Abstract Antimicrobial resistance is a global problem that threatens the success of modern medica... more Abstract Antimicrobial resistance is a global problem that threatens the success of modern medical approaches. Bacteria might exhibit several mechanisms to resist against antibiotics. Intensive antimicrobial resistance surveillance is a critical step of antimicrobial stewardship as it is the basis for detecting new trends and threats, monitoring the interventions, and developing new drugs. In this chapter, we summarize the antimicrobial resistance mechanisms of bacteria and focus on the resistance of clinically important pathogens, especially to “last resort” antibiotics in all regions of the world.
OBJECTIVES We aimed to describe the mechanisms of colistin resistance in Acinetobacter baumannii.... more OBJECTIVES We aimed to describe the mechanisms of colistin resistance in Acinetobacter baumannii. MATERIALS AND METHODS Twenty-nine patients diagnosed with colistin-resistant A. baumannii infection were included to the study. The mutations in pmrCAB, lpxA, lpxC, and lpxD genes, expression of pmrCAB, carbapenemases, and mcr-1 positivity were studied. RESULTS Twenty-seven (93%) of the patients received IV colistin therapy during their stay, and the case fatality rate was 45%. All mutations in pmrC and pmrB were found to be accompanied with a mutation in lpxD. The most common mutations were I42V and L150F in pmrC (65%), E117K in lpxD (65%), and A138T in pmrB (58.6%). The colistin minimum inhibitory concentrations (MICs) of the isolates having any of these four mutations were higher than the isolates with no mutations (p < 0.001). The two most common mutations in pmrC (I42V and L150F) were found to be associated with higher expressions of pmrA and pmrC and higher colistin MIC values (p = 0.010 and 0.031). All isolates were blaOXA-23 positive. CONCLUSION Coexistence of the lpxD mutation along with mutations in pmrCAB indicates synergistic function of these genes in development of colistin resistance in A. baumannii.
Journal of Maternal-fetal & Neonatal Medicine, Jul 24, 2013
Contrary to traditional belief, breast milk is not a sterile fluid, even in healthy women. Breast... more Contrary to traditional belief, breast milk is not a sterile fluid, even in healthy women. Breast milk may contain pathogenic bacteria that could cause serious infections especially in premature infants. There is no recommendation to evaluate breast milk routinely for pathogenic bacteria. However discontinuation of breastfeeding is not recommended even the mother had mastitis, because it is believed this will not pose a risk to infant. This is the report of a premature infant born at the 32nd gestational week who was readmitted to neonatal intensive care unit with late-onset Staphylococcus aureus sepsis. While searching for the transmission route of the infection, the breast milk was assessed. Although the mother did not have any symptoms of breast inflammation, S. aureus isolates, genetically 99% similar to those from the infant blood samples, were documented in the breast milk. Breast milk may contain pathogenic bacteria, even when expressed, stored and transported properly. When evaluating the source of a S. aureus infection in preterm infants, breast milk might be the source of the infection, even if the mother has no sign of mastitis.
ObjectivesSARS-CoV-2 infections with Omicron variants have a high capability of human-to-human tr... more ObjectivesSARS-CoV-2 infections with Omicron variants have a high capability of human-to-human transmission. Nevertheless, the duration of isolation for mild cases was shortened to 5 to 7 days. We aimed to detect the duration of viral shedding among healthcare workers (HCWs) with Omicron by using viral culture.MethodsWe prospectively included newly diagnosed nonsevere, symptomatic SARS-CoV-2 positive HCWs. Nasopharyngeal swab samples were obtained consecutively on days 5, 7,10, and 14 of onset of symptoms. The samples were examined by nucleic acid amplification test and viral culture.ResultsIn total, 55 non-severe patients with SARS-CoV-2 Omicron variant were included. The mean age of the population was 34 years (range, 23 to 54) and 78% (43/55) were female. The PCR positivity rate on days 5, 7, 10, and 14 was 96.4% (53/55), 87.3% (48/55), 74.545% (41/55), and 41.8% (23/55) consecutively, whereas the viral culture positivity rates were 83% (44/53), 52% (26/50), 13.5% (7/52), and 8% (4/50). Among the patients who became symptom-free, the viral culture positivity rates were 100% (4/4), 58% (7/12), 11% (3/27), and 5% (2/41).DiscussionWe showed that among the SARS-CoV-2 Omicron variant infected patients, viral shedding continues for ≥10 days in 13.5% of all cases and 11% in symptom-free cases. The decision for cessation of isolation according to the presence of symptoms could be reconsidered until further studies disapprove of our results. Meanwhile, the infected HCWs who give care to high-risk patients for severe COVID-19 might extend their isolations ≤10 days after the onset of symptoms, regardless of their symptoms.
