Fig 1.
Flow diagram denoting blood culture results from blood-stream infection surveillance in two rural Thai provinces from 2006–2014.
*WGS–whole genome sequencing.
Fig 2.
Distribution of previously unidentified isolates at the genus level using BD Phoenix automated identification system.
Fig 3.
Antibiotic resistance levels by organism using the BD Phoenix identification system.
Antibiotic abbreviation by drug class: Aminoglycosides: AMK–Amikacin, GEN—Gentamicin; Beta-lactam: PIP–Piperacillin, ATM–Aztreonam, TZP–Piperacillin-Tazobactam; Carbapenem: IPM–Imipenem, MEM–Meroenem; Cephalosporin: CAZ–Ceftazidime, CTX–Cefotaxime, FEP–Cefepime; CHL–Chloramphenicol; Fluoroquinolone: CIP–Ciprofloxacin, LVX–Levofloxacin; TET- Tetracycline; Folate Antagonist: SXT—Trimethoprim-Sulfamethoxazole. In the figure legend n = number of isolates for which BD Phoenix antimicrobial sensitivity test (AST) data was available/total number of species specific isolates in this study. For several isolates where AST data was not recorded the isolate grew too slowly to meet the growth control criteria cutoff. Clinical and Laboratory Standards Institute (CLSI) 2016 minimum inhibitory concentration break points were applied. Moraxella (n = 14) and Pasteurella (n = 12) species are not included in the BD Phoenix AST database and therefore this data is not available.
Table 1.
Demographic data associated with the 204 unidentified isolates processed using the BD Phoenix automated identification system, focusing on commonly identified genera.
Table 2.
Summary of patient antibiotic use prior to admission and time-to-positivity (TTP) for blood culture.
Table 3.
Summary of isolate identification using 3 different web-based platforms on whole genome sequencing short read raw data files.
Fig 4.
Taxonomer bacterial composition classifier sunburst of isolate NA45737.
Reads are classified against 16S sequences and protein sequences from Uniref50. The size of a given sector represents the relative abundance at the read level. Taxonomic ranks are hierarchical with the highest level placed in the center. Reads not classified at the species level, either because they are shared between taxa or represent novel microorganisms, are collapsed to the lowest common ancestor and shown as part of slices that terminate at higher taxonomic ranks (e.g. genus).
Table 4.
Details of One Codex analysis of taxonomic grouping for classified reads from isolate NA45737*.