Table 1.
Characteristics of patients in set 1 (training set)
| Infection, patient no. | Age | Ethnicity | Sex | Clinical disease | Bacteria vs virus | E coli vs S aureus | Acute RI | Antimicrobial therapy |
|---|---|---|---|---|---|---|---|---|
| E coli | ||||||||
| 12 | 5 mo | Black | M | Bacteremia | Fig. 1A-B | Fig. 3A-B | NA | Ceftriaxone |
| 13 | 5 mo | White | F | UTI | Fig. 1A-B | Fig. 3A-B | NA | Ceftriaxone |
| 31 | 3 mo | Hispanic | F | UTI, bacteremia | Fig. 1A-B | Fig. 3A-B | NA | Gentamicin |
| 34 | 16 y | White | F | Pyelonephritis | Fig. 1C | Fig. 3A-B | NA | Gentamicin |
| 48 | 2 mo | White | M | UTI | Fig. 1C | Fig. 3C | NA | Ampicillin, ceftriaxone |
| 57 | 3 mo | Black | F | UTI, bacteremia | Fig. 1C | Fig. 3A-B | NA | Gentamicin |
| 74 | 4 mo | Hispanic | F | UTI, bacteremia | Fig. 1A-B | Fig. 3A-B | NA | Ceftriaxone |
| 82 | 2 mo | Hispanic | M | UTI | Fig. 1C | Fig. 3A-B | NA | Ampicillin, ceftriaxone |
| 86 | 3 mo | Hispanic | M | UTI | Fig. 1A-B | Fig. 3A-B | NA | Ceftriaxone |
| 118 | 1.5 mo | White | M | UTI | Fig. 1C | Fig. 3C | NA | Test 1 and 2 |
| 120 | 1.5 mo | Hispanic | M | UTI | Fig. 1C | Fig. 3C | NA | Ampicillin, ceftriaxone |
| 133 | 2 mo | Hispanic | M | UTI | Fig. 1C | Fig. 3C | NA | Ceftriaxone |
| 139 | 1 mo | Hispanic | M | UTI | Fig. 1C | Fig. 3C | NA | Ampicillin, ceftriaxone |
| 148 | 8 y | Hispanic | F | UTI | Fig. 1C | Fig. 3A-B | NA | Ceftriaxone |
| 151 | 1.5 mo | Hispanic | M | UTI | Fig. 1C | Fig. 3C | NA | Ampicillin, gentamicin |
| 152 | 2.5 mo | Black | M | Bacteremia, meningitis | Fig. 1A-B | Fig. 3A-B | NA | Ceftriaxone, gentamicin |
| 154 | 2 mo | Hispanic | M | UTI | Fig. 1C | Fig. 3C | NA | Ceftriaxone |
| 161 | 1.7 mo | Hispanic | M | UTI | Fig. 1C | Fig. 3C | NA | Ampicillin, ceftriaxone |
| 168 | 3 mo | White | F | UTI | Fig. 1C | Fig. 3C | NA | Ceftriaxone |
| 171 | 3 mo | Hispanic | F | UTI | Fig. 1C | Fig. 3C | NA | Ceftriaxone |
| 175 | 0.5 mo | Hispanic | F | UTI, bacteremia | Fig. 1C | Fig. 3C | NA | Ceftriaxone |
| 180 | 1 mo | Hispanic | M | UTI | Fig. 1C | Fig. 3C | NA | Ampicillin, gentamicin |
| 183 | 1.5 mo | Hispanic | M | UTI | Fig. 1C | Fig. 3C | NA | Ampicillin, gentamicin, ceftriaxone |
| 184 | 0.5 mo | White | F | UTI, bacteremia | Fig. 1C | Fig. 3C | NA | Ampicillin, gentamicin |
| 188 | 1.5 mo | White | M | UTI | Fig. 1C | Fig. 3C | NA | Ampicillin, gentamicin, ceftriaxone |
| 197 | 1.25 mo | White | M | UTI | Fig. 1C | Fig. 3C | NA | Ampicillin, gentamicin |
| 219 | 5 mo | White | F | UTI, bacteremia | Fig. 1C | Fig. 3C | NA | Ceftriaxone |
| 222 | 3 mo | Hispanic | F | UTI, bacteremia | Fig. 1C | Fig. 3C | NA | Ceftriaxone, gentamicin |
| 229 | 4 mo | Hispanic | F | UTI, bacteremia | Fig. 1C | Fig. 3C | NA | Ceftriaxone |
| S aureus | ||||||||
| 5 | 10 y | Hispanic | M | Osteomyelitis | Fig. 1D | Fig. 3A-B | NA | Cefazolin |
| 24 | 3 y | Black | M | Osteomyelitis | Fig. 1D | Fig. 3C | NA | Vancomycin, rifampin |
| 30 | 15 y | Black | M | Bacteremia | Fig. 1D | Fig. 3C | NA | Vancomycin |
