Case presentation
A 68-year-old man with a past history of schizophrenia underwent laparoscopic right hemicolectomy due to carcinoma. At postoperative day 4, he was diagnosed with aspiration pneumonia as a consequence of vomiting due to intestinal obstruction and septic shock. He was transferred to the intensive care unit for further observation and treatment (see Additional file 2). At day 46, we performed microbial laboratory evaluation based on both bacterial culture and 16S rRNA gene amplicon sequencing analysis following the pipeline established by us previously [4, 5] (see Additional file 3). MinION™-based sequencing analysis just 2 h after sample collection revealed the presence of Stenotrophomonas maltophilia, Pseudomonas aeruginosa, Rhodococcus kyotonensis, Pseudoruegeria sabulilitoris, Corynebacterium simulans, and other microorganisms (see Additional file 4) (Fig. 1). Culture-based testing reported at 2 days thereafter detected Stenotrophomonas maltophilia and Pseudomonas aeruginosa.
Taxonomic assignment of the 16S rRNA genes in sputum samples. The samples were subjected to 16S rRNA amplicon sequencing using MinION™ (Oxford Nanopore Technologies, Oxford, UK), and the percentage of reads (with the abundance over 2%) belonging to the identified bacterial species is shown. Sequencing for 5 min generated 470,231 reads. A total of 41,136 reads were aligned with one of the bacterial 16S rRNA gene sequences, and 65.3% reads were aligned with Stenotrophomonas maltophilia and 15.7% reads were aligned with Pseudomonas aeruginosa