Biofire Blood Culture Identification (BCID) Panel - BCH Oakland

Modified Date: 
May 24, 2024
Document: 

Blood Culture Rapid Identification Panel (BCID-II)

The purpose of this document is to provide general guidance for empiric therapy based on the results of the rapid blood culture identification panel (BCID-II) used at BCH Oakland. 
Please note that this is general guidance and does not replace clinical judgement based on the patient's clinical presentation, history, and current clinical status.

What is BCID? 

BCID2 is an FDA-approved test called Biofire® FilmArray® Blood Culture ID Panel. It uses multiplex PCR to identify 30 bacterial and fungal pathogens and 10 antimicrobial resistance genes (Table 1), including the most common resistance gene markers (e.g. mec A for staphylococcus). The BCID2 has demonstrated 99% sensitivity and 99.8% specificity. 

What is the process for organism identification using rapid diagnostic testing in blood? 

Once a blood culture is positive, a Gram stain is performed, and the bedside nurse is informed. BCID-2 is automatically ordered by the lab if there has been no previous identification within the past 3 days. In Apex – the results will appear for clinicians to see along with guidance to call ASP M-F 8-5:30p.m. Overnight and weekend results will be paged and discussed with on-call ID.  Below is outline for current and proposed workflow 

Why is ASP/ID being consulted with BCID-II results interpretation?  

Studies has demonstrated that implementing stewardship practices alongside rapid diagnostic testing can significantly improve patient outcomes. According to a randomized trial conducted by Banerjee et al. (2015), patients who received stewardship in addition to rapid multiplex polymerase chain reaction-based blood culture identification and susceptibility testing experienced a dramatically reduced time to first appropriate de-escalation, with a median time of 21 hours (compared to 34 hours in the control group and 38 hours in the rapid multiplex group). The findings were statistically significant, with a p-value of less than 0.0001. Moreover, patients in the stewardship group were less likely to receive antibiotic treatment for contaminated blood cultures, indicating that stewardship practices can help reduce unnecessary antibiotic use and promote better patient care. This study suggests that the integration of stewardship into rapid diagnostic testing protocols can be a valuable strategy for enhancing clinical decision-making and improving patient outcomes. 

How do I interpret the results? 
Results from the BCID panel appear as a separate line below the culture result line in the viewer. Therapeutic decisions and treatment choices based on BCID results are listed in Table 2 and Table 3 (scroll below). Final susceptibilities should always be reviewed to determine if any adjustments in therapy are needed. 

What are the most common pitfalls in interpreting BCID-2 results? Pathogens are identified at a genus level (e.g. Staphylococcus, Streptococcus) and multiple family level pathogens of the Enterobacterales order. The Staphylococcus genus PCR detects numerous species of staphylococci, including S. aureusS.epidermidis, S.hominis, and others. When S. aureus is present, both genus and species will be detected. When coagulase-negative Staphylococcus such as S. hominis is detected, only the genus will be detected. 

Polymicrobial infections 

Certain infections can be polymicrobial in nature. For example, complicated intra-abdominal infections frequently have anaerobes as co-pathogens, which should not result in over-narrowing. 

Some caveats associated with resistance genes 

  • For S. aureus, the detection of mec A/C/MREJ denotes the presence of MRSA.  
  • For S. epidermidis and S. lugdunensis, the detection of mec A/C predicts beta-lactam resistance. 
  • When the Staphylococcus genus is reported without the presence of S. aureus, S. epidermidis, or S. lugdunensis, mec A/C is not reported. 
  • Detection of MCR-1 predicts colistin resistance, at this time this does not have a high clinical value for pediatric population 

Gram negative pathogen results:  Enterobacterales order 
When the Enterobacterales order is reported positive, it includes many gram-negative organisms, including E. coli, Klebsiella species, Enterobacter species, Proteus species, and Citrobacter species, among others. For example, when E. coli is reported positive, both Enterobacterales and E. coli will be positive. If an Enterobacterales order member is present but not the specific PCR target, only Enterobacterales will be reported positive. 

Other general principles applicable to all results of BCID-II  

  • Narrow based on phenotypic susceptibility results in 24-48 hours.   
  • Dosing to be adjusted based on the site and extent of infection. Refer to dosing card in table  4.  
  • Patients with carbapenemase gene resistance (KPC, OXA-48, IMP, VIM and NDM), additional susceptibility testing needs to be requested from microbiology lab.
  • For carbapenemase gene resistance - KPC, OXA-48, IMP, VIM and NDM - infection prevention needs to be informed  and place patient in contact precautions. 

