Molecular characterization of the multi-drug resistant Myroides odoratimimus isolates: a whole genome sequence-based study to confirm carbapenem resistance.

The bacteria belonging to the Myroides genus are opportunistic pathogens causing community or hospital-acquired infections that result in treatment failure due to antibiotic resistance. This study aimed to investigate molecular mechanisms of antibiotic resistance, clonal relatedness, and the biofilm forming capacity of the 51 multi-drug resistant Myroides odoratimimus. All isolates were screened for blaKPC, blaOXA, blaVIM, blaIMP, blaMUS, blaTUS, blaNDM, and blaB genes by using PCR amplification. Whole genome sequencing (WGS) was applied on three randomly selected isolates for further investigation of antibiotic resistance mechanisms. Clonal relatedness was analyzed by Pulsed-field gel electrophoresis (PFGE) and the microtiter plate method was used to demonstrate biofilm formation. All isolates were positive for biofilm formation. PCR analysis resulted in a positive for only the blaMUS-1 gene. WGS identified blaMUS-1, erm(F), ere(D), tet(X), and sul2 genes in all strains tested. Moreover, the genomic analyses of three strains revealed that genomes contained a large number of virulence factors (VFs). PFGE yielded a clustering rate of 96%. High clonal relatedness, biofilm formation, and multi-drug resistance properties may lead to the predominance of these opportunistic pathogens in hospital environments and make them cause nosocomial infections.

[Evaluation of Antibiotic Susceptibility, Biofilm Production and Clonal Analysis of Corynebacterium striatum Isolates]. / Corynebacterium striatum Izolatlarinin Antibiyotik Duyarliliklari, Biyofilm Üretimi ve Klonal Analizlerinin Degerlendirilmesi.

In this study, it was aimed to determine the possible factors affecting the clinical importance of Corynebacterium striatum isolates, which were accepted as infectious or contamination/colonization agents, by comparing their clinical and microbiological characteristics, antimicrobial susceptibility results, biofilm forming abilities and genotypic characteristics. The patients with C.striatum growth in the clinical samples sent to the laboratory were evaluated as infection or contamination/colonization with the evaluation of the examination findings and other laboratory parameters by the relevant physician. This study included 58 isolates, 29 of which were considered as infection and 29 as contamination/colonization. Length of hospital stay, presence of underlying disease [diabetes mellitus (DM), neurological disease, ischemic heart disease, chronic kidney disease, solid tumor], surgical operation status in the last month, and antibiotic use in the last three months of the patients were examined. Identification of the bacterial type was made with MALDI-TOF MS (Bruker/Germany) system. Antimicrobial susceptibility tests were performed by disc diffusion and gradient diffusion method and evaluated according to EUCAST standards. Biofilm production was determined in 96-well microtiter plates on negatively charged polystyrene surfaces. Clonal analyzes were performed by PFGE method using Xba1 enzyme. It was observed that there was no difference in terms of demographic characteristics in the two patient groups included in the study. It was observed that C.striatum strains isolated from outpatients were mostly found in the contamination/ colonization group. The presence of diabetes mellitus, ischemic heart disease, chronic kidney disease and solid tumor was not statistically different in the two patient groups. It was observed that C.striatum strains grown in the samples of patients with neurological disease were mostly found in the infectious agent group (p= 0.025). It has been observed that C.striatum strains grown purely in culture were mostly found in the infectious agent group (p= 0.001). Biofilm production was found to be significantly higher in the infectious agent group (p= 0.015). In antimicrobial susceptibility tests, it was observed that there was widespread multidrug resistance (MDR) in both groups and there was no significant difference between the groups in terms of antimicrobial susceptibility. In our study, it was determined that the strains showed very different PFGE patterns and were not clonally related to each other. In this study, it was determined that the demographic characteristics and comorbidities of the patients were not helpful in evaluating the clinical significance of C.striatum. Biofilm production was observed to be a common virulence factor in C.striatum strains. It was thought that there may be difficulties in the treatment of C.striatum in the future due to the widespread MDR detection among this bacterium strains. Our study contributes to draw attention to the increase in C.striatum infections, resistance and virulence factors.

Eggerthia catenaformis-related peritonitis in a patient with peritoneal dialysis.

Eggerthia catenaformis is a Gram-positive bacilli and an anaerobic and non-spore-forming bacterium, which rarely causes infections in humans. We present a case of peritonitis caused by E. catenaformis in a peritoneal dialysis patient. The isolate was identified as E. catenaformis with the MALDI-TOF MS method as in other cases in the literature. To the best of our knowledge, this is the first case of peritonitis caused by E. catenaformis in a human host.

[Comparision of Colistin Broth Disc Elution, Rapid Resapolymyxin NP and Broth Microdilution Methods in Determining Colistin Sensitivity in Acinetobacter, Pseudomonas and Enterobacterales species]. / Acinetobacter, Pseudomonas ve Enterobacterales Türlerinde Kolistin Duyarliliginin Belirlenmesinde Kolistin Sivi Disk Elüsyon, Hizli Resapolimiksin NP ve Sivi Mikrodilüsyon Yöntemlerinin Karsilastirilmasi.

