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    Carbapenem-resistant Acinetobacter baumannii strains in the Covid-19 pandemic: 16 S rRNA analysis, carbapenem resistance genes, and antibiotic resistance profiles
    (Springer, 2024) Acer, Omer; Bahce, Yasemin Genc; Ozudogru, Osman
    Acinetobacter baumannii was reported as a frequent pathogen leading to outbreaks of multidrug-resistant organisms both in the intensive care unit (ICU) and in non-ICU units during the coronavirus disease in 2019 (COVID-19). In this study we aimed to examine the phenotypic and molecular characteristics of clinical isolates of carbapenem-resistant A. baumannii (CrAb) obtained from Siirt Training Hospital in Siirt, Turkiye, during the Covid-19 pandemic. In our study, 31.6% of the patients whose culture was taken were Covid-19 positive. Of the 57 CrAb strains tested for antibiotic resistance, 52 (91.2%) showed extensive-drug resistance (XDR), 4 (7%) multi-drug resistance (MDR), and 1 (1.8%) pan-drug resistance (PDR). According to 16 S rRNA analysis, the sequences of the CrAb strains used in our study were 99-100% similar to the 16 S rRNA genes of the A. baumannii strains registered in GenBank. The most frequently detected carbapenem resistance gene in the species in our study was the OXA51 gene (85.7%). It's interesting to note that the blaNDM gene, which has a direct connection to the Indian Subcontinent and has recently been observed in the Middle East but has been rarely detected in Turkiye, was discovered in our study at a high rate. We think that this situation is caused by migration from the Middle East due to war in recent years. Additionally, we believe that horizontal gene transfer between bacteria is the cause of the high frequency of the blaVIM gene, whose source is primarily Pseudomonas species, in A. baumannii species in our study.
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    Carbapenem-resistant Klebsiella pneumoniae strains isolated from clinical specimens in Siirt, Türkiye; molecular characterization and antimicrobial resistance genes detection
    (Elsevier Science Inc, 2024) Gunes, Sevgi; Acer, Omer; Bahce, Yasemin Genc
    This study aimed to molecularly identify carbapenem-resistant Klebsiella pneumoniae (CRKP) strains isolated from clinical samples and to determine antibiotic resistance genes. Only carbapenem-resistant strains were included in our study. Of the 35 CRKP strains, 18 (51.4%) were extensive drug, 11 (31.4%) were multi-drug, and 6 (17.1%) were pan-drug resistances. PCR amplification revealed that 25% of the strains carried the OXA-51, 20% the OXA48, and %5 the OXA23 genes. Multilocus sequence typing (MLST) analysis based on seven house-keeping genes revealed sequence type 39. The capsule and O-antigen types were determined as KL103 and O2a, respectively. WGS analysis revealed the existence of (3-lactamase, aminoglycoside, sulfonamide, Phenicol, and Fosfomycinresistant genes. While the K. pneumoniae OmpK37 gene was detected in all 3 strains, the OmpK36 gene was detected only in the CRSU20 strain. This study is important as it is the first study to perform molecular analysis of CRKP strains from Siirt, T & uuml;rkiye.
