Development of pseudotyped VSV-SARS-CoV-2 spike variants for the assessment of neutralizing antibodies.

Aim: Serological studies with pseudotyped viruses offer a safer alternative to live SARS-CoV-2 in evaluating neutralizing antibodies, enabling research in standard labs.Methods: The SARS-CoV-2 Spike pseudotyped vesicular stomatitis virus (VSV) pseudoviruses were generated using Spike of Wuhan strain and two variants (B.1.1.7, B.1.351) and utilized to evaluate the serum neutralizing activity of human plasma samples of vaccinated (n = 13) and healthy people (n = 2) compared with a plaque assay with authentic virus.Results: Neutralizing titer of convalescent plasma resulted with a good correlation (R2 = 0.7).Conclusion: We evaluated a safe and reliable pseudotyped virus system that effectively mimics authentic virus and correlates well with traditional assays. The developed system allows easier testing of variants and has the potential to improve vaccine development.

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Frequency of Human Leukocyte Antigen-B*57:01 Allele Carriers in People Living with HIV/AIDS in Türkiye.

INTRODUCTION: Abacavir is among the first-line initial antiretroviral regimens for most patients living with HIV/AIDS (PLWHA). Although well tolerated, it is associated with hypersensitivity reaction (HSR), which is treatment-limiting and potentially life-threatening. HSR was shown to be associated with the class I MHC allele, HLA-B*57:01. In this study, we aimed to evaluate the prevalence of HLA-B*57:01 in PLWHA in Istanbul, Türkiye. MATERIAL AND METHODS: Five HIV treatment centers in Istanbul included all sequential treatmentnaïve, ≥ 18 years adult PLWHA, between December 2017- December 2021. Demographic, clinical, and laboratory data were collected at baseline and during treatment. HLA-B* 57:01 genotyping was determined with PCR-SSP. RESULTS: Eight hundred sixty-seven PLWHA were included (male:91%, mean age 39.6±11.1 years). 1.6% of patients were found to be HLA-B*57:01 positive. Among HLA-B*57:01 positive patients, 4 were initially given abacavir-containing treatment; they were switched to non-abacavir treatment upon the allele found to be positive. CONCLUSION: Although previous studies reported the HLA-B*57:01 prevalence of PLWHA in Türkiye as 3-3.6%, we have found the prevalence to be 1.6%. The current study includes higher numbers of patients than the previous studies. Furthermore, patients from all over the country apply to the centers in Istanbul; compared to the other studies, which involve patients limited to the relevant regions. It can be assumed that the number in our cohort is more representative of the country. In conclusion, the prevalence of the HLA-B*57:01 allele in PLWHA in this study is relatively low. With evident benefit in preventing abacavir HSR, HLA-B*57:01 should be screened in planning antiretroviral therapy.

Resistance Genes and Mortality in Carbapenem-resistant Klebsiella pneumoniae Bacteremias: Effects of the COVID-19 Pandemic

Background: Emerging carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) (CRKP) bacteremias are presenting significant public health risks due to limited treatment options and increased mortality. K. pneumoniae isolates exhibit carbapenem resistance rates that vary from 25% to 50% throughout the European continent, including our country. Aims: To assess the characteristics of CRKP bacteremia, a condition that has recently demonstrated an increasing prevalence in our center. We sought to ascertain the resistance rates of isolated strains to antibiotics other than carbapenems, identify the responsible carbapenemase genes, evaluate the efficacy of antibiotics, determine mortality rates, explore clonality among strains, and investigate the influence of the COVID-19 pandemic on all these factors. Study Design: Retrospective observational study. Methods: This study included patients aged 18 and older who had experienced meropenem-resistant K. pneumoniae bacteremia. Meropenem resistance was confirmed by employing the Kirby-Bauer disk diffusion method. Meropenem minimum inhibitory concentration (MIC) levels were determined using the gradient test, while colistin MIC levels were ascertained using the disk elution technique. Carbapenemase genes were evaluated via colony polymerase chain reaction (PCR), and clonality analysis was performed using the arbitrarily primed PCR technique. Results: The study comprised 230 patients, with a mean age of 63.1 ± 15.9 years, of whom 58.7% were male. Oxacillinase-48 (OXA-48) was detected in 74.8% of the patients, New Delhi metallo-beta-lactamase (NDM) in 12.6%, OXA-48 + NDM in 7.8%, and KPC in 4.8%. The 14-day and 30-day mortality rates were 57% and 69.6%, respectively. Multivariate analysis of the 30-day mortality revealed several crucial factors, including bacteremia development in the intensive care unit, the occurrence of bacteremia during the COVID-19 pandemic, polymicrobial bacteremia, the use of indwelling intravenous catheters, a platelet count of ≤ 140,000/µl, procalcitonin levels of ≥ 6 µg/l, and a Charlson comorbidity score ≥ 3. Notably, the OXA-48 and KPC genes were upregulated significantly during the COVID-19 pandemic, while the NDM gene groups were downregulated. Additionally, both 14-day and 30-day mortality rates increased significantly. Conclusion: In this study, the most prevalent carbapenemase gene was OXA-48; however, there has been a recent increase in KPC genes. No dominant epidemic strain was identified through clonality analysis. The clustering rate was 68% before the pandemic, increasing to 85.7% during the pandemic. The significance of infection control measures is underscored by the rise in both clustering and mortality rates during the COVID-19 pandemic.

