LETTER
Among molecular assays currently developed for detection and identification of pathogens (and their antimicrobial resistance genes) in positive blood cultures (BCs) (1), the BioFire FilmArray blood culture identification (BCID) panel (bioMérieux, Marcy l’Etoile, France), a multiplex PCR assay with <2 min of hands-on time and an ∼1-h turnaround time, allows for syndromic diagnosis of bloodstream infection (BSI) (2, 3). Previously, the panel could identify 24 etiological agents of BSI (11 Gram-negative bacteria, 8 Gram-positive bacteria, and 5 yeast species), as well as three antimicrobial resistance genes (mecA, vanA/B, and blaKPC, which encodes Klebsiella pneumoniae carbapenemase). Now, the BioFire FilmArray BCID2 panel encompasses 43 molecular targets associated with BSI, including 15 Gram-negative bacteria, 11 Gram-positive bacteria, 7 yeast species, and 10 antimicrobial resistance genes (https://www.biomerieux-diagnostics.com/biofire-bcid-panel). The last targets include genes encoding carbapenemases (IMP, KPC, OXA-48-like, NDM, and VIM), colistin resistance (mcr-1), extended-spectrum β-lactamase (ESBL) (CTX-M), methicillin resistance (mecA/C and, specifically for methicillin-resistant Staphylococcus aureus [MRSA], mecA/C and MREJ [mec right-extremity junction]), or vancomycin resistance (vanA/B). Unlike BCID, no published studies to date reported on BCID2 performance. This study evaluated and compared the accuracy of BCID2 with that of BCID to identify bacterial species and relative antimicrobial resistance genes directly from positive BCs.
We used archived samples from positive BCs (1.5 ml thereof mixed with 100 μl of dimethyl sulfoxide and stored at −80°C), which had prospectively been processed with the BD Bactec 9240 (BD Diagnostic Systems, Sparks, MD), BacTAlert 3D (bioMérieux), or BacTAlert Virtuo (bioMérieux) system at two hospital microbiology laboratories from January 2018 to August 2020. For BCID2 testing, samples were thawed and allowed to reach room temperature, and a 200-μl aliquot was lysed and processed following the manufacturer’s instructions. We compared BCID2 results with those of conventional identification or detection (i.e., MALDI BioTyper analysis and, relative to antimicrobial resistance genes, PCR sequencing, both performed on microbial isolates subcultured from positive BC samples), which was considered the reference method in this evaluation, or with those of the BCID. Both the reference method and the BCID had been part of a previously implemented laboratory workflow for BSI diagnosis (4). Frozen aliquots of the original BC samples were submitted to subculturing and testing of the organism(s) grown from the aliquots to confirm samples’ previous state.
We studied 90 BCs that grew clinically relevant bacterial species, of which 55 monomicrobial (55 species in total) and 35 polymicrobial (77 species in total, including 1 Candida albicans) with antimicrobial resistance determinants (53 genes in total) were identified (see Table S1 in the supplemental material). We selected BCs to ensure testing of organisms either belonging to bacterial species (e.g., Bacteroides fragilis) or carrying antimicrobial resistance genes (e.g., blaCTX-M) that were not included in the BCID. Both BCID2 and BCID assays were compared with the reference method specified above. Regarding results with on-panel organisms (Table 1), the percent agreement was 100.0% (95% confidence interval [CI], 97.2% to 100.0%) for the BCID2 and 100.0% (95% CI, 96.8% to 100.0%) for the BCID. All off-panel organisms yielded a negative result with the BCID2 (1 Ochrobactrum anthropi and 1 Brevibacterium casei) or the BCID (8 B. fragilis, 1 O. anthropi, 8 Stenotrophomonas maltophilia, and 1 B. casei). Regarding results with on-panel genes (Table 1), the percent agreement was 100.0% (95% CI, 92.3% to 100.0%) for the BCID2 and 100.0% (95% CI, 85.8% to 100.0%) for the BCID. No genes that encode ESBL- or carbapenemase-mediated β-lactam resistance (i.e., 16 CTX-M, 3 NDM, 4 OXA-48-like, and 4 VIM) were detected by the BCID. With respect to organisms targeted by both BCID2 and BCID assays, no discrepancies between the assays’ results were observed with the polymicrobial BC samples analyzed as a whole (Table S1).
