[Determination of Human Papilloma Virus (HPV) Genotype Prevalance and Distrubution in Adana: A Hospital-Based Study Between 2014-2021]. / Adana Ilinde Insan Papilloma Virüs (HPV) Genotip Prevalansi ve Dagiliminin Belirlenmesi: 2014-2021 Yillari Arasi Hastane Temelli Bir Çalisma.

Cervical cancer is the fourth most common cancer among women all over the world. It is accepted that cervical cancer is highly related to the HPV. The International Agency for Research on Cancer (IARC) has classified 13 HPV types as group 1 carcinogens (HPV 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 66), which are commonly referred to as high risk-HPVs (hr-HPVs). Among these, hr-HPV-16 is undoubtedly the most carcinogenic based in the burden of cervical cancer (CC) and its precursor lesions. In our study, we analyzed retrospectively the data of a total of 2329 female patients who applied to the obstetrics and gynecology outpatient clinic of our hospital over a seven-year-period, whose cervical smear were carried out by the polymerase chain reaction (PCR) and cytology. In this study, it was aimed to determine the data of of HPV prevalence in our region during the seven-year-period from April 2014 to April 2021 and the most common genotypes and to interpret them together with the cervical smears cytology and biopsy results if it is available. HPV 3, 6, 11, 16, 18, 21, 26, 31, 33, 35, 39, 40, 42, 45, 51, 52, 53, 54, 55, 56, 58, 59, 61, 62, 66, 67, 68, 70, 72, 73, 81, 82, 83, 84 were identified by using linear array HPV genotyping test (Roche Diagnostics, Switzerland) from April 2014 to October 2017. HPV genotypes were identified by using HPV Genotypes 14 Real-TM Quant (Qiagen, Germany) between October 2017 and April 2021. This method detected HPV genotypes 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68. The data were analyzed using IBM SPSS Statistics (Version 25.0) predictive analytics software. Continuous variables are indicated as mean ± standard deviation, and discrete variables are indicated as number [percentage (%)]. Chi-square test is used to investigate dependencies between variables. All analyzes were evaluated to provide 95% confidence level and 80% test power. p<0.05 was accepted as significant for the analysis results. Out of 2329 patients, 1283 were found to be HPV negative (54.6%) and the others were found to be HPV positive (45.4%) by using real-time PCR in the cervical smears. It was detected that out of 1046 HPV positive patients, 585 of them (55.9%) had one HPV genotype and 461 of them (44.1%) had more than one HPV genotypes. As we divided all of the patients into two groups as <30 (Group I) ve > 30 (Group II) according to age range, HPV positivity was found 134/296 (45.2%) in Group I and 912/2033 (44.8%) in Group II. When we compared the HPV positive/negative results of Groups I and II by using chi-square test, no significant difference was found between the two age groups in terms of HPV positivity (p= 0.894). In our study, the most common HPV types were HPV 16 (14.2%), HPV 68 (8.2%), HPV 56 (8.2%), HPV 52 (7.1%), HPV 51 (6.8%), HPV 31 (6.5%), HPV 66(6.1%), HPV 39 (5.8%) and HPV 18 (5.6%) among the women with normal and abnormal cytology in the cervical smears. ASC-US was the most common abnormal epithelial cell change detected with HPV16 and 18 genotypes and it was detected 26.07% and 21.88% in patients, respectively. In our study, we found HPV prevalance in our region as 45.4% and the most common type was HPV 16. As a result, we concluded that it is important to determine regional HPV prevalance data, which is an important step in cervical cancer prevention strategies, and regional data of detected HPV genotypes.

Effect of COVID-19 Pandemic on Hematopoietic Stem Cell Transplant Activity: Experience of a JACIE-Accredited Center.

