Evaluation of an expanded microarray for detecting antibiotic resistance genes in a broad range of gram-negative bacterial pathogens

Abstract

A microarray capable of detecting genes for resistance to 75 clinically relevant antibiotics encompassing 19 different antimicrobial classes was tested on 132 Gram-negative bacteria. Microarray-positive results correlated >91% with antimicrobial resistance phenotypes, assessed using British Society for Antimicrobial Chemotherapy clinical breakpoints; the overall test specificity was >83%. Microarray-positive results without a corresponding resistance phenotype matched 94% with PCR results, indicating accurate detection of genes present in the respective bacteria by microarray when expression was low or absent and, hence, undetectable by susceptibility testing. The low sensitivity and negative predictive values of the microarray results for identifying resistance to some antimicrobial resistance classes are likely due to the limited number of resistance genes present on the current microarray for those antimicrobial agents or to mutation-based resistance mechanisms. With regular updates, this microarray can be used for clinical diagnostics to help accurate therapeutic options to be taken following infection with multiple-antibiotic-resistant Gram-negative bacteria and prevent treatment failure.

Fig 1

All genes detected by microarray and the antimicrobial susceptibilities of the bacterial panel studied. For each antibiotic class, the resistance genes represented on the microarray and the antibiotic tested (indicated in capital letters) by MIC determination or the disc diffusion method are grouped, and results are given for all 132 isolates. Microarray-positive genes are indicated by black-filled cells (a blank cell indicates that no gene was detected). Genes represented by more than one probe on the microarray were considered present if at least one probe had an intensity of ≥0.4. (a) Results from the aminoglycoside and β-lactam antimicrobial groups; (b) results from the remaining antimicrobial groups. ^b, asterisks denote clinical isolates; ^c, for each antibiotic where a BSAC criterion was available, the antimicrobial susceptibility is given as susceptible (S) and resistant (R) (a blank cell indicates that no interpretive criterion was available or the test was not performed). Resistant or susceptible results which are true positive and true negative are given in shaded boxes; false-positive and false-negative results are given in black. The results of the two-by-two table analysis for each antibiotic for which data were available and the overall performance values are also given.

Fig 1

All genes detected by microarray and the antimicrobial susceptibilities of the bacterial panel studied. For each antibiotic class, the resistance genes represented on the microarray and the antibiotic tested (indicated in capital letters) by MIC determination or the disc diffusion method are grouped, and results are given for all 132 isolates. Microarray-positive genes are indicated by black-filled cells (a blank cell indicates that no gene was detected). Genes represented by more than one probe on the microarray were considered present if at least one probe had an intensity of ≥0.4. (a) Results from the aminoglycoside and β-lactam antimicrobial groups; (b) results from the remaining antimicrobial groups. ^b, asterisks denote clinical isolates; ^c, for each antibiotic where a BSAC criterion was available, the antimicrobial susceptibility is given as susceptible (S) and resistant (R) (a blank cell indicates that no interpretive criterion was available or the test was not performed). Resistant or susceptible results which are true positive and true negative are given in shaded boxes; false-positive and false-negative results are given in black. The results of the two-by-two table analysis for each antibiotic for which data were available and the overall performance values are also given.

Fig 1

All genes detected by microarray and the antimicrobial susceptibilities of the bacterial panel studied. For each antibiotic class, the resistance genes represented on the microarray and the antibiotic tested (indicated in capital letters) by MIC determination or the disc diffusion method are grouped, and results are given for all 132 isolates. Microarray-positive genes are indicated by black-filled cells (a blank cell indicates that no gene was detected). Genes represented by more than one probe on the microarray were considered present if at least one probe had an intensity of ≥0.4. (a) Results from the aminoglycoside and β-lactam antimicrobial groups; (b) results from the remaining antimicrobial groups. ^b, asterisks denote clinical isolates; ^c, for each antibiotic where a BSAC criterion was available, the antimicrobial susceptibility is given as susceptible (S) and resistant (R) (a blank cell indicates that no interpretive criterion was available or the test was not performed). Resistant or susceptible results which are true positive and true negative are given in shaded boxes; false-positive and false-negative results are given in black. The results of the two-by-two table analysis for each antibiotic for which data were available and the overall performance values are also given.

Fig 1

All genes detected by microarray and the antimicrobial susceptibilities of the bacterial panel studied. For each antibiotic class, the resistance genes represented on the microarray and the antibiotic tested (indicated in capital letters) by MIC determination or the disc diffusion method are grouped, and results are given for all 132 isolates. Microarray-positive genes are indicated by black-filled cells (a blank cell indicates that no gene was detected). Genes represented by more than one probe on the microarray were considered present if at least one probe had an intensity of ≥0.4. (a) Results from the aminoglycoside and β-lactam antimicrobial groups; (b) results from the remaining antimicrobial groups. ^b, asterisks denote clinical isolates; ^c, for each antibiotic where a BSAC criterion was available, the antimicrobial susceptibility is given as susceptible (S) and resistant (R) (a blank cell indicates that no interpretive criterion was available or the test was not performed). Resistant or susceptible results which are true positive and true negative are given in shaded boxes; false-positive and false-negative results are given in black. The results of the two-by-two table analysis for each antibiotic for which data were available and the overall performance values are also given.