[Postmortem Molecular Epidemiology of HIV-1 Strains Isolated in Turkey]. / Türkiye'de Postmortem Izole Edilen HIV-1 Suslarinda Moleküler Epidemiyoloji.

Human immunodeficiency virus (HIV) comprises two genotypes, namely HIV-1 (group M, N, O and P) and HIV-2 (group A to H), which differ in their envelope glycoproteins and other antigenic epitopes despite their morphological and biological resemblance.Group M of HIV-1 responsible for 95% of HIV infections worldwide is composed of nine subgroups. In addition to subgroups, group M contains also two recombinant forms, known as circulating recombinant form (CRF) and unique recombinant form (URF). The first case of HIV/acquired immun deficiency virus (AIDS) in Turkey was reported in 1985 and the current number of cases reached a total of 18.557 including 1736 with AIDS based upon the surveillance data of Ministry of Health between October 1985 and November 2018. The aim of this study was to determine the prevalence of HIV-1 strains isolated from HIV positive autopsy cases detected by HIV polymerase chain reaction (PCR) and determine drug resistance. Twenty eight cases [17 males, 11 female: age ranged between 3 months and 66 years (median: 35 years)] found to be HIV positive among the autopsy cases sent for HIV1 PCR study and serological screening between 2011-2017 were recruited in the study. For identification of subtypes in HIV-1 isolates, most-preferred analysis tool was used [HIVdb Stanford University Genotypic Resistance Interpretation Algorithm (www.hivdb.stanford.edu)]. Phylogenetic tree was made according to direct sequencing of HIV-1 reverse transcriptase (pol) region and phylogenetic analysis was evaluated in 23 cases. Los Alamos National Laboratory were trimmed from full-length genomes. Phylogenetic analysis of the 870 base pair of the pol gene region was performed using CLC Sequence Viewer v8.0 (Qiagen Aarhus A/S, www.qiagenbioinformatics.com) software. The phylogenetic tree was obtained according to the neighbor-joining method and the Jukes-Cantor nucleotide distance scale and bootstrap value was set at 1000. In our study, subtype B was found to be most frequent type (39.3%; 11/28). Subtype A (17.9%; 5/28), CRF02_AG (14.3%; 4/28), subtype C (10.7%; 3/28), B+CRF02_AG recombinant (3.6%; 1/28), CRF01_AE (3.6%; 1/28), subtype D (3.6%; 1/28), as well as subtype F (3.6%; 1/28) and subtype G (3.6%; 1/28) strains were also detected in the circulation. Analysis of our results showed that 32.1% (9/28) of the samples exhibited resistance mutations. Detected mutations were as follows: M41L, T215C, K65R, M184V, responsible for nucleoside reverse transcriptase inhibitor (NRTI) resistance; K103N, Y181C, G190A, responsible for non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance; D30N, M46I, responsible for protease inhibitor (PI) resistance. NRTI, NNRTI and PI mutation rates in the samples were found as 21.4%, 7.1% and 3.6%, respectively. Although number of samples analyzed in our study is low, we can propose that they resemble the strains circulating in Turkey. The results of our study; although the subtype B is still dominant in our country, it supports other studies reporting that there are non-B subtypes and an increase in CRF rates in recent years. Phylogenetic analysis is widely regarded as the gold standard technique to determine the subtypes of HIV-1. Molecular epidemiologic studies related to HIV may be important in monitoring HIV subtype patterns and spreading pathways in that country. As a result; the opportunity to collect postmortem HIV sequences in a database appears to have occurred, and as this database expands, its usability is available. Therefore, it is thought that HIV subtypes and mutation information may be useful.

[Investigation of viral respiratory tract infection agents by multiplex PCR method in autopsy cases: A five-year study]. / Otopsi olgularinda viral solunum yolu enfeksiyonu etkenlerinin multipleks PCR yöntemi ile arastirilmasi: bes yillik bir çalisma.