Urinary tract infections in older adults: associated factors for extended-spectrum beta-lactamase production.

Objective: Urinary tract infections (UTIs) due to extended-spectrum beta-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae are among the leading causes of morbidity and mortality in older adults. Identifying associated factors for ESBL production may contribute to more appropriate empirical treatment. Materials and methods: This was a prospective observational study. Hospitalized patients of age > 65 with community-onset or hospital-acquired upper UTI due to E. coli or Klebsiella pneumoniae were included. A multivariate analysis was performed. Results: A total of 97 patients were included. ESBL prevalence among UTIs with E. coli or Klebsiella pneumoniae was 69.1% (n = 67). CRP values at the time of UTI diagnosis were found to be significantly higher in the ESBL-producing group (p = 0.004). The multivariate analysis revealed that male gender (OR: 2.72, CI: 1.02-7.25), prior recurrent UTI (OR: 3.14, CI: 1.21-8.14), and the development of secondary bacteremia (OR: 4.95, CI: 1.03-23.89) were major associated factors for UTI in older adults due to ESBL-producing E. coli and Klebsiella pneumoniae. Conclusion: Severe UTI in older men with a history of recurrent UTI may be a warning to the clinician for ESBL production in the setting of high ESBL prevalence. Carbapenems may be prioritized in the empirical treatment of patients with known risk factors for ESBL.

Bone Metabolism in Men who Live with HIV Aged 50 years and Over: Impact of Infection Duration.

BACKGROUND: Early diagnosis and effective antiretroviral therapy (ART) lead to similar life expectancy in people living with HIV (PLWH) compared to the general population. This population faces problems such as decreased bone mineral density (BMD) and increased fracture risk. The aim of this study was to determine the prevalence of osteoporosis in men aged 50 years and over who were PLWH and to determine risk factors and changes in bone metabolism with bone turnover markers. METHODS: 79 male PLWH aged 50 years and over were followed up in our outpatient clinic between May 2021 and October 2021. The patients' demographic, clinical, laboratory, and DEXA data were analyzed. Serum levels of bone turnover markers were measured. RESULTS: The prevalence of osteopenia, osteoporosis, and normal BMD was found to be 55.7%, 13.9%, and 30.4%, respectively. A correlation was found between low BMD and low body mass index, elapsed time since diagnosis of HIV infection, high rate of use of ART, and long usage time of tenofovir disoproxil fumarate + protease inhibitor. A one-year increase in HIV infection duration was associated with an increased risk of low BMD by 1.246. CONCLUSION: Compared to studies conducted on the general population, the prevalence of osteoporosis in male PLWH aged 50 years and older was two times higher. The limited effect of the duration of ART use on low BMD may be due to the patients' histories of replacement therapy. Therefore, to eliminate the negative effects of ART on BMD, it may be beneficial to start replacement therapy when necessary.

Talaromyces marneffei infection in an HIV infected patient with hematological malignancy - first report from Turkey.

