Identification of bacterial species in milk by MALDI-TOF and assessment of some oxidant-antioxidant parameters in blood and milk from cows with different health status of the udder.

This study aimed to identify bacterial pathogens in milk samples from dairy cows with subclinical and clinical mastitis as well as to assess the concentrations of oxidant-antioxidant parameters [malondialdehyde (MDA), reduced glutathione (GSH), and total GSH levels] in both blood and milk samples. From a total of 200 dairy cows in 8 farms, 800 quarter milk samples obtained from each udder were tested in the laboratory for the presence of udder pathogens. Cultivated bacteria causing intramammary infection from milk samples were identified by Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF). In addition, from tested animals 60 cows were selected including 20 healthy cows that were CMT negative, 20 cows with subclinical mastitis (SM), and 20 cows with clinical mastitis (CM) for detection of MDA, GSH, and total GSH levels in blood and milk samples. Three hundred and eighty (47.5%; 380/800), 300 (37.5%; 300/800), and 120 (15%; 120/800) of milk samples, respectively were CMT positive or SM and CM, and those positives were cows from different farms. We observed that 87.4% (332/380), 25.3% (76/300), and 34.2% (41/120) of cows with CMT positive, CMT negative, and CM had bacterial growth. The most predominantly identified bacteria were Staphylococcus chromogenes (18.7%) obtained mainly from SM and Staphylococcus aureus (16.7%) as the most frequent cause of CM. According to our results, dairy cows with CM had the highest MDA levels, the lowest GSH, and total GSH levels in both blood and milk samples however, high MDA levels and low GSH levels in milk samples with SM were observed. Based on our results, lipid oxidant MDA and antioxidant GSH could be excellent biomarkers of cow's milk for developing inflammation of the mammary gland. In addition, there was no link between nutrition and MDA and GSH levels.

The Bad Bug is Back: Acinetobacter Baumannii Bacteremia Outbreak during the COVID-19 Pandemic in an Intensive Care Unit.

Background: Epidemiology of nosocomial infections may show variability because of under-estimation of infection control measures (ICMs) in coronavirus disease 19 (COVID-19) outbreak. Aim: To investigate the Acinetobacter bacteremia outbreak developed in an intensive care unit (ICU) between March 20 to May 15, 2020, examine the risk factors, and re-evaluate ICM retrospectively. Material and Methods: A retrospective cohort analysis was conducted to determine the risk factors, pulsed field gel electrophoresis (PFGE) was performed for analysis of the outbreak, ICM practices were observed by a team, and infection control interventions were undertaken. Results: Acinetobacter bacteremia developed in 17 patients (21.5%) within 79 COVID-19 patients included in the study. The mean age of the bacteremic patients was 67.3 (SD = 14.82) years, and 82.4% of them were male; of these, 15 died, leading to 88.2% mortality. The bacteremia rate was higher compared with a 14-month period preceding the COVID-19 pandemic (17/79 versus 12/580 patients, respectively). PFGE revealed that the outbreak was polyclonal. On multi-variate analysis, the bacteremia development rate was 13.7 and 5.06 times higher with central venous catheter (CVC) use and in patients with chronic obstructive pulmonary disease (COPD), respectively. The mortality rate was higher in bacteremic patients (p = 0.0016). It was observed that ICMs were not followed completely, especially change of gloves and hand hygiene. Contamination of A. baumannii was observed in 38% of the gloves. Conclusion: COPD and CVC use were determined as risk factors for Acinetobacter bacteremia development, and failures in ICM may have led to cross-contamination of endemic A. baumannii. The outbreak could be controlled within 3 weeks of interventions.

Relationship between nucleotide-binding oligomerization domain-containing protein 2 variants and severity of acute pancreatitis.

BACKGROUND AND AIM: Intestinal barrier dysfunction has been implicated in the development of infectious complications of acute pancreatitis. Nucleotide-Binding Oligomerization DomainContaining Protein 2 (NOD2) plays an important role in the proper functioning of intestinal defense mechanisms. Here, we investigated the frequency of NOD2 variants in patients with mild and severe acute pancreatitis. MATERIALS AND METHODS: Groups 1, 2 and 3 comprised healthy participants and patients with mild and severe pancreatitis, respectively. Four NOD2 variants and serum interleukin-6 (IL-6), Tumor Necrosis Factor-a (TNF-a) and lipopolysaccharide-binding protein (LBP) levels were analyzed. RESULTS: Three patients (3/32, 9.4%) in the severe pancreatitis group were positive for the p.R702W variant. This variant was negative in other groups. One, three and three patients in the healthy (1/27, 3.7%), mild (3/36, 8.3%) and severe pancreatitis (3/32, 9.4%) groups tested positive for the 1007fs variant, respectively. No significant differences in the frequencies of NOD2 variants were evident among the groups. Serum IL-6, TNF-a and LBP levels were markedly higher in the severe pancreatitis than the healthy and mild pancreatitis groups (all p<0.001). We observed no significant correlation between cytokine levels and NOD2 variants. CONCLUSION: Our results support an association between the presence of the p.R702W variant and severe pancreatitis.

