WHOLE GENOME SEQUENCING FOR STAPHYLOCOCCUS AUREUS. Claire Gordon MRC clinical research fellow Nuffield Department of Medicine, University of Oxford
|
|
|
- Rudolph Smith
- 5 years ago
- Views:
Transcription
1 WHOLE GENOME SEQUENCING FOR STAPHYLOCOCCUS AUREUS Claire Gordon MRC clinical research fellow Nuffield Department of Medicine, University of Oxford
2 Staphylococcus aureus Remains a major healthcare associated pathogen Persistently carried by 20% of population, intermittently by 30% 1 Cause of outbreaks» approximately 500 putative S. aureus outbreaks referred to Public Health England for investigation per year Multidrug resistance» MRSA» VISA/VRSA 1 Werthhiem et al, 2005 Virulent strains» USA 300» Toxin producing
3 Whole Genome Sequencing Hypothesis: whole genome sequencing (WGS) can give us all the information we need to diagnose, treat and investigate illness due to S. aureus To date we have used WGS to study outbreaks / person to person spread predict antimicrobial resistance look for virulence factors
4 Extract DNA Fragmentation, labelling and cluster generation Assembly and analysis Sequencing by synthesis
5 OUTBREAKS
6 Outbreaks studies: standard tests Find which group the strains belong to MLST spa type phage typing SCCmec typing Pulsed field gel electrophoresis
7 PFGE : gold standard? Kazakova SV et al. N Engl J Med 2005;352:
8 Why use WGS? Single platform Better resolution Turnaround times approaching those of standard techniques May give additional information
9 Calibration
10 0 5 Pairwise difference, SNVs Distribution of pairwise differences for community and hospital outbreaks Community Hospital Setting No of pairs Mean pairwise difference (SNVs) 95% CI Hospital Community P=0.00
11 % of isolates included by each SNV distance Percentage of isolates included by SNV threshold Distance from nearest neighbour Distance from index SNV threshold
12 Case study: MRSA on ITU x x x x x x x Patient A (bay 1) Patient B (bay 1) Patient C (bay 2) Nurse1 Nurse2 air sample Dr Days
13 Using epidemiology x x x x x x x Patient A (bay 1) Patient B (bay 1) Patient C (bay 2) Nurse1 Nurse2 air sample Dr Days
14 Using standard typing (spa plus PFGE) EMRSA-15, pulsotype 15b1 EMRSA-16 EMRSA-15, pulsotype 15b1
15 Using WGS
16 Using WGS
17 First broken S. aureus outbreak Demonstrates diversity within same PFGE pulsotype Unidentified source of MRSA for patient A
18 Applying WGS to complex outbreaks 30/09/ /10/ /11/ /12/ /01/ /02/ /03/2012 STM-DW STM-BG STM-TV STM-PS STM-TC STM-HB STM-KM STM-EG STM-HC STM-CG STM-RB STM-LG STM-KW STM-HD SB-HG SB-VC SB-HG SAU-PW SAU-MS SAU-BE SAU-HW SAU-RS SAU-LC SAU-AW SAN-RW SAN-SC SAN-WS SAN-RW SAN-DW SAN-HJ SAN-EW SAN-LS SAN-FF QREC-JT QEND-EC MW-LB MW-DG MW-DE MW-MJ MW-JB MW-JD MW-JH MW-GR FRD-JC FRD-SJ FRD-AS FRD-DR FRD-SC FRD-JS FRD-IC DEAL-RF DEAL-JH DEAL-BC DEAL-AR DEAL-GW DEAL-RQ DEAL-FS Deal-RD DEAL-CT CSF-ML CSF-MS CSF-SB CDU-KB CDU-IM CDU-FU CDU-DL BIS-AG BIS-GS BIS-JP BIS-LM Ward Clusters
19 PFGE WGS
20 By time (light grey-> earliest)
21 By hospital
22 WGS in real time Illumina MiSeq 12-27hr turnaround time Bench top platform
23 RESISTOTYPING
24 Genotype vs phenotype Genotyping WGS de novo assembled contigs Blasted for catalogue of resistance determinants Phenotyping disc diffusion plus automated broth dilution E-test to resolve discrepancies Isolates n=491 bacteraemia and carriage isolates sourced from clinical collections in Oxford / Brighton
25 Overall categorical agreement >99% Total of 11 cryptic genotype / phenotype mismatches Penicillin Deletions / insertions in blaz causing frameshift mutations Rapid identification of novel variants non-synonymous mutations in fusa DNA sequence alignments showing single base blaz deletions in 4 penicillin susceptible isolates
26 Overall results Phenotype: resistant Phenotype: susceptible Error Rates Genotype Genotype VME ME Antimicrobial Susceptible Resistant Susceptible Resistant (%) (%) Penicillin Methicillin Ciprofloxacin Erythromycin Clindamycin Tetracycline Vancomycin n/a 0.0 Fusidic acid Trimethoprim Gentamicin Mupirocin Rifampicin Total
27 Overall results Phenotype: resistant Phenotype: susceptible Error Rates Genotype Genotype VME ME Antimicrobial Susceptible Resistant Susceptible Resistant (%) (%) Penicillin Methicillin Ciprofloxacin Erythromycin Clindamycin Tetracycline Vancomycin n/a 0.0 Fusidic acid Trimethoprim Gentamicin Mupirocin Rifampicin Total
