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• W2913893373 abstract "Purpose: Out of more than 2400 patients with severe acute respiratory infections who travelled to the Philippines from the Middle East since 2013, only two cases were confirmed positive for the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Considering that these respiratory infections were imported into the country, it is important to determine the pathogen/s causing the disease to mitigate potential outbreaks that may overburden the country's health care system. Methods & Materials: Archived upper and lower respiratory samples (n = 203) collected from 2014 to 2016 that tested negative by MERS-CoV RT-qPCR were tested using a multiplex PCR respiratory panel to detect human viral, bacterial, and fungal pathogens. The samples that tested negative for the multiplex panel were subjected to next generation sequencing (NGS). The NGS reads were analyzed using sequence-based ultrarapid pathogen identification (SURPI) computational pipeline and Centrifuge metagenomic sequence classifier to classify the reads according to their origins for further pathogen identification and to search for divergent viruses. Results: Ninety percent of the samples were found to be positive for at least one respiratory pathogen. The most common bacteria detected were those associated with nosocomial and community-acquired pneumonia such as Klebsiella pneumoniae, Staphylococcus aureus, and Haemophilus influenza while the common viruses detected were Rhinovirus, Adenovirus, and Influenza A and B. In the 4 samples run on NGS, some of the pathogens identified were also associated with nosocomial and community-acquired infections and are important multi-drug resistant pathogens such as Pseudomonas aeruginosa, Streptococcus pneumoniae, Acinetobacter sp., Corynebacterium resistens, and Mycobacterium tuberculosis complex. Some viral and bacterial species that were supposed to be covered by the multiplex assay such as, K. pneumonia, Legionella longbeachae, L. pneumophila, Bordetella spp., Moraxella cattarhalis, Influenza A and C, and Human Metapneumovirus were also detected, highlighting the comprehensive capabilities of NGS in pathogen detection. Conclusion: Respiratory pathogens constitute important causative agents of SARI in travellers. The results puts a spotlight on the need for identification of respiratory pathogens from traveling patients to enhance monitoring of imported infections, especially those with antimicrobial resistance to mitigate possible outbreaks from novel, emerging and re-emerging infectious diseases." @default.
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• W2913893373 date "2019-02-01" @default.
• W2913893373 modified "2023-09-27" @default.
• W2913893373 title "Pathogen identification in travelling patients with severe acute respiratory infections from the Middle East to the Philippines, 2014–2016" @default.
• W2913893373 doi "https://doi.org/10.1016/j.ijid.2018.11.092" @default.
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