Prevalence of Candida africana and Candida dubliniensis, in vulvovaginal candidiasis: First Turkish Candida africana isolates from vulvovaginal candidiasis.

INTRODUCTION: Candida africana and C. dubliniensis are closely related species of C. albicans. Current phenotypic methods are not suitable to accurately distinguish all the species belonging to the C. albicans complex. Several molecular-based methods have recently been designed for discriminating among closely related Candida species. The aim of this study was to establish the prevalence of C. dubliniensis and C. africana in vulvovaginal samples with phenotypic and genotypic methods. MATERIALS AND METHODS: We re-examined 376 vulvovaginal C. albicans complex isolates. All the isolates were identified with morphological features and HWP1 gene polymorphisms. ITS and D1/D2 sequencing, carbohydrate assimilation, MALDI-TOF MS profiles and antifungal susceptibilities were evaluated for C. africana and C. dubliniensis isolates. RESULTS: Of the 376 isolates, three C. africana and three C. dubliniensis isolates (0.8% and 0.8% prevalence, respectively) were identified by molecular methods (HPW1, ITS and D1/D2) Phenotypically, C. africana differed from C. albicans and C. dubliniensis by formation of no/rare pseudohyphae, absence of chlamydospores and, the development of turquoise green colonies on CHROMagar. MALDI-TOF MS and API ID 32C could not revealed C. africana isolates. C. africana and C. dubliniensis isolates showed very low MIC values for all the tested antifungals. DISCUSSION: This first report of C. africana from Turkey provides additional data for epidemiological, phenotypic features and antimicrobial susceptibility profiles. This study also highlights the importance of using genotypic methods in combination with phenotypic methods.

Candida albicans outbreak associated with total parenteral nutrition in the neonatal unit.

BACKGROUND: The most frequently isolated fungi in patients using TPN belongs to the Candida genus. Various infections including venous catheter infections, fungemia, endocarditis and ophthalmitis may be encountered. OBJECTIVE: Upon growth of Candida in the blood cultures from the pediatric (neonatal) unit of our hospital, a surveillance was performed in this unit and involving the health care workers. Clonal relationships of the isolates were investigated with molecular tests. METHODS: Blood samples obtained from the patients in pediatric neonatal unit were studied with automatized blood culture [BacT/Alert (Bio Mιrioux, France)]. Yeast isolates from environmental surveillance cultures (TPN solutions, hands of healthcare personnel, ιtagθre, etc) and patients were identified as C. albicans with conventional methods and ID 32 C and ATB TM Fungus 3 (Biomerieux, France) kits. Clonal similarity was determined by using AP-PCR as initial method and we have also typified all strains by the method of REP-PCR (diversilab system,bioMιrieux). Finally; Pulsed Field Gel Electrophoresis (PFGE) was used for confirmation. RESULTS: C. albicans was isolated in blood cultures of seven patients. Similar antifungal susceptibility patterns were observed in all isolates. AP-PCR and REP-PCR showed that the C. albicans isolates grown in the TPN solution and from the patients' blood cultures were clonally same strains. PFGE analysis further confirmed this clonality. CONCLUSION: According to results of the molecular methods, we thought that a C. albicans outbreak had occurred in the neonatal pediatric unit, due to contamination of TPN solution.

Rapid Detection of Bloodstream Pathogens in Liver Transplantation Patients With FilmArray Multiplex Polymerase Chain Reaction Assays: Comparison With Conventional Methods.

