Meeting NewsPerspective

Diagnostic test allows outbreak testing to begin more quickly than current WGS

Vadim Sapiro
Vadim Sapiro

SAN FRANCISCO Researchers compared current whole genome sequencing methods with a new PCR diagnostic test and found that the new test provided quicker results, allowing testing during an outbreak to begin immediately, according to data presented at ASM Microbe.

“This was a proof-of-concept study to show whether the rapid molecular testing by Acuitas AMR Gene Panel in conjunction with Acuitas Lighthouse Software, both of which are for research use only, could be used as a front-line tool in clinical settings for transmission and outbreak detection,Vadim Sapiro, chief information officer of OpGen Inc., told Infectious Disease News.

According to Sapiro, the study was part of an ongoing partnership between OpGen, ILÚM Health Solutions and the New York State Department of Health’s Wadsworth Center to develop a genomic microbiology platform for statewide surveillance and control of antimicrobial resistance (AMR).

As part of the collaborative effort, researchers from OpGen and the Wadsworth Center put together a sample set of 80 clinical isolates, most of which were collected from two outbreak investigations, as well as 10 unrelated strains, representing a wide range of antibiotic resistance genes. Each strain was identified using matrix-assisted laser desorption ionization time-of-flight mass spectrometry, or MALDI-TOF, and characterized with carbapenemase production, molecular testing for carbapenemase resistance genes, and antimicrobial susceptibility testing (AST).

Additionally, whole genome sequencing (WGS) was performed, along with further evaluation using the Acuitas Lighthouse Software and Core Genome multilocus sequence typing to perform in silico analysis.

Results of the study showed that both methods accurately detected the two distinct outbreaks and classified the other strains as unrelated. However, the WGS had a longer turnaround time, though it had increased resolution when determining strain relatedness. Overall, the researchers determined that the Acuitas test in conjunction with the Acuitas Lighthouse Software can be used as a front-line tool in clinical settings for transmission and outbreak detection with follow-up confirmation of isolate relatedness by WGS.

According to Sapiro, the system’s price is similar to that of other multiplex infectious disease tests available on the market but it offers the added value of more comprehensive resistance gene coverage across more antibiotic families. He also says the system uses familiar instrumentation, as well as a standard PCR format and an intuitive cloud-based software for analysis, making it easy for hospitals to implement.

“Acuitas AMR Gene Panel and Acuitas Lighthouse Software detects AMR outbreaks quickly, rapidly confirms [carbapenem-resistant organisms] and [extended-spectrum beta-lactamase (ESBL)-producing organisms] and is being developed for rapid and accurate prediction of phenotypic AST to reduce hospital length of stay, improve patient safety and outcomes, and preserve the supply of effective antibiotics,” Sapiro concluded. – by Caitlyn Stulpin

Disclosure: Sapiro is chief information officer of OpGen Inc.

Vadim Sapiro
Vadim Sapiro

SAN FRANCISCO Researchers compared current whole genome sequencing methods with a new PCR diagnostic test and found that the new test provided quicker results, allowing testing during an outbreak to begin immediately, according to data presented at ASM Microbe.

“This was a proof-of-concept study to show whether the rapid molecular testing by Acuitas AMR Gene Panel in conjunction with Acuitas Lighthouse Software, both of which are for research use only, could be used as a front-line tool in clinical settings for transmission and outbreak detection,Vadim Sapiro, chief information officer of OpGen Inc., told Infectious Disease News.

According to Sapiro, the study was part of an ongoing partnership between OpGen, ILÚM Health Solutions and the New York State Department of Health’s Wadsworth Center to develop a genomic microbiology platform for statewide surveillance and control of antimicrobial resistance (AMR).

As part of the collaborative effort, researchers from OpGen and the Wadsworth Center put together a sample set of 80 clinical isolates, most of which were collected from two outbreak investigations, as well as 10 unrelated strains, representing a wide range of antibiotic resistance genes. Each strain was identified using matrix-assisted laser desorption ionization time-of-flight mass spectrometry, or MALDI-TOF, and characterized with carbapenemase production, molecular testing for carbapenemase resistance genes, and antimicrobial susceptibility testing (AST).

Additionally, whole genome sequencing (WGS) was performed, along with further evaluation using the Acuitas Lighthouse Software and Core Genome multilocus sequence typing to perform in silico analysis.

Results of the study showed that both methods accurately detected the two distinct outbreaks and classified the other strains as unrelated. However, the WGS had a longer turnaround time, though it had increased resolution when determining strain relatedness. Overall, the researchers determined that the Acuitas test in conjunction with the Acuitas Lighthouse Software can be used as a front-line tool in clinical settings for transmission and outbreak detection with follow-up confirmation of isolate relatedness by WGS.

According to Sapiro, the system’s price is similar to that of other multiplex infectious disease tests available on the market but it offers the added value of more comprehensive resistance gene coverage across more antibiotic families. He also says the system uses familiar instrumentation, as well as a standard PCR format and an intuitive cloud-based software for analysis, making it easy for hospitals to implement.

“Acuitas AMR Gene Panel and Acuitas Lighthouse Software detects AMR outbreaks quickly, rapidly confirms [carbapenem-resistant organisms] and [extended-spectrum beta-lactamase (ESBL)-producing organisms] and is being developed for rapid and accurate prediction of phenotypic AST to reduce hospital length of stay, improve patient safety and outcomes, and preserve the supply of effective antibiotics,” Sapiro concluded. – by Caitlyn Stulpin

Disclosure: Sapiro is chief information officer of OpGen Inc.

    Perspective
    Herbert L. DuPont

    Herbert L. DuPont

    The highly multiplexed real-time PCR employed in this comparative study appears to be effective in detecting carbapenem-resistant and ESBL-producing organisms and could be useful in hospitals where these occur in moderate to high rates. Multiplex PCR methods are ideal when you know the pathogen or virulence factor being sought. WGS is a more sophisticated approach requiring phylogenetic analysis and interpretation, and it is more useful in an outbreak investigation in which the number of potential pathogens is broad and unpredictable.

    • Herbert L. DuPont, MD, MACP
    • Infectious Disease News Editorial Board member
      Professor of epidemiology and infectious diseases
      University of Texas Health Science Center at Houston

    Disclosures: Dupont reports receiving grants from Rebiotix and being a consultant to Aries and Salix/Valeant.

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