scholarly journals Editorial Commentary: Applying a New Technology to an Old Question: Whole-Genome Sequencing and Staphylococcus aureus Acquisition in an Intensive Care Unit

2013 ◽  
Vol 58 (5) ◽  
pp. 619-621 ◽  
Author(s):  
M. Z. David ◽  
R. S. Daum
Keyword(s):  
Intensive Care Unit ◽  
Staphylococcus Aureus ◽  
Intensive Care ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
New Technology ◽  
Whole Genome ◽  
Editorial Commentary ◽  
And Staphylococcus Aureus

scholarly journals Whole-Genome Sequencing for Outbreak Investigations of Methicillin-Resistant Staphylococcus aureus in the Neonatal Intensive Care Unit: Time for Routine Practice?

2015 ◽  
Vol 36 (7) ◽  
pp. 777-785 ◽  
Author(s):  
Taj Azarian ◽  
Robert L. Cook ◽  
Judith A. Johnson ◽  
Nilmarie Guzman ◽  
Yvette S. McCarter ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Staphylococcus Aureus ◽  
Phylogenetic Analysis ◽  
Intensive Care ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Neonatal Intensive Care ◽  
Whole Genome ◽  
Genome Wide ◽  
Typing Methods

BACKGROUNDInfants in the neonatal intensive care unit (NICU) are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) acquisition. Outbreaks may be difficult to identify due in part to limitations in current molecular genotyping available in clinical practice. Comparison of genome-wide single nucleotide polymorphisms (SNPs) may identify epidemiologically distinct isolates among a population sample that appears homogenous when evaluated using conventional typing methods.OBJECTIVETo investigate a putative MRSA outbreak in a NICU utilizing whole-genome sequencing and phylogenetic analysis to identify recent transmission events.DESIGNClinical and surveillance specimens collected during clinical care and outbreak investigation.PATIENTSA total of 17 neonates hospitalized in a 43-bed level III NICU in northeastern Florida from December 2010 to October 2011 were included in this study.METHODSWe assessed epidemiological data in conjunction with 4 typing methods: antibiograms, PFGE, spa types, and phylogenetic analysis of genome-wide SNPs.RESULTSAmong the 17 type USA300 isolates, 4 different spa types were identified using pulsed-field gel electrophoresis. Phylogenetic analysis identified 5 infants as belonging to 2 clusters of epidemiologically linked cases and excluded 10 unlinked cases from putative transmission events. The availability of these results during the initial investigation would have improved infection control interventions.CONCLUSIONWhole-genome sequencing and phylogenetic analysis are invaluable tools for epidemic investigation; they identify transmission events and exclude cases mistakenly implicated by traditional typing methods. When routinely applied to surveillance and investigation in the clinical setting, this approach may provide actionable intelligence for measured, appropriate, and effective interventions.Infect. Control Hosp. Epidemiol. 2015;36(7):777–785

scholarly journals Tracking Staphylococcus aureus in the intensive care unit using whole-genome sequencing

2019 ◽  
Vol 103 (1) ◽  
pp. 13-20 ◽  
Author(s):  
S.J. Dancer ◽  
C.E. Adams ◽  
J. Smith ◽  
B. Pichon ◽  
A. Kearns ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Staphylococcus Aureus ◽  
Intensive Care ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome

scholarly journals Using whole-genome sequencing and a pentaplex real-time PCR to characterize third-generation cephalosporin-resistant Enterobacteriaceae from Southeast Queensland, Australia

2020 ◽  
Author(s):  
AG Stewart ◽  
EP Price ◽  
K Schabacker ◽  
M Birikmen ◽  
PNA Harris ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Whole Genome Sequencing ◽  
Real Time ◽  
Genome Sequencing ◽  
Real Time Pcr ◽  
Generation Cephalosporin ◽  
Whole Genome ◽  
Third Generation ◽  
Sensitivity Testing

AbstractThird-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae represent a major threat to human health. Here, we captured 288 3GC-R Enterobacteriaceae clinical isolates from 258 patients presenting at a regional Australian hospital over a 14-month period. Alongside routine mass spectrometry speciation and antibiotic sensitivity testing, isolates were examined using a rapid (~40 min) pentaplex real-time PCR assay targeting the most common extended spectrum β-lactamases (ESBLs; CTX-M-1 and CTX-M-9 groups, plus TEM, SHV, and an internal 16S ribosomal DNA control). Additionally, AmpC CMY β-lactamase prevalence was examined using a singleplex PCR. A subset of isolates, including all 3GC-R isolates obtained from the intensive care unit, were subjected to whole-genome sequencing (WGS) to assess transmission dynamics, the presence of unidentified resistance determinants, and genotyping accuracy. Escherichia coli (80.2%) and Klebsiella pneumoniae (17.0%) were dominant, with Klebsiella oxytoca, Klebsiella aerogenes and Enterobacter cloacae infrequently identified. Ceftriaxone and cefoxitin resistance was identified in 97% and 24.5% of E. coli and K. pneumoniae isolates, respectively. Consistent with global findings in Enterobacteriaceae, the majority (98.3%) of isolates harbored at least one β-lactamase gene, with 144 (50%) encoding blaCTX-M-1 group, 92 (31.9%) blaCTX-M-9 group, 48 (16.7%) blaSHV, 133 (46.2%) blaTEM, and 34 (11.8%) blaCMY. WGS of β-lactamase negative or carbapenem-resistant isolates identified uncommon ESBLs and carbapenemases, including blaNDM and blaIMP, and confirmed all PCR-positive genotypes. No evidence of transmission among intensive care unit patients was identified. We demonstrate that our PCR assays enable the rapid and cost-effective identification of ESBLs in the hospital setting, which has important infection control and therapeutic implications.

Use of whole-genome sequencing to detect an outbreak of Malassezia pachydermatis infection and colonization in a neonatal intensive care unit—California, 2015–2016

2020 ◽  
Vol 41 (7) ◽  
pp. 851-853 ◽  
Author(s):  
Nancy A. Chow ◽  
Raymond Chinn ◽  
Alice Pong ◽  
Kerry Schultz ◽  
Janice Kim ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Neonatal Intensive Care Unit ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Neonatal Intensive Care ◽  
Infection Prevention ◽  
Whole Genome ◽  
Prevention Measures ◽  
Malassezia Pachydermatis

AbstractWhole-genome sequencing confirmed the presence of a Malassezia pachydermatis outbreak among neonates in a neonatal intensive care unit. This technology supports the importance of adhering to infection prevention measures.

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