Acuitas AMR Gene Panel Electronic User Guide (EUG)

Welcome to the Acuitas AMR Gene Panel Electronic User Guide page

The Acuitas AMR Gene Panel Electronic User Guide provides performance and interpretation results for the Acuitas AMR Gene Panel as an extension of the package insert.

The Electronic User Guide primarily describes clinical performance results for detection of antimicrobial resistance (AMR) genes by the Acuitas AMR Gene Panel compared with corresponding genome sequencing and antimicrobial susceptibility test (AST) results.

As additional background information, the Electronic User Guide also includes AMR gene and AST results from an OpGen study (1) performed with clinical isolates collected through the Merck Study for Monitoring Antimicrobial Resistance Trends (SMART) (2, 3); E. coli (n=2,919), K. pneumoniae (n=1,974), P. mirabilis (n=1,150) and P. aeruginosa (n=1,484). Also included are percentages of organisms in the NCBI Pathogen Database (2019) harboring indicated AMR genes.

Querying the Electronic User Guide through search terms and/or selectable fields generates information described in the table below, which can be downloaded in XLSX format including legends, footnotes and disclaimers. Additionally, the Literature Summary, which can be downloaded in PDF format, provides a curated and referenced scientific review of AMR genes reported by the Acuitas AMR Gene Panel in terms of organisms and types of studies. Refer to the Acuitas AMR Gene Panel package insert for additional details about the Acuitas AMR Gene Panel.

Query Output		Description
Columns	Output
A	AMR Gene Target	AMR gene reported by Acuitas AMR Gene Panel.
B	Organism	Organism tested by Acuitas AMR Gene Panel.
C-D	Detection of AMR Gene Target by AMR Gene Panel versus Whole Genome Sequencing, Combined Clinical Device Performance - Stock and Prospective Isolates (from K191288)	Percent positive/negative agreement (PPA, NPA) for detection of AMR gene by Acuitas AMR Gene Panel versus genome sequencing for stock and prospective isolates from clinical study (K191288). Some stock isolates tested in replicate. Results include numbers of true/false positives and true/false negatives with 95% confidence intervals.
E	Antimicrobial	Antibiotic
F-I	Detection of AMR Gene Target by AMR Gene Panel vs AST Non-Susceptibility, Combined Clinical Device Performance - Stock and Prospective Isolates (from K191288) including only unique isolates (no replicates)	PPA, NPA and positive/negative predictive values (PPV, NPV) for detection of AMR gene by Acuitas AMR Gene Panel versus AST non-susceptibility for unique stock and prospective isolates from clinical study (K191288). Results include numbers of true/false positives and true/false negatives with 95% confidence intervals.
J-N	Detection of AMR Gene Target versus AST Non-Susceptibility in OpGen's SMART Study	PPA, NPA, PPV and NPV for detection of AMR gene by PCR versus AST non-susceptibility from OpGen’s SMART Study including numbers of true/false positives and true/false negatives with 95% confidence intervals. Column N reports percentage of study organisms positive for AMR genes including numbers of total positives and total isolates with 95% confidence intervals. Results indicate representative AMR gene variants detected by assay(s) reported as AAC, AAD, ANT, APH, CMY and DFR by Acuitas AMR Gene Panel; refer to columns A and J-N for the detailed relationship between gene tests contained in the Acuitas AMR Gene Panel and the name under which they are reported.
O	% Organisms with AMR Gene Target in NCBI Pathogen Database (2019)	Percentages of organisms in NCBI Pathogen Database (2019) with AMR gene along with total number of isolates. Results indicate representative AMR gene variants detected by assay(s) reported as AAC, AAD, ANT, APH, CMY and DFR by Acuitas AMR Gene Panel; refer to columns A and O for the detailed relationship between gene tests contained in the Acuitas AMR Gene Panel and the name under which they are reported.
P	AMR Gene Associated with AST Non-Susceptibility?	Whether organism/AMR gene associated with AST non-susceptibility in clinical study (K191288).
Q	Notes	General notes and reasons why organism/AMR gene did not associate with AST non-susceptibility in clinical study (K191288) including (a) intrinsic resistance, AST not evaluated, (b) PPV < 80%, (c) insufficient number of non-susceptible isolates by AST, (d) may have elevated MIC to imipenem due to mechanisms other than carbapenemases, and (e) OXA-9 is active against cephalosporins and penicillins according to the Comprehensive Antibiotic Resistance Database (CARD); refer to https://card.mcmaster.ca/ontology/37804.
Abbreviations: blank entry (-), intrinsic resistance (IR), not-a-number/divide-by-zero (NaN), test not performed (Not Evaluated), and result not reported (NR).

References

Predicting Antibiotic Resistance in Gram-negative Bacilli from Resistance Genes. Walker et al., (2019) Antimicrobial Agents and Chemotherapy 63 (4): e02462-18. doi: 10.1128/AAC.02462-18
A Review of Ten Years of the Study for Monitoring Antimicrobial Resistance Trends (SMART) from 2002 to 2011. Morrissey et al., (2013) Pharmaceuticals 6, 1335-1346; doi:10.3390/ph6111335
https://globalsmartsite.com/

Literature Summary

Search Term:

AMR genes:

Organisms:

Antimicrobials:

Acuitas AMR Gene Panel Electronic User Guide (v 1.0). Copyright Curetis GmbH an OpGen Group Company 2023.