The causative agents of Acute Encephalitis Syndrome remain unknown in 68-75% of the cases. In Nepal, the cases are tested only for Japanese encephalitis, which constitutes only about 15% of the ...cases. However, there could be several organisms, including vaccine-preventable etiologies that cause acute encephalitis, when identified could direct public health efforts for prevention, including addressing gaps in vaccine coverage. This study employs metagenomic next-generation-sequencing in the investigation of underlying causative etiologies contributing to acute encephalitis syndrome in Nepal. In this study, we investigated 90, Japanese-encephalitis-negative, banked cerebrospinal fluid samples that were collected as part of a national surveillance network in 2016 and 2017. Randomization was done to include three age groups (< 5-years; 5-14-years; >15-years). Only some metadata (age and gender) were available. The investigation was performed in two batches which included total nucleic-acid extraction, followed by individual library preparation (DNA and RNA) and sequencing on Illumina iSeq100. The genomic data were interpreted using Chan Zuckerberg-ID and confirmed with polymerase-chain-reaction. Human-alphaherpes-virus 2 and Enterovirus-B were seen in two samples. These hits were confirmed by qPCR and semi-nested PCR respectively. Most of the other samples were marred by low abundance of pathogen, possible freeze-thaw cycles, lack of process controls and associated clinical metadata. From this study, two documented causative agents were revealed through metagenomic next-generation-sequencing. Insufficiency of clinical metadata, process controls, low pathogen abundance and absence of standard procedures to collect and store samples in nucleic-acid protectants could have impeded the study and incorporated ambiguity while correlating the identified hits to infection. Therefore, there is need of standardized procedures for sample collection, inclusion of process controls and clinical metadata. Despite challenging conditions, this study highlights the usefulness of mNGS to investigate diseases with unknown etiologies and guide development of adequate clinical-management-algorithms and outbreak investigations in Nepal.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
BACKGROUNDIn Nepal, since the first detection of COVID-19 case in January 2020, the total cases have rose to almost a million with more than 12,000 deaths. Till now, WHO has classified 5 variants of ...SARS-Cov2 as variant of concerns at different time points causing many waves in different countries and regions at different time points. Nepal had also faced three distinct waves of COVID-19 caused by different variant of COVID 19. The objective of this study was to perform whole-genome sequencing of SARS-CoV-2 circulating in different waves of COVID-19 in Nepal and investigate its variant or lineage. METHODSIn this study, samples from 49 SARS-CoV-2 infected subjects from May 2021 to January 2022, were investigated. The methodology followed RNA extraction, real-time PCR for confirmation and whole-genome sequencing. The consensus genomes were interpreted with appropriate bioinformatics tools and databases. RESULTSSequence analysis of 49 genomes revealed to be of Delta (n=27) and Omicron Variant (n=22). The mutations in the consensus genomes contained the defining mutations of the respective lineages/variants. There were 20 genomes of Omicron sub-lineage BA.2, 1 of BA.1.1 and 1 of B.1.1.529. CONCLUSIONSThis study provides concise genomic evidence of presence of Delta and Omicron variant of COVID-19 in Nepal. Delta and Omicron variants were driving the second wave and the third wave of COVID-19 respectively in Nepal. Therefore, the genomic surveillance must be increased to clearly map out the pandemic and strategize vaccination approaches in the country.
Microorganisms with antimicrobial resistance (AMR) are prevalent among humans and animals, and also found in the environment. Though organisms with AMR can spread to humans via food from animal ...sources, the burden of AMR in food-producing animals remains largely unknown. Thus, we assessed the resistance pattern among Escherichia coli isolated from chicken cecum samples and explored issues contributing to AMR in animals in the Dhulikhel Municipality of Nepal. We conducted a mixed-methods study, comprising a cross-sectional quantitative component, with collection of chicken cecal samples from slaughter houses/shops. In addition, a descriptive qualitative component was undertaken, with a focus group discussion and key informant interviews among stakeholders involved in animal husbandry. Of the 190 chicken cecum samples collected, 170 (89%) were subjected to culture and drug sensitivity testing, of which E. coli was isolated from 159 (94%) samples. Of the 159 isolates, 113 (71%) had resistance to ≥3 antimicrobial class. Resistance to tetracycline (86%) and ciprofloxacin (66%) were most prevalent. Overuse of antimicrobials, easy availability of antimicrobials, and lack of awareness among farmers about AMR were major issues contributing to AMR. The high prevalence of resistance among E. coli in chicken cecal samples calls for rational use of antimicrobials, educating farmers, and multi-sectoral coordination.
