Performance comparison of BD Phoenix CPO detect panel with Cepheid Xpert Carba-R assay for the detection of carbapenemase-producing Klebsiella pneumoniae isolates.

BACKGROUND: We aimed to compare the performance of carbapenemase classification in carbapenem-resistant Klebsiella pneumoniae (CRKP) obtained using the BD Phoenix CPO Detect panel (CPO panel) and Cepheid Xpert Carba-R assays. We analyzed 55 CRKP strains from clinical specimens collected between November 2020 and November 2022. The CPO panel was used to detect both antibiotic susceptibility and phenotypic carbapenemase classes, while Xpert Carba-R was employed to identify KPC, NDM, VIM, OXA-48, and IMP genes. Due to the limited availability of molecular kits, we arbitrarily selected 55 isolates, identified as carbapenemase-producing according to the CPO panel and with meropenem minimum inhibitory concentration values > 8 mg/L. RESULTS: According to the Xpert Carba-R assay, 16 of the 55 isolates (29.1%) were categorised as Ambler Class A (11 of which matched CPO panel Class A identification); three isolates (5.5%) were identified as Class B and 27 isolates (49.1%) as Class D (in both cases consistent with CPO panel B and D classifications). A further eight isolates (14.5%) exhibited multiple carbapenemase enzymes and were designated as dual-carbapenemase producers, while one isolate (1.8%) was identified as a non-carbapenemase-producer. The CPO panel demonstrated positive and negative percent agreements of 100% and 85.7% for Ambler Class A, 100% and 100% for Class B, and 96.4% and 100% for Class D carbapenemase detection, respectively. CONCLUSION: While the CPO panel's phenotypic performance was satisfactory in detecting Class B and D carbapenemases, additional confirmatory testing may be necessary for Class A carbapenemases as part of routine laboratory procedures.

An evaluation of a Stenotrophomonas maltophilia outbreak due to commercial arterial blood gas collection kit.

BACKGROUND: Stenotrophomonas maltophilia is a gram-negative bacterium that can cause hospital infections and outbreaks within hospitals. This study aimed to evaluate an outbreak of Stenotrophomonas maltophilia, caused by ready-to-use commercial syringes containing liquid lithium and heparin for arterial blood gas collection in a university hospital. METHODS: Upon detecting an increase in Stenotrophomonas maltophilia growth in blood cultures between 15.09.2021 and 19.11.2021, an outbreak analysis and a case-control study (52 patients for the case group, 56 patients for the control group) were performed considering risk factors for bacteremia. Samples from possible foci for bacteremia were also cultured. Growing bacteria were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The genetic linkage and clonal relationship isolates were investigated with pulsed-field gel electrophoresis (PFGE) in the reference laboratory. RESULTS: In the case-control study, the odds ratio for the central venous catheter [3.38 (95% confidence interval [CI]: 1.444, 8.705 ; p = 0.006)], for surgery [3.387 (95% confidence interval [CI]: 1.370, 8.373 ; p = 0.008)] and for arterial blood gas collection history [18.584 (95% confidence interval [CI]:4.086, 84.197; p < 0.001)] were identified as significant risk factors. Stenotrophomonas maltophilia growth was found in ready-to-use commercial syringes used for arterial blood gas collection. Molecular analysis showed that the growths in the samples taken from commercial syringes and the growths from blood cultures were the same. It was decided that the epidemic occurred because the method for sterilization of heparinized liquid preparations were not suitable. After discontinuing the use of the kits with this lot number, the outbreak was brought under control. CONCLUSIONS: According to our results, disposable or sterile medical equipment should be included as a risk factor in outbreak analyses. The method by which injectors containing liquids, such as heparin, are sterilized should be reviewed. Our study also revealed the importance of the cooperation of the infection control team with the microbiology laboratory.

Evaluation of the combination treatments with intravenous fosfomycin for carbapenem-resistant Klebsiella pneumoniae.

