Viral Pneumonias in Forensic Autopsies: Evaluation and Classification of Histopathologic Changes With Microbiologic Correlation.

Lower respiratory infections are commonly due to viruses and are the third largest cause of death. Respiratory tract viruses have a tendency to target the specific regions in the lung and can harm the host via direct effect of the virus and the host's inflammatory response. In this study, relationships between morphologic changes in the lung and the viral agent type isolated in the lung by the polymerase chain reaction technique were investigated. This study was performed retrospectively at 113 autopsy cases in the Council of Forensic Medicine in Istanbul. Slides from the lung tissues diagnosed as interstitial pneumonia and detected viral agent in polymerase chain reaction were evaluated and reviewed under light microscope by 2 pathologists simultaneously according to predetermined bronchiolar, alveolar, and interstitial findings. Alveolar findings were detected in 108 cases (95.6%), whereas interstitial and bronchiolar findings were detected in 91 (80.5%) and 38 (33.6%) cases, respectively. Intra-alveolar edema was the most common alveolar finding. Some findings such as multinucleated syncytial cells and smudge cells can aid the search for etiologic agent. Interstitial inflammation was the most common histopathologic finding in the lung in viral infections and the most prominent clue to viral infections in the lung histopathologically without discrimination of viral agent type.

Evaluation of Virulence Factors and Antifungal Susceptibility in Yeast Isolates from Postmortem Specimens.

Invasive fungal infections are a leading cause of morbidity and mortality in immunocompromised patients, especially in cases requiring a prolonged stay in the intensive care unit. A total of 99 yeast strains were isolated from 42 postmortem cases. In this study, virulence factors and antifungal susceptibility of these species were evaluated. The isolates were identified as Candida albicans (54), C. tropicalis (15), C. glabrata (12), C. parapsilosis (6), C. lipolytica (3), C. utilis (3), C. krusei (2), C. kefyr (1), and Cryptococcus neoformans (3). The most commonly isolated species was C. albicans, and no resistant species were determined. Despite the equal number of specimens, no secretion of significant virulence factors was associated with the postmortem specimen in the Candida species. Postmortem fungal investigations in forensic autopsies are useful in explaining cause of death in such cases, also may lead to protocols for the treatment of fungal infections and contribute to fungal pathogenesis and epidemiological data.

[Characterization of class 1 and class 2 integron gene cassettes in Escherichia coli strains isolated from urine cultures: a multicenter study]. / Idrar kültürlerinden izole edilen Escherichia coli suslarinda sinif 1 ve sinif 2 integron gen kasetlerinin karakterizasyonu: Çok merkezli bir çalisma.