BACKGROUND: Bloodstream infection (BSI) is an important concern in transplant patients. Early intervention with appropriate antimicrobial therapy is critical to better clinical outcome; however, there is significant delay when conventional identification methods are used. METHODS: We aimed to determine the diagnostic performance of the FilmArray Blood Culture Identification Panel, a recently approved multiplex polymerase chain reaction assay detecting 24 BSI pathogens and 3 resistance genes, in comparison with the performances of conventional identification methods in liver transplant (LT) patients. A total of 52 defined sepsis episodes (signal-positive by blood culture systems) from 45 LT patients were prospectively studied. RESULTS: The FilmArray successfully identified 37 of 39 (94.8%) bacterial and 3 of 3 (100%) yeast pathogens in a total of 42 samples with microbial growth, failing to detect only 2 of 39 (5.1%) bacterial pathogens that were not covered by the test panel. The FilmArray could also detect additional pathogens in 3 samples that had been reported as having monomicrobial growth, and it could detect Acinetobacter baumannii in 2 samples suspected of skin flora contamination. The remaining 8 blood cultures showing a positive signal but yielding no growth were also negative by this assay. Results of MecA, KPC, and VanA/B gene detection were in high accordance. The FilmArray produced results with significantly shorter turnaround times (1.33 versus 36.2, 23.6, and 19.5 h; P < .05) than standard identification methods, Vitek II, and Vitek MS, respectively. CONCLUSIONS: This study showed that the FilmArray appeared as a reliable alternative diagnostic method with the potential to mitigate problems with protracted diagnosis of the BSI pathogens in LT patients.

Progressive Multifocal Leukoencephalopathy after Three Consecutive Liver Transplantations.

Progressive multifocal leukoencephalopathy (PML) is a lytic infection of the central nervous system caused by the reactivation of John Cunningham Virus (JCV) in severely immunosuppressed patients. Occurrence of PML after solid organ transplantations, especially after liver transplantation, is rare. If a patient has poor prognostic factors such as atypical radiological involvements or high viral load in cerebrospinal fluid (CSF), overall survival rates could be poor. Herein, we report on a patients who underwent liver transplantation three times and developed PML with unexpected radiological findings; he was also positive for JCV DNA with a high viral load. Although there are limited data about efficacy of cytarabine against JCV, it was given to the patient for five days. Despite the initiation of cytarabine and complete cessation of the immunosuppressive therapy, we lost the patient, unfortunately.

Role of endometrial concentrations of heavy metals (cadmium, lead, mercury and arsenic) in the aetiology of unexplained infertility.

OBJECTIVE: To determine the role of endometrial concentrations of heavy metals (cadmium, lead, mercury and arsenic) in the aetiology of unexplained infertility. STUDY DESIGN: Thirty-three women with unexplained infertility and 32 fertile women were recruited. Endometrial biopsies were collected during the putative window of implantation (cycle days 20-24). The concentrations of cadmium, lead, mercury and arsenic were measured in endometrial biopsy specimens using atomic absorption spectrometry. RESULTS: Cadmium was detected in 91% (30/33) of women with unexplained infertility, compared with 34% (11/32) of fertile women. The median endometrial cadmium concentration was 19.58 (interquartile range 1.46-30.23)µg/l in women with unexplained infertility, compared with 0.00 (interquartile range 0.00-0.40)µg/l in fertile women. Lead was detected in 15% (5/33) of women with unexplained infertility and 3% (1/32) of fertile women. Mercury and arsenic were not detected in any endometrial samples from either group. CONCLUSION: A significant difference in endometrial cadmium concentration was found between women with unexplained infertility and fertile women. This suggests that cadmium may be a contributing factor in the aetiology of unexplained infertility.

XPD and XRCC1 gene polymorphism in patients with normal and abnormal cervical cytology by pap smear.

AIM: The purpose of the present study was to identify the role of abnormalities in DNA repair pathways by measuring the XPD and XRCC1 gene polymorphisms. MATERIALS AND METHODS: Thirty-five patients with abnormal cervical cytology (study group) and 10 women with normal cytology (control group) were included in the study. The polymorphisms of XRCC1 Arg194Trp, XRCC1 Arg399Gln and XPD Lys751Gln genes were investigated from the blood samples. RESULTS: There was no statistically significant difference in allele frequencies of XPD gene among the groups (p = 0.097), while XRCC1R399Q gene polymorphism was strikingly more frequent in the study group than that of control cases (p = 0.029). The prevalence of XRCC1R194W gene polymorphism on the other hand, was similar between the groups (p = 0.579). CONCLUSIONS: Patients with abnormal and normal cervical cytology have similar XPD gene polymorphism. However, the frequency of gene polymorphism in XRCC1 Arg 399 Gln codon was significantly higher in abnormal cervical cytology group.

