Tıp Fakültesi / Faculty of Medicine
Permanent URI for this collectionhttps://hdl.handle.net/11727/1403
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Item Molecular Epidemiological Analysis of Bacillus Pseudo-Outbreak due to Contaminated Culture Tubes Containing Stuart Medium(2022) Asgin, Nergis; Kal-Cakmakliogullari, Elcin; Otlu, Baris; Ersoy, Omer F.; Celik, Betul; Basustaoglu, Ahmet; 35023676Background: It is challenging to determine whether Bacillus species other than Bacillus anthracis cause infections. Pseudo and true outbreaks of Bacillus spp. have been noted. Here, we present a molecular analysis of a Bacillus spp. pseudo-outbreak caused by contaminated culture tubes containing Stuart medium. Methods: Between January and March 2015, a high percentage of Bacillus spp. was isolated from the wound samples of inpatients at the Karabuk University Hospital, and an outbreak was suspected. Environmental and staff nasal samples were cultured aerobically, and Bacillus spp. were isolated from some of them. However, the isolation of Bacillus spp. in throat cultures of outpatients suggested contamination caused by culture tubes containing Stuart medium. We examined two lots of culture tubes used in the hospital. Although the culture tubes' expiry date and storage conditions were suitable, Bacillus spp. grew in one of these lots. A total of 47 Bacillus spp. isolated during this period were identified, and the clonal relationship among the isolates was investigated by arbitrarily primed polymerase chain reaction. Results: Twenty-seven strains were identified as Bacillus megaterium and 20 as Bacillus firmus. Of the four strains isolated from the Stuart medium, two were identified as B. firmus and the other two were B. megaterium. Two B. firmus strains isolated from the Stuart medium and two B. firmus strains obtained from the coronary intensive care environmental samples were matched and clustered within the same genotype. We recalled all culture tubes containing Stuart medium. After another brand's culture tubes were distributed, no growth was observed. It was then understood that the pseudo-outbreak source was contaminated culture tubes containing Stuart medium. Conclusions: Microbiological controls of medical materials and equipment should be regularly checked to prevent outbreaks (true or pseudo).Item Comparative in Vitro Activities of Omadacycline, Eravacycline and Tigecycline Against Non-ESBL- Producing ESBL- Producing and Carbapenem- Resistant Isolates of K. Pneumoniae(2022) Mirza, Hasan Cenk; Guclu, Aylin Uskudar; Ceviz, Gizem Ince; Basustaoglu, Ahmet; 0000-0002-8853-3893; 0000-0002-1872-028X; 36301611; F-1232-2015; AAU-6196-2020Introduction. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae and carbapenem-resistant Enterobacte-riaceae are characterized by the World Health Organization as pathogens for which new antibiotics are urgently needed. Oma-dacycline and eravacycline are two novel antibacterials within the tetracycline class.Gap Statement. There are limited data regarding the comparison of the activities of omadacycline, eravacycline and tigecycline against K. pneumoniae isolates with different antimicrobial susceptibility profiles.Aim. Our objective was to compare the in vitro activities of omadacycline, eravacycline and tigecycline against a collection of K. pneumoniae isolates, including non- ESBL-producing, ESBL-producing and carbapenem-resistant strains.Methodology. Ninety-four K. pneumoniae isolates, including 30 non- ESBL-producing, 30 ESBL-producing and 34 carbapenem-resistant (22 carrying blaOXA-48, 12 carrying blaNDM) strains were included in the study. ESBL and carbapenemase genes were detected by conventional PCR. Omadacycline, eravacycline and tigecycline MICs were determined by the gradient diffusion method and interpreted using US Food and Drug Administration (FDA)-defined breakpoints.Results. Overall, the percentage of tigecycline-susceptible strains (97.9 %) was higher than the percentage of omadacyline-susceptible (75.5 %) and eravacycline-susceptible (72.3 %) strains. The omadacycline and eravacycline susceptibility rates were 83.3 % among non- ESBL-producing isolates and 66.7 % among ESBL-producing isolates. The most common ESBL gene detected was blaCTX-M (90 %), followed by blaTEM (50 %) and blaSHV (50 %). The omadacycline and eravacycline susceptibility rate among isolates carrying blaTEM was 33.3 %, whereas it was 100 % among isolates that do not carry blaTEM. The omadacycline and eravacycline susceptibility rates among carbapenem-resistant isolates were 76.5 and 67.6 %, respectively. The