Mert Ahmet Kuskucu

Blood stream infections due to OXA-48-like carbapenemase-producing Enterobacteriaceae: treatment and survival

BACKGROUND Blood stream infections (BSIs) due to carbapenem-resistant Enterobacteriaceae (CRE) are associated with high hospital mortality rates and present a tremendous challenge to clinicians. The optimal treatment remains undefined. We aimed to investigate the risk factors for mortality and the correlation between different treatment modalities and outcomes. METHODS The clinical characteristics and treatment outcomes of a cohort of 36 patients with BSIs due to CRE were investigated and a retrospective nested case-control study of surviving and non-surviving patients was conducted. RESULTS Fifty percent of the cases were male and the mean patient age was 54.9 ± 15.8 years. Klebsiella pneumoniae was the etiological agent in 26 cases (72.2%), Escherichia coli in eight (22.2%), and Enterobacter aerogenes in two (5.5%). All strains were phenotypically positive for carbapenemase activity and all except two (one E. coli and one K. pneumoniae) yielded both blaOXA-48 carbapenemases and blaCTX-M-type extended-spectrum beta-lactamases (ESBLs) in PCR products. The 14-day, 28-day, and all-cause in-hospital mortality rates were 41.6%, 50%, and 58.3%, respectively. The median time to death was 8 days (range 2-52 days). No significant differences were observed between survivors and non-survivors in terms of baseline characteristics, comorbid conditions, etiologies, or sources of bacteremia, however hematological malignancies (p=0.015) and prolonged neutropenia (p=0.044) were more common in non-survivors. Microbiological eradication and clinical response within 7 days were two major determinants of 28-day attributable mortality (p=0.001 and p=0.001, adjusted r(2)=0.845). Colistin-based dual combinations, and preferably triple combinations, were associated with significantly better outcomes when compared to non-colistin-based regimens (p<0.001). Time to active treatment had a significant effect on the course of infection (p=0.014). CONCLUSION Earlier active treatment with colistin based regimens and microbiological and clinical response within 7 days are major predictors of survival in cases of BSIs due to CRE. Rectal screening offers the advantage of earlier recognition and prompt empirical treatment.

Lack of Chlamydophila pneumoniae and predominance of Alloiococcus otitidis in middle ear fluids of children with otitis media with effusion

OBJECTIVE To investigate the presence of Chlamydophila pneumoniae and other bacterial pathogens in middle ear effusion samples obtained from children with otitis media with effusion (OME). MATERIALS AND METHODS Twenty-eight children (mean age 7.03; standard deviation 2.18) with OME unresponsive to medical therapy were included in the study. All of the children underwent ventilation tube insertion under general anesthesia. Eighteen patients were bilaterally affected whereas 10 children had unilateral disease. The middle ear fluids (46 samples in total) were collected during ventilation tube insertion, and were evaluated subsequently for the presence of C. pneumoniae and other bacterial pathogens using polymerase chain reaction (PCR). RESULTS Although all samples were negative for C. pneumoniae, bacterial DNA was detected in 21 of 46 samples. Overall 40% of the patients (4/10) with unilateral involvement, and 61% of the patients (11/18) with bilateral involvement were positive for bacterial DNA. In 6 patients with bilateral OME bilateral samples were positive, whereas 5 patients with bilateral OME showed only unilateral positivity. According to the results of DNA sequencing analysis, all of the positive samples harbored only one bacterial species. In 12 of 46 samples Alloiococcus otitidis DNA (26%), in 7 Haemophilus influenzae DNA (15%), in one Streptococcus pneumoniae DNA (2%) and in one Moraxella catarrhalis DNA (2%) were present. CONCLUSIONS Our findings support that C. pneumoniae does not seem to have a role in OME in children whereas A. otitidis was found to be more frequent than the other common pathogens. Further studies are required to elucidate the exact pathogenetic role of these microorganisms in OME.

Relationship of plasma cell-free DNA level with mortality and prognosis in patients with Crimean–Congo hemorrhagic fever

