TABLE 4.

Antimicrobial resistance associations made by Explify analysis for the RPIP targeted workflow^f

Pathogen	Associated AMR marker(s)a	Susceptibility profile	Agreement
E. coli	ANT(3′), CTX-M, Dfr, MPH, OXA, Sul	ESBL; R-TMP-SMX	Agreeb (partial agreement)
E. faecalis	Erm	Pansusceptible (ampicillin, vancomycin, linezolid)	Agreec
E. faecium	APH(3′), Erm, Van	VRE; R-ampicillin, SDD-daptomycin, R-vancomycin	Agreed
M. tuberculosis	Qnr, RRS	Susceptible to first-line agents, prediction of resistance to second-line agentse	Agree
P. aeruginosa	CTX-M, Dfr, OXA	Pansusceptible	Disagree
P. aeruginosa	OXA	Pansusceptible	Disagree
P. aeruginosa	OXA	Pansusceptible	Disagree
P. aeruginosa	OXA, CrpP	Pansusceptible	Disagree
P. aeruginosa	OXA, CrpP	Pansusceptible	Disagree
P. aeruginosa	OXA, Dfr	S-meropenem, R-piperacillin-tazobactam, R-ceftazidime, R-cefepime, R-aztreonam	Disagree
S. aureus	ABC–F, APH(3′), MecA, MPH	R-oxacillin, R-erythromycin	Agree
S. aureus	Erm	R-clindamycin, R-erythromycin	Agree
S. aureus	MecA, Erm	PBP2a detected by LFA	Agree

^aAssociations are listed as reported by Explify analysis, which does not follow traditional gene-based reporting. Reported associations between AMR markers and drug classes are made by Explify as follows: ABC–F, macrolides; ANT(3′), aminoglycosides; APH(3′), aminoglycosides; CrpP, fluoroquinolones; CTX-M, cephalosporins and penicillins; Dfr, diaminopyrimidine; Erm, lincosamides and macrolides; MecA, beta-lactam/beta-lactamase inhibitors, carbapenems, cephalosporins, and penicillins; MPH, macrolides; OXA, carbapenems; Qnr, fluoroquinolones; RRS, aminoglycosides; Sul, sulfonamides; Van, glycopeptides. Associations were not made with all agents in each class.

^bSusceptible to meropenem, although OXA is associated. Macrolides were not tested for this isolate.

^cMacrolides were not tested for this isolate.

^dAminoglycosides and macrolides were not tested for this isolate.

^eSecond-line agents were moxifloxacin at an MIC of 0.25 μg/mL (at the proposed critical concentration), amikacin at an MIC of 0.5 μg/mL (below but within 1 dilution of the proposed critical concentration), and kanamycin at an MIC of 2.5 μg/mL (at the proposed critical concentration).

^fR, resistant; S, susceptible; TMP-SMX, trimethoprim-sulfamethoxazole; VRE, vancomycin-resistant Enterococcus; PBP2a, penicillin binding protein 2a; SDD = susceptible dose dependent; LFA = lateral flow assay.