We evaluated neutralizing antibodies against the Omicron variant and Anti-Spike IgG response in s... more We evaluated neutralizing antibodies against the Omicron variant and Anti-Spike IgG response in solid organ (SOT) or hematopoietic stem cell (HSTC) recipients after a third dose of BNT162b2 (BNT) or CoronaVac (CV) following two doses of CV. In total, 95 participants underwent SOT (n = 62; 44 liver, 18 kidney) or HSCT (n = 27; 5 allogeneic, 22 autologous) were included from five centers in Turkey. The median time between third doses and serum sampling was 154 days (range between 15 to 381). The vaccine-induced antibody responses of both neutralizing antibodies and Anti-Spike IgGs were assessed by plaque neutralizing assay and immunoassay, respectively. Neutralizing antibody and Anti-Spike IgG levels were significantly higher in transplant patients receiving BNT compared to those receiving CV (Geometric mean (GMT):26.76 vs. 10.89; p = 0.03 and 2116 Au/mL vs. 172.1 Au/mL; p < 0.001). Solid organ transplantation recipients, particularly liver transplant recipients, showed lower antib...
Convalescent plasma samples that can be collected from individuals after the resolution of infect... more Convalescent plasma samples that can be collected from individuals after the resolution of infection and vaccination are an invaluable source of neutralization antibodies against the virus. Although plaque reduction assay with replicative virus is the gold standard of analyzing neutralization potency of convalescent plasma, it is a technically demanding procedure requiring high biosafety level (BSL-3/4) laboratory and equipment. The abundance of neutralizing antibodies varies among individuals, therefore fast and reliable methods to identify neutralization potency of plasma samples are needed. In this paper, G-protein deficient vesicular stomatitis virus (VSV-ΔG) carrying a C-terminal 21 amino acid truncated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike protein was generated for pseudovirus neutralization assay. We analyzed SARS-CoV-2 neutralizing potency of vaccinated human convalescent plasma samples (n=13) and plasma samples of healthy people (n=2). Human con...
We aimed to describe the increased rate of Acinetobacter baumannii infections during the COVID-19... more We aimed to describe the increased rate of Acinetobacter baumannii infections during the COVID-19 pandemic and define its significance within the last five years. This study was performed in a tertiary hospital with 280 beds and included all patients infected with A. baumannii in the intensive care unit between January 1, 2018, and June 30, 2022. A. baumannii-infected patients in the intensive care unit 27 months before the pandemic and 27 months during the pandemic were included. Pulsed-field gel electrophoresis was performed to assess clonal relatedness. The infection control measures were specified based on the findings and targeted elimination. In total, 5718 patients were admitted to the intensive care unit from January 1st, 2018, to June 30th, 2022. A. baumannii infection was detected in 81 patients. Compared to the pre-pandemic era, the rate of A. baumannii infection during the pandemic was 1.90 times higher (OR: 1.90, 95% CI: [1.197, 3.033]). Clonality assessment of multidru...
