Traditionally, after a blood culture turns positive, about two days are required before the species and antibiotic sensitivity are revealed. This lag is frustrating. During this time, it may be unclear whether the culture is a false-positive (in the case of a culture revealing gram positive cocci) and whether the organisms is drug-resistant.
Verigene is a nucleic acid micro-array which can be used to provide rapid information about positive blood cultures. The array detects genetic information which may reveal the genus/species of bacteria and the presence of various resistance genes.
Different arrays are used to investigate gram-positive or gram-negative blood cultures:
Gram-negative blood culture:
- Escherechia coli
- Klebsiella pneumoniae
- Klebsiella oxytoca
- Pseudomonas aeruginosa
- Serratia marcescens
- Acinetobacter genus
- Citrobacter genus
- Enterobacter genus
- Proteus genus
- Resistance genes
- CTX-M (identifies one – but not all – extended-spectrum beta lactamase)
- IMP, KPC, NDM, OXA, VIM (carbapenemases)
Gram-positive blood culture:
- Staph genus marker (detects any Staph species)
- Staph aureus
- Staph epidermidis
- Staph lugdenesis
- Strep anginosus group
- Streptococcus genus marker (detects any Strep species)
- Strep agalactiae
- Strep pneumoniae
- Strep pyogenes
- Enterococcus faecalis
- Enterococcus faecium
- Listeria spp.
- Resistance genes:
- mecA (methicillin resistance)
- vanA, vanB (vancomycin resistance)
The identity and appropriate antibiotic may often be deduced by the pattern of genes present. For example, staphylococcus aureus which is mecA-negative must be methicillin-sensitive staph aureus (MSSA).
The test has a turn-round time of ~2.5 hours. It runs in parallel with traditional methods. Thus, Verigene provides a bit of a sneak peek at the bacteria’s identity. Traditional culture methods will return 1-2 days later, providing a double-check of the Verigene results.
The initial acquisition cost of the Verigene analyzer is considerable (~$20,000). Subsequently, each assay costs roughly $50-100. Given the ability to avoid or narrow antibiotic therapy, this tends to be cost-neutral or cost-saving. Secondary benefits include limiting antibiotic exposure, thereby reducing antibiotic resistance and C. difficile infection.
Many institutions have been using Verigene for years, so this isn’t necessarily anything incredibly new. If your shop uses this, appreciating how it works may help make sense of results coming back from the microbiology lab. Other similar products are available as well (e.g. BioFire), so if your hospital uses one of them then this post won’t apply perfectly to your practice.
The literature is strongly positive regarding the ability of Verigene to identify pathogens with high sensitivity (~97%) and specificity (~99.5%).1–3 This has been demonstrated among adult and pediatric patients, at a range of institutions across different countries.
The University of Maryland developed an algorithm for using Verigene to tailor antibiotic selection in gram-negative infections (above). Retrospectively, this algorithm was shown to achieve appropriate coverage more often than standard empiric antibiotic regimens.2
Investigators at Baylor showed that Verigene reduced the delay to appropriate antimicrobial therapy, compared to conventional techniques (figure above).4 Similar results were seen at other centers, including John Hopkins, Cleveland Clinic, and the University of Washington.5–8
There’s plenty more supportive evidence, which I’m not going to review (it gets repetitive quickly). What’s more important to fully unpack is the limitations of the assay…
Pitfalls for the clinically infected patient
Infections overall may be divided into those which are typically mono-microbial (e.g. urosepsis, pneumonia) versus those which are often poly-microbial (e.g. diverticulitis). For a mono-microbial infection, identification of the bacterial species allows focusing antibiotic therapy on that specific organism. However, for a poly-microbial infection, focusing therapy on any individual organism may be misguided.
Verigene may fail to detect all of the bacterial strains in the context of polymicrobial infection. One reason for this that Verigene is typically only performed on material from a single blood culture. Therefore, it may fail to detect bacteria present in other culture bottles.
A retrospective analysis of 1003 gram-negative bacterial cultures evaluated with Verigene found that 5.6% ultimately turned out to be polymicrobial.9 In about half of these cases (2.4% overall), Verigene failed to detect one or more bacterial species. In only 1.6% of cases could this this error have led to clinically inappropriately antibiotic selection (e.g. Verigene detected E. Coli, but missed Pseudomonas).
Bottom line? For a critically ill patient with a suspected poly-microbial infection (e.g. abdominal sepsis), it might not be wise to de-escalate therapy based on Verigene results. However, overall this is an infrequent problem.
Bacteria detection failure
Verigene has excellent sensitivity, but it will fail to detect any target in ~3% of gram-positive cultures.1,3 This seems to occur most often with Stapylococcus epidermidis and viridans group Streptococcus. If the culture is positive and Verigene is negative, a more likely possibility is that the organism is an unusual species which isn’t included in the Verigene panel at all (e.g. Corynebacterium spp, Micrococcus spp.).
Clinically this isn’t a significant problem. If Verigene fails to detect any target, then empiric antibiotics should be continued until the traditional culture/sensitivity returns.