Escherichia coli is the most common pathogen isolated from both nosocomial and community acquired urinary tract infections. Although there are many studies from different centers concerning the antibiotic susceptibility of E.coli isolates in Turkey, the studies are quite few about class 1 and class 2 integron cassettes in clinical E.coli isolates from urinary samples. The aim of the study was to investigate the antibiotic susceptibility and the carriage of integron gene cassettes in E.coli strains isolated from urinary samples. A total of 626 E.coli strains isolated from urine cultures in microbiology laboratories located at 10 provinces from different regions of Turkey (Denizli, Ankara, Kayseri, Nigde, Sanliurfa, Kahramanmaras, Tokat, Malatya, Konya and Trabzon) between June 2011-June 2012 were included in the study. The identification and antibiotic susceptibility testing of the isolates were studied by conventional methods as well as Vitek® 2 Compact (bioMérieux, France) and BD Phoenix™ 100 (Becton Dickinson, USA) systems. The antibiotic susceptibilities of all the isolates were retested by Kirby-Bauer disk diffusion method according to CLSI recommendations in the main center of the study in order to achive the standardization. The presence of integrons was detected with polymerase chain reaction (PCR) method by using specific primers targeting class 1 (intI1) and class 2 (intI2) integrase gene regions. After integron amplification the samples were cloned and subjected to DNA sequencing. When the antibiotic susceptibility of the isolates were evaluated, the highest resistance was observed against most commonly used empirical antibiotics namely ampicillin and trimethoprim-sulfamethoxazole (SXT) with the mean rate of 58.6% (range: 43.8%-73.2%) and 41.2% (range: 35.4%-45.8%), respectively. The most effective antibiotics detected against the isolates were imipenem and amikacin with the lowest resistance rates of 0.2% (range: 0%-1.1%) and 0.6% (range: 0%-3.2%), respectively. The frequency of positive IntI1 gene and class 1 integron gene cassettes were found as 25.8% (162/626) and 16.6% (104/626), respectively, whereas the frequency of positive intI2 gene II and class 2 integron gene cassettes were 5.1% (32/626) and 3% (19/626), respectively. The lowest intI1 gene frequency was detected in the isolates from Kayseri (16.6%) and the highest in the isolates from Kahramanmaras (35.4%) provinces. While there was no intI2 gene in the isolates from Denizli and Kayseri, the highest frequency was 12.1% in the isolates from Sanliurfa province. dfrA1 gene, the most frequent gene among integron gene cassettes was positive in 31 class 1 integron gene cassette alone, and positive with aadA1 gene in 18 class 1 integron gene cassettes. dfrA1 gene was positive with aadA1a just in one isolate. dfrA17 allele was positive in one isolate alone, in 28 isolates with aadA1, and in 15 isolates with aadA5. aadA1 gene was detected in four isolates. dfrA17-sat-aadA5 co-existence was detected among class 2 integron gene cassette in isolates from six provinces. dfrA1-sat-aadA1 was detected in one isolate from Ankara province and dfrA1 was detected in one isolate in Nigde province only. As a result, dfrA1 and aadA1 genes are the most common types of genes among class 1 and class 2 integron gene cassettes in E.coli isolated from urine cultures. It was concluded that high resistance against streptomycin (31.2%) and SXT (41.2%) supported the dissemination of integron-mediated genes dfr, sul1 and aad in the isolates.

Postmortem diagnosis of cytomegalovirus and accompanying other infection agents by real-time PCR in cases of sudden unexpected death in infancy (SUDI).

As an opportunistic pathogen with high mortality rates, Cytomegalovirus (CMV) may lead to fatal disseminated CMV infection of the premature and newborn; thus necessitating the demonstration of CMV-DNA with clinical history and/or histopathological findings of CMV infection and defining other bacterial and viral infection agents with real-time polymerase chain reaction (RT-PCR) in udden unexpected death in infancy (SUDI) cases as we aimed in this study. 314 (144 female, 170 male) SUDI cases were prospectively investigated from January 2013 to January 2015 in Istanbul Forensic Medicine Institution. The study includes 87 tissue samples of 39 cases for post-mortem histopathological examination of interstitial pneumonia, myocarditis, meningitis, encephalitis, hepatitis, colitis or tubulointerstitial nephritis and/or accompanying chronic sialadenitis. CMV-DNA was found positive in 35 (40.2%) salivary gland, 19 (21.8%) lung, 1 (1.1%) tonsil, and 1 (1.1%) brain tissues. CMV sialadenitis and/or CMV pneumonia associated with other viral and/or bacterial agents were detected in 23 (60%) of 39 infant cases. The demonstration of CMV-DNA would significantly clarify the cause of death and collection of epidemiological data in SUDI cases with clinical history and histopathological findings of CMV infection accompanying chronic CMV sialadenitis. Furthermore, CMV suppresses the immune system, and may predispose to other bacterial and/or viral infections in these cases. Post-mortem molecular investigations are useful in explaining cause of death in SUDI with a suspicion of infection in forensic autopsies.

[An Autopsy Case of Sudden Death Caused by Cerebral Malaria Infection]. / Serebral Malarya Enfeksiyonuna Bagli Ani Ölümle Sonuçlanan Otopsi Olgusu.

Malaria is a lethal protozoan infection which is generally diagnosed antemortem and rarely diagnosed postmortem in a few cases. A fifty five year old, Turkish citizen male has been referred for autopsy. It has been found that he has gone abroad to work a month ago, however, quitted malaria prophylaxis before the intended end and brought into the emergency department in an unconscious state.Following quinine and clindamycin treatment with the initial diagnosis of cerebral malaria, the case was reported to have died due to his general condition got worsened at the end of the third day of therapy.Histopathological evaluation of postmortem tissues was revealed haphazardly arranged minor bleedings and central vascular necrotic foci in the cerebrum, cerebelum and brain stem; light brown pigment containing cells around vasculature; and pigment containing cells in the spleen and bone marrow. Cerebral malaria has a rapid course and is rare but one of the lethal complications of infections with Plasmodium. Although domestic malaria cases has been decreasing in our country, it should be kept in mind that the malaria infection can be seen in persons travelling abroad to high endemic malarial regions and an appropriate antimalarial prophylaxis should be recommended to those overseas travellers.