28 Previous phenotyping studies Study Comparison no of isolates Categorical agreement (%) ME rate (%) VME rate (%) Ligozzi 2002 Vitek 2 vs agar dilution Fahr 2003 BD Phoenix vs broth dilution plus meca PCR Nonhoff 2005 Vitek 2 vs agar dilution Carroll 2006 BD Phoenix vs agar dilution Giani 2012 BD Phoenix vs broth dilution Bobenchik 2014 Vitek 2 vs broth dilution This study WGS vs combined disc diffusion / BD Phoenix
29 Previous phenotyping studies Study Comparison no of isolates Categorical agreement (%) ME rate (%) VME rate (%) Ligozzi 2002 Vitek 2 vs agar dilution Fahr 2003 BD Phoenix vs broth dilution plus meca PCR Nonhoff 2005 Vitek 2 vs agar dilution Carroll 2006 BD Phoenix vs agar dilution Giani 2012 BD Phoenix vs broth dilution Bobenchik 2014 Vitek 2 vs broth dilution This study WGS vs combined disc diffusion / BD Phoenix
30 Problems low frequency of resistance for some antimicrobials leading to inaccurate estimates of specificity Needs further testing with rare resistance determinants reflects resistance patterns in local population No VISA / daptomycin / linezolid resistance unknown / emerging resistance determinants
31 VIRULENCE
32 eta Virulence testing: presence / absence of known virulence genes etb etd lukpv.f lukpv.s lukm sea seb sec sed see seg enth sei sej seu selr sep tsst.1 chp sak scn virulence panel H H H H H H H H H H H H H H H H H H H H H
33 Identifying novel disease-associated mutations
34 Comparison of methods Manual Automated PCR In silico Platforms Disc diffusion, broth dilution Vitek, Phoenix, Microscan GeneXpert, IDI-MRSA, Nuclisens Easy-Q MiSeq, Ion Torrent Type of test Phenotypic Phenotypic Genotypic Genotypic No of samples Single Batch (approx 20) Single or batch Batch (currently 16) No of antimicrobials 4-6 per plate Approx Potentially unlimited Turnaround time hrs 4-24hrs 2-4hrs 27hrs
35 Current processing Resistance profile Speciation Rapid ID / MRSA PFGE for outbreaks Virulence profile, spa type
36 WGS workflow
37 Too expensive? Standard investigation WGS Culture Resistance testing Virulence testing Spa typing, PFGE Culture? Resistance profile Virulence profile Typing ~ 20 per isolate ~ 40 per isolate
38 Equipment High throughput Benchtop Palm top
39 Sequencing on your laptop?
40 Processing / bioinformatics
41 Mykrobe app: speciation and resistance prediction on a smartphone / tablet
42 Drag and drop raw data
43 Results in minutes
44
45 Turnaround times
46 Conclusions For S. aureus WGS has greater resolution than current standard typing for outbreak investigation WGS data reliably predicted antimicrobial resistance for majority of isolates tested, with overall error rates equivalent to current phenotyping tests Cost / turnaround time for WGS approaching those of standard typing
47 Enterobacteriacea, C. difficile Other organisms TB Viruses Fastidious organisms mykrobe.com
48 Acknowledgements Oxford Dr Tanya Golubchik Dr Richard Everitt John Finney Prof Tim Peto Prof Derrick Crook Prof Sarah Walker Marcus Morgan Dr David Eyre Mykrobe Phelim Bradley Dr Zam Iqbal Brighton Dr James Price Kevin Cole Dr John Paul Public Heath England Dr Bruno Pichon Prof Angela Kearns Prof Barry Cookson Outbreaks Dr Ginny Moore Dr Peter Wilson Dr James Nash
Whole genome sequencing & new strain typing methods in IPC. Lyn Gilbert ACIPC conference Hobart, November 2015
Whole genome sequencing & new strain typing methods in IPC Lyn Gilbert ACIPC conference Hobart, November 2015 Why do strain typing? Evolution, population genetics, geographic distribution 2 Why strain
Characterization of community and hospital Staphylococcus aureus isolates in Southampton, UK
Journal of Medical Microbiology (2010), 59, 1084 1088 DOI 10.1099/jmm.0.018986-0 Characterization of community and hospital Staphylococcus aureus isolates in Southampton, UK S. M. Green, 1 P. Marsh, 1
Exploring the evolution of MRSA with Whole Genome Sequencing
Exploring the evolution of MRSA with Whole Genome Sequencing PhD student: Zheng WANG Supervisor: Professor Margaret IP Department of Microbiology, CUHK Joint Graduate Seminar Department of Microbiology,
ESCMID Online Lecture by author
