EFFICIENT DIAGNOSIS OF STREPTOCOCCUS PNEUMONIA IN CEREBROSPINAL FLUID THROUGH METAGENOMICS: A BREAKTHROUGH IN CULTURE-INDEPENDENT DETECTION
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Keywords
Streptococcus pneumonia, bacterial meningitis, Metagenomic next-generation sequencing(mNGS), cerebrospinal fluid (CSF), Efficient Diagnosis, Antibiotic resistance genes, Functional annotation
Abstract
Streptococcus pneumoniae presents a major public health threat because of its high disease burden (infections and incidence), severe health outcomes (mortality and complications) and antibiotic resistance. The transmission dynamics of this noxious pathogen are very high in the vulnerable population of children causing around 800,000 mortalities per annum according to the World Health Organization (WHO). The present study highlights the severe central nervous system (CNS) infection caused byS.pneumoniaecommonly known as bacterial meningitis (BM), and the challenges associated with its conventional diagnostic methods. Despite advances in the use of culture-independent methods, many CNS pathogens still remain misdiagonsed. Metagenomic next-generation sequencing (mNGS) is considered to beaneffective diagnostic technique for cerebrospinal fluid (CSF) due to its high sensitivity and specificity. Our study investigated the implication of mNGS for the rapid diagnosis of S. pneumoniae infections from CSF samples isolated from meningitis patients.The results revealed that genomic sequencing analysis of the isolated CSF samples generated 87 contigsand provided valuable insights into the genetic structure of the S. pneumoniae strain causing BM.Functional annotation of genome sequences using tools like GenomeVx could leadtounderstanding the biology and evolutionary history of this deadly pathogen. Moreover, our results identified various antibiotic resistance genes within the assembled contigs, which could help reveal mechanisms ofresistance against various antibiotics and facilitate the treatment of this dreadful infection.
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Rehan Ali
Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi-75600, Pakistan.
Kashif Ali
Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi-75600, Pakistan
Muhammad Aurongzeb
Department of Applied Sciences, (FEST), Hamdard University Karachi 74600Pakistan.
Raheela Yasmin
HITEC-IMS Taxila/National University of Medical Sciences (NUMS) Pakistan
Ramsha Afzal
Department of Brain Science, Ajou University School of Medicine, Suwon 16499, Republic of Korea,
AmmeemaKiran
Department of Biosciences, COMSATS University, Islamabad (CUI), Pakistan
Naveed Hussain
Department of Applied Sciences, (FEST), Hamdard University Karachi 74600Pakistan.
Salman Ahmed Khan
Department of Molecular Medicine, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
Asadul Haq
Division of Rheumatology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea,(
ImdadKaleem
Department of Biosciences, COMSATS University, Islamabad (CUI), Pakistan
Turki Abualait
College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam,
Shahid Bashir
Neuroscience Center, King Fahed Specialist Hospital, Dammam