OBJECTIVES: The adoption of international quality and accreditation standards is important for the success of transplant centers. Guidelines from the Joint Accreditation Committee ISCT-Europe and EBMT (JACIE) have enabled quality management of the operations of clinical units of cellular therapy centers, including cell collection and processing, thus minimizing errors and adverse events. COVID-19 has had significant implications for immunocompromised patients, particularly hematopoietic stem cell transplant recipients, as well as their donors and caregivers. Here, we retrospectively examined measures, taken in our transplant center in Turkey during the pandemic period between March 2020 and October 2021, to investigate how JACIE accreditation has affected patient, donor, product, and employee safety. MATERIALS AND METHODS: We analyzed data on transplant activity, as well as donor, patient, product, and employee safety, during the pandemic in 3 separate 6- month periods. The measures were analyzed starting from March 2020, when the first COVID-19 case was seen in Turkey. RESULTS: Since the beginning of the pandemic, 140 patients have undergone stem cell transplant in our center. Stem cell transplant was delayed in 22 patients because of the pandemic. Transplant was also postponed due to COVID-19 positivity in 6 patients, and 2 patients died due to COVID-19 infection during the transplant process. Unrelated donor activity continued to be performed safely throughout this period. COVID- 19 infection developed in 12 of the 52 personnel working in the bone marrow transplant unit, one of whom needed intensive care due to severe pneumonia. In terms of quality management activities, the impact of the pandemic was greatest during the first month. CONCLUSIONS: Results from our retrospective study examining the impact of JACIE accreditation in a stem cell transplant center during the COVID-19 pandemic showed that, when national and international guidelines are followed, JACIE accreditation can facilitate adaptation to changing conditions in transplant centers.

[Antibody Screening and Risk Assessment of Healthcare Professionals in the COVID-19 Pandemic]. / COVID-19 Pandemisinde Saglik Çalisanlarinin Antikor Taramasi ve Risk Degerlendirmesi.

Globally 364102 healthcare professionals have been infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and 1253 of them died until 15 January 2021. Healthcare professionals serving at the forefront of combating the pandemic are in the high risk group. In our country, the data about coronavirus-2019 (COVID-19) among healthcare professionals are limited. The aim of this study was to investigate the anti-SARS-CoV-2 IgG seroprevalence in healthcare professionals, to evaluate the risks they encountered during work, and to examine their relationships with antibody positivity. A total of 572 healthcare professionals serving in various units of our hospital participated in our study and the presence of anti-nucleocapsid IgG was investigated by chemiluminescent microparticle immunoassay (SARS-CoV-2 IgG test, Abbott Laboratories Diagnostics, USA) method in serum samples collected between May 18, 2020 and June 30, 2020. The demographic characteristics, medical history, work conditions, medical procedures performed and possible risk factors were questioned with a questionnaire form. The average age of the participants was 33.5 ± 9.2 (19-61) years, and 62.9% (360/572) of them were women. In our study, the anti-SARS-CoV-2 IgG seroprevalence was 3.7% (21/572). The association of the antibody positivity with age, gender and occupational status was not statistically significant (p> 0.05). Comorbid diseases which were significantly higher in seropositive healthcare professionals were hypertension (19%) and diabetes mellitus (14.3%) (p<0.05). It was observed that antibody positivity was significantly higher in healthcare professionals working in high (52.4%) and medium risk (33.3%) areas, those who treat and/or examine patients with suspicious or positive COVID-19 (66.7%) and those who spend more than 30 minutes in COVID-19 patient rooms (76%) (p<0.05). The symptoms associated with seropositivity in healthcare workers with a history of symptoms (46%) were loss of smell (23.5%), loss of taste (20.0%) and respiratory distress (16.7%) (p<0.05). It was observed that the probability of being infected with SARS-CoV-2 increased 12 times if there was a colleague with COVID-19 in the hospital, four times if there was a patient in the house/lodging and six times if there was an infected person in the social environment (p<0.05). The rate of those who had the flu vaccine among the participants was 10.8% (62/572) and 9.7% of them were found to be anti-SARS-CoV-2 IgG positive (p<0.05, 95% CI= 1.31-9.48). The seropositivity was significantly higher in non-smokers (4.8 %) compared to smokers (0.0%) (p<0.05). In our study, it was determined that the rate of seropositivity was 12 times higher in healthcare professionals who stated that they received hydroxychloroquine prophylaxis due to risky contact compared to those who did not receive prophylaxis (p<0.05, 95% CI= 4.11-40.64). The ratio of the personnel who answered "always" to the frequency of wearing gloves, masks, goggles/face shields and overalls was 85.7%, 96.9%, 62.1% and 65.4%, respectively. In conclusion, regular and large-scale seroepidemiological screening of healthcare professionals in the COVID-19 pandemic can contribute to the control of the pandemic by providing a better understanding of transmission dynamics and risk factors.

