Objective: Each hour of delay in antibiotics administration increases mortality in sepsis. The aim of this study was to decrease the bacteria identification time to initiate appropriate antibiotic treatment as early as possible. Method: Tests were applied to 39 Gram negative bacteria isolated from blood cultures sent to our laboratory from intensive care units between November 2015- February 2016. The results of bacterial identification tested on both microarray and LFM methods were compared. Results: In the comparison of MALDI-TOF MS after sub-culture, MALDI-TOF after lysis centrifugation and microarray methods, sensitivity was determined as 82% (32/39) in LFM and as 87.1% (34/39) in the microarray method. All three methods had a concordance of 76.9% (30/39). Most common species identified in this study were Acinetobacter spp., Klebsiella spp. and Escherichia spp., and their Cohen’s Kappa coefficients for LFM and post-subculture MALDI were calculated as 0.715, 0.843, and 0.938, respectively. In addition, their BC-GN microarray and post-subculture MALDI concordance rates calculated with Cohen’s Kappa were 0.935, 0.753 and 0.938, respectively. Both methods showed good correlations with the post-culture MALDI method. Conclusion: Lysis centrifugation and microarray platforms decrease the identification time in blood culture processing successfully. Results of this study suggest that for the laboratories with MALDI-TOF mass spectrophotometer, the lysis filtration method is a fast and cost-effective method that may be suitable for routine procedures.

Giriş ve Amaç: Direkt etkili anti viral ilaçların kullanılmasıyla, hepatit C virüsü enfeksiyonunun tedavisinde başarı oranı %100’e yaklaşmıştır. Bununla birlikte, birçok hasta teşhis konulmayı beklemektedir. Biz mevcut çalışmada cerrahi öncesi hepatit C virüsü taraması yapılan hastalarda anti-hepatit C virüsü ve hepatit C virüs-RNA pozitifliğinin prevalansını belirlemeyi ve hastalığından habersiz olan hastaların oranını araştırmayı amaçladık. Gereç ve Yöntem: 2012-2015 yılları arasında cerrahi kliniklerinde anti-hepatit C virüsü pozitif saptanan hastalar, hepatit C virüs-RNA pozitifliği ve tedavi geçmişi açısından araştırıldı. Hepatit C virüs-RNA pozitifliği açısından hastane kayıtları tarandı. Tedavi bilgilerine Medula Sisteminden (Sosyal Güvenlik Sisteminden entegre bir veri tabanı) ulaşıldı. Tedavisiz anti-hepatit C virüsü pozitif hastalara telefonla pozitiflikten haberdar olup olmadıkları soruldu. Bulgular: 4 yıl boyunca 19627 hasta anti-hepatit C virüsü pozitifliği açısından tarandı. 158 hastada (%0.8) anti-hepatit C virüsü pozitif bulundu (76 erkek, 82 kadın; yaş: 58.2 ± 17.6). Hepatit C virüs-RNA 83 hastada bakılmıştı, 75 hastada hepatit C virüs-RNA testi yoktu. Ulaşılabilen 58 hastanın sadece 14’ü anti-hepatit C virüsü pozitif olduğunu biliyordu. Diğer 44 hasta gastroenteroloji veya enfeksiyon hastalıkları polikliniklerine başvurmaları konusunda uyarıldı. Sonuç: Cerrahi girişim uygulanan 19627 hastanın %0.8’inde anti-hepatit C virüsü genel Türkiye nüfusuna benzer oranda pozitif bulunmuştur. Hastaların neredeyse yarısında hepatit C virüs-RNA test edilmemiş ve çoğu hasta hepatit C virüsü-RNA’nın test edilmesi ve izlenmesi gerektiği bilgisine sahip değildir. Anti- hepatit C virüsünün cerrahi öncesi taranması yeni hastaların tespiti açısından yetersiz bulunmuştur.