Molecular epidemiology of the Bacillus anthracis isolates collected throughout Turkey from 1983 to 2011.

The main perspective of this study was to determine cross-transmissions amongst anthrax cases and provide detailed information regarding the genotypes of Bacillus anthracis isolates circulating in Turkey. A total of 251 B. anthracis isolates were obtained from human (93 isolates), animal (155 isolates), and environmental (three isolates) samples in various provinces of Turkey. All isolates were susceptible to quinolones, vancomycin, tigecycline, and linezolid, but not to ceftriaxone. Excluding human isolates, one of the animal isolates was found to be resistant to penicillin, erythromycin, and doxycycline. Multiple-locus variable-number tandem repeats analysis including 8 loci (MLVA8) revealed 12 genotypes, in which genotype 43 was observed at the highest frequency (41.8 %), followed by genotype 35 (25.5 %) and genotype 27 (10.4 %). Major subtype A3.a was the predominant cluster, including 86.8 % of the isolates. The MLVA25 analysis for the 251 isolates yielded 62 different genotypes, 33 of which had only one isolate, while the remaining 29 genotypes had 2 to 43 isolates, with a total of 218 isolates (86.9 %). These findings indicate very high cross-transmission rates within anthrax cases in Turkey. The genotypes diagnosed in Turkey are populated in the A major cluster. Penicillin prescribed as the first-choice antibiotic for the treatment of anthrax is still effective.

Outbreak of adenovirus serotype 8 conjunctivitis in preterm infants in a neonatal intensive care unit.

BACKGROUND: Adenovirus keratoconjunctivitis outbreaks have rarely been reported in preterm infants. An outbreak of adenovirus conjunctivitis occurred between 15 January and 25 February at a neonatal intensive care unit of a university hospital in Turkey. AIM: To describe the evolution, investigation and management of the outbreak. METHODS: Adenovirus type 8 was identified in 14 samples by polymerase chain reaction analysis. A case-control study was performed to determine the risk factors. FINDINGS: Fifteen preterm neonates, five healthcare workers (HCWs) and four parents suffered from conjunctivitis signs such as lacrimation, swelling and redness of the eye. A retinopathy of prematurity (ROP) examination was found to be the most important risk factor for adenovirus conjunctivitis (odds ratio: 17.5; 95% confidence interval: 1.9-163.0; P=0.012). The eyelid speculum (blepharostat) used during the ROP examination was not sterilized between each patient and was found to be the cause of contamination. CONCLUSION: The outbreak was controlled by measures such as barrier precautions, hand hygiene, sterilization of the blepharostat, suspending patient transfer to other units, and excluding infected HCWs for at least 15 days.

Epidemiological characteristics and molecular typing of Salmonella enterica serovar Typhi during a waterborne outbreak in Eastern Anatolia.

In this study, we aimed to study the molecular and epidemiological characteristics of Salmonella enterica serovar Typhi (S. Typhi) outbreak in Eastern Anatolia. Six hundred and thirty-seven patients from the same county with clinical diagnosis of typhoid fever were investigated with conventional methods from stool, urine and blood specimens. Antibiotic susceptibility tests and identifications were performed for positive specimens. Clonal relationships between the isolates were investigated using pulsed field gel electrophoresis (PFGE) method. A questionnaire was completed for the water consumption habits of patients. Of 91 culture positive specimens, 76 were blood, 13 were stool and 2 were urine. The isolates were resistant to ampicillin, ampicillin/sulbactam, chloramphenicol, cefuroxime, amikacin, gentamicin and trimethoprim-sulfamethoxazole. Although there was a single band difference in some isolates, PFGE results indicated that this was an outbreak caused by single strain according to the Tenover criteria. This outbreak thought to be associated with the consumption of tap water contaminated with sewage represents a breakdown of the basic public health and civil engineering infrastructure. Appropriate public health measures should be taken in order to avoid such outbreaks in the future.

Serum leptin concentrations are decreased and correlated with disease severity in age-related macular degeneration: a preliminary study.