Evaluation of extensively drug-resistant gram-negative bacteremia among solid-organ transplant recipients: a multicenter study

Background/aim: The aim of this study is to evaluate the distribution, sources, clinical features, and mortality rates of bacteremia due to evaluation of extensively drug-resistant (XDR) gram negative among solid-organ transplant (SOT) recipients. Materials and methods: A retrospective study of SOT recipients with bacteremia due to XDR gram-negative pathogens in 11 centers between 2016 and 2018 was conducted. Patients' records were evaluated. Results: Of 171 bacteremia that occurred in 164 SOT recipients, 93 (56.7%) were liver, 46 (28%) kidney, 14 (8.5%) heart, and 11 (6.7%) lung recipients. Bacteremia episodes were recorded in the first year in 63.7% of the patients (n = 109), early-onset bacteremia was recorded in 45% (n = 77) of the episodes. In multivariate analysis, catheter-associated bacteremia was an independent risk factor for 7-day mortality (p = 0.037), and early-onset bacteremia was found as an independent risk factor for 30-day mortality (p = 0.017). Conclusion: Difficult-to-treat infections due to XDR bacteria in SOT recipients shadow the success of transplantation. Central venous catheters seem to be the main risk factor. Judicious use of medical devices is of pivotal importance.

Diverse efficacy of CarbaNP test among OXA-48 carbapenemase producing Enterobacterales in an endemic region.

After the first description of OXA-48 type carbapenemase, it has become endemic in Europe, Mediterranean and North African countries in a short time. OXA-48 carbapenemase is the most difficult type to determine and accurate diagnosis is crucial especially in endemic areas.The CarbaNP test was described as a rapid phenotypic evaluation method of carbapenemases activity. Sensitivity and specifity of this test were high within all carbapenemases genes. In our study, we evaluated the efficacy of CarbaNP test in routine laboratories located in an endemic area of OXA-48 producing Enterobacterales.A total of 53 Enterobacterales isolates were included in this study. Antimicrobial susceptibility of the isolates to imipenem, meropenem and ertapenem was determined. Polymerase Chain Reaction (PCR) was carried out for the detection of carbapenemases genes (blaKPC, blaNDM, blaBIC, blaIMP, blaVIM, blaSPM, blaAIM, blaDIM, blaGIM, blaSIM, and blaOXA-48). The Carba NP test was performed as in the protocol described previously.Altogether 31 isolates (58.4%) were blaOXA-48 positive (18 Klebsiella pneumoniae, 8 Escherichia coli, 2 Serratia marcescens, 1 Enterobacter aerogenes, 1 Pantoea agglomerans and 1 Morganella morganii). Among these isolates 3 (5.6%) and 2 (3.7%) isolates were also positive for blaVIM and blaSPM, respectively.The sensitivity and specifity of CarbaNP test were found 64.5, and 68.2% respectively. It was observed that determination of positive isolates is hard to distinguish and subjective.The CarbaNP test has suboptimal results and low of sensitivity and specifity for detection of OXA-48 producing Enterobacterales, and not suitable for detection of blaOXA-48 positive isolates in routine laboratories in endemic areas.

[Determination of Biofilm Formation Properties of Methicillin Sensitive and Resistant Staphylococcus aureus Isolates by Conventional and Molecular Methods]. / Metisiline Duyarli ve Dirençli Staphylococcus aureus Izolatlarinin Biyofilm Olusturma Özelliklerinin Konvansiyonel ve Moleküler Yöntemlerle Belirlenmesi.

Biofilm-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.

[Results of a multicenter study investigating plasmid mediated colistin resistance genes (mcr-1 and mcr-2) in clinical Enterobacteriaceae isolates from Turkey]. / Ülkemizde klinik Enterobacteriaceae izolatlarinda plazmit aracili kolistin direnç genlerini (mcr-1 ve mcr-2) arastiran çok merkezli çalismaya ait sonuçlar.