In recent years, with the increase of carbapenem resistance in Acinetobacter, Pseudomonas, Enterobacterales species, the use of colistin in treatment has gradually increased. Since the broth microdilution method which is recommended as a reference method in colistin susceptibility tests, is laborious and expensive and other susceptibility tests do not give reliable results, all these cause laboratories to search for new methods for the determination of colistin susceptibility testing. In this study, it was aimed to compare the broth microdilution method which is the reference method with the colistin broth disc elution and rapid resapolymyxin NP tests for the determination of the susceptibility of colistin in Acinetobacter, Pseudomonas, Enterobacterales species which are common healthcare-associated infection agents.Colistin susceptibility of a total of 157 isolates isolated from patients hospitalized in Ankara City Hospital [Klebsiella pneumoniae (n= 74), Acinetobacter spp. (n= 33), Escherichia coli (n= 26), Pseudomonas aeruginosa (n= 24)] were tested by broth microdilution, colistin broth disc elution and rapid resapolymixin NP methods. The categorical and basic agreement was evaluated by comparing the broth microdilution results with the rapid resapolymyxin NP results and the colistin broth disc elution. When compared with broth microdilution, the categorical agreement of colistin broth disc elution test for Enterobacterales, Acinetobacter, Pseudomonas species was found to be 93%, 48%, 100%, respectively. When the essential agreement was evaluated the values of 95%, 45%, 100% were found, respectively. Very major error rates were found to be 10%, 70% and 0%, respectively. The categorical agreement of the rapid resapolymyxin test for Enterobacterales, Acinetobacter, Pseudomonas species was 85%, 36%, 100%, while very major error rates were found to be 10%, 88% and 0%, respectively. When compared with the reference method, both tests showed high categorical and essential agreements for P.aeruginosa. Accepted level of categorical and essential agreement was found in colistin broth disc elution method for Enterobacterales species, and low categorical agreement was found in rapid resapolymyxin NP test. For Acinetobacter species, both tests detected low categorical agreement and high rate of very major error. In addition, compared to the broth microdilution method, both colistin broth disc elution and rapid resapolymyxin NP tests were found to be cost-effective and easy to prepare. It was considered to be an additional advantage to have the results in rapid polymyxin NP test in four hours. In conclusion, in our study, it was shown that both colistin broth disc elution and rapid resapolymyxin NP test methods can be used in determining the susceptibility of colistin for P.aeruginosa and Enterobacterales species but both methods were found to be unsuccessful for Acinetobacter species.

Characteristics of candidemia in COVID-19 patients; increased incidence, earlier occurrence and higher mortality rates compared to non-COVID-19 patients.

Severe COVID-19 patients in ICU are at high risk for candidemia due to exposure to multiple risk factors for candidemia. We aimed to compare the incidence of candidemia in ICU patients with and without COVID-19, and to investigate epidemiologic and clinical characteristics of candidemia patients and risk factors for mortality in candidemia patients. This retrospective study was conducted in patients followed in the ICUs of Ankara City Hospital for 2 years, divided into pre-pandemic and pandemic periods. The incidence (event per 1000 patient-days) and epidemiology of candidemia, clinical and laboratory characteristics of patients were compared in COVID-19 and non-COVID-19 groups. Candidemia incidence was higher in the COVID-19 group (2.16, 95% CI 1.77-2.60) than the non-COVID-19 group (1.06, 95% CI 0.89-0.125) (p < .001). A total of 236 candidemia episodes (105 in COVID-19 patients and 131 in non-COVID-19 patients) were detected during the study periods. COVID-19 cases had a higher rate of corticosteroid use (63.8% vs. 9.9%, p < .001). Epidemiology of candidemia and antifungal susceptibility were similar. Candidemia developed 2 weeks earlier in COVID-19 groups and resulted in higher mortality (92.5% vs. 79.4%, p .005). One-third of candidemia patients died before receiving any antifungal treatment, and this rate was higher in the COVID-19 group. In multivariate logistic regression analysis, corticosteroid use, presence of sepsis and age older than 65 years were independent risk factors for mortality in candidemia patients. Candidemia with high mortality is a more serious problem for COVID-19 patients due to its increased incidence, earlier occurrence and a higher rate of mortality.

[Evaluation of blood culture practices: Use of system (Epicenter) data]. / Kan kültürü uygulamalarinin degerlendirilmesi: Isletim sistemi (Epicenter) verilerinin kullanimi.

Sepsis 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 hours' 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.

RS sample: Can be guide for empirical treatment of haematological malignancy patients?

