Onur Karatuna

The use of Matrix-assisted laser desorption ionization-time of flight mass spectrometry in the identification of Francisella tularensis

Francisella tularensis is the cause of the zoonotic disease tularemia and is classified among highly pathogenic bacteria (HPB) due to its low infection dose and potential for airborne transmission. In the case of HBP, there is a pressing need for rapid, accurate and reliable identification. Phenotypic identification of Francisella species is inappropriate for clinical microbiology laboratories because it is time-consuming, hazardous and subject to variable interpretation. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was recently evaluated as a useful tool for the rapid identification of a variety of microorganisms. In this study, we evaluated the use of MALDI-TOF MS for the rapid identification of Francisella tularensis and differentiation of its subspecies. Using national collection of Francisella isolates from the National Tularemia Reference Laboratory (Public Health Institution of Turkey, Ankara), a total of 75 clinical isolates were investigated by species and subspecies-specific polymerase chain reaction (PCR) test and MALDI-TOF MS. All isolates were originally identified as F. tularensis subsp. holarctica according to region of difference 1 (RD1) subspecies-specific PCR results. For all isolates MALDI-TOF MS provided results in concordance with subspecies-specific PCR analysis. Although PCR-based methods are effective in identifying Francisella species, they are labor-intensive and take longer periods of time to obtain the results when compared with MALDI-TOF MS. MALDI-TOF MS appeared to be a rapid, reliable and cost-effective identification technique for Francisella spp. Shorter analysis time and low cost make this an appealing new option in microbiology laboratories.

Six-year distribution pattern of hepatitis C virus in Turkey: a multicentre study

ABSTRACT Hepatitis C infection is a public health problem. The aim of this retrospective study was to determine the distribution of hepatitis C virus (HCV) genotypes in seven regions of Turkey, by evaluating 7002 patients with chronic HCV in a six-year period. During the 2009–2014 period, serum/plasma samples from 7002 new consecutive HCV RNA positive patients were collected. The female patients were 3867 (55.2%). The genotype distribution of HCV patiens was evaluated by ages and years. Statistical analysis was performed by using the Mann–Whitney test and the χ2 analysis. During the six-year period, genotype 1b was the most common genotype (67.7%) followed by untypeable genotype 1 (7.7%), genotype 4 (7.3%) and genotype 3 (6.7%). In 2014, genotype 3 was the second most common one (11.3%) and genotype 4 was the third most common one (9.8%). In the group with <25 years old patients, genotype 1b was most common (78.48%, 62/79) between the years of 2009 and 2011, whereas genotype 3 (34.8%, 86/247), between the years of 2012 and 2014. Genotype 1b was the most common in the groups between 26 and 35 years, 36 and 45 years, 46 and 55 years, 56 and 65 years. The rate of genotype 3 was increased from 4.78% to 10.06% and the rate of genotype 4 was increased from 1.3% to 3.84%, from 2009–2011 to 2012–2014. In recent years, genotypes 3 and 4 have gained importance. New therapeutic strategies and survey studies may be required for the modified HCV genotype pattern.

Evaluation of the Carba NP Test for the Detection of Carbapenemase Activity in Bacteroides Species

We evaluated the usefulness of the Carba NP test for rapid detection of carbapenemase activity in Bacteroides spp. The minimum inhibitory concentration (MIC) for imipenem was determined with gradient test strips, and cfiA gene was investigated by polymerase chain reaction for 27 clinical Bacteroides spp. isolates. Carba NP test was performed according to recommendations of the Clinical and Laboratory Standards Institute. Among three cfiA gene harboring clinical isolates, two imipenem resistant isolates were Carba NP test positive, while the imipenem intermediate isolate was negative. Our preliminary results suggest that the Carba NP test can be useful as a rapid test to detect carbapenemases in Bacteroides species.