Viral respiratory infections are one of the leading causes of morbidity and mortality, especially in children, elderly and immunocompromised patients. The inclusion of post-mortem studies to diagnose the infection causing mortality could be beneficial in specifying new pathogens and determining strategies for treatment and prevention. The aim of this study was to research viral etiology by applying multiplex real-time polymerase chain reaction (Rt-PCR) method in autopsy cases who have been considered to have a respiratory infection and to assess whether the viruses detected are the primary cause of the infection and whether they have any contributory effect on the mortality together with histopathological evidence. In this study, we included a total of 834 cases consisting of sudden death cases from infantile-pediatric age group and autopsy cases from > 18 year age group with suspected respiratory tract infection in our laboratory between January 2013 and May 2017. Of 834 cases, 468 (56.1%) were male and 366 (43.9%) were female, there were 191 (22.9%) cases between 0-1 months, 593 (71.1%) cases between 1 month-18 years, and 50 (6%) cases in the > 18 years age group. In 728 of 834 (87.3%) cases nasopharyngeal/tracheal swab samples and in 106 (12.7%) of them paraffin-embedded lung tissue samples were studied by the use of "FTD Respiratory 21 (Fast-Tract Diagnostics Luxemburg)" kit, with multiplex Rt-PCR method. The post-mortem samples were evaluated for human rhinovirus (HRV), parainfluenza viruses (PIV) (1, 2, 3, 4), influenza virus type A and B (INF-A, INF-B), enterovirus (EV), human bocavirus (HBoV), adenovirus (AdV), human coronavirus (HCoV 229,63,HKU,43), human metapneumovirus A ve B (HMPV-A/B), parechovirus, respiratory syncytial virus (RSV A/B) and Mycoplasma pneumoniae. In our study, at least one respiratory virus was detected by Rt-PCR in 379 (45.4%) of total 834 cases, whereas no viral agent was identified in 455 (54.6%) of the cases. One viral agent was detected in 278 (33.3%), two viral agents were detected in 83 (9.94%) and three viral agents were detected in 18 (2.16%) cases. Overall, the most common viral agent was HRV 110 (13.2%) followed by AdV 39 (4.7%) and RSV A/B 33 (4%). In pediatric cases the rate of positive results for respiratory viruses was 31.8% and in adult group it was 20% (p= 0.032). The most common virus detected among children was HRV and INF-A in adult group. In 101 (12.1%) cases infections caused by two or three agents were diagnosed. Infections with two causative agents were detected as 2.6% (5/191) in 0-1 month age group, 13% (77/593) in 1 month-18 year age group and 2% (1/50) in > 18 age group. The most frequently observed co-infections with double causative agents were HRV and INF-B, HRV and PIV, HRV and HBoV, HRV and AdV combinations. Infections with three causative agents were detected completely among 1 month-18 year age [3% (18/593)] group. In our study, 318 (38.1%) cases had no signs of infection in the postmortem histopathological examination of the lung tissues, while the most common finding was lobular pneumonia/purulent bronchitis in 233 (28%) cases and the second was interstitial pneumonia in 168 (20.1%) cases. When all cases were evaluated in terms of infection, positive results were detected in 469 (56.2%) cases. As a result; postmortem microbiological diagnosis with autopsy and histopathological detection of the patients who are thought to have respiratory tract infection will also determine the infectious agents causing death.

Cardiac Findings of Pulmonary Thromboembolism by Autopsy: A Review of 48 Cases.