T.marneffei, encountered mostly in Southeast Asia, leads to a systemic infection, especially in immunocompromised individuals such as HIV-infected patients with low CD4 level. A 32-year-old male patient, residing in Hong Kong for the last two years, admitted with fever, cough, weakness, and weight loss. Physical examination revealed bilateral cervical and axillary multiple lymph nodes and hepatosplenomegaly. Screening of the pancytopenic patient revealed HIV infection. Histopathological examination of the cervical lymph node revealed plasmoblastic lymphoma. Blood and urine cultures remained sterile. Antiretroviral therapy was started. Fungal hyphae were detected in Gram staining of hemocultures taken in the third week due to ongoing fever, and antifungal therapy was started empirically. Red pigment around colonies on Sabouraud dextrose agar and microscopic appearance arose suspicion of Talaromyces spp. T.marneffei was identified by ITS 1-4 sequence analysis. Chemotherapy was started when fungemia was controlled. On the fifth day of chemotherapy, the patient's general condition deteriorated, broad-spectrum antibiotics were started and the patient was transferred to ICU. The cultures remained sterile and he expired five days later. In conclusion, although talaromycosis is not endemic in Turkey, it should be considered in patients with travel history to endemic regions and/or an underlying immunosuppressive disease such as HIV infection.

Discontinuation of Nucleos(t)ide Analog treatment in HBeAg-Negative Non-Cirrhotic Chronic Hepatitis B Patients: Real-Life Data of 20 Years.

BACKGROUND/AIMS: Discontinuation of nucleos(t)ide analog is controversial in HBeAg-negative chronic hepatitis B patients not achieved HBsAg loss. We aimed to evaluate re-treatment rates and risk factors in non-cirrhotic HbeAg-negative chronic hepatitis B patients for whom nucleosi(t)ides analogs were discontinued. MATERIALS AND METHODS: Demographic, clinical, and laboratory data before and at the end after discontinuation of nucleos(t)ide analogs were collected retrospectively. RESULTS: Seventy-two patients followed up between January 2000 and December 2019 were included; 43 were male, with a mean age of 46.3 (±10.8). Baseline median alanine aminotransferase (ALT) and hepatitis B virus DNA levels were 55.5 IU/L and 465 925 IU/mL, respectively. The median histologic activity index was 5.5 and the fibrosis score was 2. The median duration of treatment and consolidation therapy were 59 and 56 months, respectively. The median follow-up time after discontinuation of treatment was 55 months. Among 56 patients eligible for evaluation according to proposed re-treatment criteria, 29 (51.7%) patients were re-treated. The median time for relapse was 11 months. Re-treatment was significantly common in males (P = .034) and patients treated with tenofovir/entecavir (P = .04). Baseline hepatitis B virus DNA and levels of ALT, aspartate aminotransferase (AST) at the third and sixth months of treatment and at the end of treatment were statistically significantly higher in re-treated patients. A cutoff value of ≥405 000 IU/L for hepatitis B virus DNA discriminated patients for re-treatment. HBsAg was lost permanently in 2 non-re-treated patients. CONCLUSION: In resource-limited areas where follow-up of HBsAg or other markers is not possible, nucleos(t)ide analog discontinuation can be considered in patients in the early stage, with low baseline hepatitis B virus DNA and ALT levels, after a long consolidation therapy.

Factors Influencing HIV Infection in Children Born to HIV-Infected Mothers in Turkey

Background: Human immunodeficiency virus (HIV) is still a challenge for children. About 15 to 45% of the HIV positive pregnant women can transmit the virus to their children during pregnancy, delivery and/or breastfeeding. The risk of transmission can be decreased my several measures. Aims: To identify factors associated with HIV infection in children born to HIV-infected mothers. Study Design: A multi-center retrospective cohort study. Methods: A ten-year retrospective cohort study in five dedicated HIV centers was conducted. The 325 women in our cohort were between the ages of 18 and 45. During the study period, 44 (13.5%) of these women gave birth and 51 babies were born. Of the 51 infants, 7 (13.7%) were HIV/AIDS positive. Results: Among the factors studied, breastfeeding, having a HIV-positive sibling and being on antiretroviral treatment during pregnancy and detectable HIV-RNA during delivery were found statistically significant. A multivariable logistic regression analysis showed that being on antiretroviral treatment during pregnancy is the most important predictor of mother-to-child transmission. Conclusion: Mother-to-child transmission appears to be an important route of HIV transmission in Turkey. Lack of antiretroviral treatment during pregnancy appears to be a key factor in transmission.

