Figure 5

Summary of cultivation-based, metagenomics and whole genome sequence analyses. Bacterial isolates were obtained at the hospital laboratory (1^st cultivation) from vitreous from endophthalmitis patients following cataract surgery (C1-7) and intravitreal injection (I1-7) and the taxonomic affiliation of the isolates were determined by MALDI-TOF mass spectrometry (MS). Vitreous was analyzed through metagenomics at the research laboratory using two DNA isolation methods (QIAamp DNA Mini Kit, QIA; QIAamp UCP Pathogen Mini kit, UCP) and the taxonomic affiliation of reads was determined. The detected amount of human DNA sequences in percent (%) is provided in the first column of the Metagenomics tab. In the horizontal bar charts, the taxonomic identity and relative fraction of microbial reads for the most abundant identified organisms based on the Kraken + Bracken analysis is indicated for both DNA isolation methods. The read counts for the most abundant organism according to the Kraken + Bracken (all reads) and BLASTN (forward read) analyses are indicated to the right. The read counts for the most abundant organisms per sample as determined by Kraken, Bracken and BLASTn analyses are available through figshare at https://figshare.com/s/5feabfad1d8c495bf7a3. Bacterial isolates for some samples were obtained in a second round of cultivation at the research laboratory (2^nd cultivation) and one representative per colony morphotype per vitreous sample was subjected to MS and whole genome sequencing (WGS). The taxonomic affiliation of isolates was determined through classification of assembled genomes using a k-mer based approach and genomic MLST, and antibiotic resistance genes were identified using ResFinder. Furthermore, metagenomic assemblies were generated from the shotgun metagenomic reads and analyzed with regards to taxonomic affiliation and selected functional characteristics (Supplementary Table S6). A video summary is available from figshare at https://figshare.com/s/38fe043f6a8ef1710444.