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    Evaluation of bacterial agents isolated from endotracheal aspirate cultures of Covid-19 general intensive care patients and their antibiotic resistance profiles compared to pre-pandemic conditions
    (Academic Press Ltd- Elsevier Science Ltd, 2022) Acer, Omer; Ozudogru, Osman; Bahce, Yasemin Genc
    Background: Early reports have shown that critically ill patients infected with SARS-CoV-2 have a high prevalence of nosocomial pneumonia, particularly ventilator-associated pneumonia (VAP). Method: In the present study, we determined the bacterial agents isolated from endotracheal aspirate (ETA) cultures of Covid-19 general intensive care patients and evaluated the antibiotic resistance profiles of common bacterial agents compared to the pre-pandemic period.Results: While a total of 119 significant growths with polymicrobial growths were detected in the ETA cultures of 73 (7.5%) of 971 patients hospitalized in the intensive care unit before the pandemic, 87 significant growths were detected in the ETA cultures of 67 (11.1%) of 602 patients hospitalized in the Covid-19 intensive care unit (ICU) after the pandemic. While 61 (83.6%) of patients in the ICU died before the pandemic, 63 (94.0%) of patients in the Covid-19 ICU died after the pandemic. In terms of age, gender, and mortality, there was no significant difference between the two ICUs (p > 0.05). Before the pandemic, the mean length of stay in the ICU was 33.59 +/- 32.89 days, and after the pandemic, it was 13.49 +/- 8.03 days. This was a statistically significant difference (p < 0.05). Acinetobacter baumannii (28.5%), Klebsiella pneumoniae (22.6%), Pseudomonas aeruginosa (15.9%), Staphylococcus aureus (6.7%), Escherichia coli (7.5%), Candida spp. (5.0%) were the most prevalent causal microorganisms discovered in pre-pandemic ICU ETA samples, whereas A. baumannii (54.0%), K. pneumoniae (10.3%), P. aeruginosa (6.8%), E. faecium (8%), and Candida spp.(13.7%) were the most common causative microorganisms detected in Covid-19 ICU ETA samples. Except for tigecycline, antibiotic resistance rates in A. baumannii strains increased following the pandemic. Only tobramycin showed a significant difference in the increase of resistance among these antibiotics (p = 0.037). The rate of tigecycline resistance, on the other hand, was 17.6% before the pandemic and 2.2% afterward (p < 0.05). After the pandemic, increased resistance of K. pneumoniae strains to colistin, meropenem, ertapenem, amoxicillin-clavulanic acid, piperacillin-tazobactam, ciprofloxacin, tigecycline, and cefepime antibiotics was observed. However, these increases were not statistically significant. Except for imipenem, antibiotic resistance rates in P. aeruginosa strains increased following the pandemic. The increase in resistance of ceftazidime and levofloxacin was statistically significant (p < 0.05).Conclusion: As a result, the Covid-19 pandemic requires intensive care follow-ups at an earlier age and with a more mortal course. Although the length of stay in the intensive care unit has been shortened, it is observed that this situation is observed due to early mortality. In P. aeruginosa strains, a significant difference was detected in the resistance increase of the ceftazidime and levofloxacin (p < 0.05) and with the exception of tigecycline, antibiotic resistance rates in A. baumannii strains increased following the pandemic. Only tobramycin showed a significant difference in the increase of resistance among these antibiotics (p = 0.037). Secondary infections in patients create more difficult treatment processes due to both Covid-19 and increasing antibiotic resistance today.
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    Homologous and Heterologous Covid-19 Booster Vaccinations Against SARS-CoV-2 Infection in the Elderly
    (Springer, 2024) Acer, Omer; Bahce, Yasemin Genc; Ozudogru, Osman
    A third booster doses for the 2019 coronavirus disease (COVID-19) is widely used all over the world, especially in risky individuals, with the recommendation of WHO. The purpose of this study was to evaluate the effectiveness of mRNA (BNT162b2), and CoronaVac (Sinovac Biotech) vaccines as a reminder dose following two doses of CoronaVac against COVID-19 infection, serious illness, and mortality in the geriatric population aged 75 and older during the delta variant dominant period. Our study comprised 2730 individuals the age of 75 and older in total, of which 1082 (39.6%) were male and 1648 (60.4%) were female. The vaccine effectiveness (VE) of 2 doses of CoronaVac + 1 dose of BNT162b2 vaccine combination against COVID-19 was determined as 89.2% (95% Confidence interval (CI) 80.7-93.9%), while the VE of 3 doses of CoronaVac vaccine was determined as 80.4% (95% CI 60.5-90.2%). Geriatric patients who received three doses of CoronaVac vaccine did not need intensive care. No deaths were observed in the vaccinated groups. While the VE of vaccination with 2 doses of CoronaVac + 1 dose of BNT162b2 was 41.8% (95% CI 0-74.1%) against hospitalization, 64.4% (95% CI 0-94.7%) against intensive care unit admission, the VE of vaccination with three doses of the CoronaVac was 78.2% (95% CI 0-96.5%) against hospitalization. In conclusion, our research showed that, even with the emergence of viral variants, a third dose of the CoronaVac and BNT162b2 vaccines is highly effective against symptomatic SARS-CoV-2 infection. Third-dose vaccination regimens, including heterologous and homologous vaccines, can be an effective tool in controlling the COVID-19 pandemic and the emergence of new variants.