Coronavirus Disease-19 (COVID-19) is a highly contagious infectious disease caused by the severe ... more Coronavirus Disease-19 (COVID-19) is a highly contagious infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The development of rapid antigen tests has contributed to easing the burden on healthcare and lifting restrictions by detecting infected individuals to help prevent further transmission of the virus. We developed a state-of-art rapid antigen testing system, named DIAGNOVIR, based on immune-fluorescence analysis, which can process and give the results in a minute. In our study, we assessed the performance of the DIAGNOVIR and compared the results with those of the qRT-PCR test. Our results demonstrated that the sensitivity and specificity of the DIAGNOVIR were 94% and 99.2%, respectively, with a 100% sensitivity and 96.97% specificity, among asymptomatic patients. In addition, DIAGNOVIR can detect SARS‑CoV‑2 with 100% sensitivity up to 5 days after symptom onset. We observed that the DIAGNOVIR Rapid Antigen Test’s limit of detection (...
Introduction. Aminoglycosides are used for the treatment of carbapenemase-producing Klebsiella pn... more Introduction. Aminoglycosides are used for the treatment of carbapenemase-producing Klebsiella pneumoniae (CPK) infections. 16S rRNA methyltransferases (RMTs) confer resistance to all aminoglycosides and are often cocarried with NDM. Hypothesis/Gap Statement. There is a dart of studies looking at the aminoglycoside resistance mechanisms for invasive CPK isolates, particularly in OXA-48 endemic settings. Aim. We aimed to determine the prevalence of RMTs and their association with beta lactamases and MLSTs amongst aminoglycoside-resistant CPK bloodstream isolates in an OXA-48 endemic setting. Methodology. CPK isolates (n=181), collected as part of a multicentre cohort study, were tested for amikacin, gentamicin and tobramycin susceptibility using custom-made sensititre plates (GN2XF, Thermo Fisher Scientific). All isolates were previously subjected to whole-genome sequencing. Carbapenemases, RMTs, MLSTs and plasmid incompatibility groups were detected on the assembled genomes. Results...
BackgroundIt is essential to know about immune response levels after booster doses of the two dif... more BackgroundIt is essential to know about immune response levels after booster doses of the two different types of vaccines, mRNA, and the inactivated, currently used against COVID‐19. For this purpose, we aimed to determine the effects of BNT162b2 (BNT) and CoronaVac (CV) boosters on the humoral and cellular immunity of individuals who had two doses of CV vaccination.MethodsThe study was conducted in three centers (Koc University Hospital, Istanbul University Cerrahpasa Hospital, and Istanbul University, Istanbul Medical School Hospital) in Istanbul, Turkey. Individuals who had been previously immunized with two doses of CV and no history of COVID‐19 were included. The baseline blood samples were collected 3–5 months after the second dose of CV. Follow‐up blood samples were taken 1 and 3 months after administration of third doses of CV, or one dose of BNT boosters. Neutralizing antibody titers were measured by plaque reduction assay. The CD4+ T cell, CD8+ T cell, effector CD4+CD38+CD...
European Journal of Clinical Microbiology & Infectious Diseases, 2022
We aimed to describe the effect of aminoglycosides and tigecycline to reduce the mortality in col... more We aimed to describe the effect of aminoglycosides and tigecycline to reduce the mortality in colistin- and carbapenem-resistant Klebsiella pneumoniae (ColR-CR-Kp) infections. We included the studies with defined outcomes after active or non-active antibiotic treatment of ColR-CR-Kp infections. The active treatment was defined as adequate antibiotic use for at least 3 days (72 h) after the diagnosis of ColR-CR-Kp infection by culture. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement and the checklist of PRISMA 2020 was applied. Crude and adjusted odds ratios (OR) with 95% confidence interval (CI) were calculated and pooled in the random effects model. Adding aminoglycosides to the existing treatment regimen reduced overall mortality significantly (OR 0.34, 95% CI 0.20-0.58). Overall mortality was 34% in patients treated with aminoglycoside-combined regimens and was 60% in patients treated with non-aminoglycoside regimens. Treatment with tigecycline is not found to reduce mortality (OR: 0.76, 95% CI: 0.47-1.23). Our results suggest that aminoglycoside addition to the existing regimen of colistin- and carbapenem-resistant Klebsiella pneumoniae infections reduces mortality significantly.