OBJECTIVE: The aim of this study was to evaluate the combination treatments with intravenous fosfomycin for carbapenem-resistant Klebsiella pneumoniae infections in a tertiary-care center. METHODS: Between December 24, 2018 and November 21, 2022, adult patients diagnosed with bloodstream infection or ventilator-associated pneumonia due to culture-confirmed carbapenem-resistant Klebsiella pneumoniae in the anesthesiology and reanimation intensive care units were investigated retrospectively. RESULTS: There were a total of 62 patients fulfilling the study inclusion criteria. No significant difference was recorded in 14- and 30-day mortality among different types of combination regimens such as fosfomycin plus one or two antibiotic combinations. Hypokalemia (OR:5.651, 95%CI 1.019-31.330, p=0.048) was found to be a significant risk factor for 14-day mortality, whereas SOFA score at the time of diagnosis (OR:1.497, 95%CI 1.103-2.032, p=0.010) and CVVHF treatment (OR:6.409, 95%CI 1.395-29.433, p=0.017) were associated with 30-day mortality in multivariate analysis. CONCLUSION: In our study, high mortality rates were found in patients with bloodstream infection or ventilator-associated pneumonia due to carbapenem-resistant Klebsiella pneumoniae, and no significant difference was recorded in 14- and 30-day mortality among different types of combination regimens such as fosfomycin plus one or two antibiotic combinations.

Evaluation of the combination treatments with intravenous fosfomycin for carbapenem-resistant Klebsiella pneumoniae

SUMMARY OBJECTIVE: The aim of this study was to evaluate the combination treatments with intravenous fosfomycin for carbapenem-resistant Klebsiella pneumoniae infections in a tertiary-care center. METHODS: Between December 24, 2018 and November 21, 2022, adult patients diagnosed with bloodstream infection or ventilator-associated pneumonia due to culture-confirmed carbapenem-resistant Klebsiella pneumoniae in the anesthesiology and reanimation intensive care units were investigated retrospectively. RESULTS: There were a total of 62 patients fulfilling the study inclusion criteria. No significant difference was recorded in 14- and 30-day mortality among different types of combination regimens such as fosfomycin plus one or two antibiotic combinations. Hypokalemia (OR:5.651, 95%CI 1.019-31.330, p=0.048) was found to be a significant risk factor for 14-day mortality, whereas SOFA score at the time of diagnosis (OR:1.497, 95%CI 1.103-2.032, p=0.010) and CVVHF treatment (OR:6.409, 95%CI 1.395-29.433, p=0.017) were associated with 30-day mortality in multivariate analysis. CONCLUSION: In our study, high mortality rates were found in patients with bloodstream infection or ventilator-associated pneumonia due to carbapenem-resistant Klebsiella pneumoniae, and no significant difference was recorded in 14- and 30-day mortality among different types of combination regimens such as fosfomycin plus one or two antibiotic combinations.

Investigation of the Defective Growth Pattern and Multidrug Resistance in a Clinical Isolate of Candida glabrata Using Whole-Genome Sequencing and Computational Biology Applications.

Candida glabrata is increasingly isolated from blood cultures, and multidrug-resistant isolates have important implications for therapy. This study describes a cholesterol-dependent clinical C. glabrata isolate (ML72254) that did not grow without blood (containing cholesterol) on routine mycological media and that showed azole and amphotericin B (AmB) resistance. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and whole-genome sequencing (WGS) were used for species identification. A modified Etest method (Mueller-Hinton agar supplemented with 5% sheep blood) was used for antifungal susceptibility testing. WGS data were processed via the Galaxy platform, and the genomic variations of ML72254 were retrieved. A computational biology workflow utilizing web-based applications (PROVEAN, AlphaFold Colab, and Missense3D) was constructed to predict possible deleterious effects of these missense variations on protein functions. The predictive ability of this workflow was tested with previously reported missense variations in ergosterol synthesis genes of C. glabrata. ML72254 was identified as C. glabrata sensu stricto with MALDI-TOF, and WGS confirmed this identification. The MICs of fluconazole, voriconazole, and amphotericin B were >256, >32, and >32 µg/mL, respectively. A novel frameshift mutation in the ERG1 gene (Pro314fs) and many missense variations were detected in the ergosterol synthesis genes. None of the missense variations in the ML72254 ergosterol synthesis genes were deleterious, and the Pro314fs mutation was identified as the causative molecular change for a cholesterol-dependent and multidrug-resistant phenotype. This study verified that web-based computational biology solutions can be powerful tools for examining the possible impacts of missense mutations in C. glabrata. IMPORTANCE In this study, a cholesterol-dependent C. glabrata clinical isolate that confers azole and AmB resistance was investigated using artificial intelligence (AI) technologies and cloud computing applications. This is the first of the known cholesterol-dependent C. glabrata isolate to be found in Turkey. Cholesterol-dependent C. glabrata isolates are rarely isolated in clinical samples; they can easily be overlooked during routine laboratory procedures. Microbiologists therefore need to be alert when discrepancies occur between microscopic examination and growth on routine media. In addition, because these isolates confer antifungal resistance, patient management requires extra care.