Molecular typing as a tool for the control of MDR and XDR organisms. Whole genome sequencing - already here? Martin Llewelyn Reader, Consultant Brighton and Sussex Medical School, UK m.j.llewelyn@bsms.ac.uk
Western Australian Methicillin-Resistant Staphylococcus aureus (MRSA) and Vancomycin Resistant Enterococcus (VRE) Epidemiology and Typing Report
Australian Collaborating Centre for Enterococcus and Staphylococcus Species (ACCESS) Typing and Research Microbiology and Infectious Diseases Department PathWest Laboratory Medicine-WA, Royal Perth Hospital
'The Role of the microbiology laboratory in the vision for a National Infection Service' Derrick Crook
'The Role of the microbiology laboratory in the vision for a National Infection Service' Derrick Crook 20th May 2016 Copyright of author NIS Programme Vision To develop a National Infection Service within
Received 31 January 2007/Returned for modification 29 March 2007/Accepted 12 June 2007
JOURNAL OF CLINICAL MICROBIOLOGY, Aug. 2007, p. 2554 2563 Vol. 45, No. 8 0095-1137/07/$08.00 0 doi:10.1128/jcm.00245-07 Copyright 2007, American Society for Microbiology. All Rights Reserved. The Emergence
6-8 November EICC, Edinburgh. Registration now open Abstract submission deadline: June 24th
6-8 November EICC, Edinburgh Registration now open Abstract submission deadline: June 24th An outbreak of prosthetic valve endocarditis Dr Tim Boswell Consultant Medical Microbiologist Nottingham Case
Laboratory CLSI M100-S18 update. Paul D. Fey, Ph.D. Associate Professor/Associate Director Josh Rowland, M.T. (ASCP) State Training Coordinator
Nebraska Public Health Laboratory 2008 CLSI M100-S18 update Paul D. Fey, Ph.D. Associate Professor/Associate Director Josh Rowland, M.T. (ASCP) State Training Coordinator Agenda Discuss 2008 M100- S18
Surveillance and outbreak investigation of Shiga toxin-producing Escherichia coli using whole genome sequencing- time for a change!
Surveillance and outbreak investigation of Shiga toxin-producing Escherichia coli using whole genome sequencing- time for a change! Dr Marie Anne Chattaway Deputy Head STEC Laboratory Gastrointestinal
Is Whole Genome Sequencing Really Replacing Traditional Microbiology?
Is Whole Genome Sequencing Really Replacing Traditional Microbiology? Peter Gerner-Smidt, MD, DSc Enteric Diseases Laboratory Branch InFORM II Phoenix, AZ, 18 November 2015 National Center for Emerging
Antimicrobial resistance and virulence genes in bacteria
Antimicrobial resistance and virulence genes in bacteria Johanne Ahrenfeldt PhD Student BSU course - November 2016 1 How to analyse WGS data part 2 an introduction to CGEs methods KmerFinder SpeciesFinder
Methicillin-Resistant Staphylococcus aureus (MRSA) S urveillance Report 2008 Background Methods
Methicillin-Resistant Staphylococcus aureus (MRSA) Surveillance Report 2008 Oregon Active Bacterial Core Surveillance (ABCs) Office of Disease Prevention & Epidemiology Oregon Department of Human Services
Breast and ovarian cancer in Serbia: the importance of mutation detection in hereditary predisposition genes using NGS
Breast and ovarian cancer in Serbia: the importance of mutation detection in hereditary predisposition genes using NGS dr sc. Ana Krivokuća Laboratory for molecular genetics Institute for Oncology and
Multi-clonal origin of macrolide-resistant Mycoplasma pneumoniae isolates. determined by multiple-locus variable-number tandem-repeat analysis
JCM Accepts, published online ahead of print on 30 May 2012 J. Clin. Microbiol. doi:10.1128/jcm.00678-12 Copyright 2012, American Society for Microbiology. All Rights Reserved. 1 2 Multi-clonal origin
Epidemiological and Genetic Diversity of Staphylococcus aureus Causing Bloodstream Infection in Shanghai,
Epidemiological and Genetic Diversity of Staphylococcus aureus Causing Bloodstream Infection in Shanghai, 2009-2011 Xu Chen 1., Wen-Kui Wang 2., Li-Zhong Han 1 *, Ying Liu 3, Hong Zhang 4, Jin Tang 5,
Staphylococcus aureus bacteraemia Cases in Denmark 2017
Staphylococcus aureus bacteraemia Cases in Denmark 2017 Statens Serum Institut Page 2 of 20 This report describes the laboratory and clinical characteristics of the 2,104 cases of Staphylococcus aureus
New Sequencing Technologies for Infectious Diseases
New Sequencing Technologies for Infectious Diseases Dr James Ussher Senior Lecturer, Microbiology and Immunology & Clinical Microbiologist, Southern Community Laboratories Antibiotic resistance: a 21
