Browsing by Author "Katuwal, N"
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Publication Application of hAMRonization Tool in Investigating Anti-microbial Resistance Genes to Generate Harmonized Reports(Kathmandu University, 2023) Katuwal, N; Tamrakar, D; Shrestha, RABSTRACT Background Antimicrobial resistance has become a serious threat to global public health, with the potential to cause significant morbidity and mortality. Therefore, the detection and surveillance of antimicrobial resistance genes are critical to monitor the prevalence of resistance and to guide appropriate treatment decisions. Several bioinformatics tools have been developed to facilitate the detection and investigation of antimicrobial resistance genes from sequencing data. However, these tools often require a significant amount of manual curation and provide results which can limit their intra-operability, accessibility and usability. This lack of standardization in the reporting of antimicrobial resistance genes investigation greatly hinders the comparison of results across the public health sector. Method This study focuses on the application of hAMRonize tool developed by Public Health Alliance for Genomic Epidemiology. In this study, we have implemented hAMRonization to evaluate antimicrobial resistance genes in Salmonella and compared to the results from other tools (ARIBA, RGI, amrfinderplus and abricate). Result We observed that hAMRonize was more comprehensive than other tools in predicting genes, including information on antimicrobials, drug classes, and start and end base pair of genes, among others. The hAMRonize tool also provided results in an interactive Hypertext Markup Language format. Conclusion hAMRonization is an innovative tool for investigating and sharing antimicrobial resistance data in the current field of research, where scientists use a plethora of prediction tools that provide different results and subsequent interpretations. KEY WORDS Antimicrobial resistance, Gene-prediction, hAMRonizePublication COVID 19 Vaccine Breakthrough Infection among Health Care Workers(Kathmandu University, 2023) Tamrakar, D; Katuwal, N; Adhikari, P; Banjara, M; Shrestha, N; Poudel, P; Shrestha, RABSTRACT Background Mass vaccination is considered the primary strategy for reducing the impact of COVID-19, and it has been implemented globally. Objective To study the extent of SARS-CoV-2 infection and breakthrough infection among the HCWs who were fully vaccinated for at least 14 days and investigated the relation between neutralizing antibody response and breakthrough infection. Method This study was a retrospective cohort study among health care workers at Dhulikhel Hospital Kathmandu University Hospital from December 2021 to October 2022. The interviews with semi structured questionnaire were conducted in person or over phone. Out of 1450 participants 137 fully vaccinated HCWs without breakthrough infection were randomly selected for the prospective serological cohort. Result Out of 1079 participants’ majority (51.8%) were of age 25-34 years. Two thirds (66.7%) were females. More than half of participant (54.7%) had infection with SARS-CoV-2 at least once whereas more than one third people (35%) had reported SARS-CoV-2 infection 14 days after receiving full vaccination. Infection after vaccination had less moderate and sever/critical illness and less need for hospitalization as compared to infection before vaccination. Staffs who were directly involved in patient care had higher chance of breakthrough infection compared to those not involved directly in patient care. Those who had prior infection or booster dose had relatively higher antibody level and participants with low level of antibody had higher chance for breakthrough infection (35.3%) than participants with moderate to high level of antibody (11.9%). Conclusion Vaccinations significantly decreased severe diseases and the need for hospitalizations. Breakthrough infection was higher among the health care workers involved in direct patient care and with low level of antibody. KEY WORDS Antibody level, Breakthrough infection, COVID 19, COVID 19 vaccinationPublication Molecular Investigation of Dengue Virus Serotypes in the Dengue Outbreak of 2022 in Nepal(Kathmandu University, 2024) Katuwal, N; Shrestha, A; Ranjitkar, U; Jakibanjar, S; Madhup, SK; Tamrakar, D; Shrestha, RABSTRACT Background Dengue, a viral infection highly prevalent in tropical regions, exhibits local variations in risks that are influenced by a combination of climatic, socioeconomic, and environmental factors. It is caused by four distinct, yet closely related serotypes of the dengue virus. Objective To identify the different serotypes of dengue virus responsible for the 2022 outbreak in Nepal, where dengue has been prevalent since 2006 but with limited availability of molecular information on the serotypes. Method Serum