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    Risks of catching COVID-19 according to vaccination status of healthcare workers during the SARS-CoV-2 Delta variant dominant period and their clinical characteristics
    (Wiley, 2022) Ozudogru, Osman; Acer, Omer; Bahce, Yasemin Genc
    The exposure of healthcare workers (HCWs) to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been a major concern since the beginning of the coronavirus disease 2019 (COVID-19) pandemic. The study aimed to investigate the relationship between vaccination status and the status of catching COVID-19 in HCWs working in a Training and Research Hospital in Turkey, and the clinical course of the disease in those who were caught. The vaccination status of 1279 HCWs working at Siirt Training and Research Hospital during the period when the SARS-CoV-2 Delta variant was dominant, their cases of catching COVID-19 during this period, and the clinical course of the disease in patients with COVID-19 were investigated retrospectively. We found that the rate of COVID-19 transmission was lowest in fully vaccinated HCWs (p < 0.05). The rate of COVID-19 transmission in HCWs who received two doses of BioNTech vaccine (4.4%) and two doses of CoronaVac+ one dose of BioNTech vaccines (2.7%) was considerably lower than those without vaccination (26.2%) (p < 0.05). The transmission rate was lowest among those vaccinated with two doses of CoronaVac+ one dose of BioNTech. Hospitalization was not required in fully vaccinated HCWs. The lymphocyte count was found to be significantly higher in fully vaccinated patients than incompletely vaccinated and unvaccinated patients. Although C-reactive protein (CRP), d-dimer, and ferritin values were higher in unvaccinated and partially vaccinated patients than in fully vaccinated patients, the differences were not statistically significant. As a result, the transmission rate of COVID-19 was lowest in fully vaccinated HCWs and in those vaccinated with two doses of CoronaVac+ one dose of BioNTech. In fully vaccinated HCWs, hospitalization was not needed.
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    SARS CoV-2 reinfection rate is higher in the Omicron variant than in the Alpha and Delta variants
    (Springer London Ltd, 2023) Ozudogru, Osman; Bahce, Yasemin Genc; Acer, Omer
    Background and objectives Many mutations in variants for instance Delta and Alpha are associated with immune evasion and higher infectious potential. There are uncertainties regarding Omicron. In this regard, we aimed to compare the frequency of reinfection of SARS CoV-2 variants in our hospital between April 22, 2021 and January 26, 2022. Method The reinfection rates and demographic characteristics of a total of 27,487 COVID-19 patients infected with different SARS CoV-2 variants were examined. Results Reinfection was found in 26 (0.46%) of 5554 Alpha, 209 (1.16%) of 17,941 Delta, and 520 (13.0%) of 3992 Omicron variants. A statistically significant difference was observed between the reinfection rates of the variants (p = 0.000). The mean reinfection days were calculated as 204.4 +/- 51.1 in the Alpha variant, 291.2 +/- 58.2 in the Delta variant, and 361.2 +/- 131.6 in the Omicron variant (p = 0.000). It was observed that 16.5% of reinfection cases caught COVID-19 for the second time 3-6 months after the first COVID-19 infection, 36.7% after 6-12 months, and 46.8% after more than 12 months. There was a significant difference between the times in reinfection cases. Most reinfections occurred more than 12 months apart. Among those with a reinfection time > 12 months, 0% had Alpha, 3.4% had Delta, and 96.6% had Omicron variants. Conclusion The highest reinfection rate was observed in the Omicron variant. Reinfection was approximately 30 times more frequent in the Omicron variant than in the Alpha variant and 10 times more frequent in the Delta variant.