Comparison of Hospitalized COVID-19 Patients in Terms of Disease Course According to the Presence of Gastrointestinal Symptoms Before and After Admission.

BACKGROUND: This study aimed to find the prevalence of gastrointestinal symptoms in hospitalized COVID-19 patients and to investigate the effects of gastrointestinal symptoms on the course of the disease during hospitalization. METHODS: Patients who were hospitalized due to COVID-19 were included in this retrospective study. The diagnostic method of COVID-19 was either a positive reverse transcription polymerase chain reaction test or a typical finding in chest computed tomography. This study was conducted by contacting patients by phone 1 month after they were discharged from hospital to investigate gastrointestinal symptoms. Patients' laboratory findings at the time of admission, medications they used, and clinical findings were obtained from hospital records retrospectively. Patients with gastrointestinal symptoms were divided into 2 groups according to the start of treatment: pre-treatment and post-treatment groups. RESULTS: At least 1 gastrointestinal symptom (anorexia, weight loss, diarrhea, nausea, vomiting, and abdominal pain) was present in 67.5% of 435 patients (55.6% male, mean age 52.8). If anorexia and weight loss are excluded, the rate of the presence of at least 1 gastrointestinal symptom is 54%. Gastrointestinal symptoms were present in 48.9% before the initiation of COVID-19 treatment. The most prevalent 3 symptoms were anorexia, weight loss, and diarrhea (56%, 52%, and 35.6%, respectively). Presence of pre-treatment gastrointestinal symptoms was associated with elevated C-reactive protein levels. Pre-treatment gastrointestinal symptoms were more common in those who received oxygen supply and who were intubated. Resolution of gastrointestinal symptoms takes longer time in those who were admitted to intensive care unit. Weight loss and diarrhea were more common in COVID-19 patients with gastrointestinal symptoms who were intubated than who were not intubated. Abdominal pain was not found to be a significant predictor of disease severity. CONCLUSION: The prevalence of at least 1 gastrointestinal symptom in hospitalized COVID-19 patients was 67%. The most prevalent symptoms were anorexia, weight loss, and diarrhea. Presence of pre-treatment gastrointestinal symptoms was associated with elevated C-reactive protein levels, use of oxygen supply, and intubation. Gastrointestinal symptoms persist longer in those admitted to intensive care unit.

Waning immunity to inactive SARS-CoV-2 vaccine in healthcare workers: booster required.

AIMS: Despite high vaccination rates, increasing case numbers continue to be reported with the identification of new variants of concern, and the issue of durability of the vaccine-induced immune response remains hot topic. Real-life data regarding time-dependent immunogenicity of inactivated COVID-19 vaccines are scarce. We aimed to investigate the changes in the antibody at the different times after the second dose of the CoronaVac vaccine. METHODS: The study included 175 HCWs vaccinated with inactive CoronaVac (Sinovac Life Sciences, China) SARS-CoV-2 vaccine in two doses. Anti-spike/RBD IgG levels were measured first, third, and sixth months after the second dose. Chemiluminescent microparticle immunoassay (IgG II Quant test, Abbott, USA), which is 100% compatible with plaque reduction neutralization test, was used. RESULTS: Mean age of the participants was 38 ± 11.23 years (range between 22 and 66) of whom 119 (63.9%) were female, and 56 (32%) were male. Dramatic reductions were demonstrated in median antibody levels particularly in the infection-naïve group, comprising 138 HCWs compared to those with prior history of COVID-19 infection (n = 37) (p < 0.001). There was no difference between the two groups in terms of age, gender, blood groups, BMI, and comorbid diseases. CONCLUSIONS: While antibody positivity remained above 90% in the 6th month after two doses of inactivated vaccine in HCWs, the median titers of neutralizing antibodies decreased rapidly. The decrease was more rapid and significant in those with no history of prior COVID-19 infection. In this critical phase of the pandemic, where we are facing the dominance of the Omicron variant after Delta, booster doses have become vital.

Long-term follow-up of treatment-naïve HBeAg-negative patients with chronic hepatitis B.