European Journal of Clinical Microbiology & Infectious Diseases, 2022
A prospective, multicentre observational cohort study of carbapenem-resistant Klebsiella spp. (CR... more A prospective, multicentre observational cohort study of carbapenem-resistant Klebsiella spp. (CRK) bloodstream infections was conducted in Turkey from June 2018 to June 2019. One hundred eighty-seven patients were recruited. Single OXA-48-like carbapenemases predominated (75%), followed by OXA-48-like/NDM coproducers (16%). OXA-232 constituted 31% of all OXA-48-like carbapenemases and was mainly carried on ST2096. Thirty-day mortality was 44% overall and 51% for ST2096. In the multivariate cox regression analysis, SOFA score and immunosuppression were significant predictors of 30-day mortality and ST2096 had a non-significant effect. All OXA-48-like producers remained susceptible to ceftazidime-avibactam.
Biomedical Vibrational Spectroscopy 2022: Advances in Research and Industry, 2022
The real-time polymerase chain reaction (RT-PCR) analysis using nasal swab samples is the gold st... more The real-time polymerase chain reaction (RT-PCR) analysis using nasal swab samples is the gold standard approach for COVID-19 diagnosis. However, due to the high false-negative rate at lower viral loads and complex test procedure, PCR is not suitable for fast mass screening. Therefore, the need for a highly sensitive and rapid detection system based on easily collected fluids such as saliva during the pandemic has emerged. In this study, we present a surface-enhanced Raman spectroscopy (SERS) metasurface optimized with genetic algorithm (GA) to detect SARS-CoV-2 directly using unprocessed saliva samples. During the GA optimization, the electromagnetic field profiles were used to calculate the field enhancement of each structure and the fitness values to determine the performance of the generated substrates. The obtained design was fabricated using electron beam lithography, and the simulation results were compared with the test results using methylene blue fluorescence dye. After the performance of the system was validated, the SERS substrate was tested with inactivated SARS-CoV-2 virus for virus detection, viral load analysis, cross-reactivity, and variant detection using machine learning models. After the inactivated virus tests are completed, with 36 PCR positive and 33 negative clinical samples, we were able to detect the SARS-CoV-2 positive samples from Raman spectra with 95.2% sensitivity and specificity.
Abstract Antimicrobial resistance is a global problem that threatens the success of modern medica... more Abstract Antimicrobial resistance is a global problem that threatens the success of modern medical approaches. Bacteria might exhibit several mechanisms to resist against antibiotics. Intensive antimicrobial resistance surveillance is a critical step of antimicrobial stewardship as it is the basis for detecting new trends and threats, monitoring the interventions, and developing new drugs. In this chapter, we summarize the antimicrobial resistance mechanisms of bacteria and focus on the resistance of clinically important pathogens, especially to “last resort” antibiotics in all regions of the world.
OBJECTIVES We aimed to describe the mechanisms of colistin resistance in Acinetobacter baumannii.... more OBJECTIVES We aimed to describe the mechanisms of colistin resistance in Acinetobacter baumannii. MATERIALS AND METHODS Twenty-nine patients diagnosed with colistin-resistant A. baumannii infection were included to the study. The mutations in pmrCAB, lpxA, lpxC, and lpxD genes, expression of pmrCAB, carbapenemases, and mcr-1 positivity were studied. RESULTS Twenty-seven (93%) of the patients received IV colistin therapy during their stay, and the case fatality rate was 45%. All mutations in pmrC and pmrB were found to be accompanied with a mutation in lpxD. The most common mutations were I42V and L150F in pmrC (65%), E117K in lpxD (65%), and A138T in pmrB (58.6%). The colistin minimum inhibitory concentrations (MICs) of the isolates having any of these four mutations were higher than the isolates with no mutations (p < 0.001). The two most common mutations in pmrC (I42V and L150F) were found to be associated with higher expressions of pmrA and pmrC and higher colistin MIC values (p = 0.010 and 0.031). All isolates were blaOXA-23 positive. CONCLUSION Coexistence of the lpxD mutation along with mutations in pmrCAB indicates synergistic function of these genes in development of colistin resistance in A. baumannii.