Neutropenia due to intensive chemotherapy in haematological malignancy patients leaves the host vulnerable and makes them susceptible to infections. Infections are the most important cause of morbidity and mortality especially in haematological malignancy and chemotherapy patients. In addition, the use of multiple or inappropriate antibiotics leads to the development of resistant microorganisms. Therefore, the choice of empirical treatment is of vital important in these patient groups. Escherichia coli, Acinetobacter baumannii and Klebsiella pneumoniae are among the most frequently isolated Gram negative bacteria in neutropenic patients. Rectal swab (RS) samples were obtained from haematological malignancy patients not yet on chemotherapy or have no infection on chemotherapy period, E. coli was isolated from these samples, and A. baumannii and K. pneumoniae colonization were investigated. Susceptibilities of bacteria against antibiotics used in empirical treatment and prophylaxis were determined by using Gradient test strips according to the EUCAST recommendation. All isolates were sensitive against colistin. The resistant rates of antibiotics were detected as 39.1%, 9.4%, 6.8%, 35.1%, 31%, 39.1% for ciprofloxacin, meropenem, imipenem, piperacillin-tazobactam, cefepime, ceftazidime respectively The clonal relationship between Gram negative bacteria of intestinal flora and infection agents of same patient was investigated by Pulsed-Field gel electrophoresis. Twenty-three of the 30 patients (76.6%) were found to have a clonal relationship between the bacterial isolates before and after infection. It was determined that it can be able to predict with RS samples about possible agents of infection and their antibiotic susceptibility patterns.

[Investigation of Microsporidia prevalence with calcofluor white and uvitex 2B chemiluminescence staining methods and molecular analysis of species in diarrheal patients]. / Ishalli olgularda Microsporidia sikliginin Calcofluor beyazi ve uvitex 2B kemiluminesans boyama yöntemleriyle arastirilmasi ve türlerinin moleküler yöntemle tiplendirilmesi.

Microsporidia, obligate intracellular parasites, were first defined by Nageli in 1857. Microsporidia phylum consists of 200 genus and 1500 species. They have a wide host spectrum including insects, fish, and mammals. It has been shown that they may also infect humans and may be existed both in symptomatic and asymptomatic forms. There are eight species infecting humans, which include Anncaliia (Brachiola, Nosema), Encephalitozoon, Entrocytozoon, Microsporidium, Nosema, Pleistophora, Trachipleistophor, and Vittaforma. The species most commonly infect humans are Encephalitozoon intestinalis and Enterocytozoon bieneusi. The aim of this study was to determine the prevalence of Microsporidia by using two different chemiluminescence stains, namely uvitex 2B and calcoflour and detect species by molecular analysis in diarrheal patients. For this purpose, we studied stool samples of 200 patients with diarrhea sent to Gazi University Health Practice and Research Hospital, Microbiology Laboratory and Ankara Numune Training and Research Hospital Microbiology Laboratory between 2012-2013. The stool samples were stained with chemiluminescent stains uvitex 2B and calcoflour methods; the Microsporidia prevalence was found to be 38% (77/200) by fluorescent microscopic examination. Statistically an excellent consistency was found between the chemiluminescent stains uvitex 2B and calcoflour (Cohen's kappa= 0.881). A statistical analysis for the consistency of uvitex 2B and calcoflour in terms of numerical density (low, high) and luminescence of spores (dim, bright) showed a moderate consistency between the two stains with respect to determining numerical density of spores (Cohen's kappa= 0.354), while there was no consistency in terms of luminescence of spores (Cohen's Kappa= 0.001). No significant difference was found between the Microsporidia prevalence with respect to age group or clinics (p > 0.05). A sex-based analysis showed that Microsporidia prevalence was more common in women (50%) than men (30.8%) (p< 0.05). In 77 samples that were detected positive for Microsporidia with uvitex 2B and calcoflour stains determination of genus and species level were done by using multiplex nested polymerase chain reaction (PCR) method. With this technique, seven (9.1%) of 77 isolates were detected as E.bieneusi, and 70 (90.9%) as Encephalitozoon spp. When the Microsporidia genus was considered, the Microsporidia prevalence did not show differences with respect to age, sex, and referring clinics (p> 0.05). In our study 44 (62.9%) of 70 Encephalitozoon spp. were E.intestinalis, 22 (31.4%) were E.cuniculi, and 4 (5.7%) were E. hellem. No statistical difference was found in the distribution of Encephalitozoon spp. with age, sex, and referring clinic (p> 0.05). We concluded that examination of stool samples with the chemiluminescent stain uvitex 2B and/or calcoflour would be useful for the initial stage of Microsporidia diagnosis; furthermore, the multiplex nested PCR method was considered useful for determination of genus and species. In our country, there is a small number of molecular reports about Microsporidia prevalence in stool samples. Molecular methods should be used more commonly for the evaluation of treatment options in diarrheal patients and detection of Microsporidia epidemiology.

Chronic lower extremity wound infection due to Kerstersia gyiorum in a patient with Buerger's disease: a case report.