Hydatid Disease Involved in the Heart, Liver, and Kidney That Caused Sudden Death: Case Report.

Hydatid disease is a parasitic infestation caused by ingestion of eggs of echinococcal species. For Echinococcus granulosus, the definitive host is the dog, and sheeps are the usual intermediate hosts. Humans are accidental intermediate hosts, infected by ingestion of food contaminated with eggs shed by dogs or foxes. The most common organs that hydatid disease encountered are the liver and lungs. Involvement of the kidney is rare and usually accompanies the other organ involvements. Cardiac involvement of echinococcosis is also very rare. We report the case of a 31-year-old woman with a 6-year history of asthma who collapsed after strenuous activity and died despite the interventions carried out. At autopsy, cystic masses were detected in the apex of the heart, in the right kidney, and in the liver. There were no macroscopic pathologic findings in the other organs. Microscopic examination revealed the diagnosis of hydatid cyst in the heart, right kidney, and liver besides medial hypertrophy of the lung vessels. Cause of death was attributed to hydatid cyst and its complications. Patients who have symptoms akin to asthma at clinical presentation have to be further investigated for organic cardiac and pulmonary diseases such as hydatid cyst, especially in endemic countries.

Comparison of manual and automated nucleic acid isolation methods for HBV-DNA and HCV-RNA assays.

In the diagnosis and monitoring of hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, it is important to use methods that can provide rapid and reliable results. The present study aimed to compare the automated and manual extraction methods during the nucleic acid isolation phase for HBV-DNA and HCV-RNA assays. The study included 93 serum samples, 49 of which were for the HBV-DNA assay and 44 for the HCV-RNA assay. DNA and RNA isolation from the samples was performed manually with a "QIAmpMin Elute Kit" (Qiagen, Germany) and the automated isolation system, NucliSens easyMAG (BioMérieux, France). All the extraction products were amplified using the iCycler device (Bio-Rad, USA). With both methods, compliance was found in 21 (42.8%) samples in the HBV-DNA assay; nine (18.3%) samples had a higher amount of viral nucleic acid with the manual method, whereas 19 samples (38.7%) were found to have a higher amount of nucleic acid with the automated system. For the HCV-RNA assay, total compliance was found in 31 (70.4%) samples; 12 (27.2%) samples had a higher amount of viral nucleic acid with the manual method whereas one sample (2.2%) was found to have a higher amount of nucleic acid with the automated system. It was concluded that the NucliSens easyMAG automated isolation system can be used with confidence for nucleic acid extraction due to its higher sensitivity, providing results in a shorter time, and assured standardization.

Is rapid antibacterial susceptibility testing medium reliable for routine laboratory practices?

OBJECTIVE: Early detection of antibiotic susceptibility profile of the isolates has critical importance in terms of immediate beginning of the appropriate treatment and increasing of treatment success, such as meningitis, bacteriemia and sepsis. In the present study, it was aimed to compare the antibiotic susceptibility results of Quicolor (Salubris Inc., Massachusetts, USA) and standard disk diffusion method. METHODS: One hundred twenty three isolates were included in this study (80 Enterobacteriaceae, 15 Staphylococci and 28 nonfermentative Gram-negative bacteria). Antibiotic susceptibility in clinical isolates was evaluated using Mueller-Hinton (MH) agar and Quicolor (ES and NF) agar plates. RESULTS: For Enterobacteriaceae, frequency of total concordance, major error, and minor error between the tests were found as 96.8%, 0.8%, and 2.4%, respectively. For Staphylococci, frequency of total concordance, major error, and minor error among the tests were found as 95.7%, 3.5%, and 0.8%, respectively. For non fermentative bacteria, frequency of total concordance, major error, and minor error among the tests were found as 83.9%, 9.6%, and 6.4%, respectively. CONCLUSIONS: Quicolor media provided reliable susceptibility results in enteric bacteria and Staphylococci. However, further studies including higher number of nonfermentative bacteria are required to determine whether the chromogenic media are appropriate for this group of bacteria.