BACKGROUND To identify the overall effects of pulmonary thromboembolism (PTE) on the heart, we evaluated the heart findings and clinical characteristics of deceased patients diagnosed with PTE. MATERIAL AND METHODS PTEs were classified into 2 categories: fatal and contributory. Cases with a history of cardiopulmonary disease or a finding of significant disease at autopsy, including valvular heart disease and coronary artery obstruction >50%, were excluded from the cardiac evaluation. We defined an LV wall ≥1.2 cm thick and an RV wall ≥0.8 cm thick as abnormal. RESULTS Forty-eight cases were included to the study (21 males and 27 females). The mean age was 41.42 ± 16.5 years. Of the 48 cases, 5 were excluded due to cardiopulmonary diseases for determining heart findings. The thicknesses of the LV and RV walls were not measured in some patients. In the 43 cases, cardiac hypertrophy was detected in 28 patients (65.1%). The mean heart weight was 387 ± 83.5 g. The mean thickness of the left ventricle (LV) wall was 1.40 ± 0.41 cm in 40 cases, and the mean thickness of the RV wall was 0.41 ± 0.135 cm in 41 cases. The LV walls of 35 (87.5%) cases and the RV walls of 2 cases met criteria for abnormal wall thickness. There were histopathological findings of heart in 24/43 cases (56%); these findings were necrosis, fibrosis, and hypertrophy. CONCLUSIONS The RV is affected by massive pulmonary embolism; however, the LV may also play a role in the pathogenesis of PTE.

Postmortem pathological changes in extrapulmonary organs in SARS-CoV-2 rt-PCR-positive cases: a single-center experience.

BACKGROUND: Although the lung is seen as the main target organ affected by SARS-CoV-2, other organs are also damaged. AIM: We aimed to determine the extrapulmonary findings of autopsies performed on cases with positive results with postmortem polymerase chain reaction test. METHODS: Pathological changes in extrapulmonary organs were examined with light microscopy. RESULTS: Heart, liver, spleen, kidney, pancreas, and central nervous system samples of these cases were evaluated. About 80% of the cases were men, and 20% were women. In the examination of heart, 28 of the cases had scar, 14 had acute myocardial infarction, 6 had acute and previous myocardial infarction findings, 2 had myocarditis, and 4 had interstitial mononuclear inflammatory cell infiltration. In the examination of the liver, portal inflammation was observed in 84 of the cases, steatosis in 54, centrilobular necrosis in 9, and capillary endotheliitis in the portal area in 7 of them. In the evaluation of the kidney, 37 cases had chronic pyelonephritis, 36 had tubular damage, 15 had tubulointerstitial necrosis, 16 had subcapsular microhemorrhage, 10 had capillary endothelitis, and 9 had a microvascular fibrin trombosis in their glomerular capillaries. In the central nervous system, 8 cases had infarction and liquefaction, 56 had perivascular petechial hemorrhage, 54 had acute hypoxic ischemic change, 3 had parenchymal microhemorrhage, and 52 had capillary endotheliitis. CONCLUSION: Autopsies play an important role in systematically examining the damage caused by the virus in all organs in order to elucidate the pathogenesis of SARS-CoV-2 infection and contribute to the clinical management of infected patients.

COVID-19 autopsies of Istanbul.

BACKGROUND/AIMS: The aim of this study is to share autopsy findings of COVID-19-positive cases and autopsy algorithms for safely handling of suspicious bodies during this pandemic. METHODS: COVID-19-positive cases of Istanbul Morgue Department were retrospectively analyzed. Sampling indications for PCR tests in suspicious deaths, macroscopic and microscopic findings obtained in cases with positive PCR tests were evaluated. RESULTS: In the morgue department, 345(25.8%) of overall 1336 autopsy cases were tested for COVID-19. PCR test was found positive in 26 cases. Limited autopsy procedure was performed in 7 cases, while the cause of death was determined by external examination in the remaining 19 cases. Male-to-female ratio was found 3.3:1 and mean age was 60.0 ± 13.6 among all PCR-positive cases. Cause of death was determined as viral pneumonia in fully autopsied cases. Most common findings were sticky gelatinous fluid in cavities and firm and swollen lungs, varying degrees of consolidation. In microscopy, diffuse alveolar epithelial damage, type-II pneumocyte hyperplasia, hyaline membrane formation, fibrinous exudate, and fibrinous plaques in the alveoli were the most common findings. CONCLUSIONS: In COVID-19 autopsies, pulmonary findings were found to be prominent and the main pathology was pneumonia. Older age and findings of chronic diseases indicate that the cases were in the multirisk group in terms of COVID-19 mortality.