BACKGROUND: Kerstersia gyiorum is an extremely rare pathogen of human infection. It can cause chronic infection in patients with underlying conditions. It can easily be misdiagnosed if proper diagnostic methods are not used. CASE PRESENTATION: A 47-year-old male patient with a history of Buerger's Disease for 28 years presented to our hospital with an infected chronic wound on foot. The wound was debrided, and the specimen was sent to Microbiology laboratory. Gram staining of the specimen showed abundant polymorphonuclear leukocytes and gram-negative bacilli. Four types of colonies were isolated on blood agar. These were identified as Kerstersia gyiorum, Proteus vulgaris, Enterobacter cloacae, Morganella morganii by Maldi Biotyper (Bruker Daltonics, Germany). The identification of K. gyiorum was confirmed by 16S ribosomal RNA gene sequencing. The patient was successfully recovered with antimicrobial therapy, surgical debridement, and skin grafting. CONCLUSIONS: This is the first case of wound infection due to K. gyiorum in a patient with Buerger's Disease. We made a brief review of K. gyiorum cases up to date. Also, this case is presented to draw attention to the use of new and advanced methods like MALDI-TOF MS and 16S rRNA gene sequencing for identification of rarely isolated species from clinical specimens of patients with chronic infections and with chronic underlying conditions.

A novel ELISA test for laboratory diagnosis of Blastocystis spp. in human stool specimens.

Detection of Blastocystis is routinely performed by microscopy, culture, and formyl-ether (ethyl acetate) concentration technique (FECT). Yet, these methods require special skilled personnel, are time consuming, and often involve processing that may cause misdiagnosis. The aim of this work is to demonstrate the usefulness of a newly introduced ELISA test for the detection of Blastocystis antigens in stool samples (CoproELISA(TM) Blastocystis, Savyon Diagnostics) as a proper alternative to currently used methods, especially microscopy. A cohort of 179 fresh/frozen clinical stool samples was tested by the ELISA test, and results were compared to consensus methods comprised of microscopic examination of Lugol's iodine staining, culture, and immunofluorescence assay (IFA). The new ELISA test was able to detect fewer than 10(3) cells, recognized subtypes 1, 2, 3, and 5 (comprising >95 % of human Blastocystis infections), and exhibited similar reactivity when comparing formalin-preserved samples to fresh/frozen samples. The test demonstrated 92 % sensitivity, 87 % specificity, and 89 % accuracy when culture, and IFA or microscopy consensus results were taken as reference. When the consensus was comprised of culture and IFA, the test demonstrated sensitivity, specificity, and accuracy of 82, 86, and 84 %, respectively. In contrast, the sensitivity of Lugol staining microscopy was only 18 %. This work presents a unique ELISA test that provides an alternative to the use of microscopy, currently most widely used method. The test enables high-throughput screening and diagnosis of Blastocystis, adaptation to automatic procedures.

[Investigation of the presence of Blastocystis spp. in stool samples with microscopic, culture and molecular methods]. / Diski örneklerinde Blastocystis spp. varliginin mikroskobik, kültür ve moleküler yöntemlerle arastirilmasi

Blastocystis species are enteric protozoa frequently detected in human and animals. Seventeen subtypes (STs) have now been identified, nine of them isolating from humans. The pleomorphic structure and genetic diversity of Blastocystis spp. and the absence of standardized diagnostic methods complicate the evaluation of current data. Microscopic methods such as native-lugol and trichrome staining are most frequently used methods in routine diagnosis, while culture and molecular methods are preferred for research purposes. The aims of this study were to investigate the presence of Blastocystis spp. in the stool samples of patients with gastrointestinal complaints by microscopic and culture methods, and to detect the subtypes of isolates by polymerase chain reaction (PCR). A total of 350 stool samples collected from patients with diarrhea (n= 157) and without diarrhea (n= 193) were included in the study. Presence of Blastocystis spp. in the samples were investigated by native-lugol examination, trichrome staining and direct fluorescent antibody (DFA) methods. Ringer's solution containing 10% horse serum and 0.05% asparagine was used for cultivation. The cultures were evaluated after 3-4 days of incubation at 37°C by microscopic examination. The subtypes of Blastocystis spp. strains isolated from the cultures have been identified by PCR using sequence-tagged site primers. A total of 66 (19%) stool samples, of them 26 (16.6%) were from diarrheal and 40 (21%) from non-diarrheal cases, yielded Blastocystis sp. growth in culture. Among the evaluated samples, 12% (42/350) were found positive with native-lugol examination, 17% (58/350) with trichrome staining, and 19% (66/350) with DFA method. The agreement of culture and native-lugol method was estimated as strong (κ= 0.752), while it was very strong between culture with trichrome staining and DFA methods (κ= 0.922 and κ= 1.00, respectively). When the culture was accepted as reference method, the sensitivity and specificity rates of native-lugol method were 65% and 100%, trichrome staining method were 88% and 100%, and DFA method were 100% and 100%, respectively. Forty-three (65%) of Blastocystis spp. positive samples were subtyped by PCR, while 23 isolates could not be subtyped. The most frequent detected subtype was ST3 (12/43; 28%), followed by ST1 (6/43; 13.9%), ST4 (5/43; 11.6%) and ST7 (5/43; 11.6%), ST2 (3/43; 7%) and ST6 (1/43; 2.3%). ST5 was not detected in this study and 11 (25.6%) samples have been identified to have mixed subtypes. The differences of Blastocystis spp. positivity rates and the distribution of the subtypes between the patients with or without diarrhea were not found statistically significant (p> 0.05). In our study, ST3 was the most frequently identified Blastocystis spp. subtype, similar to the previous national studies, however ST6 and ST7 have been identified for the first time. In conclusion, as the sensitivity of native-lugol examination is low, culture is time-consuming and laborious and PCR methods are costly and non-standardized, rapid, practical and high sensitive DFA is considered as the favourable method in the diagnosis of Blastocystis spp. in routine laboratories.