Cytomegalovirus (CMV), is the most common cause among congenital infections and is the most seen etiology in long-term sensorineural hearing loss (SNHL) and neurological impairment. Congenital CMV infection (CCMV) was reported in 0.15-2.2% of live-borne neonates in studies from different countries. A significant proportion of infected infants are asymptomatic after birth and might only be detected by routine screening methods during the new born period. The aim of this study was to screen the saliva of live-born neonates with areal-time PCR based method for the detection of CCMV in our hospital. Saliva samples collected in half an hour after birth by dry dacron swabs and were evaluated for CMV DNA (Rt-PCR, Abbott Molecular USA) from 1000 babies born in Ege University Faculty of Medicine Hospital Obstetrics Clinic between October 2015-October 2017. For the confirmation of CCMV, saliva positive newborns were evaluated with the same method for CMV DNA from their urine or blood within 21 days. All newborns were screened for sensorineural hearing tests. Subjects were 497 girls (49.7%) and 503 boys (50.3%), with a mean weight of 3116.8 g and mean of 37.61 birth week. CMV DNA was positive in the saliva of 16 newborns (1.6%). Fourteen newborns were weakly positive for CMV DNA in their saliva and were not confirmed for CCMV infection. Congenital CMV was confirmed in only two (0.2%) with the CMV DNA results in urine and/or blood samples. One of the two newborns with CCMV was symptomatic and had a neurosensorial hearing loss. The other one was asymptomatic. Saliva samples, taken immediately after birth with a noninvasive and easy method for the detection of CMV DNA is very important for diagnosis of CCMV. Positive samples should be confirmed with CMV DNA in urine or blood samples of these newborns. In this study, detection of positivity in saliva samples that were confirmed with other samples of our newborn population for CCMV was 0.2%. The specific diagnosis for CCMV in newborns with a noninvasive and easy collecting sample is important to avoid sequelae and for public health concerns.

Introduction: In this study, it was aimed to investigate the prevalence of rotavirus and norovirus in patients admitted to Ege University Medical Faculty Hospital with acute diarrhea in a period of about one year. Materials and Methods: Between September 2016-August 2017, stool specimens were collected from 408 (341 pediatric and 67 adult) patients with acute diarrhea. The age range of the patients was between one month to 84 years (median: 3 years, mean: 10.25 years). Stool specimens were obtained from 206 (50.5%) outpatients and 202 (49.5%) inpatients. Stool specimens of patients with acute gastroenteritis were tested by real time PCR BD MAX (TM) Enteric Viral Panel (BD Diagnostics, Baltimore, MD, USA). This is an automated in vitro diagnostic test used for the qualitative detection of norovirus (genotype I and II) and rotavirus species in stool specimens. In this multiplex PCR system, viral nucleic acid is extracted from the specimen and it undergoes reverse transcription to generate complementary DNA (cDNA). The target cDNA is amplified using real time PCR and then analyzed to detect the presence or absence of each virus in the panel. Results: Of the 408 specimens tested, 223 (54.7%) were positive for one or more gastrointestinal viruses. Of the 223 positive samples, 184 (45.1%) were rotavirus, 26 (6.4%) were norovirus genotype II, 1 (0.2%) was norovirus genotype I, and 12 (2.9%) were rotavirus/ norovirus genotype II. Of the 223 positive samples, 121 (54.3%) were outpatients and 102 (45.7%) were inpatients (p= 0.094). The rate of positivity for the rotavirus in pediatric and adult groups were 48.4% (165/341) and 46.3% (31/67) (p= 0.751), respectively. Rotavirus positivity was highest in the months of March (75%), February (70%) and January (60%). Conclusion: In conclusion, the rate of positivity for rotavirus and norovirus were found as 48% and 10%, respectively in fecal samples sent to the laboratory by viral acute gastroenteritis, especially in winter. There was no significant difference between the positivity rates of the inpatients or outpatients and the positivity rates of the pediatric or adult patients.

