Diagnose and guide treatment selection for bloodstream infection
Clinical background
Bloodstream infections are caused by blood-borne pathogens, most commonly bacteria.1 Prognosis depends on characteristics of the patient and the underlying pathogen,2 but bloodstream infections often progress to sepsis, a severe and life-threatening immune response.3 Prompt treatment with appropriate antimicrobials is critical to managing bloodstream infections and sepsis3,4; the sooner appropriate treatment begins, the better the chance of patient survival.3,5
Laboratory testing guides appropriate treatment by identifying the causative microorganism and its antimicrobial susceptibilities, but test methods and turnaround times vary.2,5 Conventional testing methods, which involve subculturing the organism, can take several days.2,4 Rapid testing methods, such as molecular panels, detect organism-specific DNA and take <3 hours.4,6,7 Rapid methods can also test for resistance markers, which are genes or enzymes that allow an organism to be resistant to certain antimicrobial treatments.5–7
Using both rapid and conventional testing methods is the standard of care for bloodstream infections5 and, when combined with support from an antibiotic stewardship program, is recommended by the Infectious Diseases Society of America (IDSA) and the Society for Healthcare Epidemiology of America (SHEA).8 This approach can improve clinical outcomes for bloodstream infections: a meta-analysis found that rapid testing methods are associated with shorter time to appropriate treatment (averaging about 5 fewer hours), shorter hospital stays (averaging about 2.5 fewer days), and lower mortality risk (odds ratio, 0.64) than conventional methods.9
Rapid molecular tests are highly accurate for identifying the organisms and resistance markers they target, showing 85% to 100% positive percent agreement and 82% to 100% negative percent agreement with conventional methods.2,6,7 However, accuracy may be lower when multiple organisms are present2,5; molecular tests may only correctly identify 50% to 75% of organisms in polymicrobial cultures, compared to >90% in monomicrobial cultures.10
The Culture, Blood with Reflex to Molecular Identification test (test code 13954) uses rapid and conventional testing methods to detect, identify, and determine the antimicrobial susceptibilities of organisms involved in bloodstream infections.2,6,7 The test begins with a blood culture (test code 389) to test for organism growth. If growth is detected, reflex tests are performed to identify the organism and determine its antimicrobial susceptibilities. Reflex testing includes
A Gram stain to classify the organism (test code 497)
A rapid molecular identification panel to test for the presence of select bacteria and resistance markers (results available within 3 hours of blood culture positivity)
Conventional (culture-based) organism identification and antimicrobial susceptibility testing (results available within 1 to 2 days of blood culture positivity)
Reflex tests are performed at additional charge and associated with additional CPT codes.
Results of the Gram stain determine which of 2 molecular identification panels (gram-positive or gram-negative) are tested. The gram-positive panel tests for 12 bacterial targets and 3 resistance markers; the gram-negative panel tests for 8 bacterial targets and 6 resistance markers (Table 1). Some bacterial targets are identified to the genus level, and some are identified to the species level. Collectively, the panels account for approximately 80% of the pathogens most commonly responsible for bloodstream infections.1,11
Table 1. Bacteria and Resistance Markers Included in Molecular Identification Panelsa
Gram-positive panel
Genera
Species
Resistance markers
Listeria
Enterococcus faecalis
mecAb
Staphylococcus
Enterococcus faecium
vanAc
Streptococcus
Staphylococcus aureus
vanBc
Staphylococcus epidermidis
Staphylococcus lugdunensis
Streptococcus agalactiae
Streptococcus anginosus (group)
Streptococcus pneumoniae
Streptococcus pyogenes
Gram-negative panel
Genera
Species
Resistance markers
Acinetobacter
Escherichia colid
CTX-M (blaCTX-M)
Citrobacter
Klebsiella oxytoca
IMP (blaIMP)
Enterobacter
Klebsiella pneumoniae
KPC (blaKPC)
Proteus
Pseudomonas aeruginosa
NDM (blaNDM)
OXA (blaOXA)
VIM (blaVIM)
a
Individual panel components cannot be ordered separately.
b
Tested only if S aureus or S epidermidis are detected.
c
Tested only if E faecalis or E faecium are detected.
d
The test cannot distinguish between E coli and Shigella species; detection of either is reported as "E coli."