[Investigation of oxacillinase genes in nosocomial multidrug-resistant Acinetobacter baumannii isolates by multiplex PCR and evaluation of their clonal relationship with Rep-PCR]. / Nozokomiyal çok ilaca dirençli Acinetobacter baumannii izolatlarinda oksasilinaz genlerinin multipleks PCR ile arastirilmasi ve klonal iliskilerinin Rep-PCR ile degerlendirilmesi.

Acinetobacter baumannii is a major nosocomial pathogen which can cause infections with high morbidity and mortality in hospitalized patients. In recent years A.baumannii has become a serious clinical problem because of the development of resistance to many antibiotics, and especially to carbapenems. The aims of this study were to investigate the oxacillinase genes responsible for carbapenem resistance in multidrug resistant (MDR) A.baumannii strains and to evaluate the clonal relationship between these strains. A total of 62 MDR A.baumannii strains isolated from various clinical specimens (24 tracheal aspirate, 14 wound, 10 blood, 7 urine, 2 abscess, 2 sputum, 2 catheter tip, 1 pleural fluid) of hospitalized patients in intensive care units (n= 42) and other inpatient clinics (n= 20) between February-March 2012, were included in the study. Identification and antibiotic susceptibility of A.baumannii isolates were performed by Vitek-2 automated system (bioMérieux, France), and the identified bacteria were confirmed by Maldi Biotyper (Bruker Daltonics, Germany) system. Imipenem, meropenem, colistin and tigecycline were additionally tested by E-test strips (bioMérieux, France). The presence of carbapenemase-producing OXA genes (blaOXA-23-like, blaOXA-40-like, blaOXA-51-like and blaOXA-58-like) were detected by multiplex PCR (hyplex® CarbOxaID test system, Amplex Diagnostics, Germany) and the clonal relationship between isolates were investigated by rep-PCR method (DiversiLab, bioMérieux, France). In our study, all isolates were found resistant to ampicillin-sulbactam, piperacillin, piperacillin-tazobactam, ceftazidime, cefepime, imipenem, meropenem, ciprofloxacin, levofloxacin and tetracycline, while the resistance rates for amikacin, gentamicin, trimethoprim-sulfamethoxazole, netilmicin and tigecycline were 88.7%, 88.7%, 82.3%, 43.5% and 27.4%, respectively. All A.baumannii isolates were susceptible to colistin. All of the strains were positive for blaOXA-23-like and blaOXA-51-like genes, while blaOXA-40-like and blaOXA-58-like genes were not detected in any of them. Simultaneous cultures from environmental samples collected from inpatient clinics in which MDR A.baumannii strains isolated were negative in terms of A.baumannii growth. In evaluation of clonal relationship between isolates, 48 strains (77.4%) showed greater than 95% similarity and formed a big cluster, named Cluster A. The remaining 14 isolates formed 3 small clusters (each had 2 isolates), named Cluster B, C and D, showing greater than 95% similarity. Majority of isolates (58.3%) in Cluster A were from patients in the surgical intensive care unit, and the first isolate from this cluster was also from a patient in the same unit. In our opinion, isolates from Cluster A may have spread to other clinics from surgical intensive care unit through transferred patients or medical and non-medical devices and equipment. Nosocomial MDR A.baumannii isolates in our hospital are highly resistant to antibiotics and all harboured blaOXA-23-like genes. The rep-PCR analysis of these isolates indicated that a large portion of A.baumannii strains were clonally closely related, and they probably from the same source and common ancestor, and separated shortly from each other. This data emphasizes that the choices of treatment are quite limited for inpatients, and the need for improvement of the infection control measures in our hospital.