BACKGROUND/AIMS: We aimed to explore long-term results of oral antiviral agents in treatment-naïve "HBeAg negative chronic hepatitis B (CHB)" and determine the factors affecting the complete virological response. METHOD: Patients with HBeAg-negative CHB who used oral antiviral agents for at least 3 years were evaluated retrospectively. RESULTS: A total of 173 patients were recorded. The mean duration of treatment was 62.2 ± 28.9 months. Complete virological responses (CVR) were 82.8% (n = 53/64) in tenofovir disoproxil fumarate (TDF), 84.4% (n = 49/58) in lamivudine (LAM), 83.9% (n = 26/31) in entecavir (ETV), 95% in telbivudine (LdT) (n = 19/20) (p = 0.290). Multivariate analysis revealed age ≤ 40 (p = 0.012, 95%CI = 1.38-13.76, OR = 4.36) and baseline HBV DNA value (p = 0.003, 95%CI = 1.23-2.63, OR = 1.78) as independent factors for CVR. Virological breakthrough was detected in 29 (50%) patients on LAM therapy, two (6.4%) patients on ETV therapy, and two (10%) patients on LdT therapy. Treatment was switched to another antiviral agent due to osteoporosis in four patients in the TDF group, muscle pain in nine patients in the LDT group, and headache in one patient in the ETV group. Hepatocelluler cancer was detected in five patients. HBsAg seroclearance developed in two patients. Anti-HBs seroconversion was not detected. CONCLUSION: CVR was achieved at similar rates with all four antiviral agents, while younger age (≤ 40) and low baseline viral load were the main factors for virological response. However, drug resistance and virological breakthrough in the LAM group and side effects in the LdT group were detected during the long-term follow-up. Moreover, HBsAg seroclearance was achieved at very low rates with oral antiviral agents.

Performance of noninvasive fibrosis indices in chronic hepatitis B during pretreatment and post-treatment periods.

Background: Pretreatment and post-treatment performances of noninvasive fibrosis indices were determined in patients with chronic hepatitis B. Method: This was a retrospective, single-center study. Results: The best area under the receiver operating characteristic curve values were detected for aspartate aminotransferase-to-alanine aminotransferase ratio (0.685) for ≥F2, Fibrosis Index (FI; 0.703) for ≥F3; FI (0.872) for ≥F4 and FI (0.864) for cirrhosis. After antiviral treatment, the best area under the receiver operating characteristic curve values were detected in aspartate aminotransferase-to-alanine aminotransferase ratio (0.615) for ≥F2; in FI based on four factors (FIB-4; 0.634) for ≥F3; in FIB-4 (0.678) for ≥F4 and in FIB-4 (0.814) for cirrhosis. Conclusion: FIB-4 and FI showed better performance in defining advanced fibrosis (≥F4) and cirrhosis.

Association of SARS-CoV-2 IgG Antibody Levels with Clinical/Laboratory Characteristics in COVID-19 Patients: Data from a Turkish Study.

BACKGROUND: COVID-19 causes clinical manifestations ranging from asymptomatic infection to multi-organ failure. It is reported that those with severe disease have higher anti-SARS-CoV-2 antibody titers compared to asymptomatic or mild cases. We evaluated the correlation of antibody responses with laboratory and clinical indicators in COVID-19 patients. METHODS: Seventy-nine male and 66 female patients (mean age: 39) with at least one positive SARS-CoV-2 RT-PCR test and SARS-CoV-2 IgG antibody result after acute infection were included. RESULTS: Seventy-six (52%), 45 (31%), and 24 (17%) patients had mild, moderate, and severe clinical findings, respectively. Patients with high body mass index and advanced age had significantly more severe disease (p < 0.001). A significant correlation was found between the increase in lymphopenia, C-reactive protein, ferritin, D-dimer, and lactate dehydrogenase and the severity of clinical findings (p = 0.0001). SARS-CoV-2 IgG antibody test was positive in 128 (88.3%) patients. A significant correlation was found between disease severity and antibody levels in the comparison of all groups (p < 0.001). CONCLUSIONS: Long-term monitoring of immune responses will be required to determine the appropriate time for the administration of new vaccines.