S. Wesley Long, MD, PhD
Basic Molecular Microbiology: A Practical Case-Based Approach S. Wesley Long, MD, PhD Center for Molecular and Translational Human Infectious Diseases Research Houston Methodist Research Institute September
In vitro assessment of dual drug combinations to inhibit growth of Neisseria gonorrhoeae
AAC Accepted Manuscript Posted Online 26 January 2015 Antimicrob. Agents Chemother. doi:10.1128/aac.04127-14 Copyright 2015, American Society for Microbiology. All Rights Reserved. 1 2 In vitro assessment
The UK s National Collection of Type Cultures: Answers to 21 st century public health questions
The UK s National Collection of Type Cultures: Answers to 21 st century public health questions Julie E. Russell Head of Culture Collections 28 th September 2016 Public Health England (PHE) Executive agency
Nosocomial transmission of community-associated methicillin-resistant Staphylococcus aureus in Danish Hospitals
J Antimicrob Chemother 2012; 67: 1775 1780 doi:10.1093/jac/dks125 Advance Access publication 20 April 2012 Nosocomial transmission of community-associated methicillin-resistant Staphylococcus aureus in
Whole genome sequencing
Downloaded from orbit.dtu.dk on: Dec 20, 2017 Whole genome sequencing Torpdahl, Mia; Löfström, Charlotta; Møller Nielsen, Eva Published in: Publication date: 2014 Document Version Publisher's PDF, also
A Norazah, S M Liew, A G M Kamel, Y T Koh, V K E Lim. O r i g i n a l A r t i c l e
Singapore Med J 2001 Vol 42(1) : 015-019 O r i g i n a l A r t i c l e DNA Fingerprinting of Methicillin-Resistant Staphylococcus Aureus by Pulsed-Field Gel Electrophoresis (PFGE): Comparison of Strains
Listeria whole-genome-sequencing EFSA Project. Anses Statens Serum Institut Public Health England University of Aberdeen
Listeria whole-genome-sequencing EFSA Project Anses Statens Serum Institut Public Health England University of Aberdeen Closing gaps for performing a risk assessment on Listeria monocytogenes in ready-to-eat
Staphylococcus aureus bacteraemia Cases in Denmark 2015
Staphylococcus aureus bacteraemia Cases in Denmark 2015 This report describes the laboratory and clinical characteristics of the 1,973 cases of Staphylococcus aureus bacteraemia (SAB) in Denmark in 2015.
A first molecular characterization of Listeria monocytogenes isolates circulating in humans from 2009 to 2014 in the Italian Veneto region
Short communication A first molecular characterization of Listeria monocytogenes isolates circulating in humans from 2009 to 2014 in the Italian Veneto region Cristiano Salata 1,2, Paola Lisotto 1, Caterina
Evaluation of MIA FORA NGS HLA test and software. Lisa Creary, PhD Department of Pathology Stanford Blood Center Research & Development Group
Evaluation of MIA FORA NGS HLA test and software Lisa Creary, PhD Department of Pathology Stanford Blood Center Research & Development Group Disclosure Alpha and Beta Studies Sirona Genomics Reagents,
2/10/2016. Evaluation of MIA FORA NGS HLA test and software. Disclosure. NGS-HLA typing requirements for the Stanford Blood Center
Evaluation of MIA FORA NGS HLA test and software Lisa Creary, PhD Department of Pathology Stanford Blood Center Research & Development Group Disclosure Alpha and Beta Studies Sirona Genomics Reagents,
Genomic epidemiology of Gram-negative pathogens: from Acinetobacter to E. coli. Professor Mark Pallen, University of Birmingham
Genomic epidemiology of Gram-negative pathogens: from Acinetobacter to E. coli Professor Mark Pallen, University of Birmingham The state we are in: diagnostic microbiology 21st Century problem, but 19th
What is new in EUCAST South Africa, May, Gunnar Kahlmeter EUCAST Technical Data Coordinator and Webmaster Sweden
What is new in EUCAST 2016 17 South Africa, May, 2016 Gunnar Kahlmeter EUCAST Technical Data Coordinator and Webmaster Sweden What is new in EUCAST 2016/17? New organisms with breakpoints (Addendum 2016)
Molecular typing insight on diversity and antimicrobial resistance of Campylobacter jejuni from Belgian chicken meat
Molecular typing insight on diversity and antimicrobial resistance of Campylobacter jejuni from Belgian chicken meat Ihab Habib Ghent University Department of Public Health and Food Safety. Contents: Molecular
Infectious Disease Case Studies: What s Lurking Out There?