omadacycline susceptibility rates among blaOXA-48-positive and blaNDM-positive isolates were 77.3 and 75.0 %, respectively. The eravacycline susceptibility rates among blaOXA-48-positive and blaNDM- positive isolates were 68.2 and 66.7 %, respectively. One carbapenem-resistant isolate was intermediate and one ESBL-producing isolate was resistant to tigecycline.Conclusion. Overall, tigecycline was the most active tetracycline against isolates. Omadacycline and eravacycline showed excellent activity against ESBL-producing K. pneumoniae isolates that do not carry blaTEM. Omadacycline showed reasonable activity against carbapenem-resistant K. pneumoniae isolates carrying blaOXA-48 or blaNDM.Item Retrospective evaluation of viral respiratory tract infections in a university hospital in Ankara, Turkey (2016-2019)(2022) Altay-Kocak, Aylin; Sarzhanova, Shakhnoza; Tapisiz, Anil; Dizbay, Murat; Basustaoglu, Ahmet; Bozdayi, Gulendam; 0000-0002-0451-0142; 35656958; AAI-8012-2021Introduction: Viruses are responsible for two-thirds of all acute respiratory tract infections. This study aims to retrospectively detect respiratory tract viruses in patients from all age groups who visited the hospital. Methodology: A total of 1592 samples from 1416 patients with respiratory tract symptoms were sent from several clinics to the Molecular Microbiology Laboratory at Gazi University Hospital from February 2016 to January 2019. Nucleic acid extraction from nasopharyngeal swabs, throat swabs or bronchoalveolar lavage (BAL) samples sent to our laboratory was done using a commercial automated system. Extracted nucleic acids were amplified by a commercial multiplex-real time Polymerase Chain Reaction (PCR) method, which can detect 18 viral respiratory pathogens. Results: Among 1592 samples, 914 (57.4%) were positive for respiratory viruses. The most prevalent were rhinovirus (25.2%) and influenza A virus (12.1%), the least prevalent was the bocavirus (2.6%). Rhinovirus was the most detected as a single agent (21.2%, 194/914) among all positive cases, followed by coronavirus (9.3%, 85/914). The detection rates of coronavirus, human adenovirus, respiratory syncytial virus A/B, human parainfluenza viruses, human metapneumovirus-A/B, human parechovirus, enterovirus and influenza B virus were 9.9%, 8%, 7.7%, 5%, 3.4%, 3.1%, 3%, and 2.8%, respectively. Conclusions: The most detected viral agents in our study were influenza A virus and rhinovirus. Laboratory diagnosis of respiratory viruses is helpful to prevent unnecessary antibiotic use and is essential in routine diagnostics for antiviral treatment. Multiplex Real-time PCR method is fast and useful for the diagnosis of viral respiratory infections.Item Antibacterial Resistance in Lower Respiratory Tract Bacterial Pathogens: A Multicenter Analysis from Turkey(2021) Guclu, Aylin Uskudar; Kocak, Aylin Altay; Ok, Mehtap Akcil; Tutluoglu, Bulent; Basustaoglu, Ahmet; 0000-0002-1872-028X; 0000-0002-0451-0142; 33690209; AAU-6196-2020; AAI-8012-2021Introduction: This study aimed to evaluate the etiology of lower respiratory tract infections (LRTIs) and their antibiotic resistance. Methodology: Bacterial culture results of LRT samples from 17 hospitals between 2016-2019 were included in the study. All isolates were identified and AST were performed by automated microbiology systems. AST was performed according to EUCAST. Results: Non-duplicate 30,051 (26,890 HA and 3156 CA) isolates detected as causative pathogen. LRTIs are caused by 85.1% Gram-negative bacterial pathogens and 14.9% Gram-positive. The most common isolates among HA pathogens were Acinetobacter spp. (27.4%), P. aeruginosa (22.2%), K. pneumoniae (17.9%); among CA pathogen S. pneumoniae (19.9%), P. aeruginosa (18.9%), H. influenzae (14.6%). ESBL rate was 62.5% in K. penumoniae; 53.1% in E.coli; 19.1% in Klebsiella spp; 13.9% in Enterobacter spp.; 8.6% in Proteus spp.; 6.3% in Citrobacter spp.; and 4.3% in Serratia spp. Resistance rates to carbapenems and colistin were 92.8% and 12.8% in A baumannii, 39.8% and 7.5% in P. aeruginosa, 47.3% and 18.5% in K. penumoniae. Among staphylococci, 27.3% of S. aureus and 82.4% of CoNS were methicillin resistant. 7.6% of E.faecium and 0.9% of E. faecalis were vancomycin resistant. Linezolid resistant S. aureus, CoNS, E. faecalis and E. faecium rates were 0.3%, 2.9%, 0.0% and 4.6%. Inducible clindamycin resistant rate was 17.2% in S. aureus 38.2% in CoNS. Non-susceptible S. pneumoniae isolate rate to penicillin was 37.0%. 