[Evaluation of the Respiratory Viral Panel PCR Test Results Before and After COVID-19 Pandemic]. / COVID-19 Pandemisi Öncesi ve Sonrasinda Solunum Yolu Virüs Paneli PCR Test Sonuçlarinin Degerlendirilmesi.

During the ongoing Coronavirus disease-2019 (COVID-19) pandemic, infections caused by other respiratory viruses continue to be seen and constitute an important health problem. In this study, it was aimed to evaluate the frequencies of respiratory tract viruses detected by respiratory tract virus panel (Allplex Respiratory Panel, Seegene, South Korea) multiplex real-time PCR test in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pre-pandemic period, and in the first and second year of the pandemic. The distribution of viral agents between these three periods was also investigated. In addition, it was planned to investigate the frequency of coinfection with SARS-CoV-2 and other respiratory tract viruses during the pandemic. When the sum of the three periods were evaluated together, it was observed that at least one respiratory tract virus was detected in 13 802 (32.7%) of 42 174 samples. While at least one respiratory tract virus was detected in 8740 (54.6%) of 16 002 samples in the pre-pandemic period, at least one respiratory tract virus was detected in 1638 (9.4%) of 17 510 samples in the first year of the pandemic, and in 3424 (39.5%) of 8662 samples in the second year of the pandemic. In the first year of the pandemic, a statistically significant difference was observed that the number of viruses detected decreased due to closure measures and the use of personal protective equipment (p<0.001). It was determined that the frequency of the detection of respiratory tract viruses other than SARS-CoV-2 started to increase again and a statistically significant difference occurred in the third period when vaccination started and the transition to normalization began by gradually loosening the closure measures (p<0.001). Rhinovirus was the most frequently detected virus in all three periods of the study (First period: 16.5%; second period: 5.9%; third period: 16.5). More than one respiratory tract virus was detected simultaneously in 2061 (14.9%) of 13 802 samples, in which at least one respiratory tract virus was detected within the scope of the study. Rhinovirus (7.3%) took the first place among the viruses found in coinfection. In the second and third periods covering the pandemic period, it was observed that the SARS-CoV-2 PCR result was also positive in 177 (4.2%) of 4219 samples whose respiratory tract virus panel PCR results were positive and simultaneously had a SARS-CoV-2 PCR test request. Therefore, it was concluded that SARS-CoV-2 coinfection can be observed in the same patient with other respiratory tract viruses in respiratory tract samples. The addition of SARS-CoV-2 to the respiratory tract virus multiplex PCR panels currently in use will enable faster detection of such coinfections. It is thought that both the incidence of respiratory tract virus infections other than SARS-CoV-2 and the rate of coinfection with other respiratory tract viruses in SARS-CoV-2 infection may increase with the relaxation of the measures taken for the control of the pandemic. For this reason, the detection of viruses that cause respiratory tract infections from clinical samples with reliable and rapid methods will ensure the measures to be taken to protect public health without delay and thus contribute to the prevention of the spread of infections.

Predictive modeling of mortality in carbapenem-resistant Acinetobacter baumannii bloodstream infections using machine learning.

Acinetobacter baumannii, a notable drug-resistant bacterium, often induces severe infections in healthcare settings, prompting a deeper exploration of treatment alternatives due to escalating carbapenem resistance. This study meticulously examined clinical, microbiological, and molecular aspects related to in-hospital mortality in patients with carbapenem-resistant A. baumannii (CRAB) bloodstream infections (BSIs). From 292 isolates, 153 cases were scrutinized, reidentified through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), and evaluated for antimicrobial susceptibility and carbapenemase genes via multiplex polymerase chain reaction (PCR). Utilizing supervised machine learning, the study constructed models to predict 14- and 30-day mortality rates, revealing the Naïve Bayes model's superior specificity (0.75) and area under the curve (0.822) for 14-day mortality, and the Random Forest model's impressive recall (0.85) for 30-day mortality. These models delineated eight and nine significant features for 14- and 30-day mortality predictions, respectively, with "septic shock" as a pivotal variable. Additional variables such as neutropenia with neutropenic days prior to sepsis, mechanical ventilator support, chronic kidney disease, and heart failure were also identified as ranking features. However, empirical antibiotic therapy appropriateness and specific microbiological data had minimal predictive efficacy. This research offers foundational data for assessing mortality risks associated with CRAB BSI and underscores the importance of stringent infection control practices in the wake of the scarcity of new effective antibiotics against resistant strains. The advanced models and insights generated in this study serve as significant resources for managing the repercussions of A. baumannii infections, contributing substantially to the clinical understanding and management of such infections in healthcare environments.