TABLE 1.
BioFire FilmArray BCID2 and BCID panel results compared to reference method results for bacterial organism identification and antimicrobial resistance gene detection from 90 positive blood culturesa
| Reference method (no. of results) | FilmArray BCID2 panel (no. of results) | FilmArray BCID panel (no. of results) |
|---|---|---|
| Gram-negative organisms (77) | ||
| Acinetobacter baumannii (3) | Acinetobacter calcoaceticus-Acinetobacter baumannii complex (3) | Acinetobacter calcoaceticus-Acinetobacter baumannii complex (3) |
| Bacteroides fragilis (8) | Bacteroides fragilis (8) | – |
| Citrobacter freundii (1) | Enterobacterales (1) | Enterobacteriaceae (1) |
| Enterobacter cloacae complex (2) | Enterobacter cloacae complex (2) | Enterobacter cloacae complex (2) |
| Escherichia coli (11) | Escherichia coli (11) | Escherichia coli (11) |
| Klebsiella aerogenes (9) | Klebsiella aerogenes (9) | Enterobacteriaceae (9) |
| Klebsiella oxytoca (3) | Klebsiella oxytoca (3) | Klebsiella oxytoca (3) |
| Klebsiella pneumoniae (14) | Klebsiella pneumoniae group (14) | Klebsiella pneumoniae (14) |
| Klebsiella variicola (8) | Klebsiella pneumoniae group (8) | Klebsiella pneumoniae (8)b |
| Ochrobactrum anthropi (1) | – | – |
| Pseudomonas aeruginosa (1) | Pseudomonas aeruginosa (1) | Pseudomonas aeruginosa (1) |
| Salmonella spp. (8) | Salmonella (8) | Enterobacteriaceae (8) |
| Stenotrophomonas maltophilia (8) | Stenotrophomonas maltophilia (8) | – |
| Gram-positive organisms (54) | ||
| Brevibacterium casei (1) | – | – |
| Enterococcus faecalis (9) | Enterococcus faecalis (9) | Enterococcus (9) |
| Enterococcus faecium (8) | Enterococcus faecium (8) | Enterococcus (8) |
| Staphylococcus aureus (9) | Staphylococcus aureus (9) | Staphylococcus aureus (9) |
| Staphylococcus epidermidis (11) | Staphylococcus epidermidis (11) | Staphylococcus (11) |
| Staphylococcus haemolyticus (4) | Staphylococcus (4) | Staphylococcus (4) |
| Staphylococcus lugdunensis (9) | Staphylococcus lugdunensis (9) | Staphylococcus (9) |
| Staphylococcus pasteurii (1) | Staphylococcus (1) | Staphylococcus (1) |
| Staphylococcus pettenkoferi (1) | Staphylococcus (1) | Staphylococcus (1) |
| Streptococcus salivarius (1) | Streptococcus (1) | Streptococcus (1) |
| Total organisms (131) | Total organisms (129) | Total organisms (113) |
| Antimicrobial resistance genes (53) | ||
| blaCTX-M-15 (11) | CTX-M (11) | – |
| blaCTX-M-27 (5) | CTX-M (5) | – |
| blaKPC-3 (6) | KPC (6) | KPC (6) |
| blaKPC-31 (2) | KPC (2) | KPC (2) |
| blaNDM-1 (3) | NDM (3) | – |
| blaOXA-23 (2) | – | – |
| blaOXA-48 (4) | OXA-48-like (4) | – |
| blaVIM-1 (4) | VIM (4) | – |
| mecA (12) | mecA/C (6),c mecA/C, and MREJ (5) | mecA (10)d |
| vanA (4) | vanA/B (4) | vanA/B (4) |
| Total genes (53) | Total genes (50) | Total genes (22) |
Including results from 55 monomicrobial and 35 polymicrobial blood cultures (BCs) from patients with clinically relevant bloodstream infection (BSI) (Table S1). Boldface indicates all molecular targets identified at the species or genus level (i.e., organisms) or detected (i.e., genes) only in the BioFire FilmArray BCID2 panel. Dashes indicate the absence of detection(s) due to off-panel organisms/genes identified/detected by the reference method and not the BioFire FilmArray BCID2 or BCID panel.