Individuals suitable for testing
Patients with suspected bloodstream infection
Methods
Blood culture: culture using automated continuous monitoring system
Gram stain: microscopic examination
Molecular identification panel: DNA hybridization microarray
Conventional identification and susceptibility testing: varies
Interpretive information
Results of the initial blood culture indicate whether organism growth was detected (positive) or not detected (negative) in the specimen.
Results of the molecular identification panel include the organism(s) detected and, if applicable, whether associated resistance markers were detected or not detected. An organism result of “not detected” indicates that none of the bacterial targets tested were detected. Because the panel can only detect the organisms it targets (Table 1), infection or coinfection with an untargeted organism cannot be ruled out.2
Detection of a resistance marker may predict that the associated organism will be resistant to certain antibiotics (Table 2). However, the predictive value of resistance markers varies:
Gram-positive resistance markers (mecA and vanA/B) have high predictive value because they are the predominant mechanisms for certain kinds of antibiotic resistance in these organisms.5,11,12 Therefore, in most cases, the presence or absence of mecA or vanA/B can reliably predict resistance or susceptibility to the associated antibiotics.5
Gram-negative organisms have multiple resistance mechanisms, not all of which are detectable by this test.5,6,11 Additionally, gram-negative resistance markers may be present but unexpressed or expressed at levels too low to cause resistance.5,11 Therefore, the presence or absence of a resistance marker in a gram-negative organism may not reliably predict antibiotic resistance or susceptibility.5,11,12
Due to the complexity of predicting phenotypic resistance from genotypic tests, the Clinical and Laboratory Standards Institute (CLSI) and IDSA/SHEA recommend that treatment changes based on molecular test results be made with guidance from an antimicrobial stewardship team.5,8
Table 2. Interpretation of Molecular Resistance Marker Results
Organism
Resistance marker
Interpretation6,7,11,13
S aureus or S epidermidis
mecA detected
Probable methicillin-resistant S aureus (MRSA) or S epidermidis (MRSE)
Organism is predictably resistant to β-lactam antibiotics
mecA not detected
mecA-mediated methicillin resistance not detected
Although rare, other resistance mechanisms cannot be ruled out
E faecium or E faecalis
vanA detected
Probable vancomycin-resistant Enterococcus (VRE)
Organism is predictably resistant to vancomycin, telavancin, dalbavancin, and teicoplanin
vanB detected
Probable vancomycin-resistant Enterococcus (VRE)
Organism is predictably resistant to vancomycin and predictably susceptible to teicoplanin
vanA and vanB not detected
vanA/B-mediated vancomycin resistance not detected
Although rare, other resistance mechanisms cannot be ruled out
Any gram-negative organism
CTX-M detected
Organism may produce extended-spectrum β-lactamase and be resistant to third- and fourth-generation cephalosporins and monobactams
Cephalosporin resistance cannot be reliably predicted, as the resistance marker may be unexpressed or expressed at low levels
CTX-M not detected
CTX-M–mediated cephalosporin resistance not detected
Cephalosporin susceptibility cannot be reliably predicted, as other resistance mechanisms cannot be ruled out
Any gram-negative organism
KPC, OXA, NDM, VIM, or IMP detected
Organism may produce carbapenemase and be resistant to carbapenems, cephalosporins, and penicillins
Carbapenem resistance cannot be reliably predicted, as the resistance marker may be unexpressed or expressed at low levels
KPC, OXA, NDM, VIM, and IMP not detected
KPC-, OXA-, NDM-, VIM-, and IMP-mediated carbapenem resistance not detected
Carbapenem susceptibility cannot be reliably predicted, as other resistance mechanisms cannot be ruled out
Results of conventional organism identification and antimicrobial susceptibility testing include the organism(s) detected and, for each organism-antimicrobial combination tested, minimal inhibitory concentrations and corresponding interpretations (susceptible, resistant, or intermediate). Interpretations are defined as follows13:
Susceptible: the organism is inhibited by standard dosing of the drug, indicating that the drug is likely to be clinically effective
Resistant: the organism is not inhibited by standard dosing of the drug, indicating that the drug is not likely to be clinically effective
Intermediate: the organism is less likely to be inhibited by standard dosing of the drug than a susceptible organism is, indicating that the drug may or may not be clinically effective
References
Verway M, Brown KA, Marchand-Austin A, et al. Prevalence and mortality associated with bloodstream organisms: a population-wide retrospective cohort study. J Clin Microbiol. 2022;60(4):e02429-21. doi:10.1128/jcm.02429-21
Dunbar SA, Gardner C, Das S. Diagnosis and management of bloodstream infections with rapid, multiplexed molecular assays. Front Cell Infect Microbiol. 2022;12:859935. doi:10.3389/fcimb.2022.859935
Tang F, Yuan H, Li X, et al. Effect of delayed antibiotic use on mortality outcomes in patients with sepsis or septic shock: a systematic review and meta-analysis. Int Immunopharmacol. 2024;129:111616. doi:10.1016/j.intimp.2024.11161
Briggs N, Campbell S, Gupta S. Advances in rapid diagnostics for bloodstream infections. Diagn Microbiol Infect Dis. 2021;99(1):115219. doi:10.1016/j.diagmicrobio.2020.115219
Clinical and Laboratory Standards Institute. Principles and procedures for blood cultures, 2nd edition. CLSI guideline M47. 2022.