| 40 | 12 y | White | M | Osteomyelitis, bacteremia | Fig. 1D | Fig. 3C | NA | Cefazolin |
| 43 | 7 y | Black | M | Hip abscess, bacteremia | Fig. 1D | Fig. 3C | NA | Vancomycin, rifampin |
| 62 | 2 y | White | M | Osteomyelitis | Fig. 1D | Fig. 3A-B | NA | Clindamycin |
| 66 | 3 mo | Black | F | Pneumonia | Fig. 1D | Fig. 3A-B | Fig. 5C | Vancomycin, gentamicin |
| 67 | 7 y | White | F | Osteomyelitis, bacteremia | Fig. 1D | Fig. 3A-B | NA | Vancomycin, rifampin |
| 69 | 9 mo | Hispanic | M | Lung abscess | Fig. 1D | Fig. 3A-B | NA | Vancomycin, cefazolin |
| 70 | 15 mo | White | F | Abscess | Fig. 1D | Fig. 3A-B | NA | Vancomycin |
| 84 | 18 y | Black | F | Abscess | Fig. 1D | Fig. 3C | NA | Cefazolin |
| 88 | 11 mo | Hispanic | M | Osteomyelitis, bacteremia | Fig. 1D | Fig. 3A-B | NA | Vancomycin |
| 89 | 4 mo | Black | F | Abscess | Fig. 1D | Fig. 3A-B | NA | Clindamycin |
| 90 | 8 mo | Black | M | Septic arthritis | Fig. 1D | Fig. 3A-B | NA | Oxacillin |
| 150 | 9 y | Black | F | Osteomyelitis, bacteremia | Fig. 1D | Fig. 3C | NA | Vancomycin, rifampin |
| 179 | 12 y | White | M | Endocarditis, bacteremia | Fig. 1D | Fig. 3C | NA | Oxacillin, gentamicin, rifampin |
| 205 | 7 y | Hispanic | M | Pneumonia, bacteremia | Fig. 1D | Fig. 3C | Fig. 5C | Vancomycin |
| 206 | 1 y | Hispanic | F | Abscess | Fig. 1D | Fig. 3C | NA | Clindamycin |
| 208 | 10 y | White | F | Osteomyelitis, bacteremia, pneumonia | Fig. 1D | Fig. 3C | Fig. 5C | Vancomycin, clindamycin, rifampin |
| 216 | 10 y | Hispanic | F | Osteomyelitis, bacteremia | Fig. 1D | Fig. 3A-B | NA | Vancomycin, rifampin |
| 220 | 11 y | Hispanic | M | Osteomyelitis, bacteremia | Fig. 1D | Fig. 3C | NA | Cefazolin, rifampin |
| 221 | 6 y | Black | F | Osteomyelitis, bacteremia | Fig. 1D | Fig. 3C | NA | Vancomycin, rifampin |
| 224 | 10 y | White | M | Osteomyelitis, bacteremia | Fig. 1D | Fig. 3C | NA | Oxacillin, rifampin |
| 241 | 10 mo | Black | F | Pneumonia, bacteremia | Fig. 1D | Fig. 3C | Fig. 5C | Vancomycin, rifampin |
| 242 | 13 mo | Black | M | Pneumonia, bacteremia | Fig. 1D | Fig. 3C | Fig. 5C* | Clindamycin |
| 258 | 8 y | White | F | Osteomyelitis, bacteremia | Fig. 1D | Fig. 3C | NA | Cefazolin |
| 262 | 13 y | Hispanic | M | Abscess, bacteremia | Fig. 1D | Fig. 3C | NA | Clindamycin |
| 264 | 13 y | Black | M | Septic arthritis | Fig. 1D | Fig. 3C | NA | Vancomycin, cefazolin, gentamicin |
| 271 | 13 y | Black | M | Osteomyelitis | Fig. 1D | Fig. 3C | NA | Clindamycin |
| 281 | 3 y | White | F | Osteomyelitis | Fig. 1D | Fig. 3C | NA | Clindamycin |
| 315 | 3 y | Hispanic | F | Cellulitis | Fig. 1D | Fig. 3C | NA | Vancomycin |
| S pneumoniae | ||||||||
| 9 | 4 mo | White | M | Abscess | Fig. 1A-B | NA | NA | Cefazolin |
| 25 | 2 mo | Hispanic | M | Meningitis | Fig. 1A-B | NA | NA | Ampicillin, ceftriaxone |
| 41 | 23 mo | White | F | Pneumonia, empyema | Fig. 1A-B | NA | Fig. 5C | Ceftriaxone |
| 64 | 10 mo | White | F | Meningitis, bacteremia | Fig. 1C | NA | NA | Ceftriaxone, vancomycin |