Colistin is a polymyxin antibiotic which is considered as one of the last line agents against infections due to multidrug resistant or carbapenem resistant gram-negative pathogens. Colistin resistance is associated with chromosomal alterations which can usually cause mutations in genes coding specific two component regulator systems. The first plasmid-mediated colistin resistance gene, mcr-1 was described in Escherichia coli and Klebsiella pneumoniae isolates in December 2015 and followed by another plasmid-mediated colistin resistance gene mcr-2 in 2016. The rapid and interspecies dissemination of plasmid-mediated resistance mechanisms through horizontal gene transfer, have made these genes considerably threatening. After the first reports, although mcr-1/mcr-2 producing Enterobacteriaceae isolates have been reported from many countries, there have been no reports from Turkey. Thus, the aim of this study was to investigate the presence of mcr-1/mcr-2 in clinical Enterobacteriaceae isolates from different parts of our country. A total of 329 Enterobacteriaceae isolates from 22 laboratories were collected which were isolated between March, 2015 and February, 2016. mcr-1/mcr-2 were investigated by polymerase chain reaction during February-March, 2016. Two hundred and seventeen of Klebsiella pneumoniae (66%), 75 of Salmonella spp. (22.8%), 31 of Esherichia coli (9.4%), 3 of Enterobacter cloacae (0.9%), 2 of Klebsiella oxytoca (0.6%) and 1 of Enterobacter aerogenes (0.3%) isolates were included to the study. Agarose gel electrophoresis results of PCR studies have shown expected band sizes for positive control isolates as 309 bp for mcr-1 and 567 bp for mcr-2. However, the presence of mcr-1/mcr-2 genes was not detected among the tested study isolates of Enterobacteriaceae. Although mcr-1/mcr-2 were not detected in our study isolates, it is highly important to understand the mechanism of resistance dissemination and determine the resistant isolates by considering that colistin is a last-line antibiotic against infections of multidrug or carbapenem resistant gram-negative bacteria. Thus, it is suggested that these mechanisms should be followed-up in both clinical and non-clinical (e.g. isolates from food animals, raw meats and environment) isolates of special populations.

Early Infections in Renal Transplant Recipients: Incidence, Risk Factors, and Causative Microorganisms.

OBJECTIVES: This study aimed to compare renal transplant recipients with and without infection with respect to demographic and clinical characteristics as well as risk factors; to determine the incidence of posttransplant infections; and to study the antibiotic resistance patterns of bacterial species identified as the causative organisms in posttransplant infections. MATERIALS AND METHODS: This study included a total of 136 patients undergoing renal transplant in a 4-year period. The patients were categorized into 2 groups. The 2 groups were compared with each other with respect to general clinical and demographic variables and the number and frequency of infectious attacks within a 1-year follow-up, infection type, and antibiotic resistance patterns. RESULTS: Ninety-two (67.6%) of the subjects were male and 44 (32.4%) were female. A total of 57 (41.9%) patients developed 128 infectious attacks. Urinary tract infections were the most common infections (42.1%). There was a significant correlation between a clinically relevant urinary culture proliferation and postoperative infection rate (P = .002). There was a significant correlation between antimicrobial resistance and the number of infectious attacks (P = .023). There was a significant correlation between the proliferation of Extended Spectrum Beta Lactamase-positive Enterobactericeae species and the number of infectious attacks (P = .000). CONCLUSIONS: Presence of a clinically relevant proliferation in the preoperative urinary culture, which was identified as a risk factor for infection, increased the number of infectious attacks. Moreover, Extended Spectrum Beta Lactamase-positive Enterobactericeae species increased the number of infections. These 2 principle results should be taken into account in patient management.

Tunnelled central venous catheter-related problems in the early phase of haematopoietic stem cell transplantation and effects on transplant outcome.

OBJECTIVE: Haematopoietic stem cell recipients need central venous catheters (CVCs) for easy administration of intravenous fluid, medications, apheresis, or dialysis procedures. However, CVCs may lead to infectious or non-infectious complications such as thrombosis. The effect of these complications on transplantation outcome is not clear. This manuscript presents the complication rates of double-lumen tunnelled CVCs and their effect on transplantation outcome. MATERIALS AND METHODS: Data from 111 consecutive patients, of whom 75 received autologous and 36 received allogeneic peripheral blood stem cell transplantations, were collected retrospectively. The data were validated by the Record Inspection Group of the related JACIE-accredited transplantation centre. RESULTS: Thrombosis developed in 2.7% of recipients (0.9 per 1000 catheter days). Catheter-related infection was identified in 14 (12.6%) patients (3.6 per 1000 catheter days). Coagulase-negative Staphylococcus was the most common causative agent. Engraftment time, rate of 100-day mortality, and development of grade II-IV graft-versus-host disease were not found to be associated with catheter-related complications. CONCLUSION: These results indicate that adverse events related with tunnelled CVCs are manageable and have no negative effects on transplant outcome.

