Investigation of drug resistance against protease, reverse transcriptase, and integrase inhibitors by next-generation sequencing in HIV-positive patients.

Our aim was to investigate the mutations in protease (PR), reverse transcriptase (RT), and integrase (IN) gene regions in human immunodeficiency virus (HIV) using a single amplicon via next-generation sequencing (NGS). The study included plasma samples from 49 HIV-1-positive patients, which were referred for HIV-1 drug resistance testing during 2017. A nested polymerase chain reaction (PCR) was performed after the RNA extraction and one-step reverse transcription stages. The sequencing of the HIV genome in the PR, RT, and IN gene regions was carried out using MiSeq NGS technology. Sanger sequencing (SS) was used to analyze resistance mutations in the PR and RT gene regions using a ViroSeq HIV-1 Genotyping System. PCR products were analyzed with an ABI3500 GeneticAnalyzer (Applied Biosystems). Resistance mutations detected with NGS at frequencies above 20% were identical to the SS results. Resistance to at least one antiretroviral (ARV) drug was 22.4% (11 of 49) with NGS and 10.2% (5 of 49) with SS. At least one low-frequency resistance mutation was detected in 18.3% (9 of 49) of the samples. Low-frequency resistance mutations resulted in virological failure in only one patient. The cost of the analyses was reduced by sample pooling and multiplex analysis using the MiSeq system. This is the first study in Turkey to use NGS technologies for the detection of resistance mutations in all three gene (PR, RT, IN) regions using a single amplicon. Our findings suggest that NGS is more sensitive and cost-effective than the SS method.

Nosocomial Non-fermentative gram negative bacteria bloodstream infections in children; Risk factors and clinical outcomes of carbapenem resistance.

INTRODUCTION: Non-fermentative Gram-negative bacterias (NFGNBs) are a major cause of life threatening infections in hospitalized children. In this study, we aimed to evaluate the demographic and clinical characteristics of NFGNBs infections and identify the risk factors and outcomes of bloodstream infections (BSIs) caused by carbapenem-resistant (CR) NFGNBs infections. METHODS: A retrospective cohort was designed to evaluate the patients with a BSI caused by NFGNBs between in January 2014 and December 2017. RESULTS: A total of 131 episodes from 115 patients were evaluated. The mean age of the patients was 4.79±(4.74) year. The most commonly isolated NFGNBs species was Acinetobacter spp. (35.9%), Pseudomonas spp. (34.4%), and Stenotrophomonas maltophilia (13%). The rate of carbapenem-resistance was 38.2% in Acinetobacter spp. and 26.6% in Pseudomonas spp. The comparison of CR group with carbapenem-susceptible (CS) group showed statistical significance for the length of hospital stay prior to onset of infection and total hospital stay (P values were 0.001, 0.008). Based on the univariate analysis, requirement of mechanical ventilation, central venous catheter, nasogastric tube, Foley catheter, severe neutropenia (<100/mm3), prolonged neutropenia (≥14 days), prior intensive care unit admission and prior antimicrobial treatment (carbapenems, colistin, glycopeptide) were more common in carbapenem-resistant NFGNBs infections (P values are 0.001, 0.012, 0.000, 0.005, 0.042, 0.027, 0.007, 0.007). In patients with NFGNBs infections 14-day and 30-day mortality rates were %16.8 and 21.4%. CONCLUSION: CR infections were more common in children with prolonged and severe neutropenia. Prior antimicrobial use and intensive care unit admission were more common in CR infections.

Clinical Reflections of Acinetobacter Infections in Children in a Quaternary-Care Hospital: A Five-Year Single-Center Experience.

OBJECTIVE: This study aimed to determine the epidemiology of Acinetobacter species in the last 5 years, the clinical diseases caused by the pathogen, the possible risk factors for infection, and the resistance pattern of the microorganism in our quaternary-care hospital. MATERIALS AND METHODS: In this retrospective cohort study, 67 pediatric cases infected with Acinetobacter species in our hospital between January 2017 and December 2021 were analyzed. Demographic characteristics and clinical and laboratory findings were analyzed. RESULTS: In pediatric patients infected with Acinetobacter spp., the median age was 36 (7-114) months, and 64.2% (n = 43) were female. Acinetobacter baumannii was grown in the cultures of 31 (46.3%) cases. When the type of infection was examined, 31 (46.3%) cases were urinary tract infections, and 29 (43.3%) cases were bloodstream infections. Extensively drug-resistant, pandrug-resistant, and multidrug-resistant A. baumannii were found in 10 (14.9%), 3 (4.5%), and 2 (3%) cases, respectively. Health-care-associated infections were found to have a significant rate of Acinetobacter resistance (P = .002). Significant antimicrobial resistance was detected in Acinetobacter-infected cases with intensive care hospitalization within the last month and carbapenem use in the previous 3 months (P < .001, both). CONCLUSION: It is necessary to act in accordance with the infection prevention and control program to reduce the incidence of health-care-associated infections with Acinetobacter species and to prevent infection with highly resistant strains. Due to health-care-associated infections and factors contributing to the increase in Acinetobacter resistance, we believe this study will help clinicians to be more cautious in the use of carbapenems. Cite this article as: Elvan-Tüz A, Tekin D, Ekemen-Keles Y, et al. Clinical reflections of acinetobacter infections in children in a quaternary-care hospital: A five-year single-center experience. Turk Arch Pediatr. 2024;59(1):38-42.