6.5% of S. maltophilia and 4.4% of B. cepacia isolates were resistant to trimethoprim/sulfamethoxazole. Conclusions: Antibiotic resistance was mainly observed among A. baumannii and K. pneumoniae and continuous surveillance of antimicrobial resistance patterns in the management of LRTIs is important.Item Predominant Mutations of SARS-CoV-2: Their Geographical Distribution and Potential Consequences(2021) Unlu, Sezin; Uskudar Guclu, Aylin; Basustaoglu, Ahmet; 0000-0001-7490-7981; 0000-0002-1872-028X; AAQ-4702-2021; AAU-6196-2020Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged in late December 2019 in Wuhan, China. More than 83 million people have been infected, and more than 1.8 million people have died, as reported to the World Health Organization on the 3rd of January, 2021. Analysis of genetic variations is critical for understanding the spreading pattern of SARS-CoV-2 across several countries. This review aimed to gather information about the prominent mutations of SARS-CoV-2 by analyzing the origin, viral pathogenesis, and mutation rate. Moreover, we concluded their potential impacts on SARS-CoV-2 therapeutics. Mutations in the spike protein (D614G, N501Y, E484K, A222V, S477N, and G485R), ORF1ab (P323L, N628N, Y455Y, A97V, and F106F), nucleocapsid protein (R203K and G204R), ORF8 (L84S), and ORF3a (Q57H and G251V) were examined in this review by analyzing relevant articles from the beginning of the current pandemic to the most recent date. A detailed analysis of articles demonstrates that D614G is the major variation distributed globally, and its frequency increased rapidly from early in March, followed by several other variations in either spike or different proteins. In addition, it was seen that the currently circulating N501Y and E484K variants revealed a public concern regarding vaccines' efficacy. Investigation of variations of SARS-CoV-2 would lead to understanding their potential mechanism of action against SARS-CoV-2, thereby suggesting suitable therapeutics. Several mechanisms were suggested to have a role in SARS-CoV-2 mutation rate and evolution. Possible therapeutics and vaccines against SARS-CoV-2 were proposed.Item In vitro Activity of Delafloxacin against Methicillin-Resistant Staphylococcus aureus Isolated from Various Clinical Specimens(2021) Mirza, Hasan Cenk; Basustaoglu, Ahmet; Yanik Yalcin, Tugba; 0000-0002-8853-3893; F-1232-2015Introduction: Delafloxacin is a novel fluoroquinolone which has anionic and weak acid character at neutral pH. Activity of delafloxacin is reported to be increased in acidic environments. Many infections are characterized by acidic pH. Staphylococcus aureus is a microorganism which can survive and multiply in mildly acidic environments. The aim of this study was to compare the activity of delafloxacin and other fluoroquinolones (ciprofloxacin, levofloxacin, moxifloxacin) against MRSA isolates at neutral (7.4) and acidic (5.5) pH. Materials and Methods: A total of 51 MRSA isolated from various clinical specimens were included in the study. Disk diffusion method was used for antimicrobial susceptibility testing. The pH of Mueller Hinton Agar was adjusted to 7.4 or 5.5, and used as the medium for antimicrobial susceptibility testing. EUCAST breakpoints were used for ciprofloxacin, levofloxacin and moxifloxacin. FDA breakpoints were used for delafloxacin. Results: The most active fluoroquinolones against MRSA isolates at neutral pH were delafloxacin and moxifloxacin. Delafloxacin and moxifloxacin susceptibility rates of isolates were same (82.4%) at neutral pH. Of the isolates, 9.8% and 17.6% were resistant to delafloxacin and moxifloxacin, respectively. Four moxifloxacin-resistant isolates were categorized as intermediate to delafloxacin. Of the isolates, 76.5% and 78.4% were 'I - susceptible, increased exposure' to ciprofloxacin and levofloxacin, respectively. Of the isolates, 23.5% and 21.6% were resistant to ciprofloxacin and levofloxacin, respectively. At acidic pH; ciprofloxacin, levofloxacin and moxifloxacin susceptibility rates of isolates were not changed. However, all delafloxacin resistant/intermediate isolates at neutral pH became susceptible to delafloxacin at acidic pH. Conclusion: Delafloxacin was the most active fluoroquinolone against MRSA isolates at acidic pH. Based on our findings, delafloxacin may represent a treatment option for MRSA infections characterized by low pH.Item Antibacterial, Antifungal and Antibiofilm Activity of Methylglyoxal: A Phytochemical from Manuka Honey Metilglioksalin Antibakteriyel, Antifungal ve Antibiyofilm Aktivitesi: Manuka Balindan Bir Fitokimyasal(2021) Uskudar-Guclu, Aylin; Simsek, Derya; Ata-Vural, Ilgin; Unlu, Sezin; Basustaoglu, Ahmet; 