Mis-identification is potentially a bigger problem than detection failure, because this could misdirect antibiotic selection. Among gram-positives, this issue seems to be restricted to species-level identification within the Streptococcus genus:
- Streptococcus mitis or Streptococcus oralis is occasionally mis-identified as Streptococcus pneumoniae.1,3
- Streptococcus pneumoniae seems to always trigger a positive genus-level Streptococcus marker, but frequently fails to be detected by the species-level Streptococcus pneumoniae marker.3
Among gram-negatives, mis-identification can occasionally occur as well:
- Klebsiella pneumoniae may be incorrectly identified as “Enterobacter.”6
- Escherichia coli cannot be differentiated from some Shigella species.
- Some other mis-identifications can occur involving rather esoteric bacterial species (for a full listing see the package insert page #19).
Overall this isn’t a big problem, as antibiotic therapy for these bacteria tends to be similar (for example, antibiotic therapy directed against “Enterobacter” will cover Klebsiella as well). Furthermore, simple awareness of these issue should minimize its impact.
Incorrect prediction of antibiotic resistance
Among gram-positives, prediction of antibiotic resistance is outstanding:
- Sensitivity for the MecA gene (conferring methicillin resistance) seems to be nearly 100%. Rarely there may be a false-positive MecA gene detection (~2% false-positive rate).1,3 So overall the detection of MecA seems to err on the side of being overly sensitive, which is good. If Verigene reports out Staph aureus with no MecA gene detected, it may be confidently concluded that MRSA coverage is unnecessary.
- Detection of vancomycin resistance seems to be excellent, essentially ~100% sensitive and specific.1,3
Among gram-negatives, detection of the CTX-M gene indicates the presence of extended spectrum beta-lactamase resistant species (ESBL). However, there are other genes can also cause extended spectrum beta-lactamase resistance (TEM, SHV). Therefore, a negative CTX-M gene doesn’t necessarily prove that the organism is susceptible to beta-lactams. For critically ill patients who are at high risk for ESBL organisms, a carbapenem might still be considered even if the CTX-M gene is negative (red box, above algorithm).2 However, a recent study suggested that screening for CTX-M was sufficient to detect the vast majority of resistant organisms (table below).10 Ideally, genetic markers such as CTX-M should be integrated into local antibiograms to maximize leverage of the Verigene system at a local level:
As shown above, Verigene cannot predict antibiotic resistance among Pseudomonas. This reflects that Pseudomonas has rather complex resistance mechanisms (which don’t involve the genes detected by Verigene). Based on these results, the following approach to Verigene data may be reasonable:2,4
The following algorithm takes into account the above pitfalls. This will apply to most critically ill patients with positive blood cultures, who are started up-front on empiric antibiotics:
To date, evidence on Veregene has focused on patients with clinical infection who have already been started on broad-spectrum antibiotics. Another application which might be even more powerful could be patients who haven’t yet been started on antibiotics.
Let’s imagine a hospitalized patient who spikes a fever, leading to a blood culture. Unfortunately, the patient is a hard stick, so only one blood culture is obtained (rather than two). The patient remains stable clinically and the fever spontaneously resolves. Two days later, the blood culture turns positive with gram positive cocci.
What do you do with a single positive blood culture for gram-positive cocci? The patient looks fine clinically, so the culture is probably a contaminant. However, we wouldn’t want to ignore the possibility of true bacteremia. In the usual course of events, this patient would probably be started on vancomycin for a couple days until the culture speciated out as Staphylococcus epidermidis.
With Verigene, the blood culture could be tested with results back within 3 hours. If the assay revealed a pathogen (e.g. methicillin-sensitive Staphylococcus aureus), then appropriate targeted antibiotics could be started. Alternatively, if the culture was consistent with contamination (e.g., Staphylcoccus epidermidis), then antibiotics could be avoided entirely.
The use of Verigine to avoid antibiotic therapy entirely has never been prospectively evaluated. However, some interesting results can be found buried in a Verigene implementation study from John Hopkins.5 Following implementation of Verigene, the median duration of therapy for coagulase negative staph fell from 19 hours to zero hours (zero!). This reveals that providers who suspected contamination were checking Verigene and, if Stapylococcus epidermidis was detected, were never giving antibiotics at all. That’s smart: the best way to avoid costs and toxicity from antibiotics is to never give a single dose.
- Verigene is a DNA micro-array which allows for prompt characterization of a positive blood culture (including detection of specific bacterial species and resistance genes).
- Verigene has proved to have high sensitivity and specificity for gram-positive and gram-negative cultures, with an impressive and rapidly growing evidence basis.
- Prompt evaluation for methicillin or vancomycin resistance facilitates rapid transition from empiric to definitive antibiotics. This may simultaneously avoid antibiotic toxicity and improve efficacy.
- Limitations to Verigene include polymicrobial infections, occasional failure to detect any organism, and difficulty sorting out specific streptococcal species. These issues are fairly minor and may be avoided if the test is applied thoughtfully.
Conflicts of Interest: Never. I've focused on Verigene because that's what is used at my hospital (trying to explore all such assays would make this post impossibly long).
- IBCC chapter:Guide to APRV for COVID-19 - April 8, 2020
- PulmCrit Theoretical Post – The COVID Severity Index (CSI 1.0) - April 2, 2020
- PulmCrit wee – Why the SCCM/AARC/ASA/APSF/AACN/CHEST joint statement on split ventilators is wrong. - March 29, 2020