Journal of Maternal-fetal & Neonatal Medicine, Jul 24, 2013
Contrary to traditional belief, breast milk is not a sterile fluid, even in healthy women. Breast... more Contrary to traditional belief, breast milk is not a sterile fluid, even in healthy women. Breast milk may contain pathogenic bacteria that could cause serious infections especially in premature infants. There is no recommendation to evaluate breast milk routinely for pathogenic bacteria. However discontinuation of breastfeeding is not recommended even the mother had mastitis, because it is believed this will not pose a risk to infant. This is the report of a premature infant born at the 32nd gestational week who was readmitted to neonatal intensive care unit with late-onset Staphylococcus aureus sepsis. While searching for the transmission route of the infection, the breast milk was assessed. Although the mother did not have any symptoms of breast inflammation, S. aureus isolates, genetically 99% similar to those from the infant blood samples, were documented in the breast milk. Breast milk may contain pathogenic bacteria, even when expressed, stored and transported properly. When evaluating the source of a S. aureus infection in preterm infants, breast milk might be the source of the infection, even if the mother has no sign of mastitis.
ObjectivesSARS-CoV-2 infections with Omicron variants have a high capability of human-to-human tr... more ObjectivesSARS-CoV-2 infections with Omicron variants have a high capability of human-to-human transmission. Nevertheless, the duration of isolation for mild cases was shortened to 5 to 7 days. We aimed to detect the duration of viral shedding among healthcare workers (HCWs) with Omicron by using viral culture.MethodsWe prospectively included newly diagnosed nonsevere, symptomatic SARS-CoV-2 positive HCWs. Nasopharyngeal swab samples were obtained consecutively on days 5, 7,10, and 14 of onset of symptoms. The samples were examined by nucleic acid amplification test and viral culture.ResultsIn total, 55 non-severe patients with SARS-CoV-2 Omicron variant were included. The mean age of the population was 34 years (range, 23 to 54) and 78% (43/55) were female. The PCR positivity rate on days 5, 7, 10, and 14 was 96.4% (53/55), 87.3% (48/55), 74.545% (41/55), and 41.8% (23/55) consecutively, whereas the viral culture positivity rates were 83% (44/53), 52% (26/50), 13.5% (7/52), and 8% (4/50). Among the patients who became symptom-free, the viral culture positivity rates were 100% (4/4), 58% (7/12), 11% (3/27), and 5% (2/41).DiscussionWe showed that among the SARS-CoV-2 Omicron variant infected patients, viral shedding continues for ≥10 days in 13.5% of all cases and 11% in symptom-free cases. The decision for cessation of isolation according to the presence of symptoms could be reconsidered until further studies disapprove of our results. Meanwhile, the infected HCWs who give care to high-risk patients for severe COVID-19 might extend their isolations ≤10 days after the onset of symptoms, regardless of their symptoms.
We evaluated neutralizing antibodies against the Omicron variant and Anti-Spike IgG response in s... more We evaluated neutralizing antibodies against the Omicron variant and Anti-Spike IgG response in solid organ (SOT) or hematopoietic stem cell (HSTC) recipients after a third dose of BNT162b2 (BNT) or CoronaVac (CV) following two doses of CV. In total, 95 participants underwent SOT (n = 62; 44 liver, 18 kidney) or HSCT (n = 27; 5 allogeneic, 22 autologous) were included from five centers in Turkey. The median time between third doses and serum sampling was 154 days (range between 15 to 381). The vaccine-induced antibody responses of both neutralizing antibodies and Anti-Spike IgGs were assessed by plaque neutralizing assay and immunoassay, respectively. Neutralizing antibody and Anti-Spike IgG levels were significantly higher in transplant patients receiving BNT compared to those receiving CV (Geometric mean (GMT):26.76 vs. 10.89; p = 0.03 and 2116 Au/mL vs. 172.1 Au/mL; p < 0.001). Solid organ transplantation recipients, particularly liver transplant recipients, showed lower antib...