Infectious Disease Case Studies: What s Lurking Out There? ASCLS-WI State Convention April 14, 2016 Case Study #2 Tim Monson, MS Microbiologist Supervisor Wisconsin State Lab of Hygiene timothy.monson@slh.wisc.edu
SUPPLEMENTAL TESTING. Tan Thean Yen
SUPPLEMETAL TESTG Tan Thean Yen To Supplement Definition: add as a supplement to what seems insufficient "supplement your diet" Why supplement? urrent methods don t work well Additional information provided
ANNUAL REPORT National Meticillin-Resistant Staphylococcus aureus Reference Laboratory
ANNUAL REPORT 2015 National Meticillin-Resistant Staphylococcus aureus Reference Laboratory INTRODUCTION... 2 ROLE OF THE LABORATORY... 3 SERVICES... 3 ISOLATES... 3 ROUTINE LABORATORY WORK... 6 REFERENCE
Methods for AST: diffusion or dilution? (pro s en con s)
7 th EURL-AR workshop 4-5 April 2013 DTU, Kgs. Lyngby, Denmark Methods for AST: diffusion or dilution? (pro s en con s) Kees Veldman Introduction Work as a senior technician at the Central Veterinary Institute
THE CARRIER STATE: METHICILLIN - RESISTANT STAPHYLOCOCCUS AUREUS A HOSPITAL STUDY "SCREENING OF HOSPITAL PERSONNEL" FOR NASAL CARRIAGE OF STAPH AUREUS
THE CARRIER STATE: METHICILLIN - RESISTANT STAPHYLOCOCCUS AUREUS A HOSPITAL STUDY "SCREENING OF HOSPITAL PERSONNEL" FOR NASAL CARRIAGE OF STAPH AUREUS Abstract Pages with reference to book, From 35 To
EpiSeq : A Next-Generation Sequencing Service for Infectious Disease Outbreak Management
EpiSeq : A Next-Generation Sequencing Service for Infectious Disease Outbreak Management CPTR 2016 Workshop Washington, DC M.Rodrigue April 7th, 2016 1 Healthcare Associated Infection A Global Burden KNOWING
Vibrio outbreak and surveillance: Maryland's collaborative approach
Vibrio outbreak and surveillance: Maryland's collaborative approach Catey Dominguez, Ph.D Developmental Scientist Maryland Department of Health Core Sequencing James Pettengill PhD Biostatistics and Bioinformatics
EDUCATIONAL COMMENTARY CLOSTRIDIUM DIFFICILE UPDATE
EDUCATIONAL COMMENTARY CLOSTRIDIUM DIFFICILE UPDATE Educational commentary is provided through our affiliation with the American Society for Clinical Pathology (ASCP). To obtain FREE CME/CMLE credits click
Pathogens in the twilight zone: Update on emerging disease issues with implications for the pork industry
Pathogens in the twilight zone: Update on emerging disease issues with implications for the pork industry Peter Davies BVSc, PhD University of Minnesota Introduction For an industry under increasing public
International Journal of Pharma and Bio Sciences
Research Article Microbiology International Journal of Pharma and Bio Sciences ISSN 0975-6299 DETECTION OF MRSA FROM NASAL CARRIER AMONG DIABETIC FOOT ULCER PATIENTS IN TERTIARY CARE HOSPITAL PUDUCHERRY
Deep-Sequencing of HIV-1
Deep-Sequencing of HIV-1 The quest for true variants Alexander Thielen, Martin Däumer 09.05.2015 Limitations of drug resistance testing by standard-sequencing Blood plasma RNA extraction RNA Reverse Transcription/
Molecular epidemiology and drug resistance mechanism of Salmonella species especially in S. Typhi strains isolated in Bangladesh
Molecular epidemiology and drug resistance mechanism of Salmonella species especially in S. Typhi strains isolated in Bangladesh Dr. Kaisar Ali Talukder Senior Scientist Icddr,b This presentation will
DIABETIC FOOT ULCERS AND Staphylococcus aureus : NEW INSIGHTS
DIABETIC FOOT ULCERS AND Staphylococcus aureus : NEW INSIGHTS Lyon 9 décembre 2010 Some important points Prevalence of diabetes mellitus in France: 3 millions (4.5% of population, 11,2% > 65 ans) In 2000,
New technologies reaching the clinic
New technologies reaching the clinic Martin Däumer May 31, 2018 Deep-sequencing Standard Sanger-sequencing...PQIYMDDHTRE... Ultra-deep-sequencing...PQIYMDDHTRE......PQIYMDDHTRE......PQIYVDDHTRE......PQIYMDDHTRE......PQIYMDDHTRE......PQIYMDDHTRE...
WGS Works! Shared Mission Different Roles APPLICATIONS SEQUENCING (WGS) Non-regulatory. Regulatory CDC. FDA and USDA. Peter Gerner-Smidt, MD ScD
PUBLIC HEALTH FOOD SAFETY APPLICATIONS FOR WHOLE GENOME SEQUENCING (WGS) Peter Gerner-Smidt, MD ScD Chief, Enteric Diseases Laboratory Branch 4 th Asia-Pacific International Food Safety Conference, Penang,
Lifting the lid on a difficile problem part 2 (Clinical) Evidence Based Practice. Problem in evolution (1) Problem in evolution (1) Interventions (2)
Lifting the lid on a difficile problem part (Clinical) Dr Philip T Mannion Consultant Microbiologist, Rhyl Evidence Based Practice Antibiotic prescribing guidance Isolation policy Hand hygiene (soap and