Evaluation of 28 cases of mucormycosis.

Mucormycosis is a rare but invasive fungal disease with high mortality. The present study aimed to retrospectively investigate the demographic characteristics, as well as the clinical, radiological and laboratory features and the results of treatment, in the patients followed in our hospital because of mucormycosis. The present study retrospectively evaluated 28 cases, which were followed in our hospital because of mucormycosis between January 2002 and July 2013. The clinical form was rhinocerebral in 27 cases (rhinoorbital in 12, nasal in 8 and rhinoorbitocerebral in 7) and disseminated in one case. With regard to predisposing factors, diabetes mellitus (n = 20), haematological malignancy (n = 6) and chronic renal insufficiency (n = 5) were the leading concomitant diseases. Seventeen (61%) of 28 cases showed atypical clinical picture. With regard to the therapeutic outcomes; it was found that 14 (50%) cases died and six cases recovered with sequel. Today, when particularly the prevalence of immunosuppressive diseases and conditions are gradually increasing, the incidence of mucormycosis is also increased. Considering that the majority of our cases had atypical clinical involvement and complications, being familiar with the characteristics of this disease could be life-saving together with early diagnosis and treatment.

Aspiration of an interesting foreign body: Myiasis.

Myiasis is a rare condition caused by the invasion of tissues by the larvae of flies. Many cases of myiasis involving various human organs have been reported. Tracheopulmonary or intratracheal myiasis is a very unusual and aberrant form of the disease in humans. We present a case of respiratory myiasis after aspiration of larvae by a healthy 8-month-old girl, which cannot be found in the English literature.

[Evaluation of the ChromID ESBL agar for the detection of ESBL-positive Enterobacteriaceae and vancomycin-resistant enterococcus isolates from urine cultures]. / GSBL Pozitif Enterobacteriaceae ve Vankomisine Dirençli Enterokoklarin Idrar Kültürlerinden Erken Tespitinde ChromID ESBL Agarin Degerlendirilmesi.

Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae strains are frequent causative agents both in community-acquired infections and in nosocomial infections. The newly developed ChromID ESBL agar (bioMerieux, Marcy I'Etoile, France) is a chromogenic medium that helps rapid identification of ESBL-positive Enterobacteriaceae species from the clinical samples. The aim of this study was to evaluate the performance of ChromID ESBL agar in the rapid identification of ESBL-positive pathogens from the urine samples of the patients with urinary tract infections. A total of 672 urine samples (437 outpatients, 235 inpatients) were included in the study. All of the samples were inoculated simultaneously to 5% sheep blood agar, McConkey agar and ChromID ESBL agar media, and evaluated after incubation at 37°C for 18-24 hours. Gram-negative pathogens were tested for ESBL both by the standard combined double-disk diffusion (CDD) method using ceftazidime and cefotaxime disks and by doubledisk synergy (DDS) test. Among 672 urine cultures, 199 yielded microbial growth in routine media (sheep blood agar and/or McConkey agar), whereas 57 yielded bacterial growth in ChromID ESBL agar. When CDD method was accepted as the reference method according to Clinical and Laboratory Standards Institute (CLSI) recommendations, the sensitivity, specificity, positive and negative predictive values for ChromID ESBL agar for the detection of ESBL-positive bacteria in urinary tract infections were estimated as 97%, 92.9%, 89.1%, and 98.1%, respectively. Additionally, we also discovered that Chrom ID ESBL agar could detect vancomycin-resistant enterococci (VRE) as well as ESBL-positive bacteria, in our study. In order to investigate this observation we inoculated a total of 203 stock strains of Enterococcus spp. (118 vancomycin-sensitive, 85 vancomycin-resistant) to this medium. None of the vancomycinsensitive Enterococcus spp. did grow in ChromID ESBL medium, while 83 of the 85 resistant isolates (97.6%) did grow in the medium. As a result, it was concluded that ChromID ESBL agar medium was advantageous since it led to the growth of VRE and ESBL-positive Enterobacteriaceae isolates in different colors and helped in early identification of these two problematic bacteria. We thought that especially early detection of VRE will accelerate the establishment of necessary measures to prevent the nosocomial spread of this microorganism.