TABLE 2.
Taxonomic identification of readsa
| Sample source, sample no. | LMAT identification(s) (no. of reads) |
||
|---|---|---|---|
| Qiagen REPLI-g single cell kit | Illustra single cell kit | Illustra V2 kit | |
| Culture-positive PJI | |||
| 980 | Streptococcus (2,694,906) | Streptococcus (286,577), Toxoplasma (489) | Streptococcus (3,075,181), Pseudomonas (232), Anaerococcus (135) |
| 982 | Staphylococcus (3,272,895), Propionibacterium (195), Mupapillomavirus (137), Finegoldia (115) | Staphylococcus (102,934), Toxoplasma (131) | Staphylococcus (9,539,147), Pseudomonas (15,292), Acinetobacter (739), Pseudoperonospora (346), Streptococcus (303), Elizabethkingia (242), Malassezia (176), Propionibacterium (142) |
| 986 | Streptococcus (37,268), Staphylococcus (26,397), Prevotella (13,472), Haemophilus (11,513), Campylobacter (3,344), Propionibacterium (2,298), Gemella (2,045), Alloprevotella (1,756), Chryseobacterium (1,531), Rothia (1,458), Neisseria (913), Capnocytophaga (911), Acinetobacter (297), Corynebacterium (248), Alloiococcus (156) | Staphylococcus (424), Toxoplasma (118) | Staphylococcus (168,046), Haemophilus (69,045), Streptococcus (66,370), Pseudomonas (58,244), Corynebacterium (18,344), Elizabethkingia (12,471), Propionibacterium (7,678), Gemella (2,298), Neisseria (2,092), Rothia (1,186), Empedobacter (835), Acinetobacter (479), Fusobacterium (434), Lactobacillus (237), Prevotella (185), Granulicatella (144), Delftia (130), Achromobacter (126) |
| 996 | Bacteroides (155,761), Clostridium (4,115), Parabacteroides (191), Corynebacterium (168), Blautia (143) | Bacteroides (11,134), Toxoplasma (669), Clostridium (454) | Bacteroides (96,154), Clostridium (4,052), Pseudomonas (1,483), Yarrowia (563), Corynebacterium (364), Propionibacterium (331), Staphylococcus (345), Parabacteroides (239), Streptococcus (116), Anaerotruncus (104) |
| 1002 | Corynebacterium (536,155), Lactococcus (2,195), Acinetobacter (187), Propionibacterium (108) | Corynebacterium (5,503), Toxoplasma (346) | Corynebacterium (1,000,810), Pseudomonas (32,865), Staphylococcus (5,704), Propionibacterium (5,396), Lactococcus (3,008), Streptococcus (2,121), Acinetobacter (1,293), Dermabacter (634), Malassezia (424), Elizabethkingia (382), Achromobacter (224), Actinobaculum (123), Delftia (108), Debaryomyces (102), Arcanobacterium (101) |
| Culture-negative PJI, 984 | Streptococcus (2,425), Acinetobacter (167) | Toxoplasma (230) | Pseudomonas (12,472), Acinetobacter (1,395), Elizabethkingia (936), Alloiococcus (706), Streptococcus (395), Staphylococcus (264), Achromobacter (205), Propionibacterium (169), Delftia (134), Malassezia (111) |
| Aseptic Failure | |||
| 983 | Streptococcus (352), Gloeocapsa (137) | Toxoplasma (442) | Pseudomonas (42,315), Acinetobacter (788), Elizabethkingia (742), Staphylococcus (630), Streptococcus (475), Propionibacterium (289) |
| 987 | Acinetobacter (5,396), Streptococcus (1,179), Prevotella (433), Propionibacterium (346), Kurthia (122) | Toxoplasma (173) | Pseudomonas (642,812), Elizabethkingia (5,283), Propionibacterium (3,271), Peptoniphilus (1,742), Acinetobacter (560), Epilithonimonas (372), Pseudoperonospora (353), Anaerococcus (255), Streptococcus (188), Capnocytophaga (172), Malassezia (158) |
| Controls | |||
| C. glutamicum | Corynebacterium (26,912,706), Rothia (1,070), Streptococcus (545), Neisseria (221), Haemophilus (240) | Corynebacterium (22,276,446), Streptococcus (333), Toxoplasma (126) | Corynebacterium (26,149,302), Pseudomonas (627), Streptococcus (289) |
| Ringer's solution | Neisseria (10,575), Streptococcus (8,441), Dolosigranulum (3,912), Haemophilus (716), Propionibacterium (385) | Streptococcus (1,192), Toxoplasma (969), Staphylococcus (929), Propionibacterium (127), Corynebacterium (123) | Pseudomonas (301,181), Staphylococcus (286,646), Streptococcus (135,065), Yarrowia (40,273), Propionibacterium (27,201), Achromobacter (15,251), Elizabethkingia (8,617), Acinetobacter (4,813), Haemophilus (4,423), Alloiococcus (2,610), Granulicatella (2,381), Malassezia (2,557), Delftia (681), Fusarium (671), Corynebacterium (593), Veillonella (498), Alloprevotella (384), Chryseobacterium (216), Dolosigranulum (234), Neisseria (177), Aspergillus (165) |
| WGA with no template | Achromobacter (5,072), Rothia (1,031), Micrococcus (451), Delftia (110) | Sphingomonas (35,596), Staphylococcus (6,414), Propionibacterium (3,596), Peptoniphilus (697), Finegoldia (196), Elizabethkingia (149) | Pseudomonas (5,297,561), Propionibacterium (1,557,410), Staphylococcus (407,691), Lactococcus (297,420), Elizabethkingia (134,333), Malassezia (89,791), Delftia (13,668), Acinetobacter (7,858), Phyllobacterium (2,808), Comamonas (3,175), Chryseobacterium (1,732), Achromobacter (1,734), Corynebacterium (1,061), Rhodococcus (1,231), Micrococcus (452), Polynucleobacter (426), Streptococcus (274), Wolbachia (223), Alternaria (220) |
a
Taxonomic identification of reads was performed using LMAT, and the reads were grouped by genus. All genera with 100 or more assigned reads are listed. Known pathogens identified by culture are in boldface.