[Evaluation of the toxoplasmosis seroprevalence in pregnant women and creating a diagnostic algorithm]. / Gebelerde toksoplazmoz seroprevalansinin degerlendirilmesi ve bir tani algoritmasinin olusturulmasi

Toxoplasma gondii, an obligatory intracellular protozoon is widely distributed around the world and can infect all mammals and birds. While acquired toxoplasmosis is usually asymptomatic in healthy subjects, acute infection during pregnancy may lead to abortion, stillbirth, fetal neurological and ocular damages. For the prevention of congenital toxoplasmosis it is recommended that a screening programme and a diagnostic algorithm in pregnant women should be implemented while considering the cost effectiveness. Thus, it is necessary to determine the seroprevalence of toxoplasmosis in pregnant women and the actual risk of T.gondii transmission during pregnancy in a certain area. The aims of this study were to detect the T.gondii seropositivity in the pregnant women admitted to our hospital and to create a diagnostic algorithm in order to solve the problems arising from interpretation of the serological test results. A total of 6140 women aged 15-49 years who were admitted to our hospital between April 1st, 2010 to July 31st, 2013, were evaluated retrospectively. In the serum samples, T.gondii IgM, IgG and IgG avidity tests were performed by VIDAS automated analyzer using TOXO IgM, TOXO IgG II and TOXO IgG avidity kits (bioMerieux, France). It was noted that, both T.gondii IgM and IgG tests were requested from 4758 (77.5%) of the pregnant women, while only IgM test from 1382 (22.5%) cases. Sole IgM positivity was found as 0.2% (11/6140), IgG as 26.4% (1278/4758) and both IgM + IgG as 0.9% (44/4758). T.gondii IgG avidity tests were requested from 12 of 44 women who were found both IgM and IgG positive and eight of them revealed high avidity and four low avidity. Avidity test was ordered for the 91 (7.1%) of 1278 sole IgG positive cases and four of them were found to have low avidity. IgG avidity test was ordered for 554 (16.2%) of IgM and/or IgG negative subjects, however, the test was not performed according to rejection criteria of the laboratory. It was noticed that no re-testing was requested for none of the seronegative cases (3428/4758; 72%) during their follow-up. In our study, total Toxoplasma seropositivity rate among pregnant women was detected as 28% (1330/4758), showing statistically significant increase (p< 0.05) with age. There was no significant difference (p> 0.05) in the seropositivity rate between the years (2010-2013). Following the evaluation of the test orders, the problems related to test orders and interpretation of the test results were determined and a diagnostic algorithm to be used in our hospital, was established to minimize such problems in toxoplasma serology. It was concluded that a diagnostic algorithm related to toxoplasmosis serology should be implemented for the appropriate evaluation of the risk of acute toxoplasmosis during pregnancy. Such an approach is necessary to support the clinical diagnosis and to minimize the anxiety in pregnant women about congenital toxoplasmosis.

Candidemia in critically ill COVID-19 patients: Risk factors and impact on mortality.

Background: Risk factors of candidemia are well-described in intensive care units (ICUs) before the Coronavirus disease 2019 (COVID-19) pandemic. The increased rates of admission to ICUs have appeared during the pandemic. Methods: Patient characteristics and laboratory data of 80 candidemia with COVID-19, 101 candidemia without COVID-19, and 100 non-candidemia with COVID-19 patients were evaluated, in this study. Results: Systemic inflammatory response syndrome (SIRS) ≥ 2, solid malignancy, total parenteral nutrition (TPN), central venous catheterization (CVC), hypotension, fever, urea, alanine aminotransferase (ALT), D-dimer, procalcitonin, ferritin, and delta neutrophil index (DNI) was found to be associated with candidemia in COVID-19 patients. TPN, hypotension, and fever were identified as independent predictors of candidemia in COVID-19, and candidemia in COVID-19 is characterized by significantly high mortality rates. Urea, lactate, and procalcitonin were defined as independent predictors of hospital mortality in candidemia patients with COVID-19. Conclusion: The presence of candidemia increases mortality in COVID-19. TPN, fever, and hypotension werefound to be the most powerful predictors of candidemia in COVID-19. Overall, these data show that candidemia in COVID-19 is characterized by significantly high mortality rates. Determination of distinctive features can prevent candidemia and mortality.

Does Formalin Disinfection Reduce Bacterial Colonization of Biopsy Needle? A Prospective Study.

OBJECTIVE: To investigate the efficacy of formalin disinfection of the needle tip in transrectal prostate biopsy (TRB) procedure to reduce infectious complications. The primary aim is to assess the impact of formalin on bacterial contamination of biopsy needle tips and its association with post-biopsy infective events. MATERIALS AND METHODS: We have employed a bacterial culture-based observational cohort design in this study. Two groups, formalin disinfection and non-formalin group, both underwent systematic 12-core TRB. In the formalin group, the biopsy needle tip was immersed in 10% formalin solution after each core, while in the non-formalin group, no formalin solution immersion was used. The primary outcomes include bacterial growth on biopsy needle tips and post-biopsy infective events. RESULTS: Formalin disinfection significantly reduced bacterial growth on needle tips (P <.001). The formalin group had no post-biopsy infections or sepsis, while the non-formalin group experienced a 7.5% infective event rate after TRB. CONCLUSION: Formalin disinfection of biopsy needle tip significantly reduces bacterial growth on biopsy needle and urinary tract infectious complications developed secondary to TRB. Further multicenter randomized controlled studies with larger cohorts are warranted to validate and establish formalin disinfection as a routine practice in TRB procedures.

