Live Tweets from Applying Advanced Molecular Techniques to Healthcare Infection Days 1-2
25 Oct 2011Here is a crude file dump of my tweets from this Wellcome Trust retreat. You will have to read them in reverse order and ignore the extraneous material, but I thought it was worth getting them archived and available here, together with relevant links
second attempt to upload slide illustrating #genomicfundamentalism featuring Lord Stanley of Bitterroot and Lady S twitpic.com/758rwq
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#AAMTHI NXL104 works against KPC-producing pathogens, in combination with other beta-lactams, even in mice Fosfomycin & ACHN-490 also active
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#AAMTHI Crystal structure of KPC-2: insights into carbapenemase activity in class A beta ncbi.nlm.nih.gov/pubmed/17441734
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#AAMTHI Robert Bonomo now talking about KPC class A beta-lactamases eats through all beta-lactams on Tn4401 novel inhibitor found
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@
@WvSchaik that's what he said, using an appropriate depth of coverage
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#AAMTHI Signing off now as will be speaking soon.
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#AAMTHI comparison with commensal OG1RF then sequenced 16 deepest nodes in E. faecalis all human disease strains >3Mbp
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#AAMTHI Took TIGR long tome to sequence first enterococcal genome v583 genome MDR strain 3.2 Mbp, three plasmids 150kB PAI 7 phages 1in core
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#AAMTHI estimated 100 bn tons of animal biomass in world; enterococci probably in most, but only know human lineage well; origins 500 Mya
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#AAMTHI enterococci also in most vertebrates and in flies Cox and Gilmore study microbiome of Drosophila ncbi.nlm.nih.gov/pubmed/17220307
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#AAMTHI insects have enterococci, including Drosophila emerged as VRE in mid 1980s 11 cases of Van R transfer into MRSA
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#AAMTHI Mike Gilmore from Harvard about to speak on MDR enterococci Q. 1 What are enterococci Q2. How get from commensal to MDR strains
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Genomic Fundamentalism! Slide from talk to explain my view of use of genome sequencing in clinical microbiology twitpic.com/756j6v
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Genomic Fundamentalism! Slide from my talk to explain my view of use of genome sequencing in clinical micro :-) twitpic.com/756j6v
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#AAMTHI 20% of SNPS in final tree captures S. african clade, but many others mixed up; global movement of strains; 1970 origin of clone
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#AAMTHI 250 genomes from ST81 First tree looks wrong; because ignores recombination; SNPs not randomly distributed. This is old stuff.
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#AAMTHI 38 of 4.5K SNPs occur independently on different branches; 11 are drug resistant Now moving to S. pneumoniae ST81 (Spanish-23F)
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#AAMTHI Parkhill says mutation rate in S. aureus 3.3. x 10-6 per site per year dN/dS = 0.69 Most changes neutral; hard to detect selection
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#AAMTHI Parkhill claiming zero false-positive SNPs in bacterial genomes sequenced by Illumina. Describing S. aureus ST329 tree
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#AAMTHI Julian Parkhill now talking on use of HTS for studying transmission chains and bacterial evolution. £36 per genome via Illumina
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#AAMTHI Stan Falkow objecting to inability of MALDI-TOF to distinguishing S. mitis and S. pneumoniae; Brian Spratt saying species overlap
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#AAMTHI MALDI-TOF can be used as epidemiological typing tool; uncertain how good it will be; likely to be crude. Not as good as genomics.
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#AAMTHI MALDI-TOF can detect beta-lactamase production in E. coli by looking for cleavage in 3 hour incubation; potential sensitivity test
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#AAMTHI 17 cases where early alterations made to patient therapy or infection control ?savings via de-escalation of therapy?
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#AAMTHI no good for mix of S. aureus and CNS. MALDI-TOF much quicker than e.g. API But does it alter patient management? Asked 4 clinicians
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#AAMTHI need 10^6 or !0^7 cfu for MALDI-TOF; cannot use scanty growth. Wenzel et al showed can detect two organisms fairly accurately
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#AAMTHI discordant result with Ps. hibiscola identified as S. maltophilia, but actually synonyms; no major errors in their study
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#AAMTHI blood culture MALDI-TOF study at Addenbrookes; 100 bottles; 95% MALDI-TOF ID at species; problems if low biomass, mixed cultures
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#AAMTHI cheap and easy technique; thin smear of colonies or BC on to MALDI target; relies on MALDI Biotyper data interpretation pipeline.
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#AAMTHI Matt Ellington talking on MALDI-TOF MS in clinical lab.Smash it & see technique. Robust ID depends on high-copy proteins (ribosomal)
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#AAMTHI Simple amplification-based assay: a nucleic aci... [J Infect Dis. 2010] - PubMed - NCBI ncbi.nlm.nih.gov/pubmed/20225949
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#AAMTHI Also avoids EtOH in preps and all reagents stable at 50°C! One closed disposable system to avoid PCR carryover.
