Research Fellow in Microbial Bioinformatics

26 Nov 2011

Research Fellow

Microbial Bioinformatics

University of Birmingham - School of Biosciences

Live Tweets from Applying Advanced Molecular Techniques to Healthcare Infection Day 3

26 Oct 2011

Here is a crude file dump of my live tweets from the third day of the Applying Advanced Molecular Techniques to Healthcare Infection. Same caveats as before: apologies for extraneous material, but something better than nothing.

Also have created newspaper of links from the meeting here: http://paper.li/mjpallen/1319610603

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#AAMTHI am signing off live tweeting and will start 3 hour drive home, skipping conference dinner; thanks for listening!

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#AAMTHI C. diff can be recovered from estuaries; same ribotypes as in human disease!

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#AAMTHI meeting closing down with last Q&A; arguing origins of Pittsburg/Montreal lineages; Lord Stan asking where C diff originated

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#AAMTHI Lawley gently dissing old-school typing methods but falling short of declaring genomic fundamentalism

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#AAMTHI in 027 lineage, 2/3 recurrences are relapses with same genotypes; 1/3 are reinfections. But even if same genotype maybe reinfection?

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#AAMTHI spread of montreal strain via Birmingham to Liverpool to Belfast incidence of 027 decreasing in Liverpool spatiotemporal clustering

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#AAMTHI phylogenomics of 027 can be reconstructed from start in Pittsburg; Montreal lineage v. spreadable; ≥4 introductions into UK

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#AAMTHI 027 strains from 19 countries sequenced pnas.org/content/107/16…

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#AAMTHI using 454 Illumina and optical mapping to do C diff genomic epidemiology via SNP trees

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#AAMTHI spores are immunogenic; spore specific abies available Wilcox report hpa.org.uk/webc/HPAwebFil…

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#AAMTHI C. diff spores very resistant and transmissible in animal house ID50 5 spores per cm2 in mice

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#AAMTHI EM images from ncbi.nlm.nih.gov/pubmed/20624955 "C. diff spores are beautiful"

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#AAMTHI Lawley now on spread of 027 strain; Canada, UK, now Australia incidence down now in UK

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#AAMTHI drinking from a fire hose? exciting stuff to come, but apparent ratio of unpublished to published work in Oxford on C. diff worrying

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#AAMTHI > 1 stool taken in 377 pts 79 cases showing mixed infections by MLST on serial samples around 20%! 2.6 new SNPs pa in trusted genome

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#AAMTHI 1500 isolates genome-sequenced good quality calls on >80% of genome error rate 1 SNP per 100 genomes

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#AAMTHI ST1 (ribotype 027) huge potential network Asked Q how many cases plausibly gained from ward contact 90% in first 2 weeks

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#AAMTHI constructed network of contacts in space/time five cases of ST63 If allow incubation period of 8 weeks get two clusters

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#AAMTHI 69 MLST types found in 984 cases at least 69 different outbreaks some rare some common clustering in time = cross infection??

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#AAMTHI 1280 C. diff cultured and MLSTed modal patients come in contact with ~300 patients within one year of C. diff

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#AAMTHI all diarrhoeal sttols tested for C diff All typed by MLST/ribotyping Research database with ethics approval 2m patients

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#AAMTHI difficult to estimate transmission parameters started with epidemiology hypothesis is that most CDI acquired by cross infection

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#AAMTHI Tim Peto on Modernising Molecular Microbiology C. difficile experience in Oxfordshire Radcliffe does tests for CDI

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#AAMTHI Atmar et al 2011 under review norovirus vaccine shows promise

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#AAMTHI ncbi.nlm.nih.gov/pubmed/21801639 Novel GII.12 norovirus strain, United States, 2009-2010

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#AAMTHI ncbi.nlm.nih.gov/pubmed/21801614 Novel surveillance network for norovirus gastroenteritis outbreaks, United States

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rnomics Fabrice Leclerc

RT @: #AAMTHI each animal has own calicivirus; reservoir for norovirus is probably... bit.ly/tZcTdE #rnomics-bioscience @MyEN

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#AAMTHI norovirus is number 1 in GI & foodborne illness 800 deaths in USA per year winter peak infectious dose 18 virions 10^10/g in stool!!

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#AAMTHI each animal has own calicivirus; reservoir for norovirus is probably humans no cell culture ~7kb +ssRNA virus

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#AAMTHI norovirus first known outbreaks probably in 1920-30s Norwalk Ohio outbreak 1972 en.wikipedia.org/wiki/Norovirus 1990 genome sequenced RT-PCR

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#AAMTHI Jan Vinje on norovirus Cruise ships ask crew to vomit over the side, not in toilets!