Cytomegalovirus (CMV), is the most common cause among congenital infections and is the most seen etiology in long-term sensorineural hearing loss (SNHL) and neurological impairment. Congenital CMV infection (CCMV) was reported in 0.15-2.2% of live-borne neonates in studies from different countries. A significant proportion of infected infants are asymptomatic after birth and might only be detected by routine screening methods during the new born period. The aim of this study was to screen the saliva of live-born neonates with areal-time PCR based method for the detection of CCMV in our hospital. Saliva samples collected in half an hour after birth by dry dacron swabs and were evaluated for CMV DNA (Rt-PCR, Abbott Molecular USA) from 1000 babies born in Ege University Faculty of Medicine Hospital Obstetrics Clinic between October 2015-October 2017. For the confirmation of CCMV, saliva positive newborns were evaluated with the same method for CMV DNA from their urine or blood within 21 days. All newborns were screened for sensorineural hearing tests. Subjects were 497 girls (49.7%) and 503 boys (50.3%), with a mean weight of 3116.8 g and mean of 37.61 birth week. CMV DNA was positive in the saliva of 16 newborns (1.6%). Fourteen newborns were weakly positive for CMV DNA in their saliva and were not confirmed for CCMV infection. Congenital CMV was confirmed in only two (0.2%) with the CMV DNA results in urine and/or blood samples. One of the two newborns with CCMV was symptomatic and had a neurosensorial hearing loss. The other one was asymptomatic. Saliva samples, taken immediately after birth with a noninvasive and easy method for the detection of CMV DNA is very important for diagnosis of CCMV. Positive samples should be confirmed with CMV DNA in urine or blood samples of these newborns. In this study, detection of positivity in saliva samples that were confirmed with other samples of our newborn population for CCMV was 0.2%. The specific diagnosis for CCMV in newborns with a noninvasive and easy collecting sample is important to avoid sequelae and for public health concerns.

Amaç: Tüberküloz yüksek morbidite ve mortaliteye neden olması nedeniyle hızlı tanı ve tedavi gerektiren bir hastalıktır. Mycobacterium tuberculosis tanısında mikroskobik inceleme önemli bir yere sahiptir. Bu çalışmada, otomatize bir mikobakteri boyama sisteminin iki farklı protokolünün manuel floresan boyama yöntemi ile performans ve boyamanın kalitesi yönünden karşılaştırılması ve otomatize boyama sistemin çapraz kontaminasyon olmadan kullanılabileceğinin gösterilmesi

Kefir microencapsulation was optimised using Box–Behnken's response surface methodology. Product yield, moisture, water activity, bulk density, hygroscopicity, colour, wettability, solubility, particle size, pH, titratable acidity and microstructure were analysed. The viable counts of lactobacilli, lactococci and yeasts in the kefir microcapsules were found in the range of 9.03–9.92 log cfu/g, 9.56–11.51 log cfu/g and 3.09–5.90 log cfu/g, respectively. Sensory evaluation indicated that reconstituted samples obtained from microencapsulated kefir samples had high and/or full scores for flavour, appearance/colour and structure/texture. Addition of hydrocolloids to kefir before spray‐drying provided sufficient stability for the powdered product.

Viral Solunum Yolu Enfeksiyonlarının Tanısında Bir Multipleks PCR Yönteminin

Although ice cream is a good vehicle to convey probiotics to human hosts, probiotics are not stable in ice cream because of milieu conditions, species- and product-related properties. Studies on the incorporation of probiotics into ice cream have been conducted; however, there is a need for development of a production method in which probiotics maintain their viability and the physicochemical properties of ice cream are preserved. In this study, the aim was to compare the physicochemical properties of ice cream containing Lactobacillus acidophilus (ATCC 4356) that was incorporated using different methods, as well as to determine the viability of L. acidophilus in the samples. Ice cream was produced using three methods: method 1, ice cream mix was fermented with L. acidophilus prior to freezing; method 2, milk (10% of total milk used in the preparation of ice cream mix) was taken and subsequently fermented with L. acidophilus ; the fermented milk was introduced to the remaining ice cream mix prior to freezing; and method 3, L. acidophilus was added to the ice cream mix and the mix was not fermented with L. acidophilus prior to freezing. The viability of L. acidophilus in ice cream was better for methods 1 and 2 of ice cream production when compared to method 3. The viable counts after 90 days of storage were higher than the target level (>10 6 cfu.g −1 ) only in samples produced using methods 1 and 2.