These results were interpreted as correct identifications because the BCID panel’s K. pneumoniae assay had been designed to detect both K. pneumoniae and K. variicola, which is a closely related species to K. pneumoniae.
The BCID2 panel uses the detection of mecA/C alone to identify staphylococci other than Staphylococcus aureus (SOSA) such as S. epidermidis and S. lugdunensis (above listed) or that of mecA/C and MREJ together to identify MRSA. However, BCID2 also signals mecA/C alone in polymicrobial BCs that grow MRSA together with S. epidermidis or S. lugdunensis. Thus, we excluded mecA/C-positive results of two BCs that grew mecA-positive S. aureus (correctly detected as MRSA) and mecA-negative S. epidermidis (Table S1). This allowed inclusion of four mecA/C-positive results in total. Additionally, three mecA genes in samples that grew S. haemolyticus (identified as Staphylococcus) were undetected because the BCID2 does not perform mecA/C detection for an organism not identified at the species level. These results were considered to be from off-panel genes and, thus, were excluded from the analysis.
The BCID panel signals the presence of mecA gene alone also in the case of polymicrobial BCs growing two different mecA-positive organisms. Thus, we included two other mecA-positive results in the analysis, which regarded two polymicrobial BCs, one growing 1 mecA-positive S. aureus plus 1 mecA-positive S. epidermidis and the other one growing 1 mecA-positive S. aureus plus 1 mecA-positive S. haemolyticus (Table S1). This allowed inclusion of 12 mecA results in total.
Regarding apparently discrepant results (all for methicillin resistance genes), three mecA genes were not detected by the BCID2, one in monomicrobial and two in polymicrobial BC samples (see IDs 54, 83, and 87 in Table S1). These samples grew Staphylococcus haemolyticus (identified as Staphylococcus) alone in one sample or together with S. aureus (1 mecA negative and 1 mecA positive) in two remaining samples. This was because the BCID2, contrary to the BCID, does not perform mecA detection for an organism not identified at the species level. Furthermore, the BCID2 detected mecA genes from two other polymicrobial BC samples that grew mecA-negative Staphylococcus epidermidis together with MRSA, for which a positive mecA/C and MREJ detection signal was provided (IDs 84 and 85 in Table S1). This was because the BCID2 also signals the mecA/C gene alone in samples that grow MRSA together with S. epidermidis or Staphylococcus lugdunensis, the two staphylococci other than S. aureus (SOSA) identified by the panel.
Here, we report that the BCID2 panel identified more bacterial species and relative antimicrobial resistance genes in positive BCs than the BCID panel while retaining similar performance for targets already included in the BCID. This was the case for BSI pathogens, such as Escherichia coli, K. pneumoniae (with the KPC gene), S. aureus (with the mecA gene), or Enterococcus faecalis (with the vanA gene), which are the most common bacterial pathogens (5). With the BCID2, the opportunity to identify MRSA (5) or S. epidermidis and S. lugdunensis (6) among SOSA may be clinically useful (7), whereas the incapacity to identify SOSA such as S. haemolyticus or other coagulase-negative Staphylococcus species may be detrimental, particularly in the presence of mecA-positive isolates (8, 9). Because the reference method helped us to interpret BCID2 (or BCID) results, we believe that the FilmArray BCID2 panel may be a valuable adjunct to culture-based diagnostics.
Supplementary Material
ACKNOWLEDGMENTS
We thank Franziska Lohmeyer for English revision of the manuscript.
bioMérieux (Marcy l’Etoile, France) provided FilmArray BCID2 panels for this evaluation, but the company had no role in study design, data collection or interpretation, or manuscript preparation.
We have no other conflicts of interest to report.
Footnotes
Supplemental material is available online only.
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