An outbreak of Ralstonia insidiosa bloodstream infections caused by contaminated heparinized syringes.

INTRODUCTION: Ralstonia insidiosa, a gram-negative waterborne bacteria able to survive and grow in any type of water source, can cause nosocomial infections, and are considered emerging pathogens of infectious diseases in hospital settings. In this study, we report an outbreak of R. insidiosa at our center related to contaminated heparinized syringes. MATERIAL AND METHODS: The present study was conducted in a tertiary care university hospital in Turkey. An outbreak analysis was performed between September 2021 and December 2021. Microbiological samples were obtained from environmental sources and from patient blood cultures. Species identification was performed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). To investigate the clonality of strains, all confirmed isolates were sent to the National Reference Laboratory and pulsed-field gel electrophoresis (PFGE) was used to perform molecular typing. RESULTS: Seventeen R. insidiosa isolates were identified from the blood cultures of 13 patients from various wards and intensive care units. Isolates from seven patient blood cultures and two heparinized blood gas syringes were characterized by PFGE. All isolates were found to belong to the same clone of R. insidiosa. CONCLUSION: R. insidiosa was identified as the cause of a nosocomial infection outbreak in our hospital, which was then rapidly controlled by the infection-control team. When rare waterborne microorganisms grow in blood or other body fluid cultures, clinicians and the infection-control team should be made aware of a possible outbreak.

Evaluation of serum indirect haemagglutination test results of suspected cystic echinococcosis cases from 2009-2017.

OBJECTIVE: This study aims to evaluate the serological, radiological and epidemiological analysis of suspected cystic echinococcosis patients, and to assess the positivity rate in the region. Methods: The retrospective study was conducted at Bursa Uludag University Hospital, Turkey and comprised data from January 2009 to December 2017 related to patients of either gender with suspected cystic echinococcosis who underwent indirect haemagglutination testing. Demographic and clinical data of patients who tested positive were analysed. Statistical analysis was done using SPSS 23. RESULTS: Of the 3910 patients with a mean age of 41.6±19.35 years (range: 0-93 years) who underwent indirect haemagglutination testing, 692(17.7%) tested positive; 390(56.4%) females, and 302(43.6%) males. The highest seropositivity rate 107(15.5%) was observed in 2011, followed by 104(15%) in 2016. Seropositive cases were predominantly seen in those aged 40-49 years 131 (18.9%), followed by those aged 50-59 years 124 (17.9%). CONCLUSIONS: Cystic echinococcosis was found to be a public health problem in South Marmara region of Turkey.

Particle scattering during otolaryngological examinations.

PURPOSE: We aimed to analyze particle scattering during common otolaryngology examination procedures which are associated with aerosol-generating procedures. MATERIALS AND METHODS: This study was conducted with 109 volunteer patients who have participated between October 2020 and January 2021. We measured aerosol and droplet production during oropharyngeal examination, anterior rhinoscopy, rigid nasopharyngoscopy, and rigid laryngoscopy. Measurements were calculated at the beginning of the examinations and during the otolaryngological examination procedures. RESULTS: There was no significant increase when we compared the particle scattering in each examination procedure with the basal measurements. But at the end of all examination methods for each patient, there was a significant increase at each micrometer. When all examination methods are compared with each other, particle increases in the oropharyngeal examination with larger particle sizes than 0,5 µm were found to be higher than other examination methods. We analyzed six patients' measurements, who coughed, gagged, or sneezed during the nasal endoscopy procedure, there was a significant increase in terms of 0,3 µm particle scattering. CONCLUSION: When all examination methods are performed together, there is a significant particle increase in all particle sizes in the examination room at the end of the examinations. This causes otolaryngologists to be exposed to a significant particle increase at each micrometer. Because of this reason, otolaryngologists should be careful and should wear personal protective equipment while examining patients.

