Epidemiological characterization of a nosocomial outbreak of extended spectrum β‐lactamase Escherichia coli ST‐131 confirms the clinical value of core genome multilocus sequence typing

Enhanced precision of epidemiological typing in clinically suspected nosocomial outbreaks is crucial. Our aim was to investigate whether single nucleotide polymorphism (SNP) analysis and core genome (cg) multilocus sequence typing (MLST) of whole genome sequencing (WGS) data would more reliably identify a nosocomial outbreak, compared to earlier molecular typing methods. Sixteen isolates from a nosocomial outbreak of ESBL E. coli ST‐131 in southeastern Sweden and three control strains were subjected to WGS. Sequences were explored by SNP analysis and cgMLST. cgMLST clearly differentiated between the outbreak isolates and the control isolates (>1400 differences). All clinically identified outbreak isolates showed close clustering (≥2 allele differences), except for two isolates (>50 allele differences). These data confirmed that the isolates with >50 differing genes did not belong to the nosocomial outbreak. The number of SNPs within the outbreak was ≤7, whereas the two discrepant isolates had >700 SNPs. Two of the ESBL E. coli ST‐131 isolates did not belong to the clinically identified outbreak. Our results illustrate the power of WGS in terms of resolution, which may avoid overestimation of patients belonging to outbreaks as judged from epidemiological data and previously employed molecular methods with lower discriminatory ability.

[1]  R. Cantón,et al.  Co-resistance: an opportunity for the bacteria and resistance genes. , 2011, Current opinion in pharmacology.

[2]  A. Mellmann,et al.  Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting , 2016, Journal of Clinical Microbiology.

[3]  Brad Spellberg,et al.  The future of antibiotics and resistance. , 2013, The New England journal of medicine.

[4]  E Feil,et al.  Guidelines for the validation and application of typing methods for use in bacterial epidemiology. , 2007, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[5]  A. Danchin,et al.  Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths , 2009, PLoS genetics.

[6]  D. Gajanana,et al.  Transmission of an Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli (Sequence Type ST131) Strain between a Father and Daughter Resulting in Septic Shock and Emphysematous Pyelonephritis , 2009, Journal of Clinical Microbiology.

[7]  E. Kristiansson,et al.  Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules , 2016, Scientific Reports.

[8]  Po-Jung Huang,et al.  Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing , 2015, BMC Genomics.

[9]  B. Finlay,et al.  Molecular mechanisms of Escherichia coli pathogenicity , 2012, Nature Reviews Microbiology.

[10]  C. Sprung,et al.  Surviving Sepsis Campaign: International Guidelines for Management of Severe Sepsis and Septic Shock 2012 , 2013, Critical care medicine.

[11]  D. Paterson,et al.  Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain. , 2011, The Journal of antimicrobial chemotherapy.

[12]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[13]  Ole Lund,et al.  Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli , 2014, Journal of Clinical Microbiology.

[14]  Ole Lund,et al.  Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria , 2012, Journal of Clinical Microbiology.

[15]  C. Jernberg,et al.  High-Resolution Melting-Curve Analysis of Ligation-Mediated Real-Time PCR for Rapid Evaluation of an Epidemiological Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli , 2011, Journal of Clinical Microbiology.

[16]  M. Levy,et al.  Surviving Sepsis Campaign: International guidelines for management of severe sepsis and septic shock: 2008 , 2007, Intensive Care Medicine.

[17]  Ole Lund,et al.  In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing , 2014, Antimicrobial Agents and Chemotherapy.

[18]  S. Beatson,et al.  Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131 , 2016, mBio.

[19]  E. Castro-Nallar,et al.  Pathogen typing in the genomics era: MLST and the future of molecular epidemiology. , 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[20]  Ö. Melefors,et al.  Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing , 2013, PloS one.

[21]  Daniel Falush,et al.  Sex and virulence in Escherichia coli: an evolutionary perspective , 2006, Molecular microbiology.

[22]  Xavier Bertrand,et al.  Escherichia coli ST131, an Intriguing Clonal Group , 2014, Clinical Microbiology Reviews.

[23]  Stefan Niemann,et al.  Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach , 2014, Journal of Clinical Microbiology.

[24]  L. Price,et al.  Complete Genome Sequence of the Epidemic and Highly Virulent CTX-M-15-Producing H30-Rx Subclone of Escherichia coli ST131 , 2013, Genome Announcements.

[25]  Dag Harmsen,et al.  Bacterial Whole-Genome Sequencing Revisited: Portable, Scalable, and Standardized Analysis for Typing and Detection of Virulence and Antibiotic Resistance Genes , 2014, Journal of Clinical Microbiology.

[26]  Carsten Friis,et al.  Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes , 2012, BMC Genomics.

[27]  James R. Johnson,et al.  WITHIN-HOUSEHOLD SHARING OF A FLUOROQUINOLONE-RESISTANT ESCHERICHIA COLI SEQUENCE TYPE ST131 STRAIN CAUSING PEDIATRIC OSTEOARTICULAR INFECTION , 2010, The Pediatric infectious disease journal.

[28]  Malbert R. C. Rogers,et al.  Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium , 2015, Journal of Clinical Microbiology.

[29]  Nicola K. Petty,et al.  BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons , 2011, BMC Genomics.

[30]  S. Rasmussen,et al.  Identification of acquired antimicrobial resistance genes , 2012, The Journal of antimicrobial chemotherapy.

[31]  A. Kasarskis,et al.  How Next-Generation Sequencing and Multiscale Data Analysis Will Transform Infectious Disease Management , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[32]  Julian Parkhill,et al.  Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission , 2015, Nature Communications.

[33]  L. Kreienbrock,et al.  Simultaneous occurrence of MRSA and ESBL-producing Enterobacteriaceae on pig farms and in nasal and stool samples from farmers. , 2017, Veterinary microbiology.

[34]  P. Gajer,et al.  The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates , 2008, Journal of bacteriology.

[35]  M. Achtman,et al.  Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[36]  J. Rothberg,et al.  Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology , 2011, PloS one.

[37]  R. Kaas,et al.  Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms , 2014, PloS one.

[38]  B. Olsson-Liljequist,et al.  Evaluation of High-Resolution Melting Curve Analysis of Ligation-Mediated Real-Time PCR, a Rapid Method for Epidemiological Typing of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Species) Pathogens , 2014, Journal of Clinical Microbiology.