GBS Screening, diagnosis and clinically relevant resistance
GBS Screening, diagnosis and clinically relevant resistance Pierrette Melin National Reference Centre for GBS Medical Microbiology, University Hospital of Liege 1 Background Evolution of culture methods
OVERVIEW OF CURRENT IDENTIFICATION SYSTEMS AND DATABASES
OVERVIEW OF CURRENT IDENTIFICATION SYSTEMS AND DATABASES EVERY STEP OF THE WAY 1 EVERY STEP OF THE WAY MICROBIAL IDENTIFICATION METHODS DNA RNA Genotypic Sequencing of ribosomal RNA regions of bacteria
MIC = Many Inherent Challenges Sensititre MIC for Antimicrobial Susceptibility Testing of Mycobacterium tuberculosis complex
MIC = Many Inherent Challenges Sensititre MIC for Antimicrobial Susceptibility Testing of Mycobacterium tuberculosis complex Marie Claire Rowlinson, PhD D(ABMM) Florida Bureau of Public Health Laboratories
Shaun Yang, PhD, D(ABMM), MLS(ASCP) CM MB CM Assistant Professor of Pathology UNM Health Sciences Center Associate Director of Infectious Disease
Shaun Yang, PhD, D(ABMM), MLS(ASCP) CM MB CM Assistant Professor of Pathology UNM Health Sciences Center Associate Director of Infectious Disease Director of Molecular Infectious Disease TriCore Reference
Host genotypes, inflammatory response and outcome of TBM Vietnam
Host genotypes, inflammatory response and outcome of TBM Vietnam Nguyen T.T. Thuong Oxford University Clinical Research Unit Ho Chi Minh City, Vietnam Tuberculous Meningitis (TBM) Diagnosis remains difficult
The Challenge of Managing Staphylococcus aureus Bacteremia
The Challenge of Managing Staphylococcus aureus Bacteremia M A R G A R E T G R A Y B S P F C S H P C L I N I C A L P R A C T I C E M A N A G E R N O R T H / I D P H A R M A C I S T A L B E R T A H E A
The Annual Surveillance of Healthcare Associated Infection Report January - December 2010
The Annual Surveillance of Healthcare Associated Infection Report January - December 2010 Health Protection Scotland is a division of NHS National Services Scotland. Health Protection Scotland website:
Escherichia coli diagnostics
Escherichia coli diagnostics Workshop on Whole Genome Sequencing and Analysis, 19-21 Mar. 2018 Learning objective: After this lecture and exercise, you should be able to describe how the CGE methods for
Diagnosis of infectious diseases and confirmation of diagnosis. Molecular epidemiology of emerging/re-emerging pathogens
LA PREPARAZIONE E LA RISPOSTA ALLE EMERGENZE INFETTIVE Padova, 20 settembre 2012 Laboratory advanced technologies in the support of Public Health interventions in infectious disease emergencies Prof. Giorgio
Infectious Disease Diagnostics in the Geisinger Health System
10X Essentials Infectious Disease Diagnostics in the Geisinger Health System NEW: Rapid GeneXpert PCR NEW Test Codes: MRSAP, MRSA Screen PCR CDIFP, C. difficile/ Epi PCR EVP, Enterovirus PCR Specimens
Received 3 November 2010/Returned for modification 26 December 2010/Accepted 1 February 2011
JOURNAL OF CLINICAL MICROBIOLOGY, Apr. 2011, p. 1240 1244 Vol. 49, No. 4 0095-1137/11/$12.00 doi:10.1128/jcm.02220-10 Copyright 2011, American Society for Microbiology. All Rights Reserved. Genotypic and
The Curious Intersection of HIV and Staphylococcus aureus with a Focus on MRSA
The Curious Intersection of HIV and Staphylococcus aureus with a Focus on MRSA Franklin D. Lowy, MD Columbia University College of Physicians & Surgeons New York, NY Topics to Be Covered Background Some
Advance Your Genomic Research Using Targeted Resequencing with SeqCap EZ Library
Advance Your Genomic Research Using Targeted Resequencing with SeqCap EZ Library Marilou Wijdicks International Product Manager Research For Life Science Research Only. Not for Use in Diagnostic Procedures.
Rapid identification and resistance assessment: The future is mass spectrometry
Rapid identification and resistance assessment: The future is mass spectrometry Dr Sanmarié Schlebusch Director of Microbiology Mater Pathology Brisbane Outline Introduction Plug and play Pre-prep and
Spectrum of vancomycin and susceptibility testing
Spectrum of vancomycin and susceptibility testing Olivier Denis Service de Microbiologie Laboratoire de bactériologie Service de Microbiologie Hôpital Erasme Glycopeptides Vancomycin 1958 < Amycolatopsis
Advances in Gastrointestinal Pathogen Detection
Advances in Gastrointestinal Pathogen Detection Erin McElvania TeKippe, Ph.D., D(ABMM) Director of Clinical Microbiology Children s Health System, Assistant Professor of Pathology and Pediatrics UT Southwestern
Dr Rick Tearle Senior Applications Specialist, EMEA Complete Genomics Complete Genomics, Inc.
