Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection.

Molecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor™ Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, Istanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor™ SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9%) were positive and 98 (22.1%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor™. Antigen Rapid Test Kit was 80.3% whereas specificity was found to be 87.8%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7%, while it increased to 95.7% in samples 20 ≤ Ct < 25 and reached 100% in samples with Ct values below 20. RapidFor™ SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.

Evaluation and comparison of eighteen SARS-CoV-2 antibody assays from seven different companies to assess its diagnostic role in SARS-CoV-2 infections.

The diagnostic performance of reverse transcriptase polymerase chain reaction (RT-PCR) decreases during the late acute stage of the corona virus disease (COVID-19) infection; hence, serological assays can be used for disease diagnosis in patients non-protected through vaccinations at this stage. The objective of this study was to assess the diagnostic accuracy of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody tests in current/past infections, determine proper testing time, and check the accuracy of cutoff values. In this study, 18 Ig (immunoglobulin) G, IgM, IgA, and total antibody serological assays were performed using 839 samples. Positive sera (n=132) were collected during the first 5 months after the patients were symptomatic and tested positive for the SARS-CoV-2 RT-PCR test; they were grouped as 0-10, 10-15, >15 days according to the symptom onset. Negative sera (N=707) were obtained from patients with lupus before the pandemic. The performance of IgG and total antibody assays was better than those of IgA, IgM, and IgA-IgM for all post-symptom groups except for 0-10 days, which showed lower Ig assay sensitivity. During 10-15 and >15 days, >70% sensitivity to IgA, IgM, IgM-IgA assays and lower sensitivity were noted, respectively. The sensitivities of IgG and total antibody assays for group C were slightly lower than that of group B. There were no significant differences, but there were higher correlations between the methods or antigenic structures. Receiving operating characteristics (ROC) analysis revealed better cutoff values. For the diagnosis of late acute/past SARS-CoV-2 infection, serological tests can be performed on unvaccinated patients showing symptoms for ≥10 days. SARS-CoV-2 IgG and total antibodies were better diagnostic markers than IgM, IgA, and IgM+IgA, which were restricted to group B.

Simple concentration method enables the use of gargle and mouthwash instead of nasopharyngeal swab sampling for the diagnosis of COVID-19 by PCR.

Since its emergence in December 2019, SARS-CoV-2 is causing one of the most devastating pandemics in human history. Currently, the most important method for definitive diagnosis of COVID-19 is identification of SARS-CoV-2 RNA in nasopharyngeal swab samples by RT-PCR. Nasopharyngeal swab sampling is a discomforting procedure sometimes with adverse effects, which also poses a risk for infection for the personnel performing the sampling. We have developed a new method for concentrating biological samples, which enabled us to use gargle and mouthwash samples to be used in RT-PCR, for the diagnosis of COVID-19, as an alternative to nasopharyngeal swab samples. We have analyzed nasopharyngeal and gargle and mouthwash samples, before and after concentration, of 363 patients by RT-PCR for the presence of SARS-CoV-2. Among 114 patients in which SARS-CoV-2 was identified in at least one of their samples, the virus was identified in 76 (66.7%), 67 (58.8%), and 101 (88.6%) of nasopharyngeal swab, gargle, and mouthwash samples before and after concentration, respectively. When concentrated by our new method, gargle and mouthwash samples can be used instead of nasopharyngeal samples in identification of SARS-CoV-2 by RT-PCR, with the same or better sensitivity. Eliminating the need for nasopharyngeal sampling will save the patients from an invasive and painful procedure and will lower the risk of infection for the healthcare personnel taking the sample. This easy sampling procedure may decrease the workload of hospitals, shorten the turnaround time of obtaining test results, and thus enable rapid isolation of infected patients.

Mesenchymal stem cell treatment in a critically ill COVID-19 patient: a case report.