Interdigital foot infections: Corynebacterium minutissimum and agents of superficial mycoses.

Interdigital foot infections are mostly caused initially by dermatophytes, yeasts and less frequently by bacteria. Erythrasma caused by Corynebacterium minutissimum can be confused with superficial mycoses. The aim of the study was to determine the prevalence of the etiologic agents of superficial mycoses and the frequency of Corynebacterium minutissimum in interdigital foot infections. All the samples obtained from the 121 patients with interdigital foot infections were examined directly with the use of 20% potassium hydroxide mounts and Gram stain under the microscope and cultured on Sabouraud's dextrose agar plates. In identification of superficial mycoses, the rate was found to be 14% with the cultural method and 14% with direct microscopic examination. Using a combination of direct microscopic examination and culture, a 33.8% ratio was achieved. In the culture of these samples, the most isolated factor was Trichophyton rubrum (33.7%). In 24 of the patients (19.8%) Corynebacterium minutissimum was detected by Gram staining, in 6 of these patients Trichophyton rubrum was found, Trichophyton mentagrophytes was found in 2 and Trichosporon spp. was found in 1. The examination of interdigital foot lesions in the laboratory, the coexistence of erythrasma with dermatophytes and yeast should be considered.

[Comparison of two different real-time PCR systems in postmortem diagnosis of tuberculosis in paraffin-embedded tissues]. / Postmortem tüberküloz tanisinda parafi ne gömülü dokularda iki farkli gerçek zamanli PCR sisteminin karsilastirilmasi

Tuberculosis (TB) is one of those infections with high morbidity and mortality in all around the world. Hundreds of people died from this disease without diagnosed or due to resistant strains in Turkey. Therefore, it is important to identify postmortem cases who have died from tuberculosis. Molecular methods have been widely used as well as conventional methods in the diagnosis of tuberculosis. The aim of this study was to compare the two different real-time polymerase chain reaction (Rt-PCR) system in the postmortem diagnosis of Mycobacterium tuberculosis infections in paraffin-embedded tissues. A total of 40 paraffin-embedded tissue samples [lung (n= 35), brain (n= 2), heart (n= 2), lymph node (n= 1)] in which histopathologic findings consistent with TB (necrotizing granulomatous inflammation, gelatinous caseous pneumonia, necrotic fibrous nodul) obtained from 37 autopsy cases (31 male, 6 female; age range: 25-85 yrs) were included in the study. Paraffin-embedded tissues were deparafinized with xylene and ethyl alcohol and then DNA isolation was done with QIAsymphony DSP Virus/Pathogen Midi kit in the QIAsymphony device. DNA amplification process was performed by Rt-PCR using the kit Artus® M. tuberculosis RG-PCR in the Rotor-Gene® Q device (Qiagen, Germany). Likewise, after deparafinization process, samples placed in the cartridge and isolation and Rt-PCR was performed by Xpert® MTB/RIF (Cepheid, USA) system, simultaneosly. Seventeen and 20 out of the 40 paraffin-embedded tissues yielded positive results with Qiagen and Xpert system, respectively. M.tuberculosis DNA was found positive in 13 (32.5%) and negative in 16 (40%) of the samples by both of the systems, exhibiting 72.5% (29/40) of concordance. On the other hand, seven (17.5%) samples that were positive with Xpert system yielded negative result with the Qiagen, while four (10%) samples that were positive with Qiagen yielded negative result with the Xpert system. Of the 20 positive cases detected with Xpert MTB/RIF system, 15 were found rifampicin-susceptible, and three were rifampicin-resistant. In two samples in which M. tuberculosis DNA was low positive, rifampicin resistance could not be detected. The identification of M.tuberculosis infections in postmortem cases will contribute epidemiological data in Turkey. In these cases, effective sampling and diagnosing of M.tuberculosis infections by acid-fast stain and culture methods are crucial. However, in cases without microbiological sampling the detection of M.tuberculosis DNA in paraffin-embedded tissues with PCR, although there are differences between PCR systems has diagnostic value. In conclusion, our data indicated that Xpert MTB/RIF system is more favourable to detect M.tuberculosis DNA in paraffin-embedded tissues, with the advantages of determination of rifampicin resistance, and detection of more positive results within a shorter time.

