Microbiology Unit

Desē, Ethiopia

Microbiology Unit

Desē, Ethiopia
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Boaretti M.,University of Verona | Boaretti M.,Microbiology Unit | Sorrentino A.,Microbiology Unit | Zantedeschi C.,University of Verona | And 4 more authors.
Journal of Clinical Virology | Year: 2013

Background: Quantification of cytomegalovirus (CMV) DNA by real-time PCR is currently considered an alternative diagnostic approach for the evaluation of active infection in transplant patients. The pp65 antigenemia assay has been used as reference test for monitoring active CMV infection and guiding preemptive therapy in transplant recipients. However, this assay suffers from some limitations: need for immediate processing of the samples, labour-intensive process, lack of standardization and subjective result interpretation. Objectives: The aim of this study was to evaluate the performance of a new commercially available real-time PCR assay coupled with a fully automated DNA extraction system (COBAS Ampliprep/COBAS Taqman CMV Test, Roche Diagnostics) for the detection of CMV-DNA in plasma comparing it with pp65 antigenemia assay for monitoring active CMV infection in solid organ transplant recipients (SOTRs). Study design: A total of 266 consecutive samples from 45 SOTRs were monitored with pp65 antigenemia and in parallel with CMV-DNA quantitation by real-time PCR assay. Results: Fifty-eight samples resulted PCR-positive, 163 negative and for 45 samples the CMV-DNA values obtained were below the lower limit of quantification (<150. copies/ml); pp65 antigen was detected in 47 samples and resulted negative in 219 specimens. Concordance between the two evaluations was 76.7%; also a good correlation was observed (. r=. 0.718). Considering the existing treatment criteria based on pp65 antigenemia evaluation corresponding to pp65 levels. ≥. 20 positive cells/200,000, preemptive therapy was administered to four asymptomatically infected patients. The corresponding cut-off value of CMV-DNA load calculated for discrimination between self-clearing infections and those requiring therapy was 2500. copies/ml (or 2275. IU/ml). Conclusion: The fully automated real-time PCR from Roche provided specific and sensitive results and represented a rapid and simple assay for the evaluation and monitoring of CMV infection in SOTRs. Further studies are required to validate the threshold level for the initiation of preemptive therapy. © 2012 Elsevier B.V.


Albuquerque L.,University of Coimbra | Rainey F.A.,Louisiana State University | Fernanda Nobre M.,University of Coimbra | da Costa M.S.,University of Coimbra | da Costa M.S.,Microbiology Unit
International Journal of Systematic and Evolutionary Microbiology | Year: 2012

Two bacterial isolates, designated AF-51T and AF-50, with an optimum growth temperature of about 45 °C and an optimum pH for growth between 6.0 and 6.5, were recovered from a hot spring in the Furnas, Área da Fonte 1825, on the Island of São Miguel in the Azores. Based on 16S rRNA gene sequence analysis, these strains were related most closely to the type strain of Hydrotalea flava at a pairwise similarity of 95.7 %. The two strains were orange-pigmented and formed non-motile, rod-shaped cells that stained Gram-negative and were aerobic and oxidaseand catalase-positive. The major fatty acids were iso-C15: 0, iso-C17: 0 3-OH and iso-C16: 0. The major respiratory quinone was menaquinone 7. Based on phylogenetic, physiological and biochemical characteristics, these strains from the Azores are considered to represent a single novel species of the genus Hydrotalea, for which the name Hydrotalea sandarakina sp. nov. is proposed. The type strain is AF-51T (=DSM 23241T=LMG 25526T). We provide emended descriptions of the genus Hydrotalea and of H. flava to reflect new results obtained in this study. © 2012 IUMS.


Antico A.,Civic Hospital | Platzgummer S.,Civic Hospital | Bassetti D.,Microbiology Unit | Bizzaro N.,Civic Hospital | And 2 more authors.
Lupus | Year: 2010