An outbreak of a new coronavirus causing severe respiratory disease (COVID-19) was first reported in China and rapidly spread worldwide. Clinical spectrum changes from asymptomatic infection to severe illness and even death, and no specific treatment is currently available. A range of antiviral, antimalarial and antibiotic agents are being used. We report a case of a COVID-19 patient that progressed to severe disease requiring intubation and intensive care. We performed mesenchymal stem cell (MSC) transplantation considering the signs showing persistent excessive immune response and deterioration despite all supportive and drug therapies. The two rounds of transplantation did not result in any severe complications and was well-tolerated. Clinical signs were improved. The use of MSC therapy may be considered for compassionate use in selected patients.

Clinical Signs and Diagnostic Tests in Acute Respiratory Infections.

OBJECTIVES: To evaluate clinical manifestations of acute respiratory system infectious diseases and specific tests for causative agents in pediatric patients. METHODS: The authors evaluated children aged 0-16 y with clinical symptoms of acute respiratory tract infections who were administered rapid strep A test and/or throat culture test and/or respiratory viral panel test, from February 2012 through January 2013 at pediatric department of Acibadem Maslak Hospital, Turkey. RESULTS: A total of 1654 patients were evaluated; 45.9 % were girls, 54.1 % were boys. Absence of cough and presence of headache were higher in the patients >6 y of age (p 0.0001, p 0.002 respectively). Positive respiratory viral panel test was higher in the patients <2 y of age (p 0.002). Both positive rapid strep A test and positive throat culture test were higher in the patients >6 y of age (p 0.0001). Positivity of rapid strep A or throat culture test were not observed in children <2 y of age. CONCLUSIONS: A clinician should mostly consider viral infections in the etiology of acute respiratory infections in children under 2 y of age and there is no need to rush for the use antibiotherapy. Bacterial etiology should be frequently considered after 6 y of age and rapid use of antibiotherapy is essential to avoid the complications.

Comparison of brucellar and tuberculous spondylodiscitis patients: results of the multicenter "Backbone-1 Study".

BACKGROUND CONTEXT: No direct comparison between brucellar spondylodiscitis (BSD) and tuberculous spondylodiscitis (TSD) exists in the literature. PURPOSE: This study aimed to compare directly the clinical features, laboratory and radiological aspects, treatment, and outcome data of patients diagnosed as BSD and TSD. STUDY DESIGN: A retrospective, multinational, and multicenter study was used. PATIENT SAMPLE: A total of 641 (TSD, 314 and BSD, 327) spondylodiscitis patients from 35 different centers in four countries (Turkey, Egypt, Albania, and Greece) were included. OUTCOME MEASURES: The pre- and peri- or post-treatment spinal deformity and neurologic deficit parameters, and mortality were carried out. METHODS: Brucellar spondylodiscitis and TSD groups were compared for demographics, clinical, laboratory, radiological, surgical interventions, treatment, and outcome data. The Student t test and Mann-Whitney U test were used for group comparisons. Significance was analyzed as two sided and inferred at 0.05 levels. RESULTS: The median baseline laboratory parameters including white blood cell count, C-reactive protein, and erythrocyte sedimentation rate were higher in TSD than BSD (p<.0001). Prevertebral, paravertebral, epidural, and psoas abscess formations along with loss of vertebral corpus height and calcification were significantly more frequent in TSD compared with BSD (p<.01). Surgical interventions and percutaneous sampling or abscess drainage were applied more frequently in TSD (p<.0001). Spinal complications including gibbus deformity, kyphosis, and scoliosis, and the number of spinal neurologic deficits, including loss of sensation, motor weakness, and paralysis were significantly higher in the TSD group (p<.05). Mortality rate was 2.22% (7 patients) in TSD, and it was 0.61% (2 patients) in the BSD group (p=.1). CONCLUSIONS: The results of this study show that TSD is a more suppurative disease with abscess formation requiring surgical intervention and characterized with spinal complications. We propose that using a constellation of constitutional symptoms (fever, back pain, and weight loss), pulmonary involvement, high inflammatory markers, and radiological findings will help to differentiate between TSD and BSD at an early stage before microbiological results are available.