Acanthamoeba Keratitis and Acanthamoeba Conjunctivitis: A Case Report.

Acanthamoeba species are vision-threatening agents by causing cornea infections known as Acanthamoeba keratitis. A 5 year-old kid with the complaints of erythema, eyelid edema, inflammation, limitation of eye movements in the right eye, and having no history of wearing contact lenses or trauma, was diagnosed of Acanthamoeba conjunctivitis through laboratory examinations in the Ophthalmology clinic. The visual sharpness of the patient improved after the treatment. A 44 year-old female patient suffering from pain, stinging, irritation, and inability to see in the left eye with the history of wearing contact lenses or trauma was diagnosed of Acanthamoeba keratitis through laboratory examinations. The agent was isolated and identified as "A. castellani" in the Genotype "T2". Examination of the left eye on the 15th day of treatment indicated that all complaints disappeared except for the cataract originated visual loss. However, the first diagnosis of Acanthamoeba keratitis appeared in the literature on a case with no history of wearing contact lenses and trauma it is found to be attention grabbing. We think that Acanthamoeba should not be ignored among microbial agents that cause eye infection with or without trauma and contact lens usage history.

Three Pentatrichomonas hominis Cases Presenting with Gastrointestinal Symptoms.

We aimed to demonstrate that Pentatrichomonas hominis may also be an agent, although rare, in diarrheal episodes. Stool samples were first examined macroscopically and microscopically during routine parasitological examinations. Samples were then evaluated by Native-Lugol and formol-ethyl acetate centrifugation method. To exclude other pathogenic bacterial agents, a bacteriological culture method was applied. Samples were evaluated using a qualitative immunochromatographic test kit for rotavirus and adenovirus. We presented three cases of 77-year-old and 10-year-old male and 9-year-old female patients. Cases 1 and 2 were admitted to the hospital with complaints of diarrhea, abdominal pain, and weakness in July 2013. Leukocytes and active P. hominis trophozoites were detected. No bacterial and other parasitic and viral agents were found in their stool specimens. Oral metronidazole treatments were administered to the patients. In Case 3, P. hominis trophozoites were detected in the cellophane band in the plastic locked bag which could survive for 48 hduring a field survey in May 2012. Case 3 was contacted and advised to visit a pediatrician. P. hominis is a rare parasitic zoonosis, and we believe that it should not be ignored among diarrheal agents.

A Clinical Scoring System for Diagnosis of Ocular Demodicosis.

BACKGROUND Demodex may cause chronic and refractory blepharitis with associated ocular surface problems, and its diagnosis and treatment can be quite challenging. In this study, our aim was to assess the efficacy of tea tree oil in Demodex treatment on caucasian patients in an industrialized region of Turkey, and to develop a systematic scoring system for extremely accurate diagnosis in the absence of advanced facilities. MATERIAL AND METHODS Charts of 412 patients with blepharitis were reviewed. A group of 39 out of 412 cases were identified as chronic and treatment-refractory, and therefore were enrolled in this study. Eyelashes from each of the lower and upper eyelids of both eyes were evaluated at ×40 and ×100 magnification using light microscopy. Treatment was started with 4% tea tree oil eyelid gel and 10% eyelash shampoo. Symptoms and findings were scored according to the most common complaints. RESULTS The mean age of the patients was 54.1±15.4 years. Seventeen (43.5%) patients were male and 22 (56.5%) patients were female. In 30 out of the 39 patients (76.9%) D. folliculorum was detected. Symptoms disappeared in 25 patients. The mean score of patients who were Demodex-negative was 2.7±1.0, and the mean score of patients who were Demodex-positive was 3.8±1.6 (p=0.047). Ninety-four percent of those with a score of 4 and over were found to be Demodex-positive (p=0.025). CONCLUSIONS Treatment with tea tree oil can be successful. If there is no facility to identify Demodex under light microscopy, we recommend starting treatment for patients who have scores of 4 and over using the scoring chart developed in this study.

Subtype distribution of Blastocystis spp. isolated from children in Eskisehir, Turkey.

