The impact of the BIOFIRE® Blood Culture Identification 2 Panel on antimicrobial treatment of children with suspected systemic inflammatory response syndrome and sepsis.

This study aimed to assess the therapeutic effects of implementing the BioFire® Blood Culture Identification 2 (BCID2) Panel (bioMérieux, Marcy l'Etoile, France) in the clinical practice of children with sepsis. This retrospective cross-sectional study included children from 15 days of age to 18 years old with sepsis and of whom the BCID2 Panel was studied from the positive blood culture. If the antimicrobial treatment was changed according to the results of BCID2 Panel, it was recorded and re-grouped as targeted antimicrobial therapy, de-escalation of the antimicrobial treatment and shifting to another antimicrobial drug if any antimicrobial resistance was detected. Seven-days and thirty-days mortality rate was recorded. Thirty-two patients with 36 septic episodes with positive BCID2 Panel results were included. The median age was 10 months 15 days (ranging from 15 days to 16.5 years). The mean difference between having positive results by the BCID2 Panel and conventional culture methods was 82.2 ± 45.4 h (ranging from 12.3 to 207 h). Effect of the BCID2 Panel on the antimicrobial treatment was detected in 69.4% of the episodes (n = 25). Glycopeptides were ceased at 6 patients, piperacillin/tazobactam was ceased at 6 patients, and cefotaxime was ceased at one patient and de-escalation was achieved in 13 episodes which formed the 36.1% of the initial antimicrobial treatment.   Conclusion: The BCID2 Panel had an important impact on the patients care and optimization according to the principles of antimicrobial stewardship. The BCID2 Panel may be one of the key items for rapid and accurate diagnosis in children with sepsis. Blood culture is still the mainstay for especially detection of antimicrobial drug resistance, while BCID2 tests had several advantages such as speed and diagnostic accuracy as good as blood culture. What is Known: • The BioFire® Blood Culture Identification 2 (BCID2) Panel (bioMérieux, Marcy l'Etoile, France) is a well-validated assay that allows for the simultaneous identification of 43 nucleic acid targets associated with bloodstream infections within about 1 h. What is New: • BCID2 Panel had a direct impact on the patient's treatment decision at the 69.4% of the sepsis episodes. • The clinicians received the microbiological results 82.2 h earlier with BCID2 panel compared to blood culture methods with antimicrobial resistance and de-escalation of the antimicrobial drugs was achieved at 13 episodes which formed the 36.1% of the initial treatment.

Distribution of spreading viruses during COVID-19 pandemic: Effect of mitigation strategies.

BACKGROUND: The study aimed to evaluate the distribution of circulating respiratory viral pathogens other than severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) during the first year of the coronavirus disease-2019 (COVID-19) pandemic with especially focusing on the effects of the national-based mitigation strategies. METHODS: This single-center study was conducted between March 11, 2020-March 11, 2021. All children who were tested by polymerase chain reaction on nasopharyngeal swabs for SARS-CoV-2 and other common respiratory viral pathogens were included in the study. RESULTS: A total of 995 children with suspected COVID-19 admitted to the study center. Of these, 513 patients who were tested by polymerase chain reaction for both SARS-CoV-2 and common respiratory viral pathogens were included in the final analysis. Two hundred ninety-five patients were (57.5%) male. The median age was 3 years of age (27 days-17 years). A total of 321 viral pathogens identified in 310 (n: 310/513, 60.4%) patients, and 11 of them (n: 11/310, 3.5%) had co-detection with more than 1 virus. The most common detected virus was rhinovirus (n: 156/513, 30.4%), and SARS-CoV-2 (n: 122/513, 23.8%) followed by respiratory syncytial virus (n: 18/513, 3.5%). The influenza virus was detected in 2 patients (0.4%). A total of 193 patients were negative for both SARS-CoV-2 and other pathogens. CONCLUSIONS: There is a decline in the frequency of all viral pathogens like SARS-CoV-2 in correlation with the national-based mitigation strategies against COVID-19 during the pandemic.

Seroprevalence of Toxoplasma gondii, Rubella virus and Cytomegalovirus among pregnant women and the importance of avidity assays.

OBJECTIVES: To determine the seroprevalence of Toxoplasma gondii (T. gondii), Rubella virus, and Cytomegalovirus (CMV) among pregnant women in Izmir, Turkey. METHODS: Medical records of pregnant women attending Izmir Tepecik Training and Research Hospital, Izmir, Turkey between January 2014 and January 2016 were analyzed in this retrospective cross-sectional study. The 7513 T. gondii IgM/IgG results, 7189 Rubella IgM/IgG results, 906 CMV IgM/IgG results and 146 avidity test results were evaluated. Specific IgM and IgG antibodies were detected by an automated chemiluminescent enzyme immunoassay method. Immunoglobulin G avidity tests were performed using a multiparametric immunoassay system. RESULTS: The rates of IgG positivity for T. gondii was 32.3%, Rubella virus 93.5%, and CMV 98.9%. Immunoglobulin M antibodies were found to be positive in 138 (1.9%) cases for T. gondii, 88 (1.2%) cases for Rubella, and 14 (1.5%) cases for CMV. Avidity tests were ordered from 146 of 218 patients who were found both IgM and IgG positive. Among 146 patients, 6 patients had a low avidity index (all for T. gondii), 11 patients showed borderline avidity, and 129 patients revealed high avidity. CONCLUSION: In our region, whereas the rates of IgG positivity for Rubella and CMV are high, most pregnant women were susceptible to T. gondii infections. In order to enhance the reliability of the serological diagnosis, avidity tests should be performed in all IgM positivities detected together with IgG positivity.