samples from suspected dengue patients visiting Dhulikhel Hospital were analyzed using Dengue Rapid Test, for the presence of IgG/IgM antibodies or NS1 Ag. The positive samples were stored at -80⁰C, and 89 samples were selected for further analysis. RNA was extracted from those positive samples and RT-PCR was performed to identify the serotypes present. Result A higher percentage of sero-positivity was observed in females(52%) compared to males. Positive cases were distributed in 14 different districts, with the highest percentage(58.4%) in Kavre. RT-PCR, of 53 out of 89 serologically positive samples, by RT-PCR revealed that DENV1 was the predominant, followed by DEN3(24.5%) and DENV2(16.9%). DENV4 was not detected in any of the samples. The average Ct-value of all serotypes was 17.6, with DENV3 having the lowest Ct-value of 16.6, indicating slightly higher viremia. Conclusion Our study, although limited in its coverage of Nepal, has provided molecular information on the serotypes responsible for the 2022 dengue outbreak. The high prevalence of DENV1 was observed, while prevalence of DENV3 was accompanied by high viral load. KEY WORDS Dengue virus, Molecular, Serotypes, NepalPublication Seroprevalence of Scrub Typhus in Patients Attending Dhulikhel Hospital, Kavre(Kathmandu University, 2021) Madhup, SK; Shrestha, R; Katuwal, N; Magar, SR; Shrestha, S; Bhandari, S; Tamrakar, DABSTRACT Background Scrub typhus is a largely ignored tropical disease and a leading cause of undifferentiated febrile illness. It is caused by Orientia tsutsugamushi. Scrub Typhus is frequently observed in South Asian countries. However, clear epidemiological information of this disease is lacking in case of Nepal. Nepal has shown steady increase in cases of Scrub Typhus since 2015. The epidemiological data related to this disease would support the decision making and surveillance design for early outbreak detection and immediate responses including prevention and treatment of scrub typhus in Nepal. Objective To understand prevalence of Scrub Typhus in subjects who had visited outpatient department at Dhulikhel Hospital. Method In this study, we have studied antibody test data (n=784) for Scrub Typhus from 2019 to 2021. The tests were performed on serum samples of patients who had visited OPD at Dhulikhel Hospital with fever lasting more than 5 days. The kit used in analysis was Scrub Typhus Detect™ IgM ELISA Kit from InBios International. Result Out of the total subjects (n=784), 133 were positive (16.9%) for IgM antibody of Scrub Typhus. The positivity in female (18.6%) was higher than the male subjects (15.3%). The positivity rate was variable among the different age groups, with highest positivity for age group 0-14 years (25%). The seasonal variation was also observed among the seropositive cases. Conclusion Scrub Typhus being a neglected tropical disease has high prevalence. It can be postulated that female subjects and subjects of age group 0-14 years are vulnerable to the infection with Scrub Typhus. There is need to increase the surveillance of Scrub Typhus to add the knowledge for diagnosis and treatment. KEY WORDS ELISA, IgM, Scrub Typhus, SeroprevalencePublication Whole Genome Sequence Analysis to Identify SARS-CoV-2 Variant in Nepal(Kathmandu University, 2021) Shrestha, R; Katuwal, N; Adhikari, N; Vanaerschot, M; Tamrakar, D; Dhimal, M; Gyanwali, P; Bhattarai, S; Madhup, SK; Devkota, BABSTRACT Background The spread of SARS-CoV-2 has become a global public health crisis. Nepal is facing the second wave of COVID-19 pandemic but, there is still a limited data on the genomic sequence of SARS-CoV-2 variants circulating in Nepal. Objective The objective of this study is to sequence the whole genome of SARS-CoV-2 in Nepal to detect possible mutation profiles and phylogenetic lineages of circulating SARS- CoV-2 variants. Method In this study, swab samples tested positive for SARS-CoV-2 were investigated. After RNA extraction, the investigation was performed through real-time PCR followed by whole genome sequencing. The consensus genome sequences were, then, analyzed with appropriate bioinformatics tools. Result Sequence analysis of two SARS-CoV-2 genomes from patient without travel history (Patient A1 and A2) were found to be of lineage B.1.1. Similarly, among other four samples from subjects returning from the United Kingdom, genomes of two samples were of lineage B.1.36, and the other two were of lineage B.1.1.7 (Alpha Variant). The mutations in the consensus genomes contained the defining mutations of the respective lineages of SARS-CoV-2. Conclusion We confirmed two genomic sequences of variant of concern VOC-202012/01 in Nepal. Our study provides the concise genomic evidence for spread of different lineages of SARS-CoV-2 – B.1.1, B.1.36 and B.1.1.7 of SARS-CoV-2 in Nepal. KEY WORDS COVID-19, Nepal, SARS-CoV-2, Variant of concern, Whole genome sequencing