Monitoring the antibiotic susceptibility pattern of Salmonella enterica serovar Typhi (S. Typhi) is important for efficiently managing cases of typhoid fever. In this study, the antimicrobial ...susceptibility patterns of 114 S. Typhi isolates, which were collected from a university hospital in Nepal during July 2009–December 2010, were investigated by disc diffusion assays. All of the S. Typhi isolates were sensitive to amoxycillin-clavulanic acid. More than 95% of the isolates were sensitive to chloramphenicol, ceftazidime, ceftriaxone, and cotrimoxazole. In addition, 1.7% of the studied isolates showed multiple drug resistance patterns. Of the 40 S. Typhi isolates, 32 strains (80%) showed nalidixic acid (NA) resistance with decreased susceptibility to ciprofloxacin (CIP). Importantly, we found the simultaneous presence of NA resistance and decreased susceptibility to CIP, suggesting that the resistance to NA is a reliable indicator of decreased CIP susceptibility (sensitivity, 97.5%; specificity, 100.0%). Furthermore, the sequencing of NA-resistant S. Typhi isolates showed a predominant amino acid alteration in the quinolone resistance-determining region (QRDR) of gyrA gene at position 83 from Ser→Phe. Two isolates with resistance to both CIP and NA had a double-mutation (Ser83→Phe and Asp87→Asn) in the QRDR of the gyrA gene, of which one had an additional amino acid mutation (Ser80→Ilu) in the QRDR of the parC gene.
Eosinophilia is common in low-resource countries and usually implies helminthiasis. Since helminthiasis is a common cause of eosinophilia and its diagnosis is cumbersome, we hypothesized that ...broad-spectrum anthelmintic therapy may decrease the eosinophil count and eventually cure helminthiasis, whether microbiologic diagnosis is established or not. We recruited patients with eosinophilia aged 5 years and older who presented to Dhulikhel hospital, Nepal. Patients were treated with albendazole and ivermectin. A stool sample for microscopy was obtained. Of a total of 113 patients, 106 had a follow-up visit and 56 were classified as responders to treatment (defined as a decrease in eosinophil count to below 500 cells/µL, or an absolute decrease of more than 1000 cells/µL). For all patients, we found an absolute decrease in the eosinophil count and for the responding group (more than 50% of the whole cohort), the eosinophil count decreased substantially. All stool samples were negative. The reason for a lack of response in the remaining patients is unclear. In order to ascertain whether eosinophilia should be an indication for anthelmintic treatment, a randomized controlled study of empirical treatment after a thorough microbiologic workup is needed.
Evidence-based decision-making to combat antimicrobial resistance (AMR) mandates a well-built community-based surveillance system for assessing resistance patterns among commensals and pathogenic ...organisms. As there is no such surveillance system in Nepal, we attempted to describe the antimicrobial resistance pattern in E. coli isolated from the fecal samples of apparently healthy individuals in Dhulikhel municipality and also explored the local drivers of AMR. We used a mixed-method design with a cross-sectional quantitative component and a descriptive qualitative component, with focus group discussion and key informant interviews as the data collection method. Fecal samples were collected from 424 individuals randomly selected for the study. E. coli was isolated from 85.9% of human fecal samples, of which 14% were resistant to ≥3 class of antimicrobials (multidrug resistant). Of the 368 isolates, resistance to ampicillin (40.0%), tetracycline (20.7%) and cefotaxime (15.5%) were most prevalent. The major drivers of AMR were: lack of awareness of AMR, weak regulations on sales of antimicrobials, poor adherence to prescribed medications, and incomplete dosage due to financial constraints. These findings indicate the need for strict implementation of a national drug act to limit the over-the-counter sales of antimicrobials. Additionally, awareness campaigns with a multimedia mix are essential for educating people on AMR.