Barlam TF, Cosgrove SE, Abbo LM, et al. Implementing an antibiotic stewardship program: guidelines by the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America. Clin Infect Dis. 2016;62(10):e51-e77. doi:10.1093/cid/ciw118
Timbrook TT, Morton JB, McConeghy KW, et al. The effect of molecular rapid diagnostic testing on clinical outcomes in bloodstream infections: a systematic review and meta-analysis. Clin Infect Dis. 2016;64(1):ciw649. doi:10.1093/cid/ciw649
Freiberg JA, Deri CR, Nesbitt WJ, et al. Identification and antibiotic susceptibility patterns of clinical blood culture isolates not identified by a rapid microarray diagnostic system. Microbiol Spectr. 2021;9(1):e00175-21. doi:10.1128/spectrum.00175-21
Banerjee R, Patel R. Molecular diagnostics for genotypic detection of antibiotic resistance: current landscape and future directions. JAC-Antimicrob Resist. 2023;5(1):dlad018. doi:10.1093/jacamr/dlad018
Yee R, Bard JD, Simner PJ. The genotype-to-phenotype dilemma: how should laboratories approach discordant susceptibility results? J Clin Microbiol. 2021;59(6):10.1128/jcm.00138-20. doi:10.1128/jcm.00138-20
Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing, 34th edition. CLSI guideline M100. 2024.
Diagnose and guide treatment selection for bloodstream infection
Clinical background
Bloodstream infections are caused by blood-borne pathogens, most commonly bacteria.1 Prognosis depends on characteristics of the patient and the underlying pathogen,2 but bloodstream infections often progress to sepsis, a severe and life-threatening immune response.3 Prompt treatment with appropriate antimicrobials is critical to managing bloodstream infections and sepsis3,4; the sooner appropriate treatment begins, the better the chance of patient survival.3,5
Laboratory testing guides appropriate treatment by identifying the causative microorganism and its antimicrobial susceptibilities, but test methods and turnaround times vary.2,5 Conventional testing methods, which involve subculturing the organism, can take several days.2,4 Rapid testing methods, such as molecular panels, detect organism-specific DNA and take <3 hours.4,6,7 Rapid methods can also test for resistance markers, which are genes or enzymes that allow an organism to be resistant to certain antimicrobial treatments.5–7
Using both rapid and conventional testing methods is the standard of care for bloodstream infections5 and, when combined with support from an antibiotic stewardship program, is recommended by the Infectious Diseases Society of America (IDSA) and the Society for Healthcare Epidemiology of America (SHEA).8 This approach can improve clinical outcomes for bloodstream infections: a meta-analysis found that rapid testing methods are associated with shorter time to appropriate treatment (averaging about 5 fewer hours), shorter hospital stays (averaging about 2.5 fewer days), and lower mortality risk (odds ratio, 0.64) than conventional methods.9
Rapid molecular tests are highly accurate for identifying the organisms and resistance markers they target, showing 85% to 100% positive percent agreement and 82% to 100% negative percent agreement with conventional methods.2,6,7 However, accuracy may be lower when multiple organisms are present2,5; molecular tests may only correctly identify 50% to 75% of organisms in polymicrobial cultures, compared to >90% in monomicrobial cultures.10
The Culture, Blood with Reflex to Molecular Identification test (test code 13954) uses rapid and conventional testing methods to detect, identify, and determine the antimicrobial susceptibilities of organisms involved in bloodstream infections.2,6,7 The test begins with a blood culture (test code 389) to test for organism growth. If growth is detected, reflex tests are performed to identify the organism and determine its antimicrobial susceptibilities. Reflex testing includes
A Gram stain to classify the organism (test code 497)
A rapid molecular identification panel to test for the presence of select bacteria and resistance markers (results available within 3 hours of blood culture positivity)
Conventional (culture-based) organism identification and antimicrobial susceptibility testing (results available within 1 to 2 days of blood culture positivity)
Reflex tests are performed at additional charge and associated with additional CPT codes.
