title: Recombinations in staphylococcal cassette chromosome mec elements compromise the molecular detection of methicillin resistance in Staphylococcus aureus.
abstract: Clinical laboratories are increasingly using molecular tests for methicillin-resistant Staphylococcus aureus (MRSA) screening. However, primers have to be targeted to a variable chromosomal region, the staphylococcal cassette chromosome mec (SCCmec). We initially screened 726 MRSA isolates from a single UK hospital trust by recombinase polymerase amplification (RPA), a novel, isothermal alternative to PCR. Undetected isolates were further characterised using multilocus sequence, spa typing and whole genome sequencing. 96% of our tested phenotypically MRSA isolates contained one of the six orfX-SCCmec junctions our RPA test and commercially available molecular tests target. However 30 isolates could not be detected. Sequencing of 24 of these isolates demonstrated recombinations within the SCCmec element with novel insertions that interfered with the RPA, preventing identification as MRSA. This result suggests that clinical laboratories cannot rely solely upon molecular assays to reliably detect all methicillin-resistance. The presence of significant recombinations in the SCCmec element, where the majority of assays target their primers, suggests that there will continue to be isolates that escape identification. We caution that dependence on amplification-based molecular assays will continue to result in failure to diagnose a small proportion (∼4%) of MRSA isolates, unless the true level of SCCmec natural diversity is determined by whole genome sequencing of a large collection of MRSA isolates.
authors: Pathogen Genomics Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney School of Public Health, University of Sydney, Sydney, Australia.
authors: Grant A
authors: GA
authors: Hill-Cawthorne
authors: Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.
authors: Lyndsey O
authors: LO
authors: Hudson
authors: Pathogen Genomics Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors: Moataz Fouad Abd
authors: MF
authors: El Ghany
authors: TwistDx Ltd., Babraham, United Kingdom.
authors: Olaf
authors: O
authors: Piepenburg
authors: Pathogen Genomics Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors: Mridul
authors: M
authors: Nair
authors: Microbiology Dept, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom.
authors: Andrew
authors: A
authors: Dodgson
authors: TwistDx Ltd., Babraham, United Kingdom.
authors: Matthew S
authors: MS
authors: Forrest
authors: Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom.
authors: Taane G
authors: TG
authors: Clark
authors: Pathogen Genomics Laboratory, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors: Arnab
authors: A
authors: Pain
mesh_terms: D001483:Base Sequence; D002876:Chromosomes, Bacterial / Q000235:genetics*; D016106:Methicillin Resistance / Q000235:genetics*; D055624:Methicillin-Resistant Staphylococcus aureus / Q000235:genetics / Q000302:isolation & purification*; D025202:Molecular Diagnostic Techniques; D008969:Molecular Sequence Data; D060885:Multiplex Polymerase Chain Reaction; D011995:Recombination, Genetic; D012680:Sensitivity and Specificity