Atypical pyogenic brain abscess evaluation by diffusion-weighted imaging: diagnosis with multimodality MR imaging.

Whether a brain abscess is apparent by imaging depends on the stage of the abscess at the time of imaging, as well as the etiology of the infection. Because conventional magnetic resonance imaging (MRI) is limited in its ability to distinguish brain abscesses from necrotic tumors, advanced techniques are required. The management of these two disease entities differs and can potentially affect the clinical outcome. We report a case having atypical imaging features of a pyogenic brain abscess on advanced MRI, in particular, on diffusion-weighted and perfusion imaging, in a patient with osteosarcoma undergoing chemotherapy.

Tuberculous meningitis presenting with nonconvulsive status epilepticus.

Nonconvulsive status epilepticus (NCSE) is an enduring epileptic condition characterized by alteration in consciousness and continuous ictal discharges on the EEG. Various etiologies have been reported. We describe the case of a 66-year-old woman with altered mental status who was diagnosed with NCSE. A workup to explain the etiology revealed tuberculous meningitis (TBM) with increased cerebrospinal fluid protein and positive tuberculous DNA polymerase chain reaction and interferon-γ assay tests. She was treated according to the status epilepticus protocol with a four-drug anti-tuberculosis regimen to which she responded. TBM is a serious disease with insidious presentation and still constitutes a diagnostic challenge with its various presentations. Among the many presentations of tuberculosis, clinicians should consider NCSE.

Carbapenem-resistant Escherichia coli and Klebsiella pneumoniae isolates from Turkey with OXA-48-like carbapenemases and outer membrane protein loss.

Treatment options are limited in infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, with carbapenems generally preferred. Disturbingly, however, carbapenem-resistant strains are emerging worldwide. Here we report two clinical isolates, one Escherichia coli and one Klebsiella pneumoniae, each with high-level carbapenem resistance (imipenem minimum inhibitory concentration of 32 microg/mL). They were isolated following imipenem therapy from two hospital patients who had received imipenem therapy in different regions of Turkey. Both isolates produced OXA-48-like carbapenemases, enzymes so far reported only from Turkey. Both isolates also had group 1 CTX-M-type ESBLs and had lost major outer membrane proteins. OXA-48-like carbapenemases appear to be scattered in Turkey and surveillance to determine their prevalence is warranted.

CTX-M-3 type beta-lactamase producing Shigella sonnei isolates from pediatric bacillary dysentery cases.

In this study, 153 clinical isolates of Shigella were screened for extended-spectrum beta-lactamase (ESBL) production by double-disk synergy test. After being confirmed by the combined disk-test and inhibitor-combined E-test strips, all positive isolates were tested for the bla gene by PCR and the enzymes by isoelectric focusing. DNA sequencing of PCR products revealed that five Shigella sonnei isolates had CTX-M-3 type ESBL enzymes. All of them were resistant to ampicillin, sulfamethoxazole and cefotaxime but susceptible to ofloxacin and ceftazidime. All isolates displayed identical patterns in pulsed-field gel electrophoresis and enterobacterial repetitive intergenic consensus PCR. This study reports multidrug-resistant (MDR) S. sonnei isolates producing CTX-M-3 type ESBL from successive pediatric bacillary dysentery patients, indicating widespread and rapid spread of CTX-M type ESBL in Shigella spp. To counter this emerging threat to public health, the surveillance of CTX-M type beta-lactamases should be considered, together with measures designed to prevent outbreaks of MDR Shigella in the community.

Rapid 4 to 6 hour detection of extended-spectrum beta-lactamases in a routine laboratory.

