Ann Clin Microbiol 2020;23:1-10. Application of 16S rRNA Gene-Targeted Next-Generation Sequencing for Bacterial Pathogen Detection in Continuous Ambulatory Peritoneal Dialysis Peritonitis
| No | Culture | NGS (> 10 % relative abundance) | Read count | Infection | Antibiotics* | Catheter removal | Clear up on day 10 | Relapse within 2 months |
|---|---|---|---|---|---|---|---|---|
| CAPD01 | Staphylococcus epidermidis | Staphylococcus spp. (20.4 %) | 14,841 | yes | cefazolin, tobramycin, vancomycin | yes | yes | no |
| CAPD02 | Escherichia coli | Escherichia spp. (99.8 %) | 96,528 | yes | rifaximin, meropenem | no | yes | yes |
| CAPD03 | No growth | Lactobacillus spp. (82.1 %) | 86,053 | no | piperacillin-tazobactam | – | – | – |
| CAPD04 | Serratia marcescens | Serratia spp. (74.6 %) | 59,609 | yes | vancomycin, ceftazidime | no | no | yes |
| CAPD05 | Micrococcus spp. | Kytococcus spp. (25.2 %) Lactobacillus spp. (19.2 %) | 13,260 | yes | cefazolin, ceftazidime | no | yes | no |
| CAPD06 | No growth | Enterobacteriaceae (11.9 %) Lactobacillus spp. (11.0 %) | 83,717 | yes | meropenem, rifaximin | no | no | no |
| CAPD07 | Staphylococcus epidermidis | Staphylococcus spp. (90.0 %) | 44,704 | yes | cefazolin, ceftazidime | no | yes | no |
| CAPD08 | Esherichia. coli | Escherichia spp. (21.4 %) Bacteroides spp. (19.9 %) | 76,720 | yes | cefazolin, ceftazidime | no | yes | no |
| CAPD09 | No growth | No dominant organism | 3,350 | no | no | – | – | – |
| CAPD10 | Enterococcus faecalis | Low read count | – | yes | cefazolin, ceftazidime | no | no | yes |
| CAPD11 | Staphylococcus epidermidis | No dominant organism | 71,751 | yes | cefazolin, ceftazidime | no | no | yes |
| CAPD12 | Staphylococcus haemolyticus | Bacteroides spp. (26.4 %) Blautia spp. (12.3 %) Collinsella spp. (10.5 %) | 74,491 | yes | cefazolin, ceftazidime | no | no | no |
| CAPD13 | No growth | No dominant organism | 58,772 | no | no | – | – | – |
| CAPD14 | No growth | Prevotella spp. (15.2 %) Streptococcus spp. (14.6 %) | 92,363 | no | no | – | – | – |
| CAPD15 | Streptococcus anginosus | Low read count | – | yes | cefazolin, ceftazidime | no | no | no |
| CAPD16 | Micrococcus spp. | Streptococcus spp. (10.0 %) | 47,182 | yes | vancomycin | yes | no | no |
| CAPD17 | Bacillus spp. | Prevotella spp. (13.3 %) Streptococcus spp. (13.2 %) Veillonella spp. (11.6 %) | 25,296 | no | no | – | – | – |
| CAPD18 | Burkholderia cepacia | Bacteroides spp. (13.6 %) | 4,174 | yes | cefazolin, ceftazidime | yes | no | yes |
| CAPD19 | Candida albicans, Enterococus avium | Enterococcus spp. (74.6 %) | 85,431 | yes | piperacillin- tazobactam | yes | no | no |
| CAPD20 | Citrobacter freundii | Low read count | – | yes | ceftazidime | yes | no | no |
| CAPD21 | Staphylococcus epidermidis | Prevotella spp. (11.5 %) | 2,800 | yes | cefazolin, ceftazidime | no | yes | yes |
*Antibiotics for CAPD peritonitis treatment (a bold form is an effective agent); -, not determined
Abbreviation: NGS, next-generation sequencing; CAPD, continuous ambulatory peritoneal dialy