Dr Rick Tearle Senior Applications Specialist, EMEA Complete Genomics Topics Overview of Data Processing Pipeline Overview of Data Files 2 DNA Nano-Ball (DNB) Read Structure Genome : acgtacatgcattcacacatgcttagctatctctcgccag
Discussion points CLSI M100 S19 Update. #1 format of tables has changed. #2 non susceptible category
Discussion points 2009 CLSI M100 S19 Update Nebraska Public Health Laboratory Changes most important to routine antimicrobial susceptibility testing. Documents available Janet Hindler discussion slide
EUROTRAVNET SCIENCE WATCH NOVEMBER-DECEMBER 2009
www.eurotravnet.eu E u r o p e a n T r a v e l a n d T r o p i c a l M e d i c i n e N e t w o r k o f t h e I n t e r n a t i o n a l S o c i e t y o f T r a v e l M e d i c i n e E u r o p e a n C e
Frequency of Nasal Carriage of Staphylococcus Aureus and Its Antimicrobial Resistance Pattern in Patients on Hemodialysis
Dialysis Frequency of Nasal Carriage of Staphylococcus Aureus and Its Antimicrobial Resistance Pattern in Patients on Hemodialysis Roya Ghasemian, 1 Narges Najafi, 1 Atieh Makhlough, 2 Mohammad Khademloo
Adenium Biotech. Management: - Peter Nordkild, MD, CEO, ex Novo Nordisk, Ferring, Egalet - Søren Neve, PhD, project director, ex Lundbeck, Novozymes
Adenium Biotech Management: - Peter Nordkild, MD, CEO, ex Novo Nordisk, Ferring, Egalet - Søren Neve, PhD, project director, ex Lundbeck, Novozymes Board of Directors: - Stephan Christgau, PhD, chairman,
A genomic dissection of travel associated ESBL producing Salmonella Typhi originating from the Philippines
A genomic dissection of travel associated ESBL producing Salmonella Typhi originating from the Philippines A one-off occurrence or threat to the effective treatment of typhoid fever? Rene S. Hendriksen,
Assessing Laboratory Performance for Next Generation Sequencing Based Detection of Germline Variants through Proficiency Testing
Assessing Laboratory Performance for Next Generation Sequencing Based Detection of Germline Variants through Proficiency Testing Karl V. Voelkerding, MD Professor of Pathology University of Utah Medical
Supplementary Appendix
Supplementary Appendix This appendix has been provided by the authors to give readers additional information about their work. Supplement to: Scarborough M, Gordon SB, Whitty CJM, et al. Corticosteroids
Received 1 August 2011; returned 30 August 2011; revised 21 October 2011; accepted 1 November 2011
J Antimicrob Chemother 2012; 67: 330 334 doi:10.1093/jac/dkr497 Advance Access publication 28 November 2011 High prevalence of spa types associated with the clonal lineage CC398 among tetracycline-resistant
Sensitivity of Surveillance Testing for Multidrug-Resistant Gram-Negative Bacteria in the
JCM Accepts, published online ahead of print on 20 August 2014 J. Clin. Microbiol. doi:10.1128/jcm.02369-14 Copyright 2014, American Society for Microbiology. All Rights Reserved. 1 2 Sensitivity of Surveillance
Analysis of phenotypic variants of the serogroup C ET-15 clone of Neisseria meningitidis by pulsed-field gel electrophoresis.
JCM Accepts, published online ahead of print on 9 May 2007 J. Clin. Microbiol. doi:10.1128/jcm.00908-07 Copyright 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study Simon R arris*, Edward J P Cartwright*, M Estée Török, Matthew T G olden, Nicholas
2.3 Invasive Group A Streptococcal Disease
2.3 Invasive Group A Streptococcal Disease Summary Total number of cases, 2015 = 107 Crude incidence rate, 2015 = 2.3 per 100,000 population Notifications In 2015, 107 cases of invasive group A streptococcal
NGS in neurodegenerative disorders - our experience
Neurology Clinic, Clinical Center of Serbia Faculty of Medicine, University of Belgrade Belgrade, Serbia NGS in neurodegenerative disorders - our experience Marija Branković, MSc Belgrade, 2018 Next Generation
Analysis of Massively Parallel Sequencing Data Application of Illumina Sequencing to the Genetics of Human Cancers
Analysis of Massively Parallel Sequencing Data Application of Illumina Sequencing to the Genetics of Human Cancers Gordon Blackshields Senior Bioinformatician Source BioScience 1 To Cancer Genetics Studies
Title: Comparison between bacteremia caused by carbapenem resistant Acinetobacter baumannii and Acinetobacter nosocomialis
Author's response to reviews Title: Comparison between bacteremia caused by carbapenem resistant Acinetobacter baumannii and Acinetobacter nosocomialis Authors: Ya-Sung Yang (ysyoung4097@gmail.com) Yi-Tzu
M E D I C A L L A B O R A T O R Y
M E D I C A L L A B O R A T O R Y E V A L U A T I O N PARTICIPANT SUMMARY 2 0 1 7 Microbiology 2017 MLE-M1 Total Commitment to Education and Service Provided by ACP, Inc. Evaluation Criteria... 2 Microbiology
Received 30 March 2005; returned 16 June 2005; revised 8 September 2005; accepted 12 September 2005
Journal of Antimicrobial Chemotherapy (2005) 56, 1047 1052 doi:10.1093/jac/dki362 Advance Access publication 20 October 2005 Evaluation of PPI-0903M (T91825), a novel cephalosporin: bactericidal activity,
A Comprehensive Study of TP53 Mutations in Chronic Lymphocytic Leukemia: Analysis of 1,287 Diagnostic CLL Samples
A Comprehensive Study of TP53 Mutations in Chronic Lymphocytic Leukemia: Analysis of 1,287 Diagnostic CLL Samples Sona Pekova, MD., PhD. Chambon Ltd., Laboratory for molecular diagnostics, Prague, Czech
Staph aureus: New nasties and how to tackle them!