The aim of this study was to evaluate the diagnostic performance of four new enzyme immunoassays (EIAs) for anti-double-stranded-DNA (anti-dsDNA) antibodies, in comparison with the Farr assay and the Crithidia luciliae immunofluorescence test (CLIFT). To this purpose, sera from four patient groups were collected: 52 sera from patients with systemic lupus erythematosus (SLE); 28 from patients with other connective tissue diseases (CTD); 36 from patients with hepatitis C virus (HCV) infection; and 24 from those with acute viral infection. All sera were tested for anti-dsDNA antibodies by four EIA methods using a different antigenic DNA source [synthetic oligonucleotide (Method A), circular plasmid (Method B), recombinant (Method C), and purified extracted (Method D)], and by CLIFT and Farr assays. The diagnostic sensitivity of the assays was as follows: 84.6% (Method A), 73% (B), 82.7% (C), 84.6% (D), 55.8% (CLIFT), and 78.8% (Farr). Specificity was 82.9% (A), 97.7% (B), 96.5% (C), 94.3% (D), 96.5% (CLIFT), and 90.9% (Farr). From these data, we can conclude that the new-generation EIA methods evaluated in this study have higher sensitivity than the CLIFT and Farr assays and, with the exception of Method A, have specificity similar to the CLIFT and slightly higher than the Farr assay. These findings suggest that EIA tests may replace CLIFT as a screening test and the Farr assay as a specific test, for anti-dsDNA antibody detection. © The Author(s), 2010.


Eckert C.,National Reference Laboratory For C Difficile | Eckert C.,University Pierre and Marie Curie | Burghoffer B.,National Reference Laboratory For C Difficile | Burghoffer B.,University Pierre and Marie Curie | And 5 more authors.
Journal of Clinical Microbiology | Year: 2013

Three selective media (chromID C. difficile agar, taurocholate cycloserine cefoxitin agar [TCCA; homemade], and CLO medium) were compared from 406 stool samples of patients suspected of having Clostridium difficile infection. The sensitivities of chromID C. difficile agar at 24 h and 48 h, CLO medium, and TCCA were 74.1%, 87%, 85.2%, and 70.4%, respectively.© 2013, American Society for Microbiology. All Rights Reserved.


Lalande V.,University Pierre and Marie Curie | Lalande V.,Microbiology Unit | Barrault L.,Microbiology Unit | Wadel S.,Microbiology Unit | And 6 more authors.
Journal of Clinical Microbiology | Year: 2011

A new assay (illumigene C. difficile; Meridian Bioscience), based on the original loop-mediated isothermal amplification (LAMP) assay, was evaluated with 472 unformed stools from patients suspected of Clostridium difficile infection. Compared to the toxigenic culture, the sensitivity, specificity, and positive and negative predictive values were 91.8, 99.1, 91.8, and 99.1% for the illumigene C. difficile assay and 69.4, 100, 100, and 96.6% for the cytotoxicity assay, respectively. Copyright © 2011, American Society for Microbiology. All Rights Reserved.


Werno A.M.,Microbiology Unit | Werno A.M.,University of Otago | Christner M.,University of Hamburg | Anderson T.P.,Microbiology Unit | And 2 more authors.
Journal of Clinical Microbiology | Year: 2012

The differentiation of species within the Streptococcus mitis group has posed a problem in the routine diagnostic microbiology laboratory for some time. It also constitutes a major weakness of recently introduced matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) fingerprinting systems. As the phylogenetic resolution of the spectral similarity measures employed by these systems is insufficient to reliably distinguish between the most closely related members of the group, the major pathogen Streptococcus pneumoniae is frequently misidentified. In this study, a comparative analysis of MALDI-TOF spectra of several species from the S. mitis group has been performed in order to identify single peaks that could be used to improve mass spectrometry-based identification of the respective species. A characteristic peak profile could be identified that unambiguously distinguished the 14 S. pneumoniae isolates studied from 33 nonpneumococcal isolates of the S. mitis group. In addition, specific peak combinations could be assigned to other members of the group. The findings of this study suggest that it is possible to distinguish different species of the S. mitis group by close analysis of their mass peak profiles. Copyright © 2012, American Society for Microbiology. All Rights Reserved.


Jennings L.C.,Microbiology Unit | Jennings L.C.,University of Otago
Influenza and other Respiratory Viruses | Year: 2013

