Comparison of two DNA microarrays for detection of plasmid-mediated antimicrobial resistance and virulence factor genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae

Walsh, Fiona; Cooke, Niamh M.; Smith, Stephen G.; Moran, Gary P.; Cooke, Fiona J.; Ivens, Alasdair; Wain, John; Rogers, Thomas R.

doi:10.1016/j.ijantimicag.2010.02.011

« Previous Next »International Journal of Antimicrobial Agents
Volume 35, Issue 6 , Pages 593-598, June 2010

Comparison of two DNA microarrays for detection of plasmid-mediated antimicrobial resistance and virulence factor genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae

Fiona Walsh
- Department of Clinical Microbiology, Sir Patrick Dun Translational Research Laboratory, School of Medicine, University of Dublin, Trinity College, St James's Hospital Campus, Dublin 8, Ireland
- These authors contributed equally to this work.
- Corresponding author. Tel.: +353 1 896 3620; fax: +353 1 896 2131.
Niamh M. Cooke
- Department of Clinical Microbiology, Sir Patrick Dun Translational Research Laboratory, School of Medicine, University of Dublin, Trinity College, St James's Hospital Campus, Dublin 8, Ireland
- These authors contributed equally to this work.
Stephen G. Smith
- Department of Clinical Microbiology, Sir Patrick Dun Translational Research Laboratory, School of Medicine, University of Dublin, Trinity College, St James's Hospital Campus, Dublin 8, Ireland
Gary P. Moran
- Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental School and Hospital, University of Dublin, Trinity College, Dublin 2, Ireland
Fiona J. Cooke
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Alasdair Ivens
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
John Wain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Thomas R. Rogers
- Department of Clinical Microbiology, Sir Patrick Dun Translational Research Laboratory, School of Medicine, University of Dublin, Trinity College, St James's Hospital Campus, Dublin 8, Ireland

Received 23 December 2009; accepted 10 February 2010. published online 31 March 2010.

Abstract

A DNA microarray was developed to detect plasmid-mediated antimicrobial resistance (AR) and virulence factor (VF) genes in clinical isolates of Enterobacteriaceae and non-Enterobacteriaceae. The array was validated with the following bacterial species: Escherichia coli (n=17); Klebsiella pneumoniae (n=3); Enterobacter spp. (n=6); Acinetobacter genospecies 3 (n=1); Acinetobacter baumannii (n=1); Pseudomonas aeruginosa (n=2); and Stenotrophomonas maltophilia (n=2). The AR gene profiles of these isolates were identified by polymerase chain reaction (PCR). The DNA microarray consisted of 155 and 133 AR and VF gene probes, respectively. Results were compared with the commercially available Identibac AMR-ve Array Tube. Hybridisation results indicated that there was excellent correlation between PCR and array results for AR and VF genes. Genes conferring resistance to each antibiotic class were identified by the DNA array. Unusual resistance genes were also identified, such as bla_SHV-5 in a bla_OXA-23-positive carbapenem-resistant A. baumannii. The phylogenetic group of each E. coli isolate was verified by the array. These data demonstrate that it is possible to screen simultaneously for all important classes of mobile AR and VF genes in Enterobacteriaceae and non-Enterobacteriaceae whilst also assigning a correct phylogenetic group to E. coli isolates. Therefore, it is feasible to test clinical Gram-negative bacteria for all known AR genes and to provide important information regarding pathogenicity simultaneously.