An investigation of clinical characteristics and antimicrobial agent susceptibility patterns in clinical Comamonas testosteroni isolates: An increasingly prevalent nosocomial pathogen.

BACKGROUND: Comamonas testosteroni is a gram-negative bacillus, known before 1987 as Pseudomonas testosteroni. Although considered as a rare pathogen, its frequency has been increasing. Data regarding its antibiotic susceptibility are insufficient. To date, forty-four cases have been reported in the literature. In this study, we identified the C. testosteroni infections observed in our hospital and evaluated their antimicrobial agent susceptibility patterns compared with cases reported in the literature. METHODS: For the purposes of the present study, patients admitted to hospital between November 2019 and December 2020 were screened. Those with clinical and laboratory signs of infection with positive C. testosteroni growth in culture were enrolled. Clinical isolates obtained from the samples processed in accordance with standard microbiological examination procedures in our laboratory were defined by MALDI-TOF mass spectrometry with 99.9% probability as C. testosteroni. RESULTS: C testosteroni infection was detected between November 2019 and December 2020 in eight patients in our hospital. Six of them had a bloodstream infection (BSI), one had pneumonia, and one had urinary tract infection due to C. testosteroni. Coexistence of COVID-19 was detected in four patients. Six out of the eight cases with BSI had hospital-acquired infection and all of the infections were healthcare-associated. When antimicrobial agent susceptibility results reported in the literature were evaluated in combination with the current results, ceftazidime and meropenem were found to be the most susceptible agents (96.1% and 80%, respectively). CONCLUSIONS: The frequency of nosocomial C. testosteroni infections and resistance to antimicrobial agents are gradually increasing. While resistance to carbapenems is on the upswing, third-generation cephalosporins are still seen as suitable treatment options.

[The rare genes related to resistance to macrolide-lincosamide and streptogramin B group antibiotics among coagulase-negative staphylococci]. / Koagülaz-Negatif Stafilokoklarda Makrolid-Linkozamid-Streptogramin B Grubu Antibiyotiklere Karsi Nadir Direnç Genlerinin Arastirilmasi

Macrolide-lincosamide-streptogramin B (MLSB) group antibiotics are recommended as first choice in the treatment of staphylococcal infections. All of those drugs bind to the 50S subunit of bacterial ribosomes, thus cross-resistance is a major concern in this group of drugs. The mechanisms associated to resistance are (a) ribosomal methylation due to the methylases encoded by erm genes, (b) active drug efflux due to msrA, msrB, vga, vgb gene activity, (c) enzymatic inactivation of the drug due to the activity of linA, vat, vatB genes. While the most common resistance genes are ermA, ermB, ermC, msrA and msrB genes; linA, vga, vgb, vat and vatB genes have also been found in some studies. In this study it was aimed to investigate the presence of the rare MLSB resistance genes and their coexistence with erm and msr genes in 454 clinical isolates of coagulase-negative staphylococci (CNS). Of them 46.5% (n= 211) were S.hominis, 30.8% (n= 140) were S.epidermidis, 12.1% (n= 55) were S.haemolyticus, 3.5% (n= 16) were S.warnerii and 7% (n= 32) were the other coagulase-negative staphylococcal species. Resistance phenotypes were determined by using D-test method according to the recommendation of Clinical and Laboratory Standards Institute (CLSI). With the D-test 107 (23.6%) strains were determined as M phenotype (resistant to erythromycin and inducible clindamycin resistance was not detected), 92 (20.3%) were iMLSB phenotype (inducible clindamycin resistance was detected by the D-test) and 110 (24.2%) were cMLSB phenotype (constitutive erythromycin and clindamycin resistance was detected). linA, vga, vgb, vat, vatB, ermA, ermB, ermC, msrA, msrB genes were investigated by polymerase chain reaction in all strains showing iMLSB (n= 92) and cMLSB (n= 110) phenotypes and 46 randomly selected strains among 107 strains exhibiting the M phenotype. linA gene was found in 91 (20%) strains as single gene or in combination with erm or msr genes, and vga gene was found in 19 (4.2%) strains. linA gene was found in 52% of iMLSB phenotype, in 26% of cMLSB phenotype and 13% of M phenotype while vga gene was found in 5.4% of iMLSB phenotype, in 12% of cMLSB phenotype and in 0.9% of M phenotype. The most common resistance gene among iMLSB and cMLSB phenotypes was ermC (32.6% and 42.7%, respectively), followed by ermC + linA gene combination (31.5% and 14.5%, respectively). The most frequent gene combination was msrA and msrB in M phenotype (34.8%) and it was followed by a combination of msrA + msrB + linA genes (19.1%). None of the strains revealed presence of vgb, vat and vatB genes. There were no previous reports about the rarely detected resistance genes against MLSB antibiotics in our country. This was the first study which reported the frequency of linA, vga, vgb, vat and vatB genes in MLSB resistant CNS. In conclusion, since linA and vga genes were detected in high frequency in MLSB resistant CNS in this study, it was thought that the investigation of these genes should be included in the further related epidemiologic gene research.