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#AAMTHI trying to squash hoods and other lab set-up into simple "pregnancy test" for HIV, HBV etc. Need simple sample preps; uses cartridges
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#AAMTHI more on Helen Lee and her work here haem.cam.ac.uk/ddu/ wellcome.ac.uk/Funding/Techno… Also has SAMBA (Simple AMplification-Based Assay)
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#AAMTHI jcm.asm.org/cgi/reprint/JC… Chlamydia test also developed. Urine collector as men who cannot aim and catch their own urine ;-)
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#AAMTHI has been avoiding venture capitalists! No FDA-approved rapid HBsAg test among WHO-recommended Developed Signal Amplificn System
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#AAMTHI Lee et al developing "Diagnostics for the Real World Ltd" idealistic goal FDA approved, 1000s of pages needed; raised $60m fr WT etc
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#AAMTHI many labs have no stable electricity, distilled h20, tap water, fridges. No incentive for development of rapid diagnostics here.
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#AAMTHI Helen Lee from U of Cambridge talking about diagnostic microbiology in Kumasi Ghana. Bloodbank has $1.5 per unit for diagnostics
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#AAMTHI control dispersal of spores ncbi.nlm.nih.gov/pubmed/20415567 Donskey shows fecal cloud cartoon closes with Dylan song cid.oxfordjournals.org/content/50/11/…
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#AAMTHI routine cleaning of skin works ncbi.nlm.nih.gov/pubmed/21460475 10% of patients asympto shedders; only 10% of them are shedding
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#AAMTHI time from diarrhoea to result 2.6 days therefore pts to be isolated when test ordered PCR on rectal swabs may be quicker than stool
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#AAMTHI what if still failing to control CDI? special approaches: preemptive isolation; bleach all rooms etc ncbi.nlm.nih.gov/pubmed/19929371
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#AAMTHI But improvements in cleaning don't improve CDI rates. 30% of thoroughly cleaned rooms still C diff +ve Need better methods to assess
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#AAMTHI monitoring of cleaning observation ATP bioluminescence flourescent maerkers (DAZO) ncbi.nlm.nih.gov/pubmed/18851687
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#AAMTHI Contaminated call button with VRE C diff ncbi.nlm.nih.gov/pubmed/17584935 ncbi.nlm.nih.gov/pmc/?term=1758… Research cleaning >> housekeeping bleach works!
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#AAMTHI why outbreak? used usual procedures ncbi.nlm.nih.gov/pubmed/18840091 Hand contamination nice picture!! ncbi.nlm.nih.gov/pubmed/18181742 cid.oxfordjournals.org/content/46/3/4…
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#AAMTHI CDI outbreak at Cleveland VA Medical Centre 2002-2004 ncbi.nlm.nih.gov/pubmed/20409374
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#AAMTHI Curtis Donskey from Cleveland Ohio now talking on Infection Control of C. difficile
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#AAMTHI MRSA colonisation rates now down to early 1990s levels in Addenbrookes; few dozen at any one time
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#AAMTHI Nick Ward closes with statement that commisioners will no longer pay for HCAI as never events en.wikipedia.org/wiki/Never_eve…
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#AAMTHI hospital-acquired MSSA rates down too in Addenbrookes and C diff!
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454Sequencing 454 Life Sciences
by
Beyond publishing papers: Why Social Media matters for scientists to spread their work | Scientific American cot.ag/nrxblN
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#AAMTHI what made the difference to MRSA rates? Central venous access team according to Nick Ward EMRSA-16 down ncbi.nlm.nih.gov/pubmed/%202003…
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#AAMTHI MRSA bacteraemia rates declined from 2006 onwards in Cambridge and nationwide. 19 per month in 2003; 2 per year so far!
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#AAMTHI mandatory MRSA bacteraemia surveillance scheme introduced Daily Mail cartoon MRSA bacteraemia as tip of iceberg Reid said halve it!
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#AAMTHI Lord Soulsby of Swaffham Prior report NAO report 2000 Lack of grip on UK MRSA media coverage
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#AAMTHI rivm.nl/earss UK came out as MRSA bad boy in EARSS report 2003; but could be ascertainment bias
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#AAMTHI bed occupancy rates much higher in UK than elsewhere (e.g. Netherlands), now ~90%
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#AAMTHI MRSA sky rocketed at Addenbrookes 1997-2003; 10% of hospital population MRSA positive!!
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#AAMTHI Hospital chief exec Sir John told by DoH not to close wards; as aside idyllic description of retired dons at Trinity college!
