Quality of MALDI-TOF mass spectra in routine diagnostics: results from an international external quality assessment including 36 laboratories from 12 countries using 47 challenging bacterial strains.

OBJECTIVES: Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a widely used method for bacterial species identification. Incomplete databases and mass spectral quality (MSQ) still represent major challenges. Important proxies for MSQ are the number of detected marker masses, reproducibility, and measurement precision. We aimed to assess MSQs across diagnostic laboratories and the potential of simple workflow adaptations to improve it. METHODS: For baseline MSQ assessment, 47 diverse bacterial strains, which are challenging to identify by MALDI-TOF MS, were routinely measured in 36 laboratories from 12 countries, and well-defined MSQ features were used. After an intervention consisting of detailed reported feedback and instructions on how to acquire MALDI-TOF mass spectra, measurements were repeated and MSQs were compared. RESULTS: At baseline, we observed heterogeneous MSQ between the devices, considering the median number of marker masses detected (range = [2-25]), reproducibility between technical replicates (range = [55%-86%]), and measurement error (range = [147 parts per million (ppm)-588 ppm]). As a general trend, the spectral quality was improved after the intervention for devices, which yielded low MSQs in the baseline assessment as follows: for four out of five devices with a high measurement error, the measurement precision was improved (p-values <0.001, paired Wilcoxon test); for six out of ten devices, which detected a low number of marker masses, the number of detected marker masses increased (p-values <0.001, paired Wilcoxon test). DISCUSSION: We have identified simple workflow adaptations, which, to some extent, improve MSQ of poorly performing devices and should be considered by laboratories yielding a low MSQ. Improving MALDI-TOF MSQ in routine diagnostics is essential for increasing the resolution of bacterial identification by MALDI-TOF MS, which is dependent on the reproducible detection of marker masses. The heterogeneity identified in this external quality assessment (EQA) requires further study.

[Investigation of Anti-HCV S/CO Value in Detecting Viremia in Patients with Hepatitis C Virus Infection]. / Hepatit C Virüsü Enfeksiyonu Olan Hastalarda Viremi Tespitinde Anti-HCV S/CO Degerinin Arastirilmasi.

Anti-HCV and HCV RNA tests are used in laboratory diagnosis of hepatitis C virus (HCV) infections. False positive results are frequently observed in anti-HCV tests used as screening tests in societies with low prevalence of HCV. The HCV RNA test, which is a confirmatory test, is not performed in every laboratory because it is a high-cost and high-tech test, which can lead to delay in the diagnosis and treatment of patients. In this study, it was aimed to obtain an optimal anti-HCV S/CO value in our laboratory for demonstrating true antibody positivity and viremia in patients by analyzing the relationship between anti-HCV, alanine aminotransferase (ALT) and HCV RNA using retrospective data. Between July 2014 and July 2017, 754.190 anti-HCV tests were performed. Patients aged 18 years or older who were reactive with anti-HCV and those with simultaneous HCV RNA and ALT prompts were included in the study. The second generation CMIA (Abbott, USA) method was used for anti-HCV detection. For quantitative HCV RNA analysis, viral nucleic acid extraction was performed with the QIAsymphony SP/AS (Qiagen, Germany) using the QIAsymphony DSP Virus/Pathogen Midi Kit; and PCR was performed by Rotor-Gene Q (Qiagen, Germany) using Artus HCV QS-RGQ kit. ARCHITECT c and AEROSET systems (Abbott, USA) were used for ALT measurement. HCV genotype determination (622 cases) was performed using GenoSen's HCV Genotyping 1/2/3/4 RG qualitative real time PCR kit (Corbett Research, Australia) and GEN-C 2.0 Reverse Hybridization Strip Assay (NLM Diagnostics, Italy) kit at different periods covered by our study. The optimal threshold value for the relationship between anti-HCV, ALT and HCV RNA was selected based on ROC analysis. Statistical significance was accepted as p<0.05. Of the anti-HCV test results, 10.679 were found to be reactive. 1754 data of 1290 cases with anti-HCV reactivity who were simultaneously tested for HCV RNA and ALT in the same serum were evaluated. Of these, 742 (42%) were found to be HCV RNA positive and 1012 (58%) were found to be HCV RNA negative. ALT and anti-HCV levels of those who were positive for HCV RNA were significantly higher than those with negative HCV RNA (p= 0.001). The threshold point for anti-HCV S/CO according to HCV RNA was found to be 7.13 (sensitivity of 97.4%, specificity of 50.3%, positive predictive value 58.9%, negative predictive value 96.4%), and the cut-off point for ALT was found to be 27.5 IU/L (sensitivity of 77.6%, specificity of 80.8%). For HCV RNA positivity, the area under the ROC curve for anti-HCV and ALT was significantly higher than 0.5 (p= 0.001). No statistically significant difference was found between HCV genotypes in terms of ALT and anti-HCV levels. By using our new threshold in the laboratory workflow, the need to verify with HCV RNA can be reduced, especially in some patients who have been screened for antiHCV for screening purposes. Anti-HCV values below 7.13 S/CO, considering the high negative predictive value of this threshold; a false positive result in a patient presenting for screening can be predicted without waiting for the HCV RNA result. In anti-HCV reactivities determined above 7.13, the possibility of absence of viremia should be considered due to the low positive predictive value.