An operational research study was conducted in 2019 to assess the quality of data submitted by antimicrobial resistance (AMR) surveillance sites in the Bagmati Province of Nepal to the National ...Public Health Laboratory for Global Antimicrobial Resistance and Use Surveillance System (GLASS). Measures were implemented to enhance the quality of AMR surveillance by strengthening capacity, improving infrastructure, implementing data sharing guidelines, and supervision. The current study examined reports submitted by surveillance sites in the same province in 2022 to assess whether the data quality had improved since 2019. The availability of infrastructure at the sites was assessed. Of the nine surveillance sites in the province, seven submitted reports in 2022 versus five in 2019. Completeness in reporting improved significantly from 19% in 2019 to 100% in 2022 ('p' < 0.001). Timely reports were received from two sites in 2019 and only one site in 2022. Specimen-pathogen consistency in accordance with the GLASS guidelines for urine, feces, and genital swab specimens improved, with >=90% consistency at all sites. Overall, the pathogen-antibacterial consistency improved significantly for each GLASS priority pathogen. The study highlights the importance of dedicated infrastructure and institutional arrangements for AMR surveillance. Similar assessments covering all provinces of the country can provide a more complete country-wide picture.
Antimicrobial resistance (AMR) is a global problem, and Nepal is no exception. Countries are expected to report annually to the World Health Organization on their AMR surveillance progress through a ...Global Antimicrobial Resistance Surveillance System, in which Nepal enrolled in 2017. We assessed the quality of AMR surveillance data during 2019-2020 at nine surveillance sites in Province 3 of Nepal for completeness, consistency, and timeliness and examined barriers for non-reporting sites. Here, we present the results of this cross-sectional descriptive study of secondary AMR data from five reporting sites and barriers identified through a structured questionnaire completed by representatives at the five reporting and four non-reporting sites. Among the 1584 records from the reporting sites assessed for consistency and completeness, 77-92% were consistent and 88-100% were complete, with inter-site variation. Data from two sites were received by the 15th day of the following month, whereas receipt was delayed by a mean of 175 days at three other sites. All four non-reporting sites lacked dedicated data personnel, and two lacked computers. The AMR surveillance data collection process needs improvement in completeness, consistency, and timeliness. Non-reporting sites need support to meet the specific requirements for data compilation and sharing.
Introduction
CSOM is defined as persistent or intermittent infected discharge of more than three months duration through the perforated or non intact tympanic membrane caused by bacteria, fungi and ...virus resulting in inflammation of mucosal lining that often results in partial or total loss of tympanic membrane and ossicles. The aim of study was to study the current bacteriological profile responsible for the disease.
Methods
This descriptive cross sectional study was carried out at the department of Ear , Nose and Throat (ENT) and Head and Neck Surgery (HNS) in a tertiary care centre from January 2019 to December 2020. Ethical approval was taken from Institutional Review Committee (Reference number 52/2021). A convenient sampling method was used and data analysis was done in Microsoft Excel . Point estimate at 95% confidence interval was calculated along with frequency and proportion for binary data.
Results
There were a total of 324 patients included in the study. The age range was from five to
sixty-eight years. Most patients were of the age group below 10 years. There were a total
of 178 males and 146 females. The most common organism isolated were Staphylococcus
aureus 145 (44.8%) and Psedomonas aeruginosa 86 (26.6%).
Conclusions
Staphylococcus aureus and Pseudomonas aeruginosa were the most common organisms
responsible for chronic suppurative otitis media in our study.
Keywords: chronic suppurative otitis media, Staphyllococcus aureus.
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