With the growing frequency of extended-spectrum beta-lactamases (ESBL) among Enterobacteriaceae, treatment of Gram-negative nosocomial infections requires rapid and reliable detection of this enzyme. Quicolor agar (QC agar) (Salubris Inc., Massachusetts, USA) is a novel chromogenic agar medium changing colour within 4 to 6 h due to the metabolic activity of growing bacteria. This study investigated the use of QC agar compared to Mueller Hinton agar (MH) for the detection of ESBL using disk diffusion and E-test. 100 Enterobacteriaceae isolated at Hacettepe University Hospital, of which 50 were predetermined to be ESBL positive and 50 as negative using the CLSI disk diffusion ESBL (phenotypic confirmatory test) criteria. For disk diffusion and E-test, cefotaxime+/-clavulanate (CT/CTL) and ceftazidime+/-clavulanate (TZ/TZL) were used, and for E-test, cefepime+/-clavulanate (PM/PML) was also used. QC agar rapid ESBL results for all strains were in agreement with the standard overnight procedure. All 50 ESBL positives were detected by both methods. For the 50 ESBL negatives, QC agar rapid results from E-test and disk diffusion were in complete accordance with the overnight MH results. Moreover, E-test detected 8 additional ESBL positive strains that disk diffusion missed. For disk diffusion, CT/CTL alone detected all 50 ESBL positives while TZ/TZL alone missed 5 ESBL positives. E-test CT/CTL alone confirmed all 50 ESBL positives and identified 4 additional ESBL-positive strains. When used together, E-test CT/CTL, TZ/TZL and PM/PML identified a total of 58 ESBL positives among the 100 strains tested. QC agar can be used for rapid and reliable ESBL detection within 4 to 6 h, using disk diffusion and E-test ESBL reagents. This rapid method should be further validated using genotype characterized ESBL and other beta-lactamase positive strains.

Evaluation of a chromogenic medium for rapid detection of extended spectrum beta-lactamase producing Salmonella spp.

BACKGROUND & OBJECTIVES: Salmonella spp. resistant to second- and third-generation cephalosporins and related antibiotics by production of various extended-spectrum beta-lactamases (ESBLs) are on the rise in Turkey. Early detection of ESBL producing Salmonella is important to institute appropriate treatment in time. In this study rapid detection of ESBL production among clinical isolates of Salmonella was evaluated using double-disk synergy test in a new chromogenic medium. The colour of the medium changes from red to yellow with bacterial growth and red circular inhibition zones are produced around disks containing antibacterials. METHODS: A total of 182 clinical isolates of Salmonella were evaluated in this study. The presence of ESBLs in clinical isolates was determined by double-disk synergy test using Mueller-Hinton (MH) agar and Quicolor E&S agar plates. RESULTS: Six isolates were shown to harbour ESBL enzymes with double disk synergy test by Mueller Hinton agar. The same results were obtained using Quicolor E&S agar after 4-6 h by changing its colour in response to the metabolic activity of growing bacteria. INTERPRETATION & CONCLUSION: Our findings showed that with this new medium, the results can be evaluated rapidly within 4-6 h and the enhancement of inhibition zones can be easily detected with the colour changes thus enabling the treating physician to institute the right treatment regimen immediately.

Molecular genotyping of methicillin-resistant Staphylococcus aureus strains in a teaching hospital in Turkey.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the major causes of nosocomial infections in our hospital. Therefore, we aimed to characterize MRSA isolates phenotypically from patients with nosocomial infections at Cumhuriyet University Hospital between December, 1999, and June, 2001, in Sivas by analysis of antibiotic patterns and genotypically using pulsed-field gel electrophoresis (PFGE) and repetitive element sequence-based polymerase chain reaction (rep-PCR). Forty-three nosocomial isolates were collected from various wards. All isolates were resistant to penicillin, tetracycline, oxacillin, and gentamicin. By rep-PCR and by separation of SmaI fragments of genomic DNA using PFGE, one major type (eight subtypes with PFGE) was identified among the strains. This clone was found to be different than some clones such as Iberian, Brazilian, and a major clone that was found in another Turkish University Hospital in Ankara. According to our results, there is a major MRSA clone with a potential to spread in our hospital. Infection control measures should be directed toward restricting the further spread of this clone. Therefore, in accordance with these findings, a surveillance culturing program should be established.

Factors affecting the antibacterial effects of Nd:YAG laser in vivo.