Crimean–Congo hemorrhagic fever (CCHF) is a viral infection. Circulating plasma cell‐free DNA (pcf‐DNA) is a novel marker indicating cellular damage. So far, the role of pcf‐DNA did not investigate in CCHF patients. In the current study, pcf‐DNA levels were investigated in CCHF patients with different clinical severity grades to explore the relationship between circulating pcf‐DNA level, virus load, and disease severity. Seventy‐two patients were categorized as mild, intermediate, and severe based on severity grading scores. The pcf‐DNA level was obtained from all participants on admission and from the survivors on the day of the discharge. The controls consisted of 31 healthy. Although the pcf‐DNA level at admission was higher in patients than in the controls, the difference was not statistically significant (P = 0.291). However, at admission and in the convalescent period, the difference between pcf‐DNA levels in mild, intermediate, and severe patient groups was significant. The pcf‐DNA level in severe patients was higher than in the others. Furthermore, compared to survivors, non‐survivors had higher pcf‐DNA levels at admission (P = 0.001). A direct relationship was found between the pcf‐DNA level and the viral load on the day of discharge in surviving patients. ROC curve analysis identified a pcf‐DNA level of 0.42 as the optimal cut‐off for prediction of mortality. The positive predictive value, negative predictive value, specificity, and sensitivity for predicting mortality was 100%, 72%, 100%, and 79%, respectively. In summary, our findings revealed that pcf‐DNA levels may be used as a biomarker in predicting CHHF prognosis. J. Med. Virol. 88:1152–1158, 2016.

Phenotypes and Genotypes of Macrolide-Resistant Streptococcus Pneumoniae

BACKGROUND Macrolide resistance in Streptococcus pneumoniae (S. pneumoniae) is a worldwide problem. AIMS The aim of this work was to analyze the phenotypes, genotypes, and clonal relatedness among macrolide-resistant S. pneumoniae strains isolated from various clinical specimens in our hospital. STUDY DESIGN Cross-sectional study. METHODS 80 non-duplicate S. pneumoniae strains were analyzed by polymerase chain reaction for both the erm (B) and mef (A) genes. RESULTS Macrolide resistance was observed in 22.5% (18 strains) of strains. Two (11.2%) isolates possessed mef (A), eight possessed erm (B) (44.4%) and eight strains (44.4%) were positive for both erm (B) and mef (A) genes. Although BOX-PCR of 18 macrolide-resistant strains revealed 11 band patterns, they clustered as seven clones with a genetic distance >10% to each other. Eight isolates possessed both erm (B) and mef (A) genes and belonged to a single clone (44.44% of all macrolide-resistant strains). CONCLUSION Increased positivity rates for both resistance genes have also been reported from other hospitals in Turkey, but this is the first study from Turkey showing the clonal dissemination of both resistance genes.

Determination of clinical significance of coagulase-negative staphylococci in blood cultures

The aim of this study was to investigate the criteria used to distinguish coagulase-negative staphylococci (CoNS) bacteremia from contamination. We evaluated 162 adult patients with CoNS-positive blood cultures (BCs). Of the 162 patients, 35 (21.6%) had at least 2 positive BCs and 127 (78.4%) had a single positive BC. According to the Laboratory-Confirmed Bloodstream Infection (LCBI) criteria, 24 (14.8%) patients with the same species of CoNS had true bacteremia, and 138 (85.2%) patients had contaminants. Despite the detection of the same CoNS species, 9 of the 24 patients had different CoNS genotypes. Using clinical assessments, only 20 patients were diagnosed with true bacteremia, 8 of them had a single positive BC. We concluded that only using the LCBI criteria or clinical evaluations of a patient were not sufficient to distinguish CoNS bacteremia from contamination. Molecular identification should also be performed as a diagnostic laboratory parameter for CoNS bacteremia.

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.

The Frequency and Associated Factors for BK Virus Infection in a Center Performing Mainly Living Kidney Transplantations

Purpose: BK virus (BKV) nephropathy has increasingly become an important cause of morbidity in renal transplant recipients. We evaluated the frequency and associated factors for BKV infection in a center performing mainly living donor transplantations over a long time period. Methods: One hundred consecutive renal transplant patients were included. Quarterly visits were planned to examine urine for decoy cells and to measure the BKV DNA in the blood and urine. Renal biopsy was performed in case of deteriorated allograft function. Serological examinations for BKV immunoglobulin G (IgG) were performed in donors. Results: Throughout the entire follow-up period, the rates of viruria, viremia, and the positivity of decoy cells were 12%, 6%, and 13%, respectively. The negative and positive predictive values of decoy cells were 93.1% and 69.2%, respectively, for viruria, and 99.2% and 45.5%, respectively, for viremia. Biopsy-proven BKV nephropathy was observed in 1 patient. The BKV IgG was positive in all living donors. Viruria and viremia were associated with deceased donor transplantation, acute rejection, and pulse steroid therapy. In addition, viremia was associated with antithymocyte globulin therapy and a short duration of the posttransplant period. Conclusions: The frequency of BKV infection was lower in our transplant unit compared to previous reports. Reduced doses of immunosuppression seem to be the main factor that may explain the reduced frequency. However, an active screening strategy is still of importance for this patient group.