Comparison of Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry with VITEK2 Gram Positive System for Identification of Beta Haemolytic Streptococci

Background: Matrix–assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is known as a successful tool for bacterial identification and suitable for clinical diagnostics. The aim of our study was to evaluate diagnostic accuracy of MALDI-TOF MS system and VITEK2 Gram Positive Identification (GP ID) system for the identification of Beta Hemolytic Streptococci (BHS). Materials and Methods: A total 148 BHS which were isolated from various clinical specimens were included in the study. Isolates were identified by Bruker Biotyper 3.4 and VITEK2 GP ID coupled to the agglutination test. Identification results for Bruker Biotyper 3.4 and VITEK2 GP ID systems were classified in three different categories as follows: correct identification, low level of discrimination, no identification/misidentification. Identification results of BHS were evaluated according to these categories. Results: BHS isolates were defined as Streptococcus pyogenes (n: 69), Streptococcus agalactiae (n: 59), Streptococcus dysgalactiae serogroup C (n: 5), and Streptococcus dysgalactiae serogroup G (n: 15) according to latex agglutination assay. MALDI-TOF MS analysis of 148 BHS isolates yielded correct identification for 89.9% of S. pyogenes , 64.4% of S. agalactiae , and 95.0% S. dysagalactiae serogroup C and G; while VITEK2 GP ID gave correct identification for 62.3% of S. pyogenes , 67.8% of S. agalactiae , and 65.0% of S. dysagalactiae serogroup C and G. Conclusions: MALDI-TOF MS-based identification provides faster and more accurate identification of beta-hemolytic streptococcal species than VITEK2 GP ID system.

Performance of “RESIST-3 O.K.N. K-SeT” immunochromatographic assay for the detection of OXA-48 like, KPC, and NDM carbapenemases in Klebsiella pneumoniae in Turkey

In this study, the performance of the “RESIST-3 O.K.N. K-SeT” (Coris BioConcept, Gembloux, Belgium) immunochromatographic assay was evaluated in 132 Klebsiella pneumoniae comprising 102 carbapenem resistant and 30 carbapenem susceptible isolates. Genotypically known isolates of Gram negative bacteria (n = 22) including various species were also tested by the assay as controls. The isolates tested by the immunochromatographic assay and also were run PCR for blaKPC, blaIMP, blaVIM, blaNDM, and blaOXA-48. The rates of blaNDM, blaOXA-48, and blaKPC in carbapenem resistant isolates were found at 52.9%, 39.2%, and 2.0%, respectively. Both blaNDM and blaOXA-48 were found in six (5.9%) isolates. The results of the assay showed 100% concordance with those obtained by PCR in 132 K. pneumoniae. The agreement between the two methods was found to be identical at the isolate level. The assay also correctly detected all genotypically known isolates of Escherichia coli, Serratia marcescens, Citrobacter freundii, Enterobacter cloacae, K. pneumoniae carrying blaKPC, blaNDM, and/or blaOXA-48. On the other hand, the assay did not exhibit any cross-reaction in control isolates harboring blaIMP and blaVIM. We conclude that the RESIST-3 O.K.N. K-SeT is a reliable, rapid, and user friendly test and we recommend it for routine diagnostic laboratories.

The Role of Microbiology Laboratory in Promoting Antimicrobial Stewardship

Abstract Microbiology laboratories are one of the major components of antimicrobial stewardship (AMS) programs. The early identification of pathogen and antimicrobial susceptibility tests helps physicians to direct the target specific therapy. Communication between laboratory staff and clinicians is essential to achieve the goals of antimicrobial stewardship program. This chapter summarizes the role of microbiology laboratory for successful AMS.

[Amoebic liver abscess in a patient initially diagnosed with pneumonia: case report and discussion of relevant literature].

In one-third of the patients with amoebiasis, amoebic liver abscess (ALA) may occur after the penetration of amoebic trophozoites through the intestinal wall. ALA is seen mostly among men aged 20-45 years with a serious clinical outcome, with fever and abdominal pain on the right upper quadrant. Most patients have no recent history of amoebic colitis; indeed, they have neither gastrointestinal complaints nor Entamoeba histolytica (E. histolytica) cysts/trophozoites in their stools. Therefore, ultrasonography and serology are primary in ALA diagnosis, while searching for E. histolytica DNA in abscess fluid using PCR has been preferred as an effective and reliable method, lately. Early antimicrobial therapy is effective; however, for cases irresponsive to therapy after 72 hours and with large abscess, drainage or surgical intervention is indicated. If left untreated, ALA may disseminate to other organs and cause death. The data concerning the extra-intestinal manifestations of amebiasis in Turkey are limited. Here, a rare case of a young man with an initial diagnosis of pneumonia followed by the identification of ALA after radiological interventions and laboratory tests is presented and the relevant literature is discussed.