Assessing blood culture contamination 

Roughly 50% of blood cultures may grow organisms not truly representing bacteremia, referred to as contaminants. Coagulase-negative staphylococci (e.g. Staphylococcus epidermidis group), viridians streptococcus are some of the common commensals.  If the patient is clinically stable with low pretest probability for bloodstream infection (e.g. lack of central venous catheter or endovascular prosthetic material), antibiotics may not be indicated. Refer to individual sections within Table 2 for further guidance. 

 

Table 1 

Gram positive bacteria 

Gram-negative bacteria 

Yeast 

Resistance Genes 

Enterococcus faecalis  
Enterococcus faecium 

Listeria monocytogenes Staphylococcus genus 

Staphylococcus aureus Staphylococcus epidermidis Staphylococcus lugdunensis 

Streptococcus genus Streptococcus agalactiae Streptococcus pneumoniae Streptococcus pyogenes 

Acinetobacter baumannii complex Bacteroides fragilis 
 
Enterobacterales Order 
Enterobacter cloacae complex Escherichia coli 
Klebsiella aerogenes 
Klebsiella oxytoca 
Klebsiella pneumoniae group  
Proteus spp. 
Salmonella spp. 
Serratia marcescens 

Haemophilus influenzae  
Neisseria meningitidis Pseudomonas aeruginosa Stenotrophomonas maltophilia 

Candida albicans  
Candida auris  
Candida glabrata  
Candida krusei  
Candida parapsilosis Candida tropicalis 

 Cryptococcus neoformans/gattii 

Carbapenemases 

IMP 
KPC  
OXA-48-like  
NDM  
VIM 

Colistin Resistance -mcr-1 

Extended spectrum beta-lactamases (ESBL) 
CTX-M 

Methicillin Resistance  
-mecA/C 
-mecA/C and MREJ (MRSA) 

Vancomycin Resistance  
-vanA/B 

 

Pathogens Detected vs Not Detected by BCID II 

Pathogens 

Pathogens Detected 

Pathogens Not-Detected 

Enterococcus  

 

E. faecium  

E. faecalis  

E. avium 
E. casseliflavus 
E. durans 
E. gallinarum 
E. hirae 
E. dispar 
E. saccharolyticus E. raffinosus 
E. mundtii  

Staphylococcus genus  

It is predicted that only 5 species will not be detected. Of those, only S. equorum has been reported in a clinical setting.  

S. equorum S. fluerettii S. lentus 
S. muscae S. rostri  

Streptococcus genus  

Designed to detect most Viridians group species and non-Group A/B beta hemolytic streptococci.  

All species within the Streptococcus genus should be amplified by one or more of the assays on the panel at positive blood culture levels.  

Some species may not be detected if present in a blood culture at low levels or if they have variant sequences (see right).  

S. equi 
S. entericus 
S. halitosis S.hyovaginalis S. minor 
S. pantholopis S. oralis 
S. sobrinus 
S. suis 
S. uberis  

Enterobacterales  

Designed to detect less 
common gram-negative bacteria within multiple families of the order Enterobacterales.  

Information about the detection of specific subspecies, strains, isolates, or serotypes of gram-negative bacteria is provided in the product instructions for use (Table 98 – Table 112) available at www.biofiredx.com/support/documents 

Cedeceae spp.  
Citrobacter spp.  
Cosenzaea spp.  
Cronobacter spp.  
Edwardsiella spp  

In silico predication)  
Enterobacter spp.  
Escherichia spp.  
Erwinia spp.  
Hafnia spp.  
Klebsiella spp.  
Kluyvera spp.  
Kosakonia spp.  
Leclerc a spp.  
Lelliottia spp.  
Mixta spp.  
Morganella spp.  
 

Pantoea spp.  
Phytobacter spp.  
Plesiomonas spp.  
Pluralibacter spp.  
Providencia spp  
Proteus spp.  
Pseudoescherchia  spp. 
Rahnella spp.  
Raoultella spp.  
Salmonella spp.  
Serratia spp.  
Sodalis spp.  
Shigella spp.  
Tatumella spp.  
Trabulsiella spp.  
Yersinia spp.  
Serratia spp.  
Sodalis spp.  
Shigella spp.  
Tatumella spp.  
Trabulsiella spp.  
Yersinia spp.  
Yokanella spp. 

Providencia heimbachae Photorhabdus asymbiotica Arsenophonus nasoniae  

       

Table 2 

BCID II Results   

Preferred therapy 

Comments 

Gram positive Pathogens 

Enterococcus faecalis 

Van A/B negative (vancomycin susceptible) 

Ampicillin +/- gentamicin 

97% of Enterococcus spp (n= 76) isolates were sensitive to ampicillin per Antibiogram 2023).  

