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. 2023 Dec 5;12(12):1701.
doi: 10.3390/antibiotics12121701.

Rapid Detection of Antimicrobial Resistance Genes in Critically Ill Children Using a Custom TaqMan Array Card

John A Clark  1   2 , Martin D Curran  3 , Theodore Gouliouris  2   3 , Andrew Conway Morris  2   4   5 , Rachel Bousfield  2   3 , Vilas Navapurkar  2 , Iain R L Kean  1 , Esther Daubney  1 , Deborah White  1 , Stephen Baker  6 , Nazima Pathan  1   2
Affiliations

Rapid Detection of Antimicrobial Resistance Genes in Critically Ill Children Using a Custom TaqMan Array Card

John A Clark et al. Antibiotics (Basel). .

Abstract

Bacteria are identified in only 22% of critically ill children with respiratory infections treated with antimicrobial therapy. Once an organism is isolated, antimicrobial susceptibility results (phenotypic testing) can take another day. A rapid diagnostic test identifying antimicrobial resistance (AMR) genes could help clinicians make earlier, informed antimicrobial decisions. Here we aimed to validate a custom AMR gene TaqMan Array Card (AMR-TAC) for the first time and assess its feasibility as a screening tool in critically ill children. An AMR-TAC was developed using a combination of commercial and bespoke targets capable of detecting 23 AMR genes. This was validated using isolates with known phenotypic resistance. The card was then tested on lower respiratory tract and faecal samples obtained from mechanically ventilated children in a single-centre observational study of respiratory infection. There were 82 children with samples available, with a median age of 1.2 years. Major comorbidity was present in 29 (35%) children. A bacterial respiratory pathogen was identified in 13/82 (16%) of children, of which 4/13 (31%) had phenotypic AMR. One AMR gene was detected in 49/82 (60%), and multiple AMR genes were detected in 14/82 (17%) children. Most AMR gene detections were not associated with the identification of phenotypic AMR. AMR genes are commonly detected in samples collected from mechanically ventilated children with suspected respiratory infections. AMR-TAC may have a role as an adjunct test in selected children in whom there is a high suspicion of antimicrobial treatment failure.

Keywords: antibacterial agents; antimicrobial resistance; child; critical illness; rapid diagnostic tests; respiratory system.

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Conflict of interest statement

M.D.C. is the inventor of a patent held by the Secretary of State for Health (UK government) EP2788503, which covers some of the genetic sequences used in this study. V.N. is a founder, director, and shareholder in Cambridge Infection Diagnostics (CID), a commercial company aimed at developing molecular diagnostics in infection and antimicrobial and AMR stewardship. A.C.M. and S.B. are members of the Scientific Advisory Board of CID. A.C.M. receives speaking fees from Boston Scientific. N.P. has received speaker fees from BioMérieux (Marcy-l’Étoile, France). All other authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Antimicrobial resistance genes detected in critically ill children with suspected lower respiratory tract infection. This figure represents antimicrobial resistance (AMR) genes identified using a custom antimicrobial resistance gene TaqMan array card. AMR genes were detected in a greater proportion of faecal samples than non-bronchoscopic bronchoalveolar lavage (mini-BAL) samples. The most commonly identified AMR gene in faecal and mini-BAL samples was ermB. If expressed, this gene can confer resistance to macrolides. Figure created at BioRender.com (accessed on 13 February 2023).
Figure 2
Figure 2
Configuration of a custom antimicrobial resistance gene TaqMan array card. This figure represents one lane of the antimicrobial resistance gene TaqMan array card (AMR-TAC). The card contains eight lanes with each configuration. The assays can detect genes conferring resistance to β-lactams, carbapenems, fluoroquinolones, glycopeptides, and macrolides.
See this image and copyright information in PMC

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