This article provides an overview of some aspects of seasonal, pre-pandemic and pandemic influenza vaccines and initiatives aimed to increase influenza vaccine use within the Asia-Pacific region. Expanding the use of influenza vaccines in the Asia-Pacific region faces many challenges. Despite the recent regional history for the emergence of novel viruses, SARS, the H5N1 and H7N9, and the generation of and global seeding of seasonal influenza viruses and initiatives by WHO and other organisations to expand influenza awareness, the use of seasonal influenza vaccines remains low. The improvement in current vaccine technologies with the licensing of quadrivalent, live-attenuated, cell culture-based, adjuvanted and the first recombinant influenza vaccine is an important step. The development of novel influenza vaccines able to provide improved protection and with improved manufacturing capacity is also advancing rapidly. However, of ongoing concern are seasonal influenza impact and the low use of seasonal influenza vaccines in the Asia-Pacific region. Improved influenza control strategies and their implementation in the region are needed. Initiatives by the World Health Organization (WHO), and specifically the Western Pacific Regional Office of WHO, are focusing on consistent vaccine policies and guidelines in countries in the region. The Asian-Pacific Alliance for the Control of Influenza (APACI) is contributing through the coordination of influenza advocacy initiates.© 2013 Blackwell Publishing Ltd.


Abejew A.A.,P.A. College | Denboba A.A.,University of Rome Tor Vergata | Mekonnen A.G.,Microbiology Unit
BMC Research Notes | Year: 2014

Background: Different studies have indicated that urinary tract infections frequently occur in both community and hospital environments and are of the most common bacterial infections in humans. the outcomes of urinary tract infections are increased hospitalization, increased direct patient costs and mortality. In Dessie, the prevalence of the commmon pathogens and antibiotic susceptibility pattern is not well studied sofar. Thus, the aim of this study is to address these gaps in the study area.Methods. Retrospective study was conducted in Dessie regional health reseacrh laboratory from January 1-March 31, 2012. All culture and antibiotic susceptibility test results of patients' diagnosed with UTI from September 2002 to September 2011 G.C were included in the study. Data were abstracted using structured questionnaires and finally, entered into SPSS Windows version 16.0, and descriptive statistics was generated to meet the study objective.Results: During the last ten years 680 (27.35%) bacteria were isolated in the regional laboratory. The most commonly isolated were E. coli 410 (60.29%), Pseudomonas species 59 (8.68%), Proteus species 53 (7.79%), S. aurous 50 (7.35%) and Klebsiella species 40 (5.88%). The E.coli were susceptible to Nitrofurantoin 43 (89.6%), furantoin 124 (87.3%), Nalidixic acid 91 (86.7%), kanamycin 116 (80%) & ciprofloxacin 66 (71.7%) but were almost resistant to Ampicillin, tetracycline, & trimethoprim-sulfamethoxazole. Similarly Pseudomonas and proteus species were resistant to almost all antibiotics except Gentamycin.Conclusion: The E.coli, pseudomonas and proteus species were the commonly isolated bacteria in the regional health research laboratory. A majority of isolated bacterial microbes were resistant to antibiotics commonly used in clinical practices and generally available in the local economy without prescription. Culture results are necessary before initiating antibiotics. © 2014 Abejew et al.; licensee BioMed Central Ltd.


Dennison A.,Microbiology Unit
Australian Journal of Medical Science | Year: 2014

The increasing incidence and severity of infections due Clostridium difficile has led to the re-evaluation of available diagnostic methods. It has become clear that the use of an enzyme immunoassay to detect C. difficile toxin in faeces cannot be used as a stand alone test to reliably exclude disease. The introduction of nucleic acid-based assays and algorithms that use two or even three separate assays have been proposed as a solution for improved sensitivity and also time to diagnosis. A review of recent literature identified testing strategies incorporating an algorithmic approach, based on screening for the presence of glutamate dehydrogenase followed by an assay to detect free toxin in faeces, could be used in most diagnostic laboratories to cost effectively optimise the sensitivity and specificity of results. Nucleic acid-based assays could be used to further stratify patients if required for infection control purposes. © 2014, Australian Institute of Medical Scientists. All rights reserved.


Saeed N.K.,Microbiology Unit
Journal of Infection in Developing Countries | Year: 2016

In this case report we described a Bahraini male patient of twenty years of age, a smoker and diagnosed with stage IV B Hodgkin lymphoma. He presented with fever, nonproductive cough, upper back pain and shortness of breath due to right upper lobe pneumonia with right encysted pleural effusion. Salmonella enterica serotype Enteritidis was isolated from the sputum. He was successfully treated with 2 weeks of ceftriaxone followed by 2 weeks of oral cefixime. This was the first case of encysted empyema caused by Salmonella enterica serotype Enteritidis reported in the Kingdom of Bahrain. The different aspects of pulmonary Salmonella infections were discussed and the literature was reviewed. © 2016 Saeed.

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