Van A/B positive 

Vancomycin resistant 

Linezolid +/- gentamicin 

ID consult 

Enterococcus faecium  

Van A/B negative  

(vancomycin susceptible)  

 

Vancomycin  

 

Van A/B Positive  

(vancomycin resistant)  

Linezolid +/- gentamicin  

ID consult 

Alternative: Daptomycin  
(99% of Enterococcus spp isolates were susceptible, Antibiogram 2023)  

Listeria monocytogenes  

Ampicillin +/- gentamicin  

ID consult 
 

Staphylococcus species   

Staphylococcus genus with all other staphylococcus species negative  

Do not start antibiotics. Likely contaminant if 1 positive blood culture, patient is hemodynamically stable without risk factors (e.g. lack of central venous catheter or endovascular prosthetic material)

 

If treatment is needed: Vancomycin  

The mecA analyte is not reported for non-S. epidermidis and S. lugdunensis coagulase-negative species (e.g. S. hominis, S. simulans, S. capitis, among others). Presume beta-lactam resistance. 

Staphylococcus aureus  

Mec A/C and MREJ negative = MSSA  

 

Preferred Cefazolin 
If CNS source suspected: Oxacillin 

ID consult  

Mec A/C and MREJ positive = MRSA 

Vancomycin  

ID consult  

Staphylococcus epidermidis   

Single positive blood culture 

Do not start antibiotics. Likely contaminant if 1 positive blood culture, patient is hemodynamically stable without risk factors (e.g. lack of central venous catheter or endovascular prosthetic material). 

Consider antimicrobial therapy if patient has risk factors for bacteremia (e.g. lack of central venous catheter or endovascular prosthetic material) 

 

Mec A/C negative 

Cefazolin  

Oxacillin is an alternative 

Mec A/C positive 

Vancomycin  

 

Staphylococcus lugdunensis 

It can be a contaminant however also capable of severe disease, ID consult is recommended. Recommend repeating blood culture  

mec A/C negative = oxacillin sensitive  

Cefazolin or if CNS source suspected Oxacillin 

 

mec A/C  positive = oxacillin resistant  

Vancomycin  

 

Streptococcus species not S. agalactiae, S. pneumoniae, or S. pyogenes 

Streptococcus genus with all other Strep species (S. agalactiae, S. pneumoniae, S. pyogenes results) negative 

Do not start antibiotics. Likely contaminant if 1 positive blood culture, patient is hemodynamically stable without risk factors. 

 

Consider antimicrobial therapy if patient has risk factors for bacteremia (e.g. lack of central venous catheter or endovascular prosthetic material). When therapy is indicated: Ceftriaxone

 

Streptococcus agalactiae  (Group B Streptococcus) 

Ampicillin  

 

Streptococcus pneumoniae 

Ceftriaxone add  

Vancomycin when CNS infection is suspected  

ID consult  

Streptococcus pyogenes(Group A Streptococcus)  

Ampicillin  

 

 

BCID II results  

Preferred Therapy 

Comments  

Gram Negative Pathogens 

Enterobacteriaceae AND/OR Eschericia coli, Klebsiella oxytoca, Klebsiella pneumoniae, Proteus, Serratia marcesens  

KPC , OXA-48, IMP, VIM, NDM Negative & CTX-M Negative  
 
CTX-M Positive (ESBL present)  

 

Oxa-48 or KPC positive (Carbapenemase) 

IMP, VIM, NDM (Carbapenemase)  

 

Ceftriaxone   


Ceftriaxone


Ertapenem or Meropenem  


Ceftazidime/avibactam 

Ceftazidime/avibactam + aztreonam  

Formerly Enterobacteriaceae. Note this is a group of possible enteric Gram-negative organisms, not a specific bacterial genus. 

See Table for list of pathogens included in this group 

ID consult is necessary for any detected resistance gene: Oxa-48, IMP, VIM, NDM, KPC  

Request susceptibility testing for ceftazidime/avibactam microbiology (x120-3536) 

Acinetobacter baumannii  

 

 

Non-CNS: Ampicillin/sulbactam  

CNS: Meropenem  

Meropenem = 100% (n=18)  (Antibiogram 2023) 
Amp/sulbactam = 100% (n=18)  (Antibiogram 2023) 

ID consult  

CTX-M or KPC positive: unusual genotype 
OXA, IMP, VIM, or NDM positive: refer to IDSA guidelines. Non-formulary medications may be needed, coordinate with pharmacy. 

Bacteroides fragilis  

Metronidazole 

ID consult.  Usually associated with abdominal source may need additional gram-negative coverage  

Enterobacter cloacae 

Cefepime 

ID consult; Amp-C producer; cefepime preferred therapy  

E. coli 

Ceftriaxone  

 

Klebsiella aerogenes 

Cefepime   

Amp-C producer cefepime preferred therapy  

Klebsiella oxytoca 

Ceftriaxone 

 

Klebsiella pneumoniae 

Ceftriaxone   

 

Proteus 

Ceftriaxone  

 

Salmonella  

Ceftriaxone 

ID consult.  