Convalescent plasma samples that can be collected from individuals after the resolution of infect... more Convalescent plasma samples that can be collected from individuals after the resolution of infection and vaccination are an invaluable source of neutralization antibodies against the virus. Although plaque reduction assay with replicative virus is the gold standard of analyzing neutralization potency of convalescent plasma, it is a technically demanding procedure requiring high biosafety level (BSL-3/4) laboratory and equipment. The abundance of neutralizing antibodies varies among individuals, therefore fast and reliable methods to identify neutralization potency of plasma samples are needed. In this paper, G-protein deficient vesicular stomatitis virus (VSV-ΔG) carrying a C-terminal 21 amino acid truncated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike protein was generated for pseudovirus neutralization assay. We analyzed SARS-CoV-2 neutralizing potency of vaccinated human convalescent plasma samples (n=13) and plasma samples of healthy people (n=2). Human con...
We aimed to describe the increased rate of Acinetobacter baumannii infections during the COVID-19... more We aimed to describe the increased rate of Acinetobacter baumannii infections during the COVID-19 pandemic and define its significance within the last five years. This study was performed in a tertiary hospital with 280 beds and included all patients infected with A. baumannii in the intensive care unit between January 1, 2018, and June 30, 2022. A. baumannii-infected patients in the intensive care unit 27 months before the pandemic and 27 months during the pandemic were included. Pulsed-field gel electrophoresis was performed to assess clonal relatedness. The infection control measures were specified based on the findings and targeted elimination. In total, 5718 patients were admitted to the intensive care unit from January 1st, 2018, to June 30th, 2022. A. baumannii infection was detected in 81 patients. Compared to the pre-pandemic era, the rate of A. baumannii infection during the pandemic was 1.90 times higher (OR: 1.90, 95% CI: [1.197, 3.033]). Clonality assessment of multidru...
Coronavirus Disease-19 (COVID-19) is a highly contagious infectious disease caused by the severe ... more Coronavirus Disease-19 (COVID-19) is a highly contagious infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The development of rapid antigen tests has contributed to easing the burden on healthcare and lifting restrictions by detecting infected individuals to help prevent further transmission of the virus. We developed a state-of-art rapid antigen testing system, named DIAGNOVIR, based on immune-fluorescence analysis, which can process and give the results in a minute. In our study, we assessed the performance of the DIAGNOVIR and compared the results with those of the qRT-PCR test. Our results demonstrated that the sensitivity and specificity of the DIAGNOVIR were 94% and 99.2%, respectively, with a 100% sensitivity and 96.97% specificity, among asymptomatic patients. In addition, DIAGNOVIR can detect SARS‑CoV‑2 with 100% sensitivity up to 5 days after symptom onset. We observed that the DIAGNOVIR Rapid Antigen Test’s limit of detection (...
Introduction. Aminoglycosides are used for the treatment of carbapenemase-producing Klebsiella pn... more Introduction. Aminoglycosides are used for the treatment of carbapenemase-producing Klebsiella pneumoniae (CPK) infections. 16S rRNA methyltransferases (RMTs) confer resistance to all aminoglycosides and are often cocarried with NDM. Hypothesis/Gap Statement. There is a dart of studies looking at the aminoglycoside resistance mechanisms for invasive CPK isolates, particularly in OXA-48 endemic settings. Aim. We aimed to determine the prevalence of RMTs and their association with beta lactamases and MLSTs amongst aminoglycoside-resistant CPK bloodstream isolates in an OXA-48 endemic setting. Methodology. CPK isolates (n=181), collected as part of a multicentre cohort study, were tested for amikacin, gentamicin and tobramycin susceptibility using custom-made sensititre plates (GN2XF, Thermo Fisher Scientific). All isolates were previously subjected to whole-genome sequencing. Carbapenemases, RMTs, MLSTs and plasmid incompatibility groups were detected on the assembled genomes. Results...
