Evaluation of Using Direct Viral Transport Medium Samples without Nucleic Acid Isolation for SARS-CoV-2 Diagnosis by RT-PCR.

BACKGROUND: Diagnosis with reverse transcriptase polymerase chain reaction (RT-PCR) test is a very important step for the control of the COVID-19 pandemic. The aim of this study is to compare the RT-PCR results of the samples taken directly from the viral transport medium (VTM) without extraction with the RT-PCR results of two different extraction methods, one automated and the other manual, in the diagnosis of COVID-19. METHODS: Among the respiratory tract samples sent to Sakarya Training and Research Hospital Microbiology Laboratory for COVID-PCR study, 20 negative and 43 positive samples with different cycle threshold (CT) values were included in the study. Both manual nucleic acid isolation with the vNAT isolation kit (Bioeksen, Turkey) and automatic nucleic acid isolation with the EZ1 Virus Mini Kit v2.0 in the isolation device were performed simulta-neously from the patient samples included in the study and the results were compared. RESULTS: The mean Ct values of the samples were found to be 21.58 using manual vNAT as the extraction method, 17.63 using the automated magnetic bead method, and 21.45 in PCR from direct VTM without extraction. When the automatic magnetic beads extraction method was taken as the reference method, the sensitivity of direct PCR was 97.3%, the specificity was 95%, the positive predictive value was 97.3%, and the negative predictive value was 95%. Phi coefficients were found to be 0.927 between vNAT and direct PCR, 1 between vNAT and EZ1, and 0.922 between direct PCR and EZ1. CONCLUSIONS: Direct PCR has advantages such as eliminating RNA extraction and purification steps, providing a shorter detection time, and using less labor and less consumables without reducing the diagnostic accuracy. It is thought that this method can help as a useful process management for the control of the epidemic in countries with limited resources.

Microbial contamination and infection risks of narghile besides hazards of tobacco.

OBJECTIVE: Water-pipe smoking has become a serious public health threat worldwide. In order to raise awareness of adverse effects and transmission of bacteria via water-pipe smoking, we aimed to identify the bacteria and their antimicrobial resistance profiles that colonize different parts of waterpipes. METHODS: We examined totally 182 water pipes from 7 lounges (in Turkey) used in public places and we collected 728 culture samples in total by microbiological methods. We used disposable sterile swabs to sample the inside and outside of the mouthpiece, and the handling piece and sterile injectors were used to collect 5 mL of water from the water pipe bowl. RESULTS: There was a significant (p < 0.05) difference in microbial contamination (growth/presence of bacteria and fungi) among the parts of the water pipes sampled. There was a significant (p < 0.05) difference in the number of bacteria growing (microbial load) among the parts of the water pipes. Only one narghile lounge out of seven, which had 13 water pipes, had a hygiene procedure. The water jars are often contaminated with Gram-negative bacteria. CONCLUSION: Water pipes, especially the interior and outer part of the mouthpieces and the handle, are colonized by microbes and pose a risk of infection. Procedures for water pipe hygiene should be developed, periods should be defined, and the owners and employees of establishments and water-pipe smokers should be educated in this regard. Water-pipe smoking is a threat to public health and should be regulated by the state.

Investigation of the In Vitro Effectiveness of Aztreonam/Avibactam, Colistin/Apramycin, and Meropenem/Apramycin Combinations Against Carbapenemase-Producing, Extensively Drug-Resistant Klebsiella pneumoniae Strains.

This study aimed at investigating the in vitro effectiveness of aztreonam/avibactam, colistin/avibactam, colistin/apramycin, and meropenem/apramycin combinations against carbapenemase-producing, extensively drug-resistant (XDR) Klebsiella pneumoniae strains. This study evaluated 38 carbapenem-resistant, carbapenemase-producing, and XDR K. pneumoniae strains. The checkerboard method was used to examine the efficacy of aztreonam/avibactam, and meropenem/apramycin combinations in all strains and the colistin/apramycin combination in colistin-resistant strains (n = 26). It was found that when used alone, aztreonam and avibactam had high minimum inhibitory concentration values in all strains and that all strains were resistant to aztreonam. Nevertheless, the aztreonam/avibactam combination was found to have a synergistic effect against all strains. Apramycin alone was effective against 30 K. pneumoniae strains (79%); however, 8 strains (21%) were found to be resistant. In the synergy testing of 26 colistin-resistant strains with the checkerboard method, the colistin/apramycin combination was found to have a synergistic effect against 4 strains (15.3%), an antagonistic effect against 8 strains (30.7%), and an additive effect against 14 strains (54%). By comparison, the meropenem/apramycin combination had a synergistic effect against 20 strains (52%) and an additive effect against 12 strains (31%). The aztreonam/avibactam combination showed a high in vitro synergistic effect on carbapenemase-producing and XDR K. pneumoniae strains, such as Metallo-ß-lactamase, and provided good prospects for the successful treatment. The meropenem/apramycin combination was also highly synergistic. The synergistic effects were low for the colistin/apramycin combination that was tested on colistin-resistant strains. However, it is promising that apramycin has low minimal inhibitory concentration values.