Results of the Gram stain determine which of 2 molecular identification panels (gram-positive or gram-negative) are tested. The gram-positive panel tests for 12 bacterial targets and 3 resistance markers; the gram-negative panel tests for 8 bacterial targets and 6 resistance markers (Table 1). Some bacterial targets are identified to the genus level, and some are identified to the species level. Collectively, the panels account for approximately 80% of the pathogens most commonly responsible for bloodstream infections.1,11
Table 1. Bacteria and Resistance Markers Included in Molecular Identification Panelsa
Gram-positive panel
Genera
Species
Resistance markers
Listeria
Enterococcus faecalis
mecAb
Staphylococcus
Enterococcus faecium
vanAc
Streptococcus
Staphylococcus aureus
vanBc
Staphylococcus epidermidis
Staphylococcus lugdunensis
Streptococcus agalactiae
Streptococcus anginosus (group)
Streptococcus pneumoniae
Streptococcus pyogenes
Gram-negative panel
Genera
Species
Resistance markers
Acinetobacter
Escherichia colid
CTX-M (blaCTX-M)
Citrobacter
Klebsiella oxytoca
IMP (blaIMP)
Enterobacter
Klebsiella pneumoniae
KPC (blaKPC)
Proteus
Pseudomonas aeruginosa
NDM (blaNDM)
OXA (blaOXA)
VIM (blaVIM)
a
Individual panel components cannot be ordered separately.
b
Tested only if S aureus or S epidermidis are detected.
c
Tested only if E faecalis or E faecium are detected.
d
The test cannot distinguish between E coli and Shigella species; detection of either is reported as "E coli."
Individuals suitable for testing
Patients with suspected bloodstream infection
Methods
Blood culture: culture using automated continuous monitoring system
Gram stain: microscopic examination
Molecular identification panel: DNA hybridization microarray
Conventional identification and susceptibility testing: varies
Interpretive information
Results of the initial blood culture indicate whether organism growth was detected (positive) or not detected (negative) in the specimen.
Results of the molecular identification panel include the organism(s) detected and, if applicable, whether associated resistance markers were detected or not detected. An organism result of “not detected” indicates that none of the bacterial targets tested were detected. Because the panel can only detect the organisms it targets (Table 1), infection or coinfection with an untargeted organism cannot be ruled out.2
Detection of a resistance marker may predict that the associated organism will be resistant to certain antibiotics (Table 2). However, the predictive value of resistance markers varies:
Gram-positive resistance markers (mecA and vanA/B) have high predictive value because they are the predominant mechanisms for certain kinds of antibiotic resistance in these organisms.5,11,12 Therefore, in most cases, the presence or absence of mecA or vanA/B can reliably predict resistance or susceptibility to the associated antibiotics.5
Gram-negative organisms have multiple resistance mechanisms, not all of which are detectable by this test.5,6,11 Additionally, gram-negative resistance markers may be present but unexpressed or expressed at levels too low to cause resistance.5,11 Therefore, the presence or absence of a resistance marker in a gram-negative organism may not reliably predict antibiotic resistance or susceptibility.5,11,12
Due to the complexity of predicting phenotypic resistance from genotypic tests, the Clinical and Laboratory Standards Institute (CLSI) and IDSA/SHEA recommend that treatment changes based on molecular test results be made with guidance from an antimicrobial stewardship team.5,8
Table 2. Interpretation of Molecular Resistance Marker Results
Organism
Resistance marker
Interpretation6,7,11,13
S aureus or S epidermidis
mecA detected
Probable methicillin-resistant S aureus (MRSA) or S epidermidis (MRSE)
Organism is predictably resistant to β-lactam antibiotics
mecA not detected
mecA-mediated methicillin resistance not detected
Although rare, other resistance mechanisms cannot be ruled out
E faecium or E faecalis
vanA detected
Probable vancomycin-resistant Enterococcus (VRE)
Organism is predictably resistant to vancomycin, telavancin, dalbavancin, and teicoplanin
vanB detected
Probable vancomycin-resistant Enterococcus (VRE)
