Table 1.
Results of the sequencing-based FISH analysis of selected abortion cases from routine diagnostic groups 1 and 2 (20).
| Species | FISH screening inclusion criteria | No. of cases screened | No. of cases of agent-associated lesions | Previous etiology (routine methods)a | Final etiology (combined methods)b |
|---|---|---|---|---|---|
| B. licheniformis | >10,000 readsc placenta and/or culture positive ≥1 organ | 4 | 4 |
B. licheniformis n = 1 Unknown n = 3 |
B. licheniformis n = 3 B. licheniformis + E. coli n = 1 |
| C. burnetii | all cases with C. burnetii readsc | 3 | 0 |
T. pyogenes n = 1 K. pneumoniae n = 1 Unknown n = 1 |
T. pyogenes n = 1 K. pneumoniae n = 1 Unknown n = 1 |
| C. jejuni | all cases with C. jejuni readsc | 1 | 0 | Unknown n = 1 | E. coli n = 1 |
| E. coli | >20,000 readsc placentad and/or pure culture positive ≥1 organ | 21 | 8 |
E. coli n = 4 N. caninum n = 6 Unknown n = 11 |
E. coli n = 6 B. licheniformis + E. coli n = 1 N. caninum n = 5 N. caninum + E. coli n = 1 Unknown n = 8 |
| F. necrophorum | >10,000 readsc placenta | 7 | 0 |
E. coli n = 1 N. caninum n = 3 Unknown n = 3 |
E. coli n = 1 N. caninum n = 3 T. pyogenes n = 2 Unknown n = 1 |
| L. monocytogenes | >10,000 readsc placenta and/or culture positive ≥1 organ | 2 | 2 | L. monocytogenes n = 2 | L. monocytogenes n = 2 |
| S. aureus | >10,000 readsc placenta and/or culture positive ≥1 organ | 4 | 3 |
S. aureus n = 3 Unknown n = 1 |
S. aureus n = 3 Unknown n = 1 |
| T. pyogenes | >10,000 readsc placentad and/or culture positive ≥1 organ | 8 | 8 |
T. pyogenes n = 5 BVDV n = 1 Unknown n = 2 |
T. pyogenes n = 7 T. pyogenes + BVDV n = 1 |
BVDV, bovine viral diarrhea virus.
The previous etiologic diagnosis was made according to the diagnostic criteria of the routine diagnostic study (20).
The final etiologic diagnosis was made based on a combined evaluation of the bacterial culture, histopathologic, sequencing, and FISH findings.
16S rDNA amplicon sequencing reads of the respective bacterial species.
If placenta was not available, the number of sequencing reads from the lung–liver pool or lung were assessed and the cases were FISH-screened if the number of reads was above the inclusion limit for placenta.
Species-specific probes were applied to evaluate the causal relationship between the pathogen and tissue lesions.