Table 7.
Bacterial identification results from 45 clinical samples based on culture and NGS of 16S-23S rRNA region.
| Sample | Sample material | Species content by NGS of 16S-23S rRNA region (% of total reads) | Species content by conventional culture and MALDI-TOF Vitek MS identification (growth) |
|---|---|---|---|
| STA1 | Pus wound deep | Streptococcus pyogenes (83.6%), Streptococcus dysgalactiae (15.5%), Streptococcus sp. (0.6%), Staphylococcus aureus (0.2%) | Staphylococcus aureus (large), Streptococcus pyogenes (large), Streptococcus group G (large) |
| STA2 | Nose | Staphylococcus aureus (65.3%), Staphylococcus epidermidis (15.2%), Corynebacterium sp. (6.4%), Cutibacterium acnes (4.4%), Staphylococcus lugdunensis (2.1%), Finegoldia sp. (1.6%), Peptoniphilus sp. (0.7%), Streptococcus sp. (0.5%), Cutibacterium sp. (0.5%), Cutibacterium granulosum (0.4%), Staphylococcus sp. (0.3%), Micrococcus sp. (0.3%), Propionibacterium sp. (0.3%), Kocuria palustris (0.2%), Herbaspirillum sp. (0.1%), Unidentified species (1.8%) | Staphylococcus aureus (medium) |
| STA3 | Nose | Corynebacterium sp. (32.9%), Staphylococcus aureus (7.8%), Corynebacterium propinquum (3.3%), Streptococcus oralis (1.9%), Streptococcus canis (1.6%), Cutibacterium acnes (1.5%), Staphylococcus epidermidis (0.8%), Streptococcus sp. (0.7%), Neisseria sicca (0.4%), Actinomyces sp. (0.4%), Finegoldia sp. (0.3%), Veillonella sp. (0.3%), Corynebacterium pseudodiphtheriticum (0.3%), Herbaspirillum sp. (0.2%), Staphylococcus sp. (0.1%), Capnocytophaga sp. (0.1%), Enterococcus sp. (0.1%), Fusobacterium hwasookii (0.1%), Anaerococcus sp. (0.1%), Unidentified species (47.0%), eukaryotic DNA (0.1%) | Staphylococcus aureus (few) |
| STA4 | Swab ulcus dig. | Staphylococcus aureus (100%) | Staphylococcus aureus (medium) |
| STA5 | Swab ulcus dig. | Staphylococcus aureus (59.6%), Streptococcus dysgalactiae (23.7%), Streptococcus sp. (3.1%), Streptococcus pneumoniae (2.7%), Herbaspirillum sp. (1.8%), Sphingomonas sanguinis (0.7%), Gemella haemolysans (0.3%), eukaryotic DNA (8.2%) | Staphylococcus aureus (medium) |
| STA6 | Pus abscess | Staphylococcus aureus (95.5%), Staphylococcus capitis (0.8%), Cutibacterium acnes (0.6%), eukaryotic DNA (3.2%) | Staphylococcus aureus (medium) |
| STA7 | Wound supperficial | Finegoldia sp. (45.6%), Anaerococcus tetradius (7.6%), Peptoniphilus harei (7.4%), Peptoniphilus coxii (7.2%), Streptococcus sp. (6.8%), Prevotella sp. (3.2%), Streptococcus agalactiae (2.1%), Anaerococcus obesiensis (1.9%), Prevotella disiens (1.6%), Anaerococcus sp. (0.7%), Unidentified species (16.0%) | Staphylococcus aureus (few), Streptococcus agalactiae (medium) |
| STA8 | Pus wound deep | Staphylococcus epidermidis (71.8%), Staphylococcus lugdunensis (17.7%), Streptococcus sp. (4.2%), Streptococcus parasanguinis (2.0%), Herbaspirillum sp. (1.0%), Streptococcus mitis (0.5%), Sphingomonas sanguinis (0.5%), Streptococcus canis (0.3%), eukaryotic DNA (2.0%) | Staphylococcus lugdunensis (few) |
