PMID- 31572571 OWN - NLM STAT- MEDLINE DCOM- 20200625 LR - 20231014 IS - 2047-2994 (Electronic) IS - 2047-2994 (Linking) VI - 8 DP - 2019 TI - Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci. PG - 153 LID - 10.1186/s13756-019-0604-5 [doi] LID - 153 AB - BACKGROUND: Recognition of nosocomial outbreaks with antimicrobial resistant (AMR) pathogens and appropriate infection prevention measures are essential to limit the consequences of AMR pathogens to patients in hospitals. Because unrelated, but genetically similar AMR pathogens may circulate simultaneously, rapid high-resolution molecular typing methods are needed for outbreak management. We compared amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) during a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VRE) that spanned 5 months. METHODS: Hierarchical clustering of AFLP profiles was performed using unweighted pair-grouping and similarity coefficients were calculated with Pearson correlation. For WGS-analysis, core single nucleotide polymorphisms (SNPs) were used to calculate the pairwise distance between isolates, construct a maximum likelihood phylogeny and establish a cut-off for relatedness of epidemiologically linked VRE isolates. SNP-variations in the vanB gene cluster were compared to increase the comparative resolution. Technical replicates of 2 isolates were sequenced to determine the number of core-SNPs derived from random sequencing errors. RESULTS: Of the 721 patients screened for VRE carriage, AFLP assigned isolates of 22 patients to the outbreak cluster. According to WGS, all 22 isolates belonged to ST117 but only 21 grouped in a tight phylogenetic cluster and carried vanB resistance gene clusters. Sequencing of technical replicates showed that 4-5 core-SNPs were derived by random sequencing errors. The cut-off for relatedness of epidemiologically linked VRE isolates was established at /=90%). The inclusion of the discrepant isolate in the outbreak resulted in the screening of 250 patients and quarantining of an entire ward. CONCLUSION: AFLP was a rapid and affordable screening tool for characterising hospital VRE outbreaks. For in-depth understanding of the outbreak WGS was needed. Compared to AFLP, WGS provided higher resolution typing of VRE isolates with implications for outbreak management. CI - (c) The Author(s). 2019. FAU - Janes, Victoria A AU - Janes VA AUID- ORCID: 0000-0001-6574-1449 AD - 1Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands. FAU - Notermans, Daan W AU - Notermans DW AD - 1Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands. FAU - Spijkerman, Ingrid J B AU - Spijkerman IJB AD - 1Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands. FAU - Visser, Caroline E AU - Visser CE AD - 1Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands. FAU - Jakobs, Marja E AU - Jakobs ME AD - 2Amsterdam UMC, University of Amsterdam, Clinical Genetics, Core Facility Genomics, Amsterdam, The Netherlands. FAU - van Houdt, Robin AU - van Houdt R AD - 3Amsterdam UMC, Vrije Universiteit, Medical Microbiology, Amsterdam, The Netherlands. FAU - Willems, Rob J L AU - Willems RJL AD - 4Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands. FAU - de Jong, Menno D AU - de Jong MD AD - 1Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands. FAU - Schultsz, Constance AU - Schultsz C AD - 1Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands. AD - 5Amsterdam UMC, University of Amsterdam, Global Health - Amsterdam Institute for Global Health and Development (AIGHD), Amsterdam, The Netherlands. FAU - Matamoros, Sebastien AU - Matamoros S AD - 1Amsterdam UMC, University of Amsterdam, Medical Microbiology, Amsterdam, The Netherlands. LA - eng PT - Comparative Study PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20190923 PL - England TA - Antimicrob Resist Infect Control JT - Antimicrobial resistance and infection control JID - 101585411 RN - 0 (Bacterial Proteins) RN - 0 (VanB protein, Enterococcus) SB - IM MH - Amplified Fragment Length Polymorphism Analysis/*methods MH - Bacterial Proteins/genetics MH - Carrier State/diagnosis/microbiology MH - Cluster Analysis MH - Cross Infection/*microbiology MH - Disease Outbreaks MH - Enterococcus faecium/classification/genetics/isolation & purification MH - Genome, Bacterial MH - Gram-Positive Bacterial Infections/*diagnosis MH - Humans MH - Molecular Typing MH - Phylogeny MH - Polymorphism, Single Nucleotide MH - Retrospective Studies MH - Tertiary Care Centers MH - Time Factors MH - Vancomycin-Resistant Enterococci/classification/genetics/*isolation & purification MH - Whole Genome Sequencing/*methods PMC - PMC6757385 OTO - NOTNLM OT - AFLP OT - Molecular typing OT - Nosocomial outbreak OT - VRE OT - WGS COIS- Competing interestsThe authors declare that they have no competing interests. EDAT- 2019/10/02 06:00 MHDA- 2020/06/26 06:00 PMCR- 2019/09/23 CRDT- 2019/10/02 06:00 PHST- 2019/02/18 00:00 [received] PHST- 2019/08/30 00:00 [accepted] PHST- 2019/10/02 06:00 [entrez] PHST- 2019/10/02 06:00 [pubmed] PHST- 2020/06/26 06:00 [medline] PHST- 2019/09/23 00:00 [pmc-release] AID - 604 [pii] AID - 10.1186/s13756-019-0604-5 [doi] PST - epublish SO - Antimicrob Resist Infect Control. 2019 Sep 23;8:153. doi: 10.1186/s13756-019-0604-5. eCollection 2019.