0000-0002-1872-028X; AAU-6196-2020Introduction: Honey has been known for its ability to promote wound healing for a long time. It is utilized for several skin and soft tissue infections caused by a wide range of microorganisms due to its antimicrobial property. Methylglyoxal (MGO), the unique antibacterial compound contained by Manuka honey, is believed as the reason for the antimicrobial activity of Manuka honey. This study aims to identify the antibacterial, antifungal and anti-adherent activity of MGO in changing concentrations and determine the viable number of bacteria and fungi in biofilm after the treatment of MGO. Materials and Methods: Antibacterial and antifungal activity of MGO was determined by broth microdilution method for identifying minimum inhibitory and bactericidal and fungicidal concentrations (MIC, MBC and MFC, respectively). Percentage of biofilm formation inhibition and the number of viable microorganisms in biofilm after the MGO treatment was determined by the colony-forming unit method. Results: Minimum inhibitory concentration values for the bacterial strains ranged from 0.0078 to 0.125010 (v/v), while MBC ranged from 0.0312 to 2010 (v/v). Among fungi, MIC and MFC values were higher than those for tested bacterial strains; MIC values ranged from 0.0156 to 1010 (v/v), while MFC values ranged from 0.0625 to 2010 (v/v). Methylglyoxal was able to prevent biofilm formation in the all tested biofilm forming isolates. Number of viable bacteria, even in the sub-inhibitory doses of MGO, reduced remarkably. Conclusion: Unique compound of Manuka honey, MGO, exerts significant antimicrobial and antibiofilm activity against clinically important strains of both bacteria and fungi which may be utilized for the search of promising alternatives for antibiotics and may lead to combat antibiotic resistance.Item Determination of Biofilm Formation Properties of Methicillin Sensitive and Resistant Staphylococcus aureus Isolates by Conventional and Molecular Methods(2020) Hortac Istar, Elvan; Aliskan, Hikmet Eda; Basustaoglu, Ahmet; 0000-0002-2571-0637; 0000-0001-9060-3195; 32723278; AAI-8926-2021; AAE-2282-2021Biofilm-related infections are considered as among the foremost causes of treatment failure nowadays. One of the most common causes of biofilm-related infections is Staphylococcus aureus. It becomes extremely difficult to determine the appropriate treatment protocol while biofilm-related infections are coexisting with bacterial methicillin resistance. The aim of this study was to observe the potential of biofilm formation of methicillin-sensitive and -resistant S.aureus strains isolated from different clinical specimens and to determine reliable and effective methods for biofilm detection. A total of 200 S.aureus strains (100 methicillin-resistant and 100 methicillin-susceptible) isolated from 107 wound, 93 blood and catheter specimens, which were accepted as causative agents, included in the study. In order to determine the methicillin sensitivity, oxacillin minimal inhibitory concentration value obtained by an automated system and cefoxitin disc diffusion method were evaluated together. Biofilm formation was investigated by modified Christensen (MC), MTT, BioTimer and Congo Red Agar (CRA) methods, and the presence of ica operon responsible for biofilm formation was also observed by polymerase chain reaction. It has been shown that methicillin-resistant isolates produce biofilms in a shorter time and higher rate, and their biofilm structure is denser than methicillin-sensitive isolates in all MC, MTT and BioTimer methods. There was no difference between blood and wound isolates in biofilm formation. The most sensitive and specific conventional methods were MTT and BioTimer methods respectively. There was no significant difference between the isolates containing a gene region of icaADBC operon and the biofilm forming isolates according to MC, MTT, BioTimer and CCA methods. There was a high correlation between the presence of biofilm and ica positivity, and the tendency to form biofilm augmented as the number of ica genes increased. It has been emphasized that more virulent strains such as methicillin-resistant S.aureus have a higher tendency to form biofilm, and these two resistance mechanisms have been shown to support each other as cascade. ica detection may be an important reagent in itself for the detection of virulent strains, thus detection of the ica presence may be an early marker of treatment decisions, determination of protection strategies, and struggle with