| STA9 | Swab wound deep | Streptococcus agalactiae (28.3%), Staphylococcus aureus (24.3%), Peptoniphilus harei (12.7%), Finegoldia magna (7.3%), Anaerococcus sp. (6.7%), Peptoniphilus coxii (4.8%), Anaerococcus vaginalis (2.9%), Fastidiosipila sp. (2.8%), Porphyromonas bennonis (0.6%), Actinotignum sp. (0.6%), Corynebacterium sp. (0.4%), Varibaculum cambriense (0.2%), Fastidiosipila sanguinis (0.2%), Cutibacterium acnes (0.1%), Staphylococcus capitis (0.1%), Streptococcus sp. (0.1%), Unidentified species (7.5%), eukaryotic DNA (0.4%) | Staphylococcus aureus (medium), Streptococcus agalactiae (few) |
| STA10 | Wound supperficial | Staphylococcus epidermidis (81.9%), Herbaspirillum sp. (5.6%), Sphingomonas sanguinis (5.4%), Streptococcus thermophilus (2.2%), Paracoccus sp. (1.1%), Unidentified species (0.7%), eukaryotic DNA (3.0%) | Staphylococcus epidermidis (few) |
| STA11 | Nose | Staphylococcus epidermidis (45.2%), Psychrobacter alimentarius (29.3%), Corynebacterium accolens (15.2%), Peptoniphilus sp. (2.9%), Anaerococcus sp. (2.5%), Corynebacterium sp. (1.3%), Cutibacterium granulosum (1.1%), Corynebacterium pseudodiphtheriticum (0.7%), Propionibacterium sp. (0.3%), Sphingomonas sanguinis (0.1%), Kocuria rhizophila (0.1%), Herbaspirillum sp. (0.1%), Unidentified species (1.1%) | Staphylococcus epidermidis (few) |
| STA12 | Swab ulcus dig. | Staphylococcus aureus (55.0%), Streptococcus oralis (28.2%), Pseudomonas aeruginosa (10.1%), Finegoldia magna (4.9%), Morganella morganii (0.7%), Streptococcus pneumoniae (0.3%), Herbaspirillum sp. (0.2%), Anaerococcus sp. (0.2%), Staphylococcus sp. (0.1%), Unidentified species (0.2%) | Staphylococcus aureus (medium), Pseudomonas aeruginosa (medium) |
| STA13 | Cervix/vagina post partum | Megasphaera sp. (33.8%), Atopobium sp. (6.4%), Lactobacillus sp. (3.8%), Aerococcus sp. (1.5%), Peptostreptococcus sp. (1.4%), Staphylococcus sp. (0.9%), Anaerococcus tetradius (0.3%), Prevotella sp. (0.3%), Peptoniphilus sp. (0.3%), Gemella asaccharolytica (0.2%), Arcanobacterium sp. (0.2%), Streptococcus sp. (0.2%), Finegoldia sp. (0.2%), Dialister sp. (0.2%), Corynebacterium sp. (0.1%), Unidentified species (50.3%) | Staphylococcus haemolyticus (sporadic), Staphylococcus epidermidis (large) |
| STA14 | Throat | Faecalibacterium prausnitzii (10.8%), Streptococcus salivarius (5.9%), Staphylococcus epidermidis (4.9%), Oscillibacter sp. (3.2%), Bacteroides vulgatus (2.9%), Bacteroides uniformis (2.6%), Alistipes sp. (2.0%), Staphylococcus lugdunensis (1.9%), Lactobacillus sp. (1.7%), Escherichia coli (1.7%), Roseburia sp. (1.6%), Eubacterium sp. (1.2%), Barnesiella sp. (1.0%), Enterococcus faecium (0.9%), Eubacterium rectale (0.8%), Acutalibacter sp. (0.7%), Porphyromonas bennonis (0.7%), Monoglobus pectinilyticus (0.5%), Longibaculum sp. (0.5%), Blautia sp. (0.5%), Eubacterium