Antimicrobial susceptibilities of Escherichia coli isolates as agents of community-acquired urinary tract infection (2008-2014).

OBJECTIVE: Urinary tract infections (UTIs) are among the most frequently seen community-acquired infections worldwide. E. coli causes 90% of urinary system infections. To guide the empirical therapy, the resistance pattern of E. coli responsible for community-acquired UTI was evaluated throughout a seven-year period in this study. MATERIAL AND METHODS: The urine cultures of patients with urinary tract infections admitted to outpatient clinics between 1(st) January 2008 and 31(st) December 2014 were analyzed. Presence of ≥10(5) colony-forming units/mL in urine culture media was considered as significant for UTI. Isolated bacteria were identified by standard laboratory techniques or automated system VITEK2 (BioMerieux, France) and BD PhoenixTM 100 (BD, USA), as required. Antibiotic susceptibility testing was performed by Kirby-Bauer disk diffusion method using Clinical Laboratory Standard Institute (CLSI) criteria. RESULTS: A total of 13281 uropathogens were isolated. Overall E. coli accounted for 8975 (67%) of all isolates. Resistance rates of E. coli to antimicrobial agents was demonstrated to be as follows: ampicillin 66.9%, cefazolin 30.9%, cefuroxime 30.9%, ceftazidime 14.9%, cefotaxime 28%, cefepime 12%, amoxicillin-clavulanic acid 36.9%, trimethoprim-sulfamethoxazole (TMP-SXT) 20%, ciprofloxacin 49.9%, amikacin 0.3%, gentamycin 24%, nitrofurantoin 0.9%, and fosfomycin 4.3%. There was no resistance to imipenem nor meropenem. The frequency of ESBL-producing E. coli strains was 24%. CONCLUSION: It is concluded that fosfomycin and nitrofurantoin are appropriate empirical therapy for community-acquired UTI empirical therapy, but the fluoroquinolones and the TMP-SXT shall not be used in the emprical treatment of UTI at this stage. In conclusion, as resistance rates show regional differences, it is necessary to regularly examine regional resistance rates to determine the appropriate empiric antibiotic treatment and national antibiotic usage policies must be reorganized according to data obtained from these studies.

Investigation of West Nile virus among healthy blood donors in the western part of Turkey.

BACKGROUND/AIM: THE West Nile virus (WNV) is a mosquito-borne flavivirus causing different forms of infection among humans, varying from asymptomatic illness to fetal central nervous system infection. Turkeylies within an endemic region for WNV. Transfusion of infected blood products is another well-documented major route of transmission. The aim of our study was to investigate the presence of WNV viremia among a healthy donor population from the western part of the country. MATERIALS AND METHODS: A total of 438 healthy volunteer blood donors were included in the study. The presence of WNV RNA was investigated by quantitative real-time reverse-transcriptase polymerase chain reaction (qRT-PCR) and anti-WNV IgG was detected by a commercial ELISA test. RESULTS: Ages of volunteer donors were 18-62 years (mean: 34.7) and 34 (7.76%) were women. All samples were negative for WNV RNA by qRT-PCR. Eleven (2.51%) samples, 1 of which was borderline, were positive for anti-WNV IgG. All positive samples were from the western part of the country and 9 of them were from Izmir. CONCLUSION: Although all donor samples were negative for WNV RNA by qRT-PCR, the risk of WNV transmission via blood products should not be ignored in endemic regions.

Regulatory effects of alanine-group amino acids on serine alkaline protease production by recombinant Bacillus licheniformis.

Influences of the concentration and addition time of alanine-group amino acids, i.e. alanine, leucine and valine, on serine alkaline protease (SAP) synthesis were investigated by Bacillus licheniformis (DSM 1969) carrying pHV1431:: sub C in a defined medium to identify the amino acids creating intracellular reaction-rate limitation in SAP production. While the precursors of alanine-group amino acids, pyruvate and alanine, did not affect SAP production considerably within the range 0-15 mM, the addition of leucine decreased both SAP production and cell formation, because of the inhibition of valine synthesis. Although valine inhibits reactions starting with pyruvate towards 2-oxo-isovalerate, due to conversion of valine into 2-oxo-isovalerate and from 2-oxo-isovalerate to leucine, valine did not inhibit leucine synthesis. Val (7.5 mM) supply at t =0 h increased SAP activity to an activity of 1070 units.cm(-3) which was 1.3-fold higher than that of the reference production medium. The highest cell growth yield on substrate (Y (X/S)) was obtained as 0.24 g.g(-1) with the supply of alanine; and the highest product formation yield on substrate was obtained as 0.134 units.g(-1) with the supply of valine. By using the results obtained, strategies for increasing SAP production and complex medium design were also discussed.