Interdigital foot infections: Corynebacterium minutissimum and agents of superficial mycoses

Interdigital foot infections are mostly caused initially by dermatophytes, yeasts and less frequently by bacteria. Erythrasma caused by Corynebacterium minutissimum can be confused with superficial mycoses. The aim of the study was to determine the prevalence of the etiologic agents of superficial mycoses and the frequency of Corynebacterium minutissimum in interdigital foot infections. All the samples obtained from the 121 patients with interdigital foot infections were examined directly with the use of 20% potassium hydroxide mounts and Gram stain under the microscope and cultured on Sabouraud's dextrose agar plates. In identification of superficial mycoses, the rate was found to be 14% with the cultural method and 14% with direct microscopic examination. Using a combination of direct microscopic examination and culture, a 33.8% ratio was achieved. In the culture of these samples, the most isolated factor was Trichophyton rubrum (33.7%). In 24 of the patients (19.8%) Corynebacterium minutissimum was detected by Gram staining, in 6 of these patients Trichophyton rubrum was found, Trichophyton mentagrophytes was found in 2 and Trichosporon spp. was found in 1. The examination of interdigital foot lesions in the laboratory, the coexistence of erythrasma with dermatophytes and yeast should be considered.

[Investigation of cytomegalovirus positivity in the peripheral blood samples of risky patients by shell-vial cell culture, antigenemia test and real-time polymerase chain reaction]. / Riskli Hastalarin Periferal Kan Örneklerinde Sitomegalovirus Varliginin "Shell Vial" Hücre Kültürü, Antijenemi Testi ve Gerçek Zamanli Polimeraz Zincir Reaksiyonu ile Arastirilmasi

Cytomegalovirus (CMV) infections in immunocompromised patients and congenital infections in infants have high morbidity and mortality while it may lead to asymptomatic infections in immunocompetent subjects. Serological tests, culture methods, antigenemia tests and molecular methods are applied in the diagnosis of CMV infection. The aim of this study was to investigate the presence of CMV in peripheral blood samples of patients who were at risk for CMV disease by shell vial cell culture, antigenemia test and real-time polymerase chain reaction (RT-PCR) methods. A total of 141 blood specimens obtained from 91 patients (33 female, 58 male) with suspected CMV disease were included to the study. Five of the patients were newborns and the others aged between 17-79 years old were bone morrow (n= 81), kidney (n= 4) and liver (n= 1) transplantation patients. Shell vial (Vircell, Spain) cell culture method was applied for CMV isolation from the samples, while the detection of pp65 antigen in blood leukocytes was investigated by indirect immunofluorescence method (CINAkit Argene, Biosoft, France). The presence of CMV DNA in plasma samples was detected by RT-PCR (CMV QNP 2.0 kit; Fluorion, Iontek, Turkey) method. CMV was found positive in 72 (51%) of 141 samples by shell vial, 82 (58.2%) by antigenemia test and 49 (34.8%) by RT-PCR. Considering cell culture as the gold standard, the sensitivity and specificity of antigenemia test were calculated as 81.9% and 66.6%, respectively; and for PCR those rates were 43% and 73.9%, respectively. In addition DNA sequencing (ABI Prism 310 Genetic Analyzer; Perkin Elmer, USA) was performed for the samples of randomly selected three patients out of 15, who were yielded positive results with cell culture and antigenemia tests but negative CMV DNA by RT-PCR. In this analysis CMV DNA was found positive in three of the samples that were found negative by RT-PCR in spite of CMV isolation and positive antigenemia. DNA sequencing of those samples revealed multiple mutations in the probe binding region (gB) of CMV QNP 2.0 kit. It was concluded that for the detection of CMV viremia and viral load in patients under risk for CMV disease, antigenemia and PCR based methods could be applied, however, negative results obtained by PCR targeting CMV gB gene, should remind the possible presence of mutations in the related site and the results should be confirmed by sequence analysis.

[Investigation of herpes simplex virus (HSV) by three different methods in the clinical specimens of patients with suspected HSV infections]. / Herpes simpleks virus (HSV) enfeksiyonu süphesi olan hastalarin klinik orneklerinde uç farkli yöntemle HSV varliginin arastirilmasi.