Staph aureus: New nasties and how to tackle them! Brenda Dale Health Protection Unit, Dartington Adam Brown Doncaster and Bassetlaw Hospitals NHS Foundation Trust Hosted by Maria Bennallick maria@webbertraining.com
CHARACTERISATION OF STAPHYLOCOCCUS AUREUS BLOODSTREAM ISOLATES FROM GAUTENG AND WESTERN CAPE PROVINCES, SOUTH AFRICA, 2016 AND 2017
CHARACTERISATION OF STAPHYLOCOCCUS AUREUS BLOODSTREAM ISOLATES FROM GAUTENG AND WESTERN CAPE PROVINCES, SOUTH AFRICA, 2016 AND 2017 Ashika Singh-Moodley 1,2 and Olga Perovic 1,2 1 Centre for Healthcare-associated
PATIENT DEMOGRAPHICS. Surname. Given name. Pacific Islander (non-maori) ADMISSION DETAILS
Reviewer / hospital Date review started PATIENT DEMOGRAPHICS MRN DOB Sex Patient sticky label if available, else enter details here Surname Post-code Given name Australian Aborigine / TSI Middle Eastern
Mutation Detection and CNV Analysis for Illumina Sequencing data from HaloPlex Target Enrichment Panels using NextGENe Software for Clinical Research
Mutation Detection and CNV Analysis for Illumina Sequencing data from HaloPlex Target Enrichment Panels using NextGENe Software for Clinical Research Application Note Authors John McGuigan, Megan Manion,
A Guideline for the Molecular Typing of Canadian Epidemic Methicillin-Resistant Staphylococcus aureus Using spa Typing.
A Guideline for the Molecular Typing of Canadian Epidemic Methicillin-Resistant Staphylococcus aureus Using spa Typing. George R. Golding National Microbiology Laboratory Winnipeg, Manitoba AMMI-CACMID
Key words: superantigen, Staphylococcus aureus, TSST-1, enterotoxin, neonatal exanthematous disease
Key words: superantigen, Staphylococcus aureus, TSST-1, enterotoxin, neonatal exanthematous disease Fig. 1 Clinical course and laboratory findings in a typical case of new neonatal exanthematous disease
Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel meca homologue mecc
Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel meca homologue mecc Ewan M. Harrison, Gavin K. Paterson, Matthew T.G. Holden, Jesper Larsen, Marc Stegger, Anders
10/4/16. mcr-1. Emerging Resistance Updates. Objectives. National Center for Emerging and Zoonotic Infectious Diseases. Alex Kallen, MD, MPH, FACP
National Center for Emerging and Zoonotic Infectious Diseases Emerging Resistance Updates Alex Kallen, MD, MPH, FACP Lead Antimicrobial Resistance and Emerging Pathogens Team Prevention and Response Branch
Original Article Clinical Microbiology INTRODUCTION
Original Article Clinical Microbiology Ann Lab Med 2019;39:158-166 https://doi.org/10.3343/alm.2019.39.2.158 ISSN 2234-3806 eissn 2234-3814 Impact of Community-Onset Methicillin-Resistant Staphylococcus
APPENDIX: NATIONAL SURVEILLANCE DATA AND TRENDS
2008 Annual Surveillance Report Notifiable and Other s in New Zealand 49 APPENDIX: NATIONAL SURVEILLANCE DATA AND TRENDS COMPARISON OF NOTIFIABLE DISEASE CASES AND RATES FOR 2007 AND 2008 Table 37. Number
New York State Health Department's experience with implementing Whole Genome Cluster Analysis for Salmonella outbreak investigations
New York State Health Department's experience with implementing Whole Genome Cluster Analysis for Salmonella outbreak investigations William Wolfgang Wadsworth Center NYSDOH InForm 2013 11/20/13 Current
Abstract. Optimization strategy of Copy Number Variant calling using Multiplicom solutions APPLICATION NOTE. Introduction
Optimization strategy of Copy Number Variant calling using Multiplicom solutions Michael Vyverman, PhD; Laura Standaert, PhD and Wouter Bossuyt, PhD Abstract Copy number variations (CNVs) represent a significant
T&T WG. June 2018 San Diego, CA
T&T WG June 2018 San Diego, CA Co-Chairs Jana Swenson Shelley Campeau Secretary Carey-Ann Burnham Members Andrea Ferrell Janet Hindler Melissa Jones Peggy Kohner Dyan Luper Linda Mann Susan Munro Barth
Örebro University Hospital
Örebro University Hospital Department of Laboratory Medicine Susanne Jacobsson Date: 2015-02-18 Page 1 (8) Neisseria meningitidis 2014 Annual report concerning serogroup, genosubtype and antibiotic susceptibility
Consortium partners key persons
Consortium partners key persons Statens Serum Institut: Eva Møller Nielsen, project leader Jonas Larsson Kristoffer Kiil Public Health England: Tim Dallman Kathie Grant Anais Painset Corinne Amar Anses:
ANNUAL REPORT National Meticillin-Resistant Staphylococcus aureus Reference Laboratory
ANNUAL REPORT 2016 National Meticillin-Resistant Staphylococcus aureus Reference Laboratory CONTACT DETAILS National MRSA Reference Laboratory St. James s Hospital, James s Street, Dublin 8 Ireland Tel:
Performance Characteristics BRCA MASTR Plus Dx
Performance Characteristics BRCA MASTR Plus Dx with drmid Dx for Illumina NGS systems Manufacturer Multiplicom N.V. Galileïlaan 18 2845 Niel Belgium Table of Contents 1. Workflow... 4 2. Performance Characteristics