Manufacture of ice cream using cold-and heat-adapted Lactobacillus acidophilus was studied. Temperature-time combinations at 4 degrees C for 18 h and at 45 degrees C for 15 min were set as the adaptation conditions for below and above the optimum growth temperature (37 degrees C), respectively. Ice cream was produced by two different methods: method 1, ice cream mix was fermented with cold-and heat-adapted L. acidophilus prior to freezing; method 2, cold-and heat-adapted L. acidophilus was added to ice cream mix but the mix was not fermented with L. acidophilus prior to freezing. The lowest reduction ratio was found in the samples produced by using method 1 and cold-adapted L. acidophilus, adapted at 4 degrees C for 18 h. L. acidophilus survived at the required levels (>10(6) cfu g(-1)), with or without an adaptation. The adaptation conditions improved stability of L. acidophilus in the samples, but the magnitude of improvement was small. (C) 2016 Elsevier Ltd. All rights reserved.

Amaç: Bu çalışmada, üst ve alt solunum yolu enfeksiyonu olan hastalarda multipleks PCR tanı yöntemi ile kısa sürede solunum virüslerinin saptanması amaçlandı. Gereç ve Yöntem: Bu çalışmaya, Ocak 2007-Ağustos 2013 tarihleri arasında, üst veya alt solunum yolu enfeksiyonu ön tanısı alan, toplam 1708 (1220 çocuk, 488 erişkin) hasta (%45.1 kadın, %54.9 erkek, yaş aralığı 5 gün-94 yaş) dahil edildi. Hastaların solunum yolu örneklerindeki solunum virüsleri, mültipleks PCR yöntemi ile araştırıldı. Bulgular: Toplam 1708 hastanın, 620'sinde (%36.3) bir veya birden fazla solunum virüsü pozitif, 1088'inde (%63.7) negatif bulundu. Bu hastaların 63'ünde (%3.7) çoklu etken saptandı. Çoklu etken saptanan örneklerin %89.5'i çocuk hastalardı. Solunum yolu örneklerinin 387'si (%22.7) poliklinik hastalarından, 1321'i (%77.3) yatan hastalardan elde edildi. Poliklinik hastalarının %48.5'i, yatan hastaların %32.7'sinde (p

The aim of this study was to investigate the prevalence and seasonal distribution of respiratory viruses in pediatric and adult outpatients and inpatients who were admitted to hospital with the symptoms of upper and lower respiratory tract infections, during a 12-year period. A total of 5102 clinical samples (4372 nasopharyngeal swabs, 316 bronchoalveolar lavages, 219 transtracheal aspirates, 163 nasopharyngeal aspirates, 20 sputum, 10 nasal swabs) examined in our laboratory between January 1st 2002 and July 17th 2014, were evaluated retrospectively. Of the specimens, 1107 (21.7%) were obtained from outpatients and 3995 (78.3%) from hospitalized patients. Of the patients, 2851 (55.9%) were male and 2251 (44.1%) were female, while 1233 (24.2%) were adults and 3869 (75.8%) were children (age range: 1 day - 93 years; median: 3 years). Respiratory samples were investigated for the presence of respiratory syncytial virus (RSV), influenza virus type A and B (INF-A, INF-B), adenovirus (AdV), parainfluenza viruses (PIV types 1-4), human rhinoviruses (HRV), human coronaviruses (HCoV), human metapneumovirus (HMPV) and human bocavirus (HBoV). All specimens were tested by both direct immunofluorescence antibody (DFA) and shell vial cell culture (SVCC) methods. In DFA assay the samples were initially screened by fluorescent-labeled polyclonal antibodies, and the positive ones were typed by using monoclonal antibodies (Light Diagnostics, Merck Millipore, USA). In SVCC, HEp-2, MDCK, A-549 and Vero cell lines were used for the isolation of viruses. In addition to these methods, real-time multiplex PCR methods (RealAccurate®, Respiratory RT PCR, PathoFinder, Netherlands and Seeplex® RV15 ACE Detection, Seegene, South Korea) were used for the detection of respiratory viruses in samples (n= 2104) obtained from 2007 to 2014. Respiratory viruses were detected in a total of 1705 (33.4%) patients, of them 967 (19%) were male and 738 (14.4%) were female. Three hundred and eighteen (18.6%) of the 1705 patients were infected with multiple respiratory viruses. The most frequently observed co-infections were RSV+INF-A (40/318; 12.6%), and RSV+PIV (33/318; 10.4%). The rate of positivity for the respiratory viruses in pediatric and adult groups were 35.4% (1369/3869) and 27.3% (336/1233), respectively (p< 0.000). The most frequently detected virus in pediatric group was RSV (336/1369; 24.5%), followed by influenza viruses (314/1369; 22.9%), PIV (197/1369; 14.4%), HRV (118/1369; 8.6%), AdV (75/1369; 5.5%) and the others (49/1369; 3.6%). On the other hand the most frequently detected virus in adult group was influenza viruses (181/336; 53.8%) followed by AdV (37/336; 11%), RSV (24/336; 7.1%), PIV (24/336; 7.1%), HRV (23/336; 6.8%) and the others (9/336; 2.7%). The rate of multiple virus infections in pediatric and adult groups were 7.2% (280/3869) and 3% (38/1233), respectively. Most of the coinfections (280/318; 88%) were detected in children. Respiratory viruses were detected positive in 40.2% (445/1107) of outpatients, and in 31.5% (1260/3995) of inpatients (p< 0.000). The most frequent viruses detected in pediatric outpatients and inpatients were HRV and RSV, respectively, while influenza viruses were the first in line among both adult outpatients and inpatients. During the study period, a PIV-3 outbreak (n= 96) have emerged between December 2004-April 2005, and an influenza A (H1N1)pdm09 outbreak (n= 207) between November 2009-January 2010. When the seasonal distribution was considered, the isolation rates of 1705 respiratory viruses in winter, spring, summer and autumn were 44.4%, 27%, 8.3% and 20.3%, respectively. RSV was most frequently detected from December to March, influenza viruses from November to March, HRV from December to June, and mixed infections from January to February. In conclusion, the data of our study obtained in about 12-year period indicated that the prevalence of respiratory viruses in acute respiratory infections is 33.4%, and they typically active during the months of winter and early spring in our region.