siraeum (0.5%), Parabacteroides distasonis (0.4%), Staphylococcus sp. (0.4%), Bacteroides sp. (0.4%), Ruminococcus sp. (0.3%), Peptoniphilus sp. (0.3%), Herbaspirillum sp. (0.3%), Dialister sp. (0.3%), Intestinimonas sp. (0.3%), Parabacteroides sp. (0.3%), Sphingomonas zeae (0.2%), Colidextribacter massiliensis (0.2%), Odoribacter splanchnicus (0.2%), Unidentified species (45.0%), eukaryotic DNA (4.6%) | Escherichia coli (medium), Staphylococcus spp. (few) |
| STA15 | Urine | Actinotignum sp. (68.2%), Staphylococcus epidermidis (31.1%), Actinotignum schaalii (0.1%), Unidentified species (0.6%) | Staphylococcus epidermidis (≥10e5 CFU/ml.) |
| STA16 | Urine | Lactobacillus sp. (98.5%), Lactobacillus iners (0.8%), Unidentified species (0.7%) | Staphylococcus haemolyticus (≥10e5 CFU/ml.) |
| STA17 | Sputum | Prevotella melaninogenica (76.9%), Staphylococcus haemolyticus (10.0%), Leptotrichia sp. (5.7%), Veillonella sp. (0.1%), Prevotella jejuni (0.1%), Prevotella sp. (0.1%), Unidentified species (7.1%) | Staphylococcus haemolyticus (medium) |
| STA18 | Cathether | Staphylococcus epidermidis (90.8%), Enterococcus faecalis (4.1%), Enterococcus hirae (1.7%), Herbaspirillum sp. (1.2%), Sphingomonas sanguinis (0.9%), Roseateles sp. (0.5%), Ralstonia insidiosa (0.2%), eukaryotic DNA (0.6%) | Staphylococcus epidermidis (≥ 15 CFU), Enterococcus faecium (1 CFU) |
| STA19 | Urine | Staphylococcus epidermidis (91.9%), Herbaspirillum sp. (5.6%), Sphingomonas sanguinis (1.6%), Streptococcus oralis (0.6%), Rhizobacter sp. (0.2%), Delftia acidovorans (0.2%) | Staphylococcus epidermidis (≥10e5 CFU/ml.) |
| STA20 | Cathether | Staphylococcus epidermidis (76.4%), Herbaspirillum sp. (8.4%), Janthinobacterium svalbardensis (2.0%), Sphingomonas sanguinis (1.2%), Staphylococcus capitis (1.2%), Roseateles sp. (0.7%), Corynebacterium accolens (0.5%), Pseudomonas sp. (0.4%), Rhizobacter sp. (0.3%), Unidentified species (2.3%), eukaryotic DNA (6.5%) | Staphylococcus capitis (≥15 CFU), |
| Staphylococcus epidermidis (≥15 CFU) | |||
| STA21 | Urine | Staphylococcus epidermidis (72.5%), Bacteroides dorei (20.2%), Bacteroides fragilis (6.6%), Unidentified species (0.8%) | Staphylococcus epidermidis (≥10e5 CFU/ml.) |
| STA22 | Urine | Staphylococcus haemolyticus (65.1%), Dialister sp. (4.2%), Actinomyces sp. (1.6%), Solobacterium moorei (1.5%), Cutibacterium acnes (1.1%), Peptoniphilus lacrimalis (1.1%), Prevotella sp. (0.9%), Actinotignum sp. (0.9%), Porphyromonas bennonis (0.7%), Herbaspirillum sp. (0.7%), Eubacterium saphenum (0.5%), Peptoniphilus grossensis (0.5%), Peptoniphilus urinimassiliensis (0.4%), Kallipyga sp. (0.4%), Eubacterium sp. (0.4%), Jonquetella anthropic (0.3%), Peptoniphilus koenoeneniae (0.3%), Actinomyces turicensis (0.3%), Criibacterium bergeronii (0.2%), Ezakiella sp. (0.2%), Prevotella colorans (0.2%), Roseateles sp. (0.2%), Sphingomonas sanguinis (0.2%), Moryella indoligenes (0.1%), Howardella sp. (0.1%), Unidentified species (17.8%) | Staphylococcus heamolyticus (≥10e4 CFU/ml.) |
