Bacterial whole-genome sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes.
Multidrug-resistant nosocomial pathogens present a major burden for hospitals. Rapid cluster identification and pathogen profiling, i.e., of antibiotic resistance and virulence genes, are crucial for effective infection control. Methicillin-resistant Staphylococcus aureus (MRSA), in particular, is now one of the leading causes of nosocomial infections. In this study, whole-genome sequencing (WGS) was applied retrospectively to an unusual spike in MRSA cases in two intensive care units (ICUs) over the course of 4 weeks. While the epidemiological investigation concluded that there were two separate clusters, each associated with one ICU, S. aureus protein A gene (spa) typing data suggested that they belonged to single clonal cluster (all cases shared spa type t001). Standardized gene sets were used to extract an allele-based profile for typing and an antibiotic resistance and toxin gene profile. The WGS results produced high-resolution allelic profiles, which were used to discriminate the MRSA clusters, corroborating the epidemiological investigation and identifying previously unsuspected transmission events. The antibiotic resistance profile was in agreement with the original clinical laboratory susceptibility profile, and the toxin profile provided additional, previously unknown information. WGS coupled with allelic profiling provided a high-resolution method that can be implemented as regular screening for effective infection control.
Institute of Hygiene, University of Münster, Münster, Germany.
Shana R
SR
Leopold
Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska, USA.
Richard V
RV
Goering
Leibniz Institute for Arteriosclerosis, University of Münster, Münster, Germany.
Anika
A
Witten
Department of Periodontology, University of Münster, Münster, Germany.
Dag
D
Harmsen
Institute of Hygiene, University of Münster, Münster, Germany mellmann@uni-muenster.de.
Alexander
A
Mellmann
D015373:Bacterial Typing Techniques / Q000379:methods*; D003428:Cross Infection / Q000453:epidemiology / Q000382:microbiology*; D024881:Drug Resistance, Bacterial; D016680:Genome, Bacterial; D006801:Humans; D007362:Intensive Care Units; D055624:Methicillin-Resistant Staphylococcus aureus / Q000145:classification* / Q000187:drug effects / Q000235:genetics / Q000302:isolation & purification; D017720:Molecular Epidemiology / Q000379:methods; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D013203:Staphylococcal Infections / Q000453:epidemiology / Q000382:microbiology*