Archive for October 26, 2016

Next-Generation Sequencing: a Diagnostic One-Stop Shop for Hepatitis C?

Journal of Clinical Microbiology October 2016 V.54 N.10 P.2427-2430

Mario Poljak

Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia

Before starting chronic hepatitis C treatment, the viral genotype/subtype has to be accurately determined and potentially coupled with drug resistance testing.

Due to the high genetic variability of the hepatitis C virus, this can be a demanding task that can potentially be streamlined by viral whole-genome sequencing using next-generation sequencing as demonstrated by an article in this issue of the Journal of Clinical Microbiology by E. Thomson, C. L. C. Ip, A. Badhan, M. T. Christiansen, W. Adamson, et al. (J Clin Microbiol. 54:2455–2469, 2016)

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http://jcm.asm.org/content/54/10/2427.full.pdf+html

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October 26, 2016 at 8:09 am

Molecular Epidemiology of Staphylococcus aureus in the General Population in Northeast Germany: Results of the Study of Health in Pomerania (SHIP-TREND-0)

Journal of Clinical Microbiology November 2016 V.54 N.11 P.2774-2785

Silva Holtfreter, Dorothee Grumann, Veronika Balau, Annette Barwich, Julia Kolata, André Goehler, Stefan Weiss, Birte Holtfreter, Stephanie S. Bauerfeind, Paula Döring, Erika Friebe, Nicole Haasler, Kristin Henselin, Katrin Kühn, Sophie Nowotny, Dörte Radke, Katrin Schulz, Sebastian R. Schulz, Patricia Trübe, Chi Hai Vu, Birgit Walther, Susanne Westphal, Christiane Cuny, Wolfgang Witte, Henry Völzke, Hans Jörgen Grabe, Thomas Kocher, Ivo Steinmetz, and Barbara M. Bröker

aDepartment of Immunology, University Medicine Greifswald, Greifswald, Germany

bFriedrich-Loeffler Institute for Medical Microbiology, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany

cDepartment of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University of Greifswald, Greifswald, Germany

dDepartment of Restorative Dentistry, Periodontology, Endodontology and Pedodontics, University Medicine Greifswald, Greifswald, Germany

eInstitute for Community Medicine, University Medicine Greifswald, Greifswald, Germany

fCentre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany

gRobert Koch Institute, Wernigerode Branch, National Reference Center for Staphylococci, Wernigerode, Germany

hDepartment of Psychiatry und Psychotherapy, University Medicine Greifswald, Greifswald, Germany

Population-based studies on Staphylococcus aureus nasal colonization are scarce.

We examined the prevalence, resistance, and molecular diversity of S. aureus in the general population in Northeast Germany.

Nasal swabs were obtained from 3,891 adults in the large-scale population-based Study of Health in Pomerania (SHIP-TREND).

Isolates were characterized using spa genotyping, as well as antibiotic resistance and virulence gene profiling. We observed an S. aureus prevalence of 27.2%.

Nasal S. aureus carriage was associated with male sex and inversely correlated with age.

Methicillin-resistant S. aureus (MRSA) accounted for 0.95% of the colonizing S. aureus strains.

MRSA carriage was associated with frequent visits to hospitals, nursing homes, or retirement homes within the previous 24 months. All MRSA strains were resistant to multiple antibiotics.

Most MRSA isolates belonged to the pandemic European hospital-acquired MRSA sequence type 22 (HA-MRSA-ST22) lineage.

We also detected one livestock-associated MRSA ST398 (LA-MRSA-ST398) isolate, as well as six livestock-associated methicillin-susceptible S. aureus (LA-MSSA) isolates (clonal complex 1 [CC1], CC97, and CC398). spa typing revealed a diverse but also highly clonal S. aureus population structure.

We identified a total of 357 spa types, which were grouped into 30 CCs or sequence types. The major seven CCs (CC30, CC45, CC15, CC8, CC7, CC22, and CC25) included 75% of all isolates. Virulence gene patterns were strongly linked to the clonal background.

In conclusion, MSSA and MRSA prevalences and the molecular diversity of S. aureus in Northeast Germany are consistent with those of other European countries.

The detection of HA-MRSA and LA-MRSA within the general population indicates possible transmission from hospitals and livestock, respectively, and should be closely monitored.

PDF

http://jcm.asm.org/content/54/11/2774.full.pdf+html

October 26, 2016 at 8:07 am

Application of Mass Spectrometry Technology to Early Diagnosis of Invasive Fungal Infections

Journal of Clinical Microbiology November 2016 V.54 N.11 P.2786-2797

Alexandre Mery, Boualem Sendid, Nadine François, Marjorie Cornu, Julien Poissy, Yann Guerardel, and Daniel Poulain

aSATT Nord-de-France, Lille, France

bUniversité Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France

cCHU Lille, Service de Parasitologie-Mycologie, Lille, France

dUniversité Lille, U995-LIRIC-Lille Inflammation Research International Centre, Lille, France

eINSERM, U995-Team 2, Lille, France

fCHU Lille, Pôle de Réanimation, Lille, France

gCHU Lille, Délégation à la Recherche Clinique et à l’Innovation, Lille, France

We recently developed a mass spectrometry (MS) procedure based on the detection of a serum disaccharide (MS-DS) in patients with invasive candidiasis (IC).

Here, we compare the performance of MS-DS for the diagnosis of IC, invasive aspergillosis (IA), and mucormycosis (MM) with those of commercially available antigen detection tests.

This retrospective study included 48 patients (23 IC patients [74 serum samples], 15 IA patients [40 serum samples], and 10 MM patients [15 serum samples]) and 49 appropriate controls (102 serum samples). MS-DS, mannan (Mnn), galactomannan (GM), and (1,3)-β-D-glucan (BDG) were detected by matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) MS, Platelia, and Fungitell assays, respectively.

For IC, the sensitivity and specificity of the MS-DS index, BDG detection, and Mnn detection were 62% and 84%, 82% and 60%, and 33% and 94% per serum sample and 83% and 69%, 96% and 31%, and 39% and 86% per patient, respectively.

For IA, the corresponding values in comparison to BDG and GM detection were 83% and 81%, 62% and 95%, and 62% and 100% per serum sample and 93% and 76%, 87% and 90%, and 93% and 100% per patient, respectively. Nine of the 10 MM patients had a positive MS-DS result. MS-DS gave an early diagnosis in IC (73% positivity before blood culture), IA (positive before GM detection in six patients), and MM (positivity mainly preceded the date of diagnosis) patients.

For IC, persisting MS-DS was associated with a poor prognosis. The different biomarkers were rarely detected simultaneously, suggesting different kinetics of release and clearance. For IA, MS-DS provided better complementation to GM monitoring than BDG monitoring. MS-DS detects panfungal molecules circulating during invasive fungal infections.

The performance of MS-DS compared favorably with those of biological tests currently recommended for monitoring at-risk patients. Further validation of this test in multicenter studies is required.

PDF

http://jcm.asm.org/content/54/11/2786.full.pdf+html

October 26, 2016 at 8:05 am


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