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Published on: October 29, 2014
Surveillance of Enterobacter cloacae complex colonization and comparative analysis of different typing methods on a
Andreas F Wendel1,2, Daniel Peter3,4, Frauke Mattner3,4
1Institute of Hygiene, Cologne Merheim Medical Centre, University Hospital of Witten/Herdecke, Ostmerheimer Strasse 200, 51109, Cologne, Germany. wendela@kliniken-koeln.de.
Insights
Whole genome sequencing (WGS) is the most effective method for tracking Enterobacter cloacae complex outbreaks in neonatal intensive care units. Traditional methods like PFGE and RAPD/rep-PCR also offer reliable results for infection control.
Area of Science:
- Microbiology
- Infectious Diseases
- Genomics
Background:
- Enterobacter cloacae complex poses a significant opportunistic threat in neonatal intensive care units.
- Rising colonization rates necessitate effective surveillance and typing methods.
- High-risk preterm neonates require active microbiological screening.
Purpose of the Study:
- To evaluate the performance of various bacterial typing techniques.
- To establish whole genome sequencing (WGS) as the reference standard for E. cloacae complex typing.
- To assess typing methods for detecting transmission events and guiding infection control.
Main Methods:
- Isolates from clinical and screening specimens were identified and tested for antibiotic susceptibility.
- Bacterial typing was performed using RAPD/rep-PCR, PFGE, and Fourier-transform infrared (FTIR) spectroscopy.
- Whole genome sequencing (WGS) with SNP-based clustering served as the reference method for comparison.
Main Results:
- Whole genome sequencing (WGS) demonstrated the highest discriminatory power.
- RAPD/rep-PCR and PFGE showed good concordance with WGS results.
- FTIR spectroscopy yielded mediocre performance; polyclonal spread and two dominant clonal clusters were identified.
Conclusions:
- Bacterial typing is crucial for implementing targeted infection control during E. cloacae complex outbreaks.
- WGS is the most discriminatory typing method, but PFGE and RAPD/rep-PCR are reliable alternatives.
- Further research is needed for rapid species-level identification of E. cloacae complex in clinical laboratories.
Background:
Enterobacter cloacae complex is a group of common opportunistic pathogens on neonatal intensive care units. Active microbiological screening to guide empirical antimicrobial treatment or to detect transmission events is recommended in high-risk preterm neonates. A rise in colonization with E. cloacae complex was observed in a German perinatal centre. The aim of this study was to evaluate the performance of different typing techniques using whole genome sequencing (WGS) as a reference.
Methods:
Enterobacter cloacae complex isolates from clinical and screening specimens with an epidemiological link to the neonatal intensive care units were further assessed. Identification and antibiotic susceptibility testing was performed by a combination of VITEK2 (bioMérieux) and MALDI-TOF (Bruker Daltonics), followed by RAPD/rep-PCR and PFGE (XbaI). Retrospectively, all isolates were analyzed by Fourier-transform infrared (FTIR) spectroscopy (IR Biotyper, Bruker Daltonics). Whole genome sequencing with SNP-based clustering was used as the reference method. Furthermore, resistome analysis, sequence type and species identification were derived from the WGS data. Transmission analysis was based on epidemiological and typing data.
Results:
Between September 2017 and March 2018 32 mostly preterm neonates were found to be colonized with E. cloacae complex and 32 isolates from 24 patients were available for further typing. RAPD/rep-PCR and PFGE showed good concordance with WGS whereas FTIR displayed mediocre results [adjusted rand index (ARI) = 0.436]. A polyclonal increase and two dominant and overlapping clonal clusters of two different E. hormaechei subspecies were detected. Overall, four different species were identified. Genotyping confirmed third-generation cephalosporin resistance development in isolates of the same patient. During the six-month period several infection prevention interventions were performed and no E. cloacae complex isolates were observed during the following months.
Conclusions:
Interpretation of the microbiological results alone to detect transmission events is often challenging and bacterial typing is of utmost importance to implement targeted infection control measures in an epidemic occurrence of E. cloacae complex. WGS is the most discriminatory method. However, traditional methods such as PFGE or RAPD/rep-PCR can provide reliable and quicker results in many settings. Furthermore, research is needed to quickly identify E. cloacae complex to the species level in the microbiological laboratory.