BACKGROUND AND OBJECTIVES: One of the main advantages of laser surgery is it's bactericidal effect which reduces the risk of postoperative infections. Several study designs have been set to investigate this effect. Aim of this study was to research if the bactericidal effect of laser tool was affected from several factors in vitro studies. STUDY DESIGN/MATERIALS AND METHODS: To determinate and investigate the bactericidal effect of laser in an original model, alpha-hemolytic streptococcus, Bacterioides fragilis, Neisseria, Streptococcus salivarius, Staphylococcus aureus, and Candida albicans were prepared in 10(4), 10(6) and 10(8) inoculum and placed in Mueller-Hinton Broth which have five different proportions of sheep blood. Samples which exposed with various energy levels of Nd:YAG laser were spread on agar plates, and at the end of an incubation time the colonization counted comparatively. The lowest energy level without colonization was accepted as minimal bactericidal energy level. RESULTS: Highest minimum bactericidal energy level is used for alpha-hemolytic streptococcus and lowest values for neisseria. Bactericidal effect decreased on suspensions, of which population of microorganisms are high and hemoglobin concentration was high in the broth. CONCLUSIONS: These findings suggest that the Nd:YAG laser has a higher bactericidal effect when sheep blood is added to the media. Factors like population and type of bacteria in the irradiated suspension affect minimum bactericidal energy level.

[Comparison of routine sensitivity tests and mecA gene analysis for determination of methicillin resistance in Staphylococcus aureus isolates]. / Staphylococcus aureus izolatlarinin metisilin direncinin saptanmasinda rutin duyarlilik testleri ve mecA gen analizi sonuçlarinin karsilastirilmasi.

Currently, oxacillin disk diffusion test is the most frequently employed method to detect the methicillin resistance of Staphylococcus aureus isolates. However, due to some of the test conditions, errors may occur during the detection of heteroresistant bacteria. It is now widely accepted that lower incubation temperatures (< or = 35 degrees C) and media with a NaCl concentration of 2-4%, could facilitate detection. In our study, methicillin (oxacillin) susceptibilities of 125 S. aureus isolates were determined by the disk diffusion and microdilution tests as defined by National Committee for Clinical Laboratory Standards (NCCLS), and the results were compared with those of mecA gene analysis. In the routine susceptibility tests, 75 isolates were found to be methicillin resistant (MRSA), whereas 50 were found to be susceptible (MSSA). Various induction tests were performed to investigate the heterogeneous resistance among methicillin-susceptible isolates. These induction tests showed that the MIC values of seven isolates reached to the resistant levels, therefore these isolates should be accepted as "borderline oxacillin resistant S. aureus" isolates lacking the mecA gene. The susceptibility tests and mecA gene analysis of the remaining isolates yielded compatible results. In conclusion, susceptibility tests, when performed according to NCCLS recommendations, are found to be reliable and decisive, for the detection of methicillin resistance of S. aureus.

Clinical importance of extended-spectrum beta-lactamase (PER-1-type)-producing Acinetobacter spp. and Pseudomonas aeruginosa strains.

Recently, an extended-spectrum beta-lactamase (PER-1) was found to be disseminated among Acinetobacter spp. and Pseudomonasaeruginosa isolates in Turkey. A population-based cohort study was conducted to elucidate predictive mortality factors in patients with nosocomial infections caused by Acinetobacter spp. and P. aeruginosa, with particular reference to PER-1-type extended-spectrum beta-lactamase (ESBL) production. The study group comprised 16 and 21 non-survivors and 82 and 126 survivors in cohorts infected with Acinetobacter and P. aeruginosa, respectively. In the Acinetobacter-infected cohort, nosocomial pneumonia, hypotension and infection with a PER-positive isolate were independent predictors of mortality. In the P. aeruginosa-infected cohort, impaired consciousness, a PER-positive isolate, male sex and (with a negative relative risk) urinary tract infection were independent predictors of death. This study demonstrated the relationship of PER-1-type ESBL-producing Acinetobacter spp. and P. aeruginosa with poor clinical outcome.