biofilm-related infections. In cases where molecular methods are not available, the existence of quick, easy-to-apply and reliable conventional methods to detect biofilm formation is extremely important. All conventional methods used in this study seem to be sufficient in this respect. MC and MTT methods stand out in terms of biofilm quantitation. BioTimer method is a very new and remarkable test used to detect biofilm formation. In conclusion, determining the potential of biofilm formation of colonizing or causative agents and taking essential precautions before interventional procedures will decrease biofilm related infections and related morbidity and mortality.Item Prevention of Candida biofilm formation over polystyrene by plasma polymerization technique(2020) Kaleli-Can, Gizem; Hortac-Istar, Elvan; Ozguzar, Hatice Ferda; Mutlu, Mehmet; Mirza, Hasan Cenk; Basustaoglu, Ahmet; Gocmen, Julide Sedef; 0000-0002-8853-3893; 0000-0002-2571-0637; F-1232-2015; AAI-8926-2021This work investigates the antifungal effect of plasma polymer films produced by low-pressure RF-generated plasma system using acrylic acid, 2-hydroxyethyl methacrylate, and diethyl phosphite (DEP). Unmodified and plasma-modified polystyrene (PS) microplate wells were tested by 30 biofilm-positive Candida spp. isolated from blood samples and two control strains using a quantitative plaque assay method. Regardless of the precursors and plasma parameters, biofilm formation was inhibited for all plasma-modified microplate wells. The most significant anti-biofilm effect was observed on PS modified by DEP at 90 W plasma power with the inhibition of all Candida species' biofilm formation.Item Evaluation of Blood Culture Practices: Use of System (Epicenter) Data(2019) Basustaoglu, Ahmet; Suzuk Yildiz, Serap; Mumcuoglu, Ipek; Karahan, Zeynep Ceren; Ogunc, Dilara; Kaleli, Ilknur; Kursun, Senol; Evren, Ebru; Ozhak, Baysal Betil; Demir, Melek; Murray, Patrick; 30683035Sepsis is a serious clinical problem and estimated to be responsible for 18 million annual deaths worldwide. Therefore, the use and the rapid processing of blood cultures are important for the transition from empiric therapy to directed therapy. The aim of this study was to assess the best blood culture practices in Turkey. We have examined the collection practices and techniques at four different hospitals, and a total of 165.443 blood culture bottles were evaluated (2013-2015). At the preanalytical phase most of the data which were important and which could support hospital quality systems/practices were not entered into the HIS and EpiCenter system. At the analytical phase loading of the bottles and removal of positive bottles primarily occurred between 6:00 and 9:00 AM but the positivity rate of the bottles showed a homogeneous distribution throughout the day. In other words, there were significant delays at processing positive blood culture bottles related to laboratory workers. The effect of education regarding best practices, transition from single bottle to two bottle cultures was successful in all hospitals. Single bottle usage decreased below 10% in all hospitals. Significantly more positive cultures were detected at multiple cultures when compared with the single bottle collection practice. In retrospective patient records, it was seen that all the laboratories reported the results of Gram staining to the clinics. However, these data were not recorded to the Epicenter. The contamination rates of Ankara Numune Hospital and Akdeniz University Faculty of Medicine Hospital are 6.2% and 5.4% respectively, contamination rates were not reported in other hospitals. The most common isolates detected in blood cultures were Escherichia coli, Klebsiella pneumoniae, Enterococcus faecium, Staphylococcus aureus, and Acinetobacter baumannii. The mean time for the detection of these organisms were less than 20 hours in the aerobic bottle and anaerobic bottles. A total of 79.6% of facultative anaerobic isolates were detected in both bottles; 9.8% were detected only in the aerobic bottles; 10.6% of the isolates were detected only in the anaerobic bottles. As a result, the educational efforts in Turkey have met with success for transition from collecting single bottle blood culture sets to two bottle blood cultures. However, further efforts are needed to increase the number of blood culture sets collected during a 24 hour's period. In addition, errors at the preanalytical, analytical and postanalytical periods (taking samples, loading bottles into the system and processing positive blood cultures) should be eliminated.