Heterologous booster COVID-19 vaccination elicited potent immune responses in HCWs.

The objective of our study was to evaluate the antibody responses of health care workers (HCWs) who were vaccinated with booster dose BNT162b2 6 months after 2 doses of the CoronoVac vaccine. The study included 318 HCWs vaccinated with inactive CoronaVac SARS-CoV-2 vaccine in 2 doses. Anti-spike/RBD IgG levels were measured immediately before and 1 month after the booster dose. In the sixth month after CoronaVac vaccination, the median of antibody levels of 1212.02 AU/ML, while it was 9283 AU/mL after BNT162b2 vaccination. IgG antibody titers of over 1050 AU/mL (which is equivalent to 1:80 dilution in the plaque reduction neutralization test) were detected in HCWs 15.09% and 97.8%, respectively. Our results showed that antibody titers increased 8-fold after the booster dose. We believe that the administration of the mRNA vaccine as a booster dose can provide more effective protection against COVID-19 infection, especially in individuals with risk factors.

Incidence, Risk Factors, and Prognosis of Bloodstream Infections in COVID-19 Patients in Intensive Care: A Single-Center Observational Study.

BACKGROUND: Critically ill COVID-19 patients are prone to bloodstream infections (BSIs). AIM: To evaluate the incidence, risk factors, and prognosis of BSIs developing in COVID-19 patients in the intensive care unit (ICU). METHODS: Patients staying at least 48 h in ICU from 22 March 2020 to 25 May 2021 were included. Demographic, clinical, and laboratory data were analyzed. RESULTS: The median age of the sample (n = 470) was 66 years (IQR 56.0-76.0), and 64% were male. The three most common comorbidities were hypertension (49.8%), diabetes mellitus (32.8%), and coronary artery disease (25.7%). Further, 252 BSI episodes developed in 179 patients, and the BSI incidence rate was 50.2 (95% CI 44.3-56.7) per 1000 patient-days. The source of BSI is central venous catheter in 42.5% and lower respiratory tract in 38.9% of the episodes. Acinetobacter baumannii (40%) and carbapenem-resistant Klebsiella pneumoniae (21%) were the most common pathogens. CRP levels were lower in patients receiving tocilizumab. Multivariable analysis revealed that continuous renal replacement therapy, extracorporeal membrane oxygenation, and treatment with a combination of methylprednisolone and tocilizumab were independent risk factors for BSI. The estimated cumulative risk of developing first BSI episode was 50% after 6 days and 100% after 25 days. Of the 179 patients, 149 (83.2%) died, and a statistically significant difference (p < 0.001) was found in the survival distribution in favor of the group without BSI. CONCLUSION: BSI is a common complication in COVID-19 patients followed in the ICU, and it can lead to mortality. Failure in infection control measures, intensive immunosuppressive treatments, and invasive interventions are among the main factors leading to BSIs.

A pan-resistant Myroides odoratimimus catheter-related bacteremia in a COVID-19 patient and review of the literature.

Myroides spp. are opportunistic environmental Gram-negative bacteria. These affect mostly immunocompromised hosts and generally lead to soft tissue, and urinary tract infections. Bacteremia most commonly develop secondary to soft tissue or catheter related infections and may lead rarely to mortality. Myroides spp. are generally suscetible to fluoroquinolones, piperacillin/tazobactam, trimethoprim/sulfamethoxazole, carbapenems or tetracyclines however, pan-resistant isolates and multiple resistance genes have been reported in clinical isolates of Myroides spp. We report a pan-resistant Myroides odoratimimus bacteremia in a patient with severe COVID-19 ending with fatality and in this context a review of reported Myroides bacteremias are also described. In this study, a 64-year old male patient with history of coronary artery bypass was admitted to ICU with severe COVID-19 pneumonia accompanied by pneumomediastinum and pneumopericardium. Continous renal replacement therapy and extracorporeal membraneous-oxygenation were initiated due to acute renal failure and persistent hypercarbia/hypoxia, respectively. Within four weeks of hospitalization various episodes of bacteremia developed and multiple antibiotics were used. On the 5th week of follow-up, acute phase reactants increased and empirical broad spectrum antibiotics were initiated. Blood culture revealed Gram-negative rods. The patient became hypotensive and despite maximum medical care he was lost due to cardiac arrest. M. odoratimimus was identified by MALDI-TOF and the bacterium was pan-resistant. According to Center for Genomic Epidemiology results the strain was identified as M. odoratimimus PR63039 and the genome analysis revealed antibiotic resistance genes associated with resistance to beta-lactams (bla OXA-347, bla MUS-1, bla EBR-1), tetracyclines (tetX), sulfonamides (sul2), macrolides (ereD), (ermF).

