Table 2.
Typical and atypical bacteria detected, with PPAs and NPAs
| Typical bacteria | Culture (n) | FA-PP (n) | PPA (95% CI) | NPA (95% CI) |
|---|---|---|---|---|
| H. influenzae | 5 | 43 | 100 (57–100) | 64 (55–73) |
| S. aureus | 1 | 30 | 100 (5–100) | 74 (65–81) |
| S. pneumoniae | 4 | 28 | 100 (51–100) | 78 (69–85) |
| Klebsiella pneumoniae | 1 | 27 | 100 (5–100) | 77 (68–83) |
| Enterobacter cloacae complex | 2 | 18 | 100 (18–100) | 85 (78–91) |
| Acinetobacter calcoaceticus-baumannii complex | 2 | 16 | 100 (18–100) | 87 (80–92) |
| P. aeruginosa | 4 | 11 | 100 (51–100) | 94 (87–97) |
| Escherichia coli | 0 | 10 | — | 91 (84–95) |
| Moraxella catarrhalis | 0 | 9 | — | 92 (85–96) |
| Proteus species | 0 | 6 | — | 95 (89–98) |
| Klebsiella oxytoca | 0 | 4 | — | 96 (91–99) |
| Serratia marcescens | 1 | 4 | 100 (5–100) | 97 (92–99) |
| Klebsiella aerogenes | 0 | 3 | — | 97 (92–99) |
| Streptococcus agalactiae | 0 | 3 | — | 97 (92–99) |
| Streptococcus pyogenes | 0 | 2 | — | 98 (94–100) |
| Total | 20 | 214 | 100 (84–100) | 88 (87–90) |
| Atypical bacteria | Culture (n) | FA-PP (n) | ||
| L. pneumophila | 4a | 4 | ||
| Chlamydia pneumoniae | N/A | 0 | ||
| Mycoplasma pneumoniae | N/A | 0 | ||
| Total | 4 | |||
| Viral pathogens | PCR (n) | FA-PP (n) | ||
| Human rhinovirus/enterovirus | N/A | 19 | ||
| Parainfluenza virus | N/A | 5 | ||
| Coronavirus | N/A | 4 | ||
| Respiratory syncytial virus (RSV) | N/A | 4 | ||
| Adenovirus | N/A | 2 | ||
| Human metapneumovirus | N/A | 0 | ||
| Influenza A | N/A | 0 | ||
| Influenza B | N/A | 0 | ||
| Middle East respiratory syndrome coronavirus (MERS) | N/A | 0 | ||
| Total | 34 | |||
| Resistance genes | Phenotypic (n) | FA-PP (n) | ||
| CTX-M | 3b,c | 16 | ||
| mecA/C and MREJ | 0 | 6 | ||
| NDM | 2c,d | 5 | ||
| OXA-48-like | 0 | 3 | ||
| IMP | 0 | 0 | ||
| KPC | 0 | 0 | ||
| VIM | 0 | 0 | ||
| Total | 5 | 30 | ||
N/A, not applicable.
Two out of the four L. pneumophila detections confirmed with positive L. pneumophila serogroup 1 urinary antigen test, the rest confirmed with a PCR test for atypical pneumonia by the NICD as non-serogroup 1.
Carbapenem-susceptible P. aeruginosa (WT) was detected by routine laboratory testing, but FA-PP detected CTX-M, NDM and OXA-48-like genes in the presence of Acinetobacter calcoaceticus-baumannii complex, K. pneumoniae and P. aeruginosa. Assumption made that P. aeruginosa only associated with CTX-M.
Carbapenem-resistant A. baumannii detected by routine laboratory testing, but FA-PP detected CTX-M and NDM genes in the presence of Acinetobacter calcoaceticus-baumannii complex and K. pneumoniae. Assumption that A. baumannii associated with both genes.
Carbapenem-resistant A. baumannii detected by routine laboratory testing, but FA-PP detected the NDM gene in the presence of Acinetobacter calcoaceticus-baumannii complex and P. aeruginosa. Assumption made that A. baumannii associated with the NDM gene.