Organism is predictably resistant to vancomycin and predictably susceptible to teicoplanin
vanA and vanB not detected
vanA/B-mediated vancomycin resistance not detected
Although rare, other resistance mechanisms cannot be ruled out
Any gram-negative organism
CTX-M detected
Organism may produce extended-spectrum β-lactamase and be resistant to third- and fourth-generation cephalosporins and monobactams
Cephalosporin resistance cannot be reliably predicted, as the resistance marker may be unexpressed or expressed at low levels
CTX-M not detected
CTX-M–mediated cephalosporin resistance not detected
Cephalosporin susceptibility cannot be reliably predicted, as other resistance mechanisms cannot be ruled out
Any gram-negative organism
KPC, OXA, NDM, VIM, or IMP detected
Organism may produce carbapenemase and be resistant to carbapenems, cephalosporins, and penicillins
Carbapenem resistance cannot be reliably predicted, as the resistance marker may be unexpressed or expressed at low levels
KPC, OXA, NDM, VIM, and IMP not detected
KPC-, OXA-, NDM-, VIM-, and IMP-mediated carbapenem resistance not detected
Carbapenem susceptibility cannot be reliably predicted, as other resistance mechanisms cannot be ruled out
Results of conventional organism identification and antimicrobial susceptibility testing include the organism(s) detected and, for each organism-antimicrobial combination tested, minimal inhibitory concentrations and corresponding interpretations (susceptible, resistant, or intermediate). Interpretations are defined as follows13:
Susceptible: the organism is inhibited by standard dosing of the drug, indicating that the drug is likely to be clinically effective
Resistant: the organism is not inhibited by standard dosing of the drug, indicating that the drug is not likely to be clinically effective
Intermediate: the organism is less likely to be inhibited by standard dosing of the drug than a susceptible organism is, indicating that the drug may or may not be clinically effective
References
Verway M, Brown KA, Marchand-Austin A, et al. Prevalence and mortality associated with bloodstream organisms: a population-wide retrospective cohort study. J Clin Microbiol. 2022;60(4):e02429-21. doi:10.1128/jcm.02429-21
Dunbar SA, Gardner C, Das S. Diagnosis and management of bloodstream infections with rapid, multiplexed molecular assays. Front Cell Infect Microbiol. 2022;12:859935. doi:10.3389/fcimb.2022.859935
Tang F, Yuan H, Li X, et al. Effect of delayed antibiotic use on mortality outcomes in patients with sepsis or septic shock: a systematic review and meta-analysis. Int Immunopharmacol. 2024;129:111616. doi:10.1016/j.intimp.2024.11161
Briggs N, Campbell S, Gupta S. Advances in rapid diagnostics for bloodstream infections. Diagn Microbiol Infect Dis. 2021;99(1):115219. doi:10.1016/j.diagmicrobio.2020.115219
Clinical and Laboratory Standards Institute. Principles and procedures for blood cultures, 2nd edition. CLSI guideline M47. 2022.
Barlam TF, Cosgrove SE, Abbo LM, et al. Implementing an antibiotic stewardship program: guidelines by the Infectious Diseases Society of America and the Society for Healthcare Epidemiology of America. Clin Infect Dis. 2016;62(10):e51-e77. doi:10.1093/cid/ciw118
Timbrook TT, Morton JB, McConeghy KW, et al. The effect of molecular rapid diagnostic testing on clinical outcomes in bloodstream infections: a systematic review and meta-analysis. Clin Infect Dis. 2016;64(1):ciw649. doi:10.1093/cid/ciw649
Freiberg JA, Deri CR, Nesbitt WJ, et al. Identification and antibiotic susceptibility patterns of clinical blood culture isolates not identified by a rapid microarray diagnostic system. Microbiol Spectr. 2021;9(1):e00175-21. doi:10.1128/spectrum.00175-21
Banerjee R, Patel R. Molecular diagnostics for genotypic detection of antibiotic resistance: current landscape and future directions. JAC-Antimicrob Resist. 2023;5(1):dlad018. doi:10.1093/jacamr/dlad018
Yee R, Bard JD, Simner PJ. The genotype-to-phenotype dilemma: how should laboratories approach discordant susceptibility results? J Clin Microbiol. 2021;59(6):10.1128/jcm.00138-20. doi:10.1128/jcm.00138-20
Clinical and Laboratory Standards Institute. Performance standards for antimicrobial susceptibility testing, 34th edition. CLSI guideline M100. 2024.