Blastocystis spp. is the most common enteric protist found in human feces. The pathogenic role of Blastocystis remains controversial and it has been suggested that the symptomatology of Blastocystis is associated with its subtypes (ST). However, only few studies have investigated the relationship between the symptomatology and subtypes of Blastocystis in children. This study aimed to investigate the prevalence of Blastocystis in children aged 3 to 13years with or without gastrointestinal complaints and determine the distribution of the subtypes of Blastocystis. A total of 303 stool samples obtained from symptomatic (n=84) and asymptomatic (n=219) children were included in the study. The presence of Blastocystis was investigated using native-lugol examination, trichrome staining and real-time PCR method. Using the real-time PCR method, 115 samples were found positive for Blastocystis. Subtyping was successfully performed on 46 samples using sequenced-tagged site (STS) primers and PCR. The remaining 69 samples could not be subtyped. The most frequently detected subtype was ST3 (43.4%) followed by ST1 (26.1%), ST4 (10.9%) and ST2 (8.7%). The mixed subtypes were identified in five samples (10.9%) as; ST1+ST3 (n=3), ST1+ST2 (n=1) and ST2+ST3 (n=1). None of the samples had ST5, ST6 or ST7. No statistically significant difference was found between the symptomatic and asymptomatic groups in terms of the Blastocystis positivity and the distribution of subtypes (p>0.05). To our knowledge, this is the first study to investigate the subtype distribution of Blastocystis in children in Turkey and the results are in agreement with the related data available in Turkey.

[Comparison of direct microscopy, culture, ELISA and molecular methods for diagnosis of Entamoeba histolytica]. / Entamoeba histolytica'nin tanisinda direkt mikroskopi, kültür, ELISA ve moleküler yöntemlerin karsilastirilmasi

Amebiasis, a parasitic infection caused by Entamoeba histolytica, is one of the most common parasitic infections worldwide. Since it is still an important public health problem in developing countries, rapid differential diagnosis of amebiasis is crucial in terms of treatment. The most frequently used method for laboratory diagnosis is direct microscopy, however more reliable and specific methods are needed in order to differentiate the apathogenic Entamoeba dispar under the microscope. This study was conducted to compare the results of different methods namely, direct microscopy, culture, ELISA and PCR for the detection of E.histolytica in stool samples and to evaluate the performances of those methods. A total of 1049 stool samples collected from pediatric and adult patients who were admitted to hospital with diarrhea complaint between January 2011-March 2013, and randomly selected samples from primary school children, were included in the study. Direct microscopic examination was performed by native-lugol, physiological saline, modified formol-ethyl acetate sedimentation and trichrome staining methods. The stool samples were also inoculated into TYI-S-33 media for axenic cultivation of amoeba. The presence of amebic antigens in the samples were screened by a commercial ELISA kit (TechLab, E.histolytica II, USA). For the molecular diagnosis, a multiplex tandem real-time PCR (MT-PCR) kit (AusDiagnostics Pty Ltd, Australia) was used, after the extraction of DNAs with QIAamp DNA Stool Mini Kit (Qiagen, USA). A total of 354 samples which could be evaluated by all of the methods, were included in the study. Of the 354 stool samples, 84 (23.7%) were found E.histolytica/E.dispar positive by direct microscopy, 61 (17.2%) by trichrome staining, 46 (12.9%) by culture, 31 (8.7%) by ELISA and 9 (2.5%) by MT-PCR. Of direct microscopy positive samples 54.7% (46/84) were also positive with trichrome staining, 39.3% (33/84) with culture, 15.5% (13/84) with ELISA and 7.1% (6/84) with MT-PCR methods. On the other hand, of the nine MT-PCR positive samples, six were positive with direct microscopy, four with trichrome staining and culture, and one with ELISA. It was remarkable that only one (0.3%) sample yielded positive results with all of the diagnostic methods used. When MT-PCR was considered as the reference method, the sensitivity and specificity values of direct microscopy, trichrome staining, culture and ELISA methods were estimated as; 66.7% and 77.4%, 44.4% and 83.5%, 44.4% and 87.8%, 11.1% and 91.3%, respectively. In conclusion, if the circumstances allow, the use of all methods in combination and evaluation together with the clinical symptoms seems to be the best approaches for the laboratory diagnosis of patients with amebiasis.