[Phenotypic and genotypic traits of vancomycin-resistant enterococci in a public hospital: the first vanB-positive Enterococcus faecium isolates]. / Bir Devlet Hastanesinde Vankomisine Dirençli Enterokok Suslarinin Fenotipik ve Genotipik Olarak Degerlendirilmesi: Ilk vanB-Pozitif Enterococcus faecium Izolatlari

Thirty eight vancomycin resistant enterococci (VRE) were isolated in one year surveillance study for hospital infection control programme in a state hospital in Ankara, Turkey. All isolates were identified as Enterococcus faecium by VITEK2 system (bioMerieux, France). Vancomycin and teicoplanin resistant 30 strains were defined as vanA phenotype while vancomycin-resistant teicoplanin-susceptible eight strains were defined as vanB phenotype. vanA genes were found in 30 strains while vanB genes were found in five strains by using PCR method. Those five strains were the first vanB positive E.faecium strains in our country. VRE strains revealed six different band patterns by PFGE, while six isolates could not be classified. All isolates with vanB type resistance were found in the same cluster. Source of vanB positive strains was considered as the hemodialysis unit. When the previous national reports related to vancomycin-resistant enterococci were considered, this was the first report of vanB positive E.faecium isolates in our country. This emphasized that both the diversity of VRE and the isolation rate was increasing. In order to eliminate the spread of VRE, effective surveillance studies should be performed and protective measures should be established promptly.

Diagnostic value of ß-D-glucan alone or combined with Candida score, colonization index and C-reactive protein for candidemia.

INTRODUCTION: Candidemia causes high mortality and is occuring at increasing rate in intensive care units (ICUs). (1,3)- ß-D-glucan (BDG) testing is recommended in neutropenic patients. However the usefulness of BDG in ICUs is unclear. METHODOLOGY: This study was conducted to compare the diagnostic value of Candida score (CS), colonization index (CI), serum BDG detection, and routine laboratory parameters in ICU patients. Characteristics and laboratory data of 83 patients (15 patients with candidemia and 68 patients without candidemia) were evaluated. RESULTS: Median serum BDG was significantly higher in the candidemia group (129 pg/mL vs. 36 pg/mL, p < 0.001). BDG assay with standard cut-off value ≥ of 80 pg/mL had 93.33% sensitivity and 64.18% specificity (Areas under the ROC curve (AUC): 0.788). This study concluded that the optimal cut-off value for BDG assay was 112 pg/mL with sensitivity of 86.67% and specificity of 82.09% (AUC: 0.844). C-reactive protein (CRP) with optimal cut-off value ≥ 85 mg/L and BDG ≥ 80 pg/mL had the highest AUC (0.862, 95% CI: 0.768 - 0.928) with sensitivity 93.33% and specificity 79.1%. CONCLUSIONS: Predicting candidemia is essential in critically ill patients who are at high risk and have high mortality rates. The results of this study suggest that BDG testing is useful for predicting candidemia in ICU. However, BDG combined with CRP may be a stronger predictor for candidemia.

An outbreak of Ralstonia pickettii bloodstream infection among pediatric leukemia patients.

BACKGROUND: Ralstonia pickettii is an opportunistic waterborne microbe which can survive in many kinds of solutions. Contamination of these solutions may result as outbreaks, which can be mortal for immuncompromised patients. Herein we report an outbreak of R. pickettii related to contaminated saline infusion in our center. METHODS: This study was conducted in Ankara Pediatric City Hospital. An outbreak occured in Pediatric Hematology and Oncology Unit between August 28, 2019 and September 13, 2019. When the outbreak occured, infection control team began an investigation. Environmental samples were collected in order to find the source of the outbreak. RESULTS: A total of 11 patients with catheter related blood stream infection caused by R. pickettii who were diagnosed with leukemia were affected. None of the patients infected with R. pickettii died during the outbreak. A total of seventy environmental samples were cultured with the purpose of finding the source of outbreak. R. pickettii grew in normal saline solution culture and all isolates had the same clone of R. pickettii. The outbreak lasted two weeks and was controlled by stopping the usage and sending back the saline solutions belonging to the same manufacturing batch. CONCLUSIONS: We reported an outbreak of R. pickettii BSIs in highly immunocompromised patients due to contaminated intravascular solution, which was rapidly controlled by infection control measures. Vigilant surveillance by hospital infection control teams and prompt investigation to identify the source of nosocomial infections are crucial to stop an outbreak.