Prevalence of Transmitted Drug Resistance among HIV-1 Patients in the Aegean Region: Results from the Western Part of Turkey.

OBJECTIVES: This study aimed to analyze the antiretroviral drug resistance in antiretroviral treatment-naïve HIV-positive patients in the Aegean Region of Turkey from 2012 to 2019. METHODS: The study included 814 plasma samples from treatment-naïve HIV-positive patients. Drug resistance analysis was performed by Sanger sequencing (SS) between 2012-2017 and by next-generation sequencing sequencing (NGS) between 2018-2019. SS was used to analyze resistance mutations in the protease (PR) and reverse transcriptase (RT) gene regions using a ViroSeq HIV-1 Genotyping System. PCR products were analyzed with an ABI3500 GeneticAnalyzer (Applied Biosystems). The sequencing of the HIV genome in the PR, RT, and integrase gene regions was carried out using MiSeq NGS technology. Drug resistance mutations and subtypes were interpreted using the Stanford University HIV-1 drug resistance database. RESULTS: Transmitted drug resistance (TDR) mutation was detected in 34/814 (4.1 %) samples. Nonnucleoside reverse transcriptase inhibitor (NNRTI), nucleoside reverse transcriptase inhibitor (NRTI), and protease inhibitor (PI) mutations were identified in 1.4 % (n =12), 2.4 % (n =20), and 0.3 % (n = 3) of samples, respectively. The most common subtypes were B (53.1 %), A (10.9%), CRF29_BF (10.6%), and B + CRF02_AG (8,2%). The most common TDR mutations were E138A (3.4%), T215 revertants (1.7%), M41L (1.5%), and K103N (1.1%). CONCLUSION: Transmitted drug resistance rate in the Aegean Region is compatible with national and regional data. Routine surveillance of resistance mutations may guide the safe and correct selection of initial drug combinations for antiretroviral therapy. The identification of HIV-1 subtypes and recombinant forms in Turkey may contribute to international molecular epidemiological data.

Why is it important to report early possible COVID-19 PET/CT findings in cancer patients? Explaining with a case series.

BACKGROUND: Coronavirus disease-2019 (COVID-19) causing a pandemic mostly results in mild symptoms; however, it can evolve into serious complications. It is emphasized that if the term from the recent anticancer treatment to the diagnosis of COVID-19 was short, the probability of serious events increased in cancer patients. Therefore, early detection of COVID-19 and prevention of serious events is very important. We aimed to investigate whether it is possible to detect COVID-19 early by positron emission tomography (PET)/computed tomography (CT). METHODS: We retrospectively evaluated the images and clinical findings of patients who underwent PET/CT due to malignancy and whose COVID-19 polymerase chain reaction (PCR) test were detected positive subsequently. RESULTS: Eight cancer patients with positive COVID-19 PCR tests were included in the study. PET/CT revealed subpleural ground-glass opacities (GGOs) showing mild fluorodeoxyglucose (FDG) uptake that could be compatible with COVID-19 in 4 of 8 patients. The number of affected lobes ranged from 1-4. All patients were diagnosed with COVID-19 by PCR test when symptoms and/or lung findings worsened on the days after PET/CT. The time interval between the last anticancer treatment and COVID-19 diagnosis in five patients was ≤7 days. During the follow-up, six of the cases (75%) needed mechanical ventilation and died later. CONCLUSION: COVID-19 may be recognised early by detecting incidental findings in PET/CT, especially in asymptomatic cancer patients. Potential complications may be prevented by early diagnosis and anticancer therapy changes. Therefore, possible COVID-19 findings in PET/CT should be reported and the patient should be referred to relevant clinician.