods correctly identified serogroups for 69 to 98% of IMD isolates.

In contrast, only 47% of carriage isolates were groupable by genotypic methods, due to mutations within the capsule operon; of the isolates identified by genotypic methods, ≤43% were serogroupable with any of the phenotypic methods tested.

These observations highlight the difficulties in the serogrouping and capsular genogrouping of meningococcal carriage isolates. Based on our findings, WGS is the most suitable approach for the characterization of meningococcal carriage isolates.

PDF

http://jcm.asm.org/content/54/1/25.full.pdf

February 21, 2017 at 3:29 pm

Unveiling New Aspects of Meningococcal Carriage and Disease Prevention

Journal of Clinical Microbiology January 2016 V.54 N.1 P.2-4

Commentaries

Magnus Gottfredsson

Department of Infectious Diseases, Landspitali University Hospital, and Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland

Recently, two protein-based vaccines have been approved for the prevention of invasive meningococcal disease caused by Neisseria meningitidis serogroup B (MenB).

It is therefore important to study carefully if and how these pathogens respond to widespread vaccination.

Traditionally, meningococci have been classified on the basis of capsular phenotypes, but variable levels of capsule expression can influence the results, mainly among MenB strains.

In this issue, Jones and colleagues (J Clin Microbiol 54:25–34, 2016, http://dx.doi.org/10.1128/JCM.01447-15) compare whole-genome sequencing to traditional phenotypic methods of classifying meningococci.

They demonstrate that for MenB in particular, sequencing-based methods are far superior to traditional methods, especially when it comes to characterizing carriage isolates. This has important implications for future surveillance.

PDF

http://jcm.asm.org/content/54/1/2.full.pdf

February 21, 2017 at 3:27 pm

Role of Serologic and Molecular Diagnostic Assays in Identification and Management of Hepatitis C Virus Infection

Journal of Clinical Microbiology February 2016 V.54 N.2 P.265-273

Minireviews

Gavin Cloherty, Andrew Talal, Kelly Coller, Corklin Steinhart, John Hackett Jr., George Dawson, Juergen Rockstroh, and Jordan Feld

aAbbott Diagnostics, Abbott Park, Illinois, USA

bUniversity at Buffalo, Buffalo, New York, USA

cViiV Healthcare, Research Triangle Park, North Carolina, USA

dUniversity Bonn, Bonn, Germany

eUniversity of Toronto, Toronto, Canada

The drugs available for the treatment of hepatitis C virus (HCV) have evolved to provide shorter treatment duration and higher rates of sustained virologic response (SVR), and the role of HCV infection diagnostic tests has had to evolve in order to meet changing clinical needs. This review gives an overview on the role of HCV infection diagnostic testing (molecular and serological tools) used in the diagnosis and management of HCV infection. All of this critical information guides physician decisions to optimize patient clinical outcomes. Also discussed is the future direction of diagnostic testing in the context of further advances in drug development.

PDF

http://jcm.asm.org/content/54/2/265.full.pdf

February 21, 2017 at 3:25 pm

Flow Cytometry To Assess Cerebrospinal Fluid Fungal Burden in Cryptococcal Meningitis

Journal of Clinical Microbiology March 2016 V.54 N.3 P.802-804

Mycology

James E. Scriven, Lisa M. Graham, Charlotte Schutz, Thomas J. Scriba, Robert J. Wilkinson, David R. Boulware, Graeme Meintjes, David G. Lalloo, and Britta C. Urban

aLiverpool School of Tropical Medicine, Liverpool, Merseyside, United Kingdom

bWellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, United Kingdom

cClinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa

dDepartment of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa

eSouth African TB Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa

fDepartment of Medicine, Imperial College, London, United Kingdom

gFrancis Crick Institute, Mill Hill Laboratory, London, United Kingdom

hDepartment of Medicine, University of Minnesota, Minnesota, USA

James E. Scriven, jscriven@liv.ac.uk

Fungal burden in the cerebrospinal fluid is an important determinant of mortality in cryptococcal meningitis, but its use in aiding clinical decision making is hampered by the time involved to perform quantitative cultures. Here, we demonstrate the potential of flow cytometry as a novel and rapid technique to address this issue.

PDF

http://jcm.asm.org/content/54/3/802.full.pdf

February 21, 2017 at 3:24 pm


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