| STA23 | Urine | Staphylococcus saprophyticus (96.9%), Veillonella sp. (1.1%), Streptococcus agalactiae (0.8%), Herbaspirillum sp. (0.2%), Moraxella osloensis (0.2%), Streptococcus sp. (0.2%), Streptococcus mitis (0.2%), Acidovorax sp. (0.1%), Brevundimonas vesicularis (0.1%) | Staphylococcus saprophyticus (≥10e4 CFU/ml.) |
| STA24 | Swab eye | Cutibacterium acnes (47.5%), Corynebacterium sp. (9.7%), Staphylococcus epidermidis (4.4%), Streptococcus sanguinis (4.3%), Herbaspirillum sp. (4.2%), Simonsiella sp. (1.6%), Veillonella sp. (1.3%), Sphingomonas sanguinis (1.2%), Corynebacterium jeikeium (1.2%), Roseateles sp. (0.9%), Gordonia sp. (0.8%), Fusobacterium nucleatum (0.8%), Finegoldia sp. (0.6%), Aquabacterium sp. (0.5%), Kocuria palustris (0.5%), Methylobacterium sp. (0.4%), Kocuria rhizophila (1.5%), Propionibacterium acnes (0.4%), eukaryotic DNA (18.2%) | Staphylococcus epidermidis (unknown) |
| STA25 | Nose | Staphylococcus epidermidis (69.3%), Finegoldia magna (7.9%) Sphingomonas sanguinis (3.6%), Herbaspirillum sp. (3.4%), Pseudomonas fluorescens (2.4%), Staphylococcus haemolyticus (1.8%), Streptococcus sanguinis (1.6%), | Staphylococcus pasteuri (unknown) |
| Enterococcus faecalis (1.5%), Staphylococcus sp. (1.2%), Kocuria palustris (1.0%), Staphylococcus hominis (0.7%), Niastella sp. (0.6%), Staphylococcus pasteuri (0.6%), Corynebacterium sp. (0.4%), Propionibacterium acnes (0.4%), Staphylococcus capitis (0.3%), Janthinobacterium sp. (0.2%), Roseateles sp. (0.2%), Campylobacter concisus (0.2%), Streptococcus sp. (0.2%), Actinomyces neuii (0.2%), Unidentified species (1.5%), eukaryotic DNA (0.8%) | |||
| STA26 | Urine | Staphylococcus lugdunensis (100%) | Staphylococcus lugdunensis (≥10e5 CFU/ml.) |
| STA27 | Urine | Staphylococcus epidermidis (97.3%), Pseudomonas putida (2.6%), Unidentified species (0.1%) | Staphylococcus epidermidis (≥10e5 CFU/ml.) |
| STA28 | Urine | Aerococcus urinae (95.7%), Staphylococcus sp. (3.6%), Unidentified species (0.7%) | Staphylococcus epidermidis (≥10e5 CFU/ml.), Aerococcus urinae (≥10e5 CFU/ml.) |
| STA29 | Pus wound deep | Staphylococcus haemolyticus (43.1%), Herminiimonas sp. (11.2%), Propionibacterium acnes (9.2%), Sphingomonas sanguinis (6.6%), Staphylococcus epidermidis (6.3%), Paracoccus yeei (3.4%), Janthinobacterium sp. (1.7%), Herbaspirillum sp. (1.6%), Pseudomonas sp. (0.3%), Pseudomonas lurida (0.3%), Staphylococcus aureus (0.3%), Unidentified species (0.6%), eukaryotic DNA (15.5%) | Staphylococcus haemolyticus (few), Staphylococcus epidermidis (few) |
| STA30 | Insertion opening | Corynebacterium sp. (52.0%), Peptoniphilus harei (31.5%), Corynebacterium tuberculostearicum (1.6%), Cutibacterium acnes (1.1%), Anaerococcus sp. (0.7%), Finegoldia sp. (0.7%), Herbaspirillum sp. (0.5%), Corynebacterium pseudogenitalium (0.2%), Herbaspirillum rubrisubalbicans (0.1%), Unidentified species (11.5%), eukaryotic DNA (0.1%) | Staphylococcus hominis (few), Corynebacterium tuberculostearicum (Medium) |