BACKGROUND: Age-related maculopathy (ARM) or degeneration (ARMD) is the leading cause of irreversible blindness in developed countries. Despite several studies on the morphology of ARMD, the aetiology is unknown and factor(s) contributing to the pathogenesis remain to be characterised. More recent studies have demonstrated that cholesterol esters and lipids are present within Bruch's membrane deposits and drusen, and dietary fat intake is associated with ARMD. The product of Ob gene, leptin, is a recently discovered peptide participating in human metabolism. There is a direct relationship between serum leptin and diet, and lipoprotein metabolism, but the role of leptin in the course of ARMD has not previously been investigated. PURPOSE: This cross-sectional case-control study investigated whether serum leptin level was associated with ARMD as a new possible risk factor and to assess its relationship with disease severity. Methods A total of 32 patients with ARM or ARMD (17 men, 15 women) and 20 age- and sex-matched healthy control subjects without ARMD (11 men, nine women) from a similar ethnic background were enrolled in this multicentre study. Body mass index (BMI) (weight (kg)/height (m(2))) was calculated for each group. The presence of maculopathy was assessed on the basis of colour fundus photographs using an international classification system. Patients were classified as early-ARM (n=16) or late-ARMD (n=16) using clinical examination and grading of photographs. Serum leptin levels were measured by an enzyme-linked immunosorbent assay kit. The Mann-Whitney U test or chi(2) test was used for statistics as indicated, and P&<0.05 was considered to be significant. RESULTS: The age, sex ratio, and BMI between groups were comparable. Patients with maculopathy had significantly (P&<0.001) lower leptin levels (mean+/-SD, 6.01+/-2.55 ng/ml) than control subjects (13.21+/-2.27 ng/ml). In addition, late-ARMD patients had significantly lower leptin levels (3.81+/-0.58 ng/ml) than early-ARM patients (8.21+/-1.68 ng/ml, P&<0.001) or control subjects (P&<0.001). CONCLUSION: Leptin seems to be a possible newly associated factor in the course of ARM and may be involved in the lipid composition of the macular lesions, especially in late-ARMD.

Detection of Alloiococcus otitidis in the nasopharynx and in the outer ear canal.

Alloiococcus otitidis has been recovered from the middle ear of children with otitis media with effusion, but its natural habitat is not known. To determine whether the nasopharynx and the outer ear canals are the natural habitats of A. otitidis, 145 swabs (50, nasopharynx; 95 outer ear canal) collected from 50 children were screened by polymerase chain reaction. A. otitidis DNA was detected in seven (4.8%) of the 145 specimens, of which four were nasopharynx, and three outer ear canal. These results indicate that the nasopharynx and outer ear canal may be the body sites for localization of A. otitidis.

Effect of multiple freezing and thawing of serum on TT virus and hepatitis B virus DNA positivity.

This study was done to determine the effect of freezing and thawing of serum on the stability of TTV and HBV DNA levels. Seven TTV DNA positive samples were randomly selected among the sera having HBV DNA with concentrations ranging from 12 pg/ml to 4162 pg/ml and they were frozen and thawed up to eight times and then analyzed for changes on TTV- and HBV DNA levels. TTV DNA positivity and HBV DNA concentrations were tested by using semi-nested PCR and Digene hybrid capture system, respectively. Seven cycles of freezing and thawing did not significantly change HBV DNA concentrations and TTV DNA positivity in any of the samples tested. After eight cycles, only three samples were tested, and all were positive for HBV DNA, but negative for TTV DNA. Our results show that both TTV- and HBV DNA positives continued until the seventh cycle of freezing and thawing in all samples tested.

Bacterial etiology of otitis media with effusion; focusing on the high positivity of Alloiococcus otitidis.

The etiology of otitis media with effusion (OME) is unclear. The bacterial analyses of middle ear effusion (MEE) in OME may reveal important information regarding its etiology. Alloiococcus otitidis, Heamophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis were investigated by using microbiologic culture and a multiplex PCR method in the middle ear fluid of 32 children (54 samples) with chronic OME. PCR yielded positive results in 18 (33.3%) middle ear effusions while culture resulted positive for 3 (5.6%). The PCR method detected A. otitidis in 10 (18.5%) specimens, H. influenzae in 7 (13%), M. catarrhalis in 4 (7.4%) and S. pneumoniae in 2 (3.7%) specimens. The multiplex PCR method enhances the detection rate significantly compared to that of the conventional culture method. A. otitidis is the most common detected pathogen in the MEE of the OME.

Nosocomial infections in a new medical center, Turkey.

Nosocomial infection was found in 255 (2.5%) of 10,164 inpatients in a new medical center with a 310-bed capacity. The infection rate was 12.5% in the intensive care unit, 9.5% in neurology, 5.5% in general surgery, and 4.0% in orthopedics. Rates in the other services were lower. Hospital-acquired infections in our medical center frequently involved multiply resistant Enterobacteriaceae and staphylococci.