scholarly journals Sink drains as reservoirs of VIM-2 metallo-β-lactamase-producing Pseudomonas aeruginosa in a Belgian intensive care unit: relation to patients investigated by whole genome sequencing

2021 ◽  
Author(s):  
Deborah De Geyter ◽  
Robin Vanstokstraeten ◽  
Florence Crombé ◽  
Jan Tommassen ◽  
Ingrid Wybo ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Pseudomonas Aeruginosa ◽  
Intensive Care ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome

Whole Genome Sequencing in Real-Time Investigation and Management of a Pseudomonas aeruginosa Outbreak on a Neonatal Intensive Care Unit

2015 ◽  
Vol 36 (9) ◽  
pp. 1058-1064 ◽  
Author(s):  
Rebecca J. Davis ◽  
Slade O. Jensen ◽  
Sebastiaan Van Hal ◽  
Björn Espedido ◽  
Adrienne Gordon ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Pseudomonas Aeruginosa ◽  
Intensive Care ◽  
Infection Control ◽  
Neonatal Intensive Care Unit ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Neonatal Intensive Care ◽  
Neonatal Unit ◽  
Whole Genome

OBJECTIVETo use whole genome sequencing to describe the likely origin of an outbreak of Pseudomonas aeruginosa in a neonatal unit.DESIGNOutbreak investigation.SETTINGThe neonatal intensive care unit service of a major obstetric tertiary referral center.PATIENTSInfants admitted to the neonatal unit who developed P. aeruginosa colonization or infection.METHODSWe undertook whole genome sequencing of P. aeruginosa strains isolated from colonized infants and from the neonatal unit environment.RESULTSEighteen infants were colonized with P. aeruginosa. Isolates from 12 infants and 7 environmental samples were sequenced. All but one of the clinical isolates clustered in ST253 and no differences were detected between unmapped reads. The environmental isolates revealed a variety of sequence types, indicating a large diverse bioburden within the unit, which was subsequently confirmed via enterobacterial repetitive intergenic consensus–polymerase chain reaction typing of post-outbreak isolates. One environmental isolate, obtained from a sink in the unit, clustered within ST253 and differed from the outbreak strain by 9 single-nucleotide polymorphisms only. This information allowed us to focus infection control activities on this sink.CONCLUSIONSWhole genome sequencing can provide detailed information in a clinically relevant time frame to aid management of outbreaks in critical patient management areas. The superior discriminatory power of this method makes it a powerful tool in infection control.Infect. Control Hosp. Epidemiol. 2015;36(9):1058–1064

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.

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

Sign in / Sign up

Export Citation Format

Share Document