Drug Resistance


Current trends in diagnostic microbiology testing for drug resistant organisms

With the rising problem of global antibiotic resistance, the role that the diagnostic microbiology laboratory plays in detecting drug resistant organisms and acquiring information for treatment is absolutely critical. “One of the keys to diagnosing and treating antimicrobial resistant organisms is, the faster we can get an identification and susceptibility, the faster we can make sure our patient is on appropriate therapy,” said Scott Wesley Long, MD, PhD, associate director of Diagnostic Microbiology at Houston Methodist Hospital. “We know from clinical data that the earlier we get a patient on appropriate therapy, the better the outcome.”

Currently, the most common means of identifying antimicrobial resistance is through automated susceptibility testing, a liquid-based system that is dependent upon growth of the organism. However, Long said, many advancements on the horizon may lead to acquiring susceptibility information faster.


According to Long, the use of MALDI-TOF technology has been one of the greatest advances in microbiology in the last 30 years, virtually revolutionizing bacterial identification. “It allows us to identify organisms much faster, and since we can identify those faster, we can get the susceptibilities faster,” he said.

Although MALDI-TOF has not directly advanced susceptibility testing, the ability to acquire identification faster allows lab to provide susceptibility results much more quickly. Some labs are also experimenting with MALDI-TOF for susceptibility testing, Long said, but at this point, the results of those research studies have been mixed.

An additional avenue being explored in order to obtain susceptibility results faster involves devices that monitor real-time growth of organisms in the presence of antibiotics. “It’s similar to how our current instruments work,” Long said. “Although it’s faster, there are limitations.”

Whole-Genome Sequencing

“In terms of diagnosis, I think one of the things that’s on the horizon is the increasing use of next-generation sequencing in clinical diagnostic microbiology,” Long said. As next-generation sequencing instrumentation gets smaller, cheaper, and faster per sample, and labs move towards real-time sequencing of microorganisms—especially once they have the possibility of sequencing organisms from primary specimens without having to culture them first—that may greatly speed up their ability to identify antimicrobial resistance, he said.

Houston Methodist Hospital is the flagship hospital of Houston Methodist. Located in the Texas Medical Center in Houston, Texas, Houston Methodist Hospital was established in 1919 as an outreach ministry of Methodist Episcopal Church.

Although Long thinks it’s unlikely that next-generation sequencing will replace culture, numerous new molecular tests are already available for the identification of particular resistance elements for certain pathogens. “We’re certainly seeing, already, in the world of molecular microbiology diagnostics, the addition of particular resistance elements to these molecular panels that give us rapid susceptibility results on a molecular basis,” he said.

As next-generation sequencing technology improves, Long believes it will start to move into the laboratory as a routine practice and allow labs to acquire results even faster. “The nice thing about whole-genome sequencing is that it doesn’t restrict you to particular targets like a PCR assay does,” Long said. “You’re sequencing all the genetic material that is there and looking at what genes are present or absent, what mutations might be present or absent.”

The only caveat within sequencing technology, which is also the caveat with PCR-based technology, Long said, is that identification of resistance elements is limited to what is known. This makes it difficult to identify novel resistance mechanisms. However, if labs get to the point to where they sequence all organisms, it will create very powerful means for the identification of novel resistance mechanisms in close to real-time. “It’s certainly an informatics challenge,” Long said, “but the bio-informatics community is getting very savvy at dealing with these large data sets.”

According to Long, several publications have shown that whole-genome sequencing works quite well and correlates with current methods of automated susceptibility testing. “There are some very exciting things coming in the future using whole-genome sequence data to define antimicrobial resistance,” he said. “Right now we need to culture organisms, preferably a pure culture, to get a good sequencing result. If we can push back to where we can sequence the organisms from primary specimens, that’ll really be the turning point in bringing whole-genome sequencing into more routine clinical practice.”

In 2013, Long’s lab published a paper with the purpose of proving that whole-genome sequencing could be performed as routine practice. “At the time, it was a difficult sell because people didn’t think it was practical,” Long recalled. Although his lab does not routinely sequence everything right now, Long said that whole genome sequencing in clinical microbiology is “certainly something that’s becoming more commonplace.”

“We’re very much all-in on MALDI technology for identification, but occasionally we get something on the MALDI that it can’t identify, so we sequence those organisms for identification,” Long said. “We selectively pick and choose now which organisms to sequence, usually to gain some advantage either in identifying something we couldn’t identify by another method or to identify something faster than sending it out.”

How many labs are doing whole-genome sequencing? “At this point I would say it’s probably a handful of labs that are doing routine sequencing in clinical microbiology, and it’s probably special cases,” Long said.

Although Long’s lab initially received “a lot of push back” that whole-genome sequencing wasn’t practical, was too expensive and too slow, since then, several review articles have discussed the application of whole-genome sequencing for microbiology. “It’s gone from being a very controversial idea to now entering main stream acceptance and being operationalized. We have realized these benefits and enhancements over the past three years,” Long said. “I think in another three to five years it’s something that’s going to be much more commonplace.”

Infection Control

To manage the spread of drug resistance, Long stressed the need for additional federal investment for antimicrobial resistance research, new antibiotics, and geographically comprehensive real-time surveillance. “We really need surveillance across the country and around the world to detect these new resistance mechanisms and resistant organism trends as they occur so we can be more proactive and less reactive,” he said.

Antimicrobial stewardship is another important piece of this effort. “We have a very active antimicrobial stewardship program here at Houston Methodist, in partnership with our infectious disease pharmacists, that has been key in helping us take our ability to rapidly diagnose resistant organisms in the clinical lab and very rapidly translate that into action at the patients’ bedside to make sure patients are on appropriate therapy,” Long said. “Because no matter how good we are in the clinical lab, no matter how fast I am at identifying antibiotic resistant organisms, if no one acts on that information, clinically, then I haven’t done enough to help to the patient. That’s the really critical part.”

At Houston Methodist, a team of infectious disease pharmacists is on call 24/7 so that the lab can relate critical antimicrobial susceptibility results on organisms of concern. This allows the team to act on that data and immediately determine if a patient is on appropriate therapy, rather than waiting for the patient’s primary team to respond to a result. “If we get a result at 1 a.m. and no one sees that result until 9 a.m., that’s a potential 8 hour delay,” Long said. “That’s time lost that we could be helping patients. If you have active antimicrobial stewardship and rapid action taken on your clinical laboratory results, that’s how you get the benefit to the patients’ bedside, and that’s absolutely critical.”

Ultimately, it all works together. “You need the rapid diagnostics, you need to leverage new technologies to decrease the time to identification and time to susceptibility results, and you need the active stewardship piece to decrease the time to the patient being on appropriate therapy,” Long concluded. “That’s how you get better outcomes in patients.”

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