| STA31 | Wound supperficial | Streptococcus dysgalactiae (98.8%), Corynebacterium sp. (0.5%), Finegoldia sp. (0.4%), Unidentified species (0.3%) | Staphylococcus aureus (medium), Streptococcus group C (large) |
| STA32 | Throat | Staphylococcus aureus (98.4%), Corynebacterium striatum (1.0%), Peptostreptococcus anaerobius (0.4%), Streptococcus sp. (0.2%) | Staphylococcus aureus (medium) |
| STA33 | Ear | Finegoldia sp. (37.6%), Gemella haemolysans (11.5%), Anaerococcus sp. (7.2%), Streptococcus pneumoniae (4.0%), Staphylococcus sp. (2.3%), Enterococcus sp. (1.9%), Peptoniphilus harei (1.2%), Prevotella sp. (1.0%), Eikenella corrodens (0.9%), Corynebacterium sp. (0.6%), Staphylococcus aureus (0.4%), Auricoccus sp. (0.4%), Prevotella melaninogenica (0.3%), Unidentified species (29.9%), eukaryotic DNA (0.9%) | Staphylococcus aureus (large) |
| STA34 | Urine | Staphylococcus aureus (68.7%), Peptostreptococcus anaerobius (7.6%), Anaerococcus tetradius (2.2%), Anaerococcus sp. (1.4%), Peptoniphilus harei (0.6%), Corynebacterium simulans (0.5%), Herbaspirillum sp. (0.2%), Sphingomonas sanguinis (0.2%), Corynebacterium sp. (0.2%), Pedobacter sp. (0.2%), Unidentified species (16.9%), eukaryotic DNA (1.8%) | Staphylococcus aureus (≥ 10e5 CFU/ml.) |
| STA35 | Urine | Staphylococcus aureus (98.4%), Staphylococcus haemolyticus (1.0%), Staphylococcus epidermidis (0.5%) | Staphylococcus aureus (≥ 10e5 CFU/ml.), Candida parapsilosis (10e4 CFU/ml.) |
| STA36 | Urine | Staphylococcus aureus (100%) | Staphylococcus aureus (≥ 10e5 CFU/ml.) |
| STA37 | Sputum | Staphylococcus aureus (62.4%), Streptococcus sp. (16.6%), Fusobacterium sp. (5.2%), Fusobacterium nucleatum (3.6%), Veillonella atypica (3.2%), Gemella morbillorum (1.3%), Prevotella sp. (0.9%), Prevotella conceptionensis (0.6%), Prevotella melaninogenica (0.5%), Parvimonas micra (0.5%), Streptococcus salivarius (0.4%), Capnocytophaga sp. (0.2%), Lactobacillus gasseri (0.2%), Streptococcus parasanguinis (0.2%), Unidentified species (1.4%), eukaryotic DNA (2.8%) | Staphylococcus aureus (large) |
| STA38 | Urine | Klebsiella sp. (61.5%), Pseudomonas sp. (29.6%), Staphylococcus aureus (2.7%), Stenotrophomonas sp. (0.6%), Acinetobacter sp. (0.3%), Enterobacter sp. (0.3%), Klebsiella oxytoca (0.3%), Pseudomonas azotoformans (0.1%), Unidentified species (4.7%) | Staphylococcus aureus (≥ 10e5 CFU/ml.), Klebsiella oxytoca (≥ 10e5 CFU/ml.) |
| STA39 | Sputum | Streptococcus anginosus (32.0%), Prevotella sp. (26.9%), Moraxella catarrhalis (13.9%), Staphylococcus aureus (8.5%), Prevotella oris (3.5%), Solobacterium moorei (1.6%), Streptococcus sp. (1.1%), Peptoniphilus harei (0.6%), Corynebacterium sp. (0.5%), Parvimonas micra (0.4%), Finegoldia sp. (0.3%), Streptococcus oralis (0.3%), Pseudomonas sp. (0.1%), Unidentified species (9.1%), eukaryotic DNA (1.3%) | Staphylococcus aureus (large), Pseudomonas aeruginosa (medium), Klebsiella oxytoca (few) |
