Pathogen identification in endotracheal aspire sample using metatranscriptomics

Pneumonia pathogen identification and drug sensitivity can help diagnoses and effective treatment. Metatranscriptomics sequence (MTS) on pneumonia pathogen identification is rarely seen. We use MTS and Metagenomic sequence (MGS) analyze the same sample, comparing the results with clinical culture and drug sensitivity test (DST), aiming to preliminary explore the use of MTS in endotracheal aspire (ETA) sample. <bold>Materials and Methods:</bold> ETA was collected from pneumonia patients, and divided for microbial culture and DST, RNA extraction, and DNA extraction. Both RNA and DNA sample were sequenced using Illumina. <bold>Results:</bold> Klebsiella pneumoniae (KPN) was the most abundant pathogen in MTS (592 reads), consistent with MGS (68 reads) (Table 1). Drug resistance genes identification were almost the same (MGS&MTS: SHV-11, oqxA, KpnE, KpnF; MTG:AcrS, soxR). However, the DST only showed resistance to tetracycline, and sensitive to rest of them. (Figure 1) <bold>Conclusion:</bold> We successfully performed MTS on ETA. MTS, MGS and microbial culture were consistent at species identification. However, MTS and MGS had more resistance genes without corresponding resistance phenotypes. How to utilize MTS and MGS for rapid identification of pathogen antimicrobial resistance phenotypes requires further research. Table 1 Top 3 abundant species <table-wrap><object-id>erj;64/suppl_68/PA1497/TB1</object-id><object-id>T1</object-id><object-id>TB1</object-id><table><colgroup><col></col><col></col></colgroup><tbody><tr><td>MTS</td><td>MGS</td></tr><tr><td>Homo sapiens</td><td>Homo sapiens</td></tr><tr><td>Klebsiella pneumoniae</td><td>Klebsiella pneumoniae</td></tr><tr><td>Corynebacterium simulans</td><td>Escherichia coli</td></tr></tbody></table></table-wrap> <fig><object-id>erj;64/suppl_68/PA1497/F1</object-id><object-id>F1</object-id><object-id>F1</object-id><graphic></graphic></fig>