Background: Culture-based identification and AMR-testing requires up to 72h. In addition, respiratory samples may have low sensitivities due to (i) small sample amounts being cultured and (ii) background (over)growth of oropharyngeal flora. Broad-panel PCR assays may overcome these gaps. We aim to evaluate the microbiological performance of the BIOFIRE® Pneumonia plus Panel (PNplus Panel) compared to culture-based techniques.
Materials/methods: We used consecutive collected bronchoalveolar lavage (BAL) and tracheal secretion (TS) samples from February-August 2019. Detection rates of the PNplus Panel (200uL per sample) was compared to culture (BAL: 1uL and TS: approx. 50uL; internal gold-standard) on 5% sheep blood agar, CNA, Haemophilus, and MacConkey plates. The PNplus Panel covered 15 bacterial (semi-quantitative), 3 atypical bacterial and 9 viral and 7 AMR targets (qualitative) and was performed according to company instructions.
Results: We compared 690 respiratory samples, corresponding to 18,630 PNplus Panel targets. PNplus Panel detected 517 targets (347 bacteria, 2 atypical bacteria, and 168 viruses). In comparison to culture, the PNplus Panel found significantly more bacterial targets (+114%, 347/690 vs. 162/690). Some species were more frequently detected with PNplus Panel: Haemophilus influenzae, Moraxella catarrhalis, Streptococcus agalactiae, Streptococcus pyogenes, and Staphylococcus aureus with additional 375%, 533%, 100%, 250% and 89%, respectively. These were often detected at low quantities in PCR (104 to 105 CFUs/mL). Samples with higher background flora (>50,000 CFUs/mL) showed a higher mismatch between the culture and PNplus Panel results. Overall specificity and sensitivity were 98.1% and 89.9%, respectively. We detected only 5 AMR genes (3x CTX-M/2x mecA), of which 3 were confirmed by culture (2x CTX-M/1x mecA).
Conclusions: PNplus Panel allows a rapid assessment of most common pneumonia pathogens and AMR genes. The difference in detection rates is most likely due to substantial differences in the culture workup or small quantities of target bacteria overgrown by oropharyngeal flora. The question remains if S. aureus and H. influenzae are pathogens or bystanders at low concentrations or presence of substantial background flora. Careful evaluation of clinical evidence for infection should be considered to avoid overtreatment of patients. The PNplus Panel may benefit from a background flora target.