BackgroundIt is essential to know about immune response levels after booster doses of the two dif... more BackgroundIt is essential to know about immune response levels after booster doses of the two different types of vaccines, mRNA, and the inactivated, currently used against COVID‐19. For this purpose, we aimed to determine the effects of BNT162b2 (BNT) and CoronaVac (CV) boosters on the humoral and cellular immunity of individuals who had two doses of CV vaccination.MethodsThe study was conducted in three centers (Koc University Hospital, Istanbul University Cerrahpasa Hospital, and Istanbul University, Istanbul Medical School Hospital) in Istanbul, Turkey. Individuals who had been previously immunized with two doses of CV and no history of COVID‐19 were included. The baseline blood samples were collected 3–5 months after the second dose of CV. Follow‐up blood samples were taken 1 and 3 months after administration of third doses of CV, or one dose of BNT boosters. Neutralizing antibody titers were measured by plaque reduction assay. The CD4+ T cell, CD8+ T cell, effector CD4+CD38+CD...
European Journal of Clinical Microbiology & Infectious Diseases, 2022
We aimed to describe the effect of aminoglycosides and tigecycline to reduce the mortality in col... more We aimed to describe the effect of aminoglycosides and tigecycline to reduce the mortality in colistin- and carbapenem-resistant Klebsiella pneumoniae (ColR-CR-Kp) infections. We included the studies with defined outcomes after active or non-active antibiotic treatment of ColR-CR-Kp infections. The active treatment was defined as adequate antibiotic use for at least 3 days (72 h) after the diagnosis of ColR-CR-Kp infection by culture. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement and the checklist of PRISMA 2020 was applied. Crude and adjusted odds ratios (OR) with 95% confidence interval (CI) were calculated and pooled in the random effects model. Adding aminoglycosides to the existing treatment regimen reduced overall mortality significantly (OR 0.34, 95% CI 0.20-0.58). Overall mortality was 34% in patients treated with aminoglycoside-combined regimens and was 60% in patients treated with non-aminoglycoside regimens. Treatment with tigecycline is not found to reduce mortality (OR: 0.76, 95% CI: 0.47-1.23). Our results suggest that aminoglycoside addition to the existing regimen of colistin- and carbapenem-resistant Klebsiella pneumoniae infections reduces mortality significantly.
European Journal of Clinical Microbiology & Infectious Diseases, 2022
A prospective, multicentre observational cohort study of carbapenem-resistant Klebsiella spp. (CR... more A prospective, multicentre observational cohort study of carbapenem-resistant Klebsiella spp. (CRK) bloodstream infections was conducted in Turkey from June 2018 to June 2019. One hundred eighty-seven patients were recruited. Single OXA-48-like carbapenemases predominated (75%), followed by OXA-48-like/NDM coproducers (16%). OXA-232 constituted 31% of all OXA-48-like carbapenemases and was mainly carried on ST2096. Thirty-day mortality was 44% overall and 51% for ST2096. In the multivariate cox regression analysis, SOFA score and immunosuppression were significant predictors of 30-day mortality and ST2096 had a non-significant effect. All OXA-48-like producers remained susceptible to ceftazidime-avibactam.
Biomedical Vibrational Spectroscopy 2022: Advances in Research and Industry, 2022
The real-time polymerase chain reaction (RT-PCR) analysis using nasal swab samples is the gold st... more The real-time polymerase chain reaction (RT-PCR) analysis using nasal swab samples is the gold standard approach for COVID-19 diagnosis. However, due to the high false-negative rate at lower viral loads and complex test procedure, PCR is not suitable for fast mass screening. Therefore, the need for a highly sensitive and rapid detection system based on easily collected fluids such as saliva during the pandemic has emerged. In this study, we present a surface-enhanced Raman spectroscopy (SERS) metasurface optimized with genetic algorithm (GA) to detect SARS-CoV-2 directly using unprocessed saliva samples. During the GA optimization, the electromagnetic field profiles were used to calculate the field enhancement of each structure and the fitness values to determine the performance of the generated substrates. The obtained design was fabricated using electron beam lithography, and the simulation results were compared with the test results using methylene blue fluorescence dye. After the performance of the system was validated, the SERS substrate was tested with inactivated SARS-CoV-2 virus for virus detection, viral load analysis, cross-reactivity, and variant detection using machine learning models. After the inactivated virus tests are completed, with 36 PCR positive and 33 negative clinical samples, we were able to detect the SARS-CoV-2 positive samples from Raman spectra with 95.2% sensitivity and specificity.
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