Human immunodeficiency virus type 1 impairs sumoylation.

During infection, the human immunodeficiency virus type 1 (HIV-1) manipulates host cell mechanisms to its advantage, thereby controlling its replication or latency, and evading immune responses. Sumoylation is an essential post-translational modification that controls vital cellular activities including proliferation, stemness, or anti-viral immunity. SUMO peptides oppose pathogen replication and mediate interferon-dependent anti-viral activities. In turn, several viruses and bacteria attack sumoylation to disarm host immune responses. Here, we show that HIV-1 impairs cellular sumoylation and targets the host SUMO E1-activating enzyme. HIV-1 expression in cultured HEK293 cells or in CD4+ Jurkat T lymphocytes diminishes sumoylation by both SUMO paralogs, SUMO1 and SUMO2/3. HIV-1 causes a sharp and specific decline in UBA2 protein levels, a subunit of the heterodimeric SUMO E1 enzyme, which likely serves to reduce the efficiency of global protein sumoylation. Furthermore, HIV-1-infected individuals display a significant reduction in total leukocyte sumoylation that is uncoupled from HIV-induced cytopenia. Because sumoylation is vital for immune function, T-cell expansion and activity, loss of sumoylation during HIV disease may contribute to immune system deterioration in patients.

Detection of SARS-CoV-2 RNA in Upper Respiratory Swap Samples by Pooling Method

Background: Widespread and effective use of molecular diagnostic tests is indispensable for protecting public health and containing the severe respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. More than 1 year into the pandemic, as resources have reached a point of depletion, grouping samples in pools of certain sizes appears to be a reasonable method to reduce both the costs and the processing time without necessitating additional training, equipment, or materials. Aims: To assess whether the pooling strategy that was used in past outbreaks and is used in blood tests prior to transfusion for screening large populations can also be used in SARS CoV-2 tests. Study Design: Diagnostic accuracy study. Methods: This prospective study was conducted with 2815 samples, sent to the coronavirus disease 2019 (COVID-19) Laboratory of our hospital between February 12 and 21, 2021, to be tested for the presence of SARS-CoV-2. The samples were examined individually and in pools of five 100 µl taken from each sequential sample, using 3 different SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) kits, the Allplex™ 2019-nCoV Assay kit (Seegene, Republic of Korea), the GeneMAP™ 2019-nCoV detection V.3 kit (GenMark, Türkiye), and the Bio-Speedy™ SARS-CoV-2 Double Gene™ RT-qPCR kit (Bioeksen, Türkiye) on the BioRAD CFX96™ Touch (Bio-Rad Laboratories Inc., Hercules, CA, USA) platform available in our laboratory. Results: Following the extraction of serial dilutions prepared from the SARS-CoV-2 RNA positive (cycle of threshold: 20) sample, the standard curves of RT-PCR were analyzed. By evaluating the efficiency (E) values, all 3 kits showed high sensitivity and similar results; while the highest level was detected with the Allplex™ 2019-nCoV Assay kit in the nucleocapsid (N) gene (E: 124%), the lowest was detected with the Double Gene™ RT-qPCR kit in the N and ORF 1ab genes (E: 90%). Of the samples included in the study, only 1 positive sample with low viral load was found to be negative when studied by pooling. The total number of kits to be used in pooled tests and then to individually retest the 5 samples in positive pools was calculated as 827 and the savings rate as 69.91% (1968/2815). Conclusion: The pooling strategy is an effective approach to extend the impact of limited testing resources and reagents available in certain periods of the COVID-19 pandemic. Testing by pooling samples requires improvement of RNA extraction methods and careful monitoring of RT-PCR test sensitivity to avoid missing low-positive entities. Therefore, based on the prevalence of COVID-19 in their regions, laboratories should conduct their own validation of pooling studies for RNA extraction and amplification methods they use.