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#AAMTHI use SNP thresholds rather than precise numbers of SNPs Ben Cooper clearly clever enough to come work at @unibirmingham :-)

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#AAMTHI better results with sequence data; 100 SNPs; most connections make sense in light of epidemiology but some don't; need to combine

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#AAMTHI who infects who with or without sequence data ncbi.nlm.nih.gov/pubmed/18394654 Generation interval contraction and epidemic data analysis

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#AAMTHI estimates of daily per host transmission probability possible applied to WGS SNPs ! patient has cloud of strains 50 SNPs apart

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#AAMTHI ncbi.nlm.nih.gov/pubmed/21488764 Veterans Affairs initiative to prevent methicillin-resistant Staphylococcus aureus infections

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#AAMTHI ncbi.nlm.nih.gov/pubmed/21980062 Screening, isolation, decolonisation strategies in the control of MRSA in ICU: cost effectiveness evaluation

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#AAMTHI Cooper cites An augmented data method for the analysis of nosocomial infection data ncbi.nlm.nih.gov/pubmed/18635575

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#AAMTHI Ben Cooper talking about S. aureus transmission & models in Thailand cites ncbi.nlm.nih.gov/pubmed/19197054

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#AAMTHI After a morning talk about faecal microbiome transplants they serve this for lunch! twitpic.com/75lqjr

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#AAMTHI at last lunch; conclusion so far is that genomic epidemiology & culture-independent diagnosis hot topics, but lots of opportunities

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#AAMTHI mtz triggers VRE dominance; dominance in bowel microbiota predicts type of bacteraemia; VRE vs proteobacteria

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#AAMTHI aha, now some work on 16S V1-3 via 454 ncbi.nlm.nih.gov/pmc/articles/P… VRE domination of intestinal microbiota enabled by antibiotic treatment

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#AAMTHI S. viridans was problem then vanco prophylaxis led to VRE surge; surge in GNRs after quinolone prophylaxis stopped in 2010

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#AAMTHI Bactaermia common in pre-engraftment ≤10 days post-transplant; usually GI organisms VRE, Kleb, E coli, Enterobact etc VRE ++ > 2003

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#AAMTHI choice between deleting T-cells or not; if done, means less GVH, more odd opportunistic infections

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#AAMTHI now talk on allogeneic haematopoietic stem cell transplantation (allo-HSCT) and infection

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#AAMTHI ir.viropharma.com/releasedetail.… ViroPharma Initiates Phase 2 Study of VP 20621 for Prevention of Recurrence of CDI

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#AAMTHI old stuff being presented ncbi.nlm.nih.gov/pubmed/12447764 Colonization for the prevention of Clostridium difficile disease in hamsters

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#AAMTHI I find live tweeting is the only way to keep awake and alert at scientific meetings; cures ADHD and ensures CPD

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#AAMTHI ncbi.nlm.nih.gov/pubmed/19303570 New approach to the management of C. difficile infection: colonisation with non-toxigenic C. difficile...

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#AAMTHI Dale Gerding on use of non-toxigenic C diff. Looks like microbiological version of E. O. Wilson :-)

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#AAMTHI more on autism and microbiome udaan.org/drugs/vancocin… ncbi.nlm.nih.gov/pubmed/2152471… I remain skeptical...

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#AAMTHI now Louie claiming you can claiming autism by vancomycin or faecal microbiome transplant !?! Starting to get cranky!

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#AAMTHI Bacteriotherapy for chronic relapsing Clostridium difficile diarrhoea in six patients ncbi.nlm.nih.gov/pubmed/2566734 not much progress since

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#AAMTHI anecdotal stuff on which taxa change after faecal transplant; no consistent picture

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#AAMTHI 79/82 cases of CDI arrested after faecal transplant; low-level microbial ecology studies have been carried out, showing shifts

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#AAMTHI Louie explored various protocols, moved from enemas to oral capsule delivery of microbiome ncbi.nlm.nih.gov/pmc/articles/P…

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#AAMTHI The FECAL trial, Fecal therapy to Eliminate Clostridium difficile Associated Longstanding diarrhoea. trialregister.nl/trialreg/admin…

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#AAMTHI Treating Clostridium difficile Infection With Fecal Microbiota Transplantation ncbi.nlm.nih.gov/pubmed/21871249

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#AAMTHI faeces is the ultimate probiotic since 1950s known that shit stops diarrhoea 300 cases; varying metjods; enema, inoculum

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#AAMTHI revulsion common problem with this kind of research; poor legal framework; "chinese" takeaway home delivery service of human shit -)

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#AAMTHI Tom Louie on fecal microbiome transplants, i.e. eating shit coprophagy: a reboot of the microbiome common in animals

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#AAMTHI in Q&A, issue of whether metabolomics disturbance less important than disturbance of innate immunity effects from biota

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#AAMTHI Vince Young playing homage to Lord Stanley of Bitterroot alumni