Herpes simplex virus (HSV) infections are a common clinical problem worldwide. HSV infections have a severe and rapidly progressive course especially in immunocompromised patients, leading to significant morbidity and mortality. Therefore, rapid and reliable laboratory diagnosis of HSV infections is of crucial importance for the initiation of early antiviral therapy. In this study the aim was to investigate the presence of HSV type 1 and type 2 in clinical specimens by cell culture, in-house polymerase chain reaction (PCR) and direct fluorescein antibody (DFA) methods. The study was conducted at Erciyes University Gevher Nesibe Hospitals between March 2006 and june 2007. A total of 65 clinical specimens, 38 of them being cerebrospinal fluid (CSF) samples obtained from meningoencephalitis suspected cases and 27 being vesicular/conjunctival/genital swabs obtained from patients with different clinical presentations (13 herpes labialis, 5 keratoconjunctivitis, 4 gingivostomatitis, 3 eczama herpeticum, 1 herpetic whitlow, 1 genital ulcer). The age range of the 65 patients varied between 1-68 years, 20 being children. All the samples except CSF were investigated by 3 of the test methods, however, CSF samples were tested only by cell culture and PCR since DFA is not recommended. HSV was found positive in 48.1% (13/27) of the 27 swab specimens by DFA, in 66.6% (18/27) by PCR and in 51.8% (14/27) cytopathic effect consistent with HSV was observed. HSV positivity was detected in 7.8% (3/38) of the 38 CSF specimens by cell culture and in 47.4% (18/38) by in-house PCR. Viral growth in cell cultures showing cytopathic effect were further confirmed by DFA method using HSV-1 and HSV-2 specific fluorescein monoclonal antibodies (Monofluo, Bio-Rad Laboratories, USA). Agreement between the methods were investigated by Kappa analysis. Moderate level agreement was determined for both swab (K = 0.7) and CSF (K = 0.6) specimens for the tested methods when cell culture was considered as the reference method. In conclusion for swab specimens, primarily DFA which is a practical and rapid method, could be applied. This step might be followed by PCR and cell culture techniques sequentially. On the other hand CSF specimens should be investigated by the rapid and more sensitive PCR method.

[The investigation of Toxoplasma gondii seropositivity in women in the Kayseri province]. / Kayseri'de kadinlarda Toxoplasma gondii seropozitifliginin arastirilmasi.

Toxoplasmosis is a parasitic disease caused by a protozoon, Toxoplasma gondii. Its prevalence varies according to geographical status, age, eating habits and life style. The aim of this study was to determine seropositivity of Toxoplasma gondii in women who presented at the Kayseri Obstetric and Children Hospital. Anti-Toxoplasma IgG and IgM antibodies were investigated with the microparticle enzyme immunoassay (MEIA) method in sera of 2235 women from August 2005 to December 2008. It was found that Toxoplasma seropositivity was 33.42% and that increases in the seropositivity rate is statistically significant in regard to the increase in age (p<0.05).

In vitro pharmacodynamic activities of root canal sealers on Enterococcus faecalis.

AIM: The aim of this study was to evaluate the antimicrobial efficiency of different root canal sealers on Enterococcus faecalis (E. Faecalis) at different time intervals. METHODS AND MATERIALS: All sealers used were mixed according to the manufacturers' instructions then 75 mg of each sealer was added to different sterile tubes and evaluated at 20 minutes, 24 hours, 7 days, and 30 days. A time-kill assay (TKA) was used to determine the antimicrobial efficiency of the sealers. RESULTS: AH Plus and MCS were found to be bactericidal at 20 minutes and 24 hours, but only MCS was bactericidal at the seventh and thirtieth days. Epiphany and Sealapex were found to be bacteriostatic at the seventh and thirtieth days but indifferent at 20 minutes and 24-hours. MCS and AH Plus were both found to be bactericidal in freshly mixed samples, but only MCS was bactericidal at longer time periods. Epiphany Sealer and Sealapex were found to be bacteriostatic at longer time periods but indifferent at 20 minutes and 24 hours. CONCLUSION: The antibacterial effect of MCS was greater than the other sealers evaluated. CLINICAL SIGNIFICANCE: Sealers containing eugenol and epoxy resin might be preferable due to their antibacterial effect.