Kefir has a long tradition in human nutrition due to its presupposed health promoting effects. To investigate the potential contribution of bioactive peptides to the physiological effects of kefir, comprehensive analysis of the peptide profile was performed by nano-ESI-LTQ-Orbitrap MS coupled to nano-ultrahigh-performance liquid chromatography. Thus, 257 peptides were identified, mainly released from β-casein, followed by αS1-, κ-, and αS2-casein. Most (236) peptides were uniquely detected in kefir, but not in raw milk indicating that the fermentation step does not only increase the proteolytic activity 1.7- to 2.4-fold compared to unfermented milk, but also alters the composition of the peptide fraction. The influence of the microflora was determined by analyzing kefir produced from traditional kefir grains or commercial starter culture. Kefir from starter culture featured 230 peptide sequences and showed a significantly, 1.4-fold higher proteolytic activity than kefir from kefir grains with 127 peptides. A match of 97 peptides in both varieties indicates the presence of a typical kefir peptide profile that is not influenced by the individual composition of the microflora. Sixteen of the newly identified peptides were previously described as bioactive, including angiotensin-converting enzyme (ACE)-inhibitory, antimicrobial, immunomodulating, opioid, mineral binding, antioxidant, and antithrombotic effects. BIOLOGICAL SIGNIFICANCE:The present study describes a comprehensive peptide profile of kefir comprising 257 sequences. The peptide list was used to identify 16 bioactive peptides with ACE-inhibitory, antioxidant, antithrombotic, mineral binding, antimicrobial, immunomodulating and opioid activity in kefir. Furthermore, it was shown that a majority of the kefir peptides were not endogenously present in the raw material milk, but were released from milk caseins by proteases of the microbiota and are therefore specific for the product. Consequently, the proteolytic activity and the composition of the peptide profile can be controlled by the applied microflora (grains or starter culture). On the other hand, a considerable portion of the peptide profile was identified to be typical for kefir in general and independent from production parameters. In summary, the generated kefir peptide profile helped to reveal its origin and to identify bioactive peptides in kefir, which may advance the understanding of health benefits of this food product. The results further indicate that subsets of the kefir peptide list can be used as markers to control food authenticity, for example, to distinguish different types of kefir.