Inactive SARS-CoV-2 vaccine generates high antibody responses in healthcare workers with and without prior infection.

BACKGROUND AND OBJECTIVES: Healthcare workers (HCWs) were among the first groups to be vaccinated in Turkey. The data to be obtained by the vaccination of HCWs would guide wide spread vaccination programs. MATERIALS AND METHODS: The study included 330 HCWs working at Istanbul University-Cerrahpasa, Cerrahpasa Medical Faculty Hospital and vaccinated with inactive CoronaVac (Sinovac Life Sciences, China) SARS-CoV-2 vaccine in two doses (28 days apart). Anti-Spike /RBD IgG levels were measured 14 days after the first dose and 28 days after the second dose. Chemiluminescent microparticle immunoassay (CMIA) (ARCHITECT IgG II Quant test, Abbott, USA), which is 100% compatible with plaque reduction neutralization test (PRNT), was used. RESULTS: Of the participants, 211 (63.9%) were female, 119 (36.1%) were male, and mean age was 39.6 ± 7.7 years. In those without prior COVID-19 history; (n = 255) antibody positivity was detected as 48.2% (95% CI: 42.1-54.3) 14 days after the first dose of vaccine, and 99.2% (95% CI: 98.1-100) at day 28 after the second dose. Antibody titers were significantly lower in patients with hypertension (p = 0.011). In those with prior history of COVID-19 (n = 75); both the antibody positivity rates after the first vaccine (48.2% vs 100%, p = 0.000) and the anti-spike/RBD antibody levels after the second vaccine (with a ≥ 1050 AU/mL titer equivalent to PRNT 1/80 dilution) was significant than infection-naive group (25.9% vs. 54.7%, p = 0.000). Antibody positivity after two doses of vaccination for all study group was 99.4% (95% CI: 98.6-100). CONCLUSIONS: Two doses CoronaVac produce effective humoral immunity in HCWs. Antibody response is significantly higher in those with prior history of COVID-19 than infection-naive group. Given no significant benefit of the second dose, a single shot of vaccination may be sufficient for those with prior history of COVID-19. Monitoring humoral and cellular immune responses, considering new variants, is required to validate this approach.

Dermatological lesions among people living with HIV in Turkey.

This study aimed to document the dermatoses and their relationships with CD4+ T lymphocyte counts and clinical stages of disease among people living with HIV followed by our Clinical Department, to investigate the effect of antiretroviral therapy (ART) on findings and to compare with real-world data. Medical records of people living with HIV were analyzed retrospectively in our outpatient clinic from January 2005 to June 2017. A total of 500 patient files were examined. 179 patients with dermatoses were included in the study. Demographic data, clinical and laboratory findings, dermatological findings, type and distribution of lesions, serological and histopathological examinations, diagnosis, treatment, and follow-up of patients were transferred to data forms. 84.4% of the patients were male and the mean age was 38.65 ± 11.6 years. The median CD4+ T lymphocyte count was 253/mm3 (range:0-1067). At least one dermatosis was present in 69.3% of the patients. Compared with their median CD4+ T lymphocyte counts, the ratio of CD4+ T lymphocytes was significantly lower in the group with three or more dermatoses (p = 0.019). Condyloma acuminatum (15.1%), drug eruption (13.4%), seborrheic dermatitis (11.7%), oral candidiasis (11.2%), dermatophytoses (11.2%), syphilis (8.4%), Kaposi's sarcoma (8.4%), and telogen effluvium (8.4%) were the most common dermatoses. Kaposi sarcoma (KS), oral candidiasis, onychomycosis, and molluscum contagiosum were significantly higher in the CD4+ T lymphocyte <200/mm³ group when CD4+ T lymphocyte threshold value was determined as 200/mm³. Compared with other TDF/FTC-containing regimens, a significantly higher proportion of alopecia was reported in patients receiving TDF/FTC/EVG/c (p = 0.007). Dermatoses may be a good clinical marker for detecting clinical stage and diagnosing HIV infection; also, there may be a significant increase in the number of dermatoses in advanced stages. Although there are only a few studies in the literature, it should be kept in mind that ART-associated alopecia rates may increase nowadays when ART is targeted at everyone.