| 96 | 16 mo | Hispanic | M | Pneumonia, empyema | Fig. 1A-B | NA | Fig. 5C | Ceftriaxone, azithromycin |
| 113 | 7 mo | Hispanic | F | Septic arthritis | Fig. 1A-B | NA | NA | Ceftriaxone, clindamycin |
| 155 | 3 mo | Hispanic | M | Meningitis | Fig. 1A-B | NA | NA | Ceftriaxone, vancomycin |
| 261 | 13 y | White | M | Meningitis | Fig. 1C | NA | NA | Ceftriaxone, vancomycin |
| 268 | 3 y | Hispanic | M | Pneumonia, empyema | Fig. 1C | NA | NA | Ceftriaxone, clindamycin |
| 265 | 2 y | White | F | Pneumonia, empyema | Fig. 1C | NA | Fig. 5C | Ceftriaxone, vancomycin |
| 277 | 16 y | White | M | Pneumonia, empyema | Fig. 1C | NA | Fig. 5C | Ceftriaxone, vancomycin |
| 287 | 3 y | White | F | Pneumonia, bacteremia | Fig. 1C | NA | Fig. 5C | Ceftriaxone, vancomycin |
| 289 | 2 y | Hispanic | M | Pneumonia, bacteremia | Fig. 1C | NA | Fig. 5C | Ceftriaxone, vancomycin |
| Influenza A | ||||||||
| 55 | 11 mo | Hispanic | M | Respiratory distress | Fig. 1A-B | NA | Fig. 5C | Cefuroxime |
| 87 | 19 mo | White | F | Fever, hypoxia | Fig. 1A-B | NA | Fig. 5C | Cefuroxime |
| 92 | 1 mo | Hispanic | F | Fever | Fig. 1A-B | NA | Fig. 5C | Ampicillin, ceftriaxone |
| 95 | 4 y | Hispanic | M | Fever | Fig. 1C-D | NA | Fig. 5C | None |
| 101 | 4 mo | Hispanic | M | Fever, URI | Fig. 1A-B | NA | Fig. 5C* | Cefuroxime, oseltamivir |
| 104 | 17 mo | Hispanic | M | Seizures, fever, respiratory failure | Fig. 1A-B | NA | Fig. 5C | Ceftriaxone |
| 105 | 4 y | Hispanic | F | Fever, encephalopathy | Fig. 1C-D | NA | Fig. 5C* | Ceftriaxone, acyclovir, oseltamivir |
| 107 | 1.5 mo | Asian | M | Fever, lethargy | Fig. 1A-B | NA | Fig. 5C | Ampicillin, ceftriaxone |
| 108 | 5 mo | Hispanic | M | Fever | Fig. 1A-B | NA | Fig. 5C | Ceftriaxone |
| 112 | 1 mo | Hispanic | M | Fever, URI | Fig. 1C-D | NA | Fig. 5C | Ampicillin, gentamicin |
| 114 | 18 mo | Black | F | Respiratory distress, fever | Fig. 1A-B | NA | Fig. 5C | Cefuroxime, oseltamivir |
| 115 | 20 mo | White | M | Seizures | Fig. 1A-B | NA | Fig. 5C | Amoxicillin |
| 116 | 2 y | White | M | Fever, URI | Fig. 1C-D | NA | NA | Cefuroxime, clindamycin |
| 117 | 24 y | White | F | Fever | Fig. 1C-D | NA | Fig. 5C | None |
| 128 | 11 mo | Hispanic | F | Fever, hypoxia | Fig. 1A-B | NA | Fig. 5C* | Cefuroxime |
| 132 | 6 mo | White | M | Respiratory distress, fever | Fig. 1A-B | NA | Fig. 5C* | Oxacillin, tobramycin |
| 259 | 3 mo | Hispanic | F | Pneumonia | Fig. 1C-D | NA | Fig. 5C | None |
| 266 | 36 y | White | F | Fever, cough | Fig. 1C-D | NA | NA | None |
For E coli (n = 29), median age, 2 months (range, 2 weeks to 16 years); S aureus (n = 31), median age, 7 years (range, 3 months to 18 years); S pneumoniae (n = 13), median age, 1.9 years (range, 2 months to 16 years); and influenza A (n = 18), median age, 14 months (range, 3 weeks to 36 years).
RI indicates respiratory infection; NA, not applicable; UTI, urinary tract infection; URI, upper respiratory infection.
*
These samples were characterized by a mixed signature.