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.

Postoperative keratitis due to Paecilomyces: a rare pediatric case.

Fungal infections like Paecilomyces keratitis have emerged in childhood recently. The diagnosis and treatment of Paecilomyces keratitis is difficult and the outcome is usually poor. Corneal culture should be performed on fungal media such as Sabouraud glucose neopeptone agar (SDA) as soon as possible for diagnosis. We report a rare case of Paecilomyces keratitis in an immunocompetent child, which was unresponsive to amphotericin B. The case was managed by a multidisciplinary approach involving the departments of ophthalmology, microbiology and pediatric infectious diseases. We want to draw attention once again that fungal keratitis caused by unusual agents are increasing. Physicians should consider fungal causes of keratitis, in patients with some predisposing factors like ocular surgery and prolonged use of topical corticosteroids.

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.

Detection of Human Bocavirus DNA by Multiplex PCR Analysis: Postmortem Case Report.

BACKGROUND: Human bocavirus (HBoV) is a virus belonging to the Parvoviridae family, which has been newly discovered to be associated with respiratory tract infections in children. There are many reports worldwide on the endemicity of this virus. Since it is relatively new, it is not routinely detected in clinical laboratory investigations. CASE REPORT: We demonstrated that HBoV infection caused the death of a 5-month-old girl with a history of high fever and wheezing. Human bocavirus (HBoV 1/2/3/4) was found in a nasopharyngeal swab, paraffin-embedded lung tissue and stool samples by multiplex PCR methods using postmortem microbiological analysis. CONCLUSION: This case suggests that lower respiratory tract infections due to HBoV may cause severe and life-threatening diseases. Postmortem microbiology is useful in both clinical and forensic autopsies, and allows a suspected infection to be confirmed. To our knowledge, this report is the first document of a HBoV postmortem case in Turkey.

Determination of standard number, size and weight of mediastinal lymph nodes in postmortem examinations: reflection on lung cancer surgery.

BACKGROUND: Mediastinal lymph node dissection is an essential component of lung cancer surgery. Literature lacks established information regarding the number and size of the healthy lymph nodes. In this postmortem autopsy study, we aim to define the number, size and weight of the lymph nodes in each mediastinal lymph node station. To implement the data for the clinical practice, we analyzed the possible number of nodes to be dissected in a systematic mediastinal lymph node dissection from the right and left sides during lung cancer surgery. METHODS: Sixty-two samples obtained from cadavers who did not die from chest malignancies, extrathoracic malignancies, any kind of infections or previous hospitalization before the death were included to the study. The locations of the nodes were recorded according to the American Thoracic Society Mediastinal Lymph Node Map. The number, size and weight of the nodes were determined at each station. RESULTS: Median age of the cadavers was 39 years. Primary causes of death were asphyxia in 10 (16.1%) subjects, trauma in 29 (46.8%) subjects, cardiovascular problems in 10 (16.1%) subjects, and undetermined in 13 (21%) subjects. The median number of lymph nodes resected from each patient was 23 (range: 11-54). The right sided paratracheal lymph nodes (Station 2R and 4R) were more frequent, heavier and longer than left sided lymph nodes (Station 2L and 4L) at the paratrecheal region. Right sided inferior mediastinal lymph nodes were heavier and longer than the left ones; however, their availability was more often on the left. CONCLUSIONS: The properties of mediastinal lymph nodes at particular stations are different for number, size and weight. Station 4R and 7 have the highest number of nodes followed by stations 5 and 6. We recommend removing the lymph nodes of these stations completely in lung cancer patients to rule out the possibility of micrometastatic disease. Diameter of normal lymph node may be 1 cm for the stations other than 4R and 7, but the definition of normal diameter of a lymph node at the stations 4R and 7 may be changed as 1,5 cm and 2,0 cm, respectively. Weight of the nodes may be a new subject to study and may be defined as a new modality to define a staging to be more accurate and the issue needs further investigations.