Problems encountered in conventional HIV 1/2 Algorithms: lack of necessity for immunoblot assays to confirm repeated ELISA reactive results

Background The use of conventional (serologically based) HIV 1/2 diagnostic algorithms has become controversial in recent years. Objectives Sera from patients who underwent verification tests were evaluated because repeated ELISA-reactive results demonstrated a HIV1+HIV2 positive band pattern. Methods The line immunoassay (LIA) test was used for repeated HIV enzyme immunoassays (EIA)-reactive sera in patients at three centers. The Bio-Rad Geenius™ HIV 1/2 and the HIV-1 RNA tests were used. HIV-1 and RNA HIV-2 were investigated using PCR. Results LIA was used to evaluate 3,224 out of 10,591 samples with repeated ELISA reactivity (30%). We found that 32 (1%) of the sera, along with HIV1 bands and HIV2 gp36 bands, were positive. Only 28 of the 32 verified serum samples with gp36 bands were repeated, and no gp36 band positivity was detected using the Bio-Rad Geenius™ HIV-1/2 confirmatory assay in these serum samples. The HIV-2 proviral DNAs were also negative. Therefore, we excluded the possibility of HIV1+2 co-infection. All samples from the 32 patients were positive for HIV-1 RNA. Conclusion Our findings highlight the need to exclude confirmatory tests like the LIA test from the current diagnostic HIV algorithm and replace it with rapid HIV-1 and HIV-2 confirmatory immunochromotographic tests.

Emergence of E138 mutations among treatment naïve HIV-infected patients in Istanbul

No: 1689 Presentation at ESCV 2015: Poster 2 Interlaboratory comparison of BK virus DNA load assays M. Solis1,2,∗, M. Meddeb1, C. Sueur1,2, P. Domingo-Calap2, E. Soulier2, A. Chabaud1, P. Perrin3, B. Moulin4, S. Bahram4, S. Caillard3, F. Stoll-Keller1, S. Fafi-Kremer1 1 Laboratoire de Virologie, Hopitaux Universitaires de Strasbourg, Strasbourg, France 2 Inserm UMR S1109, LabEx Transplantex, Federation de Medecine Translationnelle de Strasbourg (FMTS), France 3 Departement de Nephrologie – Transplantation, Hopitaux Universitaires de Strasbourg, France 4 LabEx Transplantex, Federation de Medecine Translationnelle de Strasbourg (FMTS), Universite de Strasbourg, France Background: International guidelines recommend screening of kidney transplant recipients for BK virus (BKV) replication and define BKV viremia ≥4 log10 copies/ml as presumptive BKV-associated nephropathy (BKVN) and a cutoff for therapeutic intervention. Hence, BKV DNA load (BKVL) assays need to be comparable to ensure appropriate patient care. Methods: To assess interlaboratory variability in BKV viruria and viremia testing, 27 laboratories were sent 15 (5 urine, 5 whole blood and 5 plasma) and 8 (4 urine, 2 whole blood and 2 plasma) clinical specimens in 2013 and 2014, respectively. Results: Nine BKVL assays were used, including 5 commercial kits and 4 in-house methods. The majority (71%) of laboratories targeted the StAg while the LTAg was targeted by 17% of the laboratories and 3 other techniques used a different target gene (VP1, VP2-VP3 or VP1+StAg). Assuming that±0.5 log10 variation relative to the expected result is acceptable, 68% of the reported results fell within this range. Laboratories using commercial assays reported significantly more results within the acceptable range (76%) than laboratories using in-house assays (39%) (p<0.0001). High interlaboratory variability was observed, with a variation ranging from 1.73 to 4.65 log10 copies/ml (mean=2.55 log10 copies/ml). The number of mutations and the distance from the 3′ end of the primers largely contributed to this variability, and most mutations (88.2%)were genotype-specific. Genotype II and IV samples displayedhigher variability due to polymorphismon the target gene and were incorrectly quantified by all in-house assays. The calibration material also contributed to interlaboratory variability. Recalibration with a common calibrator significantly reduced the bias in comparisons between assays. Furthermore, the extraction apparatus had only a limited impact on interlaboratory variability. Conclusion: Polymorphism of the amplification target gene and the use of different calibration material contribute largely to interlaboratory variability. This variabilitymay significantly impact patient care and calls for presumptive BKVN cutoff reevaluation. The development of an International Standard for BKVL assay calibration and increased awareness of BKV polymorphism would reduce interlaboratoryvariabilityandallowadequateBKV infection monitoring. http://dx.doi.org/10.1016/j.jcv.2015.07.264