Serratia marcescens 

Ceftriaxone  

 

Haemophilus influenzae 

Ceftriaxone  

H. flu type B may require prophylaxis of contacts (review Red Book) 

Neisseria meningitidis 

Ceftriaxone  

ID consult  

N. meningitidis requires prophylaxis of contacts (review Red Book) 

Pseudomonas aeruginosa 

 

NDM/IMP/VIM Positive  

Cefepime  

 

Ceftazidime/avibactam + Aztreonam  

Immunocompromised patients with severe sepsis consider meropenem until susceptibility returns.  

Request susceptibility testing for ceftazidime/avibactam microbiology (x120-3536) 

CTX-M, KPC, OXA positive: unusual genotype

IMP, VIM, or NDM positive additional treatment options may need to be considered. 

Refer to IDSA guidelines, further modification to therapy may be indicated.

 

BCID Result Fungal  

Antimicrobial Recommendations  

Candida auris  

<2 months of age: amphotericin B deoxycholate 1 mg/kg daily 
≥2 months of age: micafungin 10 mg/kg/day IV; maximum 100 mg IV daily  

Candida glabrata  

Neonate: amphotericin B deoxycholate 1mg/kg daily   
Non-neonate: micafungin 10 mg/kg/day, maximum 100 mg IV daily  

Candida krusei  

Neonate: amphotericin B deoxycholate 1mg/kg daily  
Non-neonate: micafungin 10 mg/kg/day, maximum 100 mg IV daily 

Candida parapsilosis  

Neonate: amphotericin B deoxycholate 1mg/kg daily  
Non-neonate: micafungin 10 mg/kg/day, maximum 100 mg IV daily 

Candida tropicalis  

Neonate: amphotericin B deoxycholate 1 mg/kg daily  
Non-neonate: micafungin 10 mg/kg/day, maximum 100 mg IV daily  

Cryptococcus neoformans/gattii  

Liposomal amphotericin B (5–7.5 mg/kg/day) is indicated in combination with oral flucytosine (25 mg/kg/dose, 4 times/day when renal function is normal) as first-line induction therapy for pediatric patients with meningeal and/or other serious cryptococcal infections 

 

 

Table 3 Dosing table recommendations is for pediatric population (>3 mo), for neonatal dosing please refer to idmp neonatal dosing 

Antibiotic  

Dose 

Maximum Dose 

Ampicillin 

50 mg/kg/dose IV q6h  

2000 mg/dose 

Ampicillin/sulbactam 

50 mg ampicillin/kg/dose IV q6h 

2000 mg ampicillin/dose 

Aztreonam 

35 mg/kg/dose IV q8h 

2000 mg/dose 

Cefazolin 

50 mg/kg/dose IV q8h 

2000 mg/dose 

Cefepime 

50 mg/kg/dose IV q8h 

2000 mg/dose 

Ceftazidime/Avibactam 

≥ 3 to <6 mo: IV: 40 mg ceftazidime/kg/dose IV q8h 

≥ 6 mo: 50 mg ceftazidime/kg/dose IV q8h 

2000 mg ceftazidime/dose 

Ceftriaxone 

50 mg/kg/dose IV q24h 

2000 mg/dose 

Daptomycin 

< 7 yo: 12 mg/kg/dose IV q24h 

7 yo to < 12 yo: 9 mg/kg/dose IV q24h 

≥12 yo: 7 mg/kg/dose IV q24h 

N/A 

Ertapenem 

≥ 3 mo to < 12 yo: 15 mg/kg/dose IV q12h 

≥ 12 yo: 1000 mg IV q24h 

≥ 3 mo to ≤ 11 yo: 500 mg/dose 

≥ 12 yo: 1000 mg/dose 

Gentamicin 

7 mg/kg/dose IV q24h 

N/A 

Linezolid 

<12 yo: 10 mg/kg/dose IV q8h 

≥12 yo: 10 mg/kg/dose IV q12h 

600 mg/dose 

Meropenem 

20 mg/kg/dose IV q8h 

1000 mg/dose 

Oxacillin 

50 mg/kg/dose IV q6h 

2000 mg/dose 

Vancomycin 

1 to 2 mo: 15 mg/kg/dose IV q6h 

3 mo to < 12 yo: 17.5 mg/kg/dose IV q6h 

≥ 12 yo: 15 mg/kg/dose IV q6h 

Initial max 4000 mg/DAY