First Detection of Klebsiella pneumoniae Isolate Co-Harboring Fosfomycin Resistance Gene fosA3 and blactx-m Among Gram Negative Urine Isolates in a Turkish Hospital.

The most common gram-negative pathogens in urinary tract infections are Escherichia coli and Klebsiella pneumoniae. Therapy that is often empirical relies on local antibiotic resistance data, hence monitorization of antimicrobial resistance periodically in each hospital is a requirement. In this study, antibiotic susceptibility profiles of consecutive urinary isolates (E. coli [n = 235] and K. pneumoniae [n = 56]) of adult patients collected between February 2018 and February 2019 from inpatients in Hacettepe University Hospital were assessed. Isolates resistant to fosfomycin (minimum inhibitory concentration >32 mg/L) were further investigated for the presence of fosA, fosA3, and fosC2. Fosfomycin susceptibility was determined by agar dilution method. Broth microdilution method was performed for amikacin, gentamicin, ceftazidime, ceftriaxone, meropenem, ciprofloxacin, tigecycline, trimethoprim/sulfamethoxazole (TMP/SMX), colistin, and piperacillin/tazobactam (PIP/TAZ). PCR method was employed to investigate fosA, fosA3, fosC2, and blaCTX-M. Existence of fosA3 gene was confirmed by sequencing. Resistance rates to amikacin, gentamicin, ceftazidime, ceftriaxone, meropenem, ciprofloxacin, tigecycline, TMP/SMX, colistin, and PIP/TAZ were 2.7%, 18.5%, 25.4%, 33.0%, 3.4%, 45.4%, 2.4%, 43.6%, 6.2%, and 23.7%, respectively. Sixteen isolates (5.5%) were resistant to fosfomycin. Resistance was most frequently observed in K. pneumoniae (n = 9). fosA3 gene was detected in one fosfomycin-resistant K. pneumoniae isolate. This isolate also carried blaCTX-M. fosC2 and fosA genes could not be detected in any of the isolates. In this study, we report for the first time the existence of fosA3 in Turkey and its association with the blaCTX-M gene. As a result of increasing blaCTX-M producing Enterobacterales isolates globally, increase in fosfomycin resistance may be expected in near future.

Critical appraisal of air pouch infection model in rats.

The aim of this study was to assess the efficacy and pharmacokinetic profiles of gentamicin, vancomycin, and levofloxacin in a rat air pouch model, in which Staphylococcus aureus (ATCC 25293) was used as the test organism. Antibiotic treatments (i.p.) were started 1 hour after bacterial inoculation and continued for 5 days. Bacterial counts and antibiotic concentrations were determined in pouch exudates that were obtained on the 5th day of antibiotic treatment. The following observations were made: 1) The concentrations of gentamicin or vancomycin in the exudate were found to be below the detection limit. 2) Levofloxacin and ciprofloxacin exhibited a dose-dependent effect on bacterial counts in the exudate. 3) The antibacterial efficacy of levofloxacin was found to be enhanced when the total daily dose of 10 mg was divided into smaller parts. The present study also showed that the air pouch infection model was a valuable tool to assess the pharmacokinetic and pharmacodynamic properties of antibiotics.