| STA40 | Sputum | Staphylococcus aureus (8.5%), Leptotrichia sp. (2.3%), Streptococcus thermophilus (1.7%), Herbaspirillum sp. (1.5%), eukaryotic DNA (85.9%) | Staphylococcus aureus (few), Candida albicans (few) |
| STA41 | BAL | Leptotrichia sp. (37.4%), Prevotella sp. (13.5%), Streptococcus sp. (10.7%), Veillonella atypica (5.2%), Fusobacterium sp. (1.4%), Selenomonas sp. (1.3%), Actinomyces sp. (0.8%), Parvimonas sp. (0.8%), Megasphaera sp. (0.7%), Atopobium sp. (0.6%), Streptococcus salivarius (0.5%), Tannerella sp. (0.3%), Lactobacillus sp. (0.3%), Cryptobacterium sp. (0.3%), Porphyromonas sp. (0.3%), Aerococcus sp. (0.2%), Prevotella melaninogenica (0.2%), Alloprevotella tannerae (0.2%), Dialister sp. (0.2%), Dialister pneumosintes (0.2%), Fretibacterium fastidiosum (0.2%), Mogibacterium sp. (0.2%), Stomatobaculum longum (0.2%), Centipeda sp. (0.2%), Peptostreptococcus sp. (0.1%), Prevotella nigrescens (0.1%), Streptococcus mitis (0.1%), Actinomyces odontolyticus (0.1%), Anaeroglobus sp. (0.1%), Atopobium parvulum (0.1%), Solobacterium sp. (0.1%), Eubacterium sp. (0.1%), Unidentified species (23.6%) | Staphylococcus aureus (few), Aspergillus fumigatus (few) |
| STA42 | Pus abscess labia | Staphylococcus aureus (30.8%), Mobiluncus curtisii (5.1%), Dialister sp. (1.8%), Anaerococcus sp. (1.7%), Actinomyces sp. (1.4%), Peptoniphilus coxii (1.1%), Herbaspirillum sp. (0.8%), Peptoniphilus sp. (0.6%), Peptoniphilus harei (0.6%), Peptostreptococcus anaerobius (0.5%), Unidentified species (16.7%), eukaryotic DNA (38.7%) | Staphylococcus aureus (medium) |
| STA43 | Cervix/vagina post partum | Lactobacillus sp. (50.7%), Prevotella sp. (17.4%), Parvimonas sp. (5.7%), Streptococcus anginosus (1.3%), Gemella sp. (1.1%), Solobacterium sp. (0.7%), Anaerococcus obesiensis (0.4%), Peptoniphilus sp. (0.3%), Lactobacillus iners (0.2%), Solobacterium moorei (0.1%), Unidentified species (22.1%), eukaryotic DNA (0.1%) | Staphylococcus aureus (large), Escherichia coli (large), Prevotella disiens (medium) |
| STA44 | Wound supperficial | Streptococcus agalactiae (65.5%), Finegoldia sp. (10.2%), Anaerococcus sp. (3.4%), Actinotignum sp. (0.5%), Peptoniphilus sp. (0.4%), Actinomyces sp. (0.1%), Enterococcus sp. (0.1%), Unidentified species (19.9%) | Staphylococcus aureus (large), Streptococcus agalactiae (large) |
| STA45 | Swab ulcus dig. | Staphylococcus aureus (63.4%), Streptococcus oralis (23.4%), Staphylococcus sp. (7.0%), Finegoldia magna (3.5%), Pseudomonas aeruginosa (0.4%), Anaerococcus murdochii (0.2%), Corynebacterium striatum (0.2%), Actinomyces neuii (0.2%), Unidentified species (1.8%) | Staphylococcus aureus (medium), Pseudomonas aeruginosa (medium) |
All detected Staphylococcus species are indicated in bold.