[Surveillance of resistance in the intensive care units using a cumulative antibiogram]. / Yogun bakim ünitelerinde kümülatif antibiyogram ile antibiyotik direncinin izlenmesi.

Empiric treatment with broad-spectrum antibiotics exerts condensed pressure in intensive care units (ICUs) for the selection of multidrug-resistant bacteria. Multidrug-resistant gram-negative bacteria became the focus of interest owing to limited treatment options and negative effects on patient survival. Cumulative antibiograms can guide selection of correct empiric treatment, de-escalation treatment according to antibiogram results and development of policies in fight against antibiotic resistance. In this study, we aimed to determine the antibiotic resistance rates of gram-negative bacilli in the intensive care units of the public hospitals in the region where we are connected by using the cumulative antibiogram result and to show the change of resistance over the years and to determine whether there is any difference between the hospitals. Gram-negative bacilli were isolated from ICUs of state hospitals in the second Istanbul State Hospitals Association area during 2014-2016. Isolates were identified using Vitek MS (bioMérieux, France) system and tested for antibiotic susceptibility with Vitek 2 (bioMérieux, France) system according to the Clinical and Laboratory Standards Institute (CLSI) criteria followed during those years. Cumulative antibiogram reports for these strains were prepared according to the CLSI M39-A4 guide. Gram-negative bacilli were divided into three groups: non-fermentative, urinary enteric, and non-urinary enteric bacilli. Total number of strains isolated during three years from these groups were 2626, 1390 and 2011, respectively. Annual trends of susceptibility during the aforementioned years were evaluated. Hospitals were also classified into five groups and differences were evaluated in the susceptibility profiles of these hospitals. Among the non-fermentative bacilli, Acinetobacter baumannii complex was the most commonly isolated species and the most resistant bacteria against antibiotics. The susceptibility rates of A.baumannii complex against the beta-lactam group of antibiotics were < 10%. Colistin susceptibility rates of A.baumannii complex and Pseudomonas aeruginosa isolates were over 98%. Among the non-urinary enteric bacilli, K.pneumoniae was the most commonly isolated species displaying maximum antibiotic resistance. Susceptibility rates for colistin, which is the last resort for treating resistant gram-negative bacteria, ranged between 73% and 80%. Escherichia coli, which was the second most common isolated species among non-urinary bacilli, had susceptibility rates over 90% to carbapenems along with colistin and tigecycline. Although E.coli was the most commonly isolated species among urinary enteric bacilli, K.pneumoniae and Proteus mirabilis were the most resistant isolates. A statistically significant decrease in susceptibility rates against all antibiotics was observed in P.mirabilis isolates between the years 2015-2016. Carbapenem susceptibility rates decreased below 70%. E.coli, Serratia spp., and Stenotrophomonas maltophilia had similar susceptibility profiles among different hospitals, indicating homogenous distribution, whereas other species had different profiles, indicating a more heterogenic distribution, among hospitals. The reports of this study were generated according to a standard guide and they clearly revealed the seriousness of antibiotic resistance in our region which represents approximately one-fourth area of Istanbul. When all the results were considered, best empiric treatment option for enteric bacilli except K.pneumoniae was carbapenems. For K.pneumoniae infections there is no reliable choice other than colistin but a de-escalation treatment can be planned according to antibiogram results. Similarly colistin is the first choice in empiric treatment of infecitons due to non-enteric bacilli. However, the heterogeneity of the susceptibility profile observed in the hospitals, which are geographically close to each other, indicated the difference in the flora of the intensive care unit of hospitals. It would be appropriate to prepare cumulative antibiogram reports similar to those in the present study, to prevent complications, reduce costs and improve patient prognosis in the intensive care units of hospitals and these reports should become part of the infection control policies applied in hospitals.