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#AAMTHI Nick Ward 1994 large outbreak of EMRSA-15; 30 pts; inability to cope; bottom of waiting list league table for surgery!
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#AAMTHI EMRSA-3, -15, -16 all seen in Cambridge Biomedical campus First MRSA in 1990. Usual isolation in neg pressure/ward closure/clearance
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#AAMTHI Nick Brown now talking about MRSA in Addenbrookes; loss of control of MRSA and then regained control ncbi.nlm.nih.gov/pubmed/9893757
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#AAMTHI Livermore pointing out that trip from Sweden to India led to long term colonisation with ESBL producers in many travellers
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#AAMTHI CDC guy pointed out that we controlled SARS, so should be possible for HCAI MDR bacteria; has been done in Israel. Call for openness
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#AAMTHI Q & A discussion over legality/morality of quarantine even if rapid accurate diagnosis
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#AAMTHI Opportunities with new methods MALDI-TOF; 454; MiSeq Low looking for a bioinformatician in sunny Toronto! microbiology.mtsinai.on.ca/staff/dlow.sht…
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#AAMTHI One Indian patient had NDM1 in three different enterobacterial species in three different sites!!
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#AAMTHI Low advocates use of 454 sequencing for carbapenemase characterisation! Livermore playing Cassandra again on Oxa-48!
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#AAMTHI use battery of inhibitors, but tricky and no good for OXA-48, which is emerging problem ncbi.nlm.nih.gov/pubmed?term=ox…
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#AAMTHI carbapenenmases new threat; Hodge test in lab. works most of time, but not always, e..g. NDM1 ncbi.nlm.nih.gov/pubmed/21624908
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#AAMTHI outbreak in Toronto and elsewhere in Canada with vanA PCR+ve van sensitive clone; truncated operon; why so spreadible? No worry?
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#AAMTHI VRE big deal; complex-17 ampR and hosp-associated; carries VanR gene cluster, D-lactate in PG
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#AAMTHI 2005 resp infection outbreak; "mystery virus"; turned out to be legionellosis; mol methods would have speeded up response
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#AAMTHI Low says mol methods maybe too sensitive and too expensive. Toronto labelled plague city in 2003 SARS outbreak. Good for funding!
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#AAMTHI Low says mol methods now routine & driven by cost impacts. e.g. cepheidinternational.com/tests-and-reag… But means no isolates recovered!
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#AAMTHI Donald Low from Toronto speaking on Healthcare Infections Challenges in Diagnostic lab SARS led to creation of Public Health Ontario
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#AAMTHI Ontario government spending $4m on hand washing in hospitals. Hard to spend that much money!
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#AAMTHI Livermore points out Canadian MRSA rates not yet declining like in US/UK, but absolute rates have always been lower.
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#AAMTHI ~20 NDM isolates so far in Canada. Mulvey questions definitions in genomic epidemiology and is somewhat skeptical
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#AAMTHI rise of community-acquired MRSA in Canada but epidemiology unlike USA. ncbi.nlm.nih.gov/pubmed/20237572
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#AAMTHI Almost no speakers keeping to time with 30 minute talks; most having to skip slides! Why can't intelligent people get this right :-(
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#AAMTHI 90% of CDI treated with Mtz not vanc in Canada NAP1 pulsotype predominates since 2004 More on Canadian CDI here ncbi.nlm.nih.gov/pubmed/19191641
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#AAMTHI Apparent 4X rise in incidence of C. diff infection in Canada 1997-2004 Ribotype O27 to blame. But came down after that.
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#AAMTHI Mulvery describing massive rise in colonisation rates with VRE since 2006; 87% vanA E. faecium Hasn't bothered to type isolates!
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#AAMTHI Mulvey describing The Canadian Nosocomial Infection Surveillance Program phac-aspc.gc.ca/nois-sinp/surv…
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#AAMTHI Mike Mulvey on antibiotic resistance in Canada. 50% of ESBL E. coli there are ST131 CTX-M-15 ncbi.nlm.nih.gov/pubmed?term=ST…
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#AAMTHI unexplained decline of MRSA infection rates in several parts of world, UK and USA and Asia
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#AAMTHI David Livermore bemoaning lack of microbiology on most infections & irresistible rise of ESBL-producing E. coli ncbi.nlm.nih.gov/pubmed/21303394
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#AAMTHI Ed Kuijper talk on C. difficile covered C. difficile in pigs, which was new to me. ncbi.nlm.nih.gov/pubmed?term=ku…
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#AAMTHI Sharon Peacock gave storming talk showing how genomics can recover transmission chains and reveal heterogeneous infns with S. aureus
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At WT retreat on applying advanced mol techniques to Healthcare infections (#AAMTHI) at Hinxton. Few surprises so far.
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