Table 4 Detection method details.

From: Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture

CategoryClassification group (CRC)aNumber of samples
PrevalencebReported by standard cultureReportable by direct NGS16ScPlate wash positive by NGS16S
Current culture conditions sufficient for detectionviridans streptococci141313131213
Staphylococcus aureus222222
Neisseria species444414
Bacillus species, not Bacillus anthracis11 1 1
Current culture conditions insufficient for detectionPrevotella species*14 101414 
Veillonella species*13 1213133
aerobic non-sporeforming Gram-positive rods111 12102
Campylobacter species*10 61010 
Atopobium species*7  77 
Capnocytophaga species*7 2651
Lachnoanaerobaculum species*6  66 
Lactobacillus species*5  55 
Megasphaera species*6 355 
Solobacterium moorei*6 166 
Fusobacterium species*5 3441
Oribacterium species*5  55 
Selenomonas species*4  44 
Porphyromonas species*3 3331
Stomatobaculum species*3  33 
Alloprevotella species*2 122 
Dialister species*2  22 
Leptotrichia species*2 122 
Parvimonas micra*2  22 
Peptostreptococcus species*2  22 
[Eubacterium] sulci*1  11 
[Eubacterium] yurii*1  11 
Anaeroglobus species*1  11 
Marmoricola aurantiacus*1 1   
Peptoanaerobacter species*1  11 
Skermanella aerolata*1 1   
Poor correlation between culture report and growth on standard culture mediaActinomyces species*154815158
Rothia species117211 11
Staphylococcus, coagulase negative710754
Haemophilus species645636
Dermacoccus species31 3 3
Dermabacter species1  1 1
Eikenella corrodens1  111
Special case organismsYeast/fungi11    
Tropheryma whipplei1 1   
  1. aTo facilitate comparisons between culture and NGS16S analysis, organisms were assigned to classification groups as detailed in Table 1 and Supplementary Table S1. Anaerobes are noted with an*.
  2. bNumber of positive study specimens (total number of specimens = 20); positive is defined as reportable by standard culture or NGS16S, and/or recovered in at least one culture plate wash.
  3. cas evaluated by UWMC Clinical Microbiology; note that in some cases reads may be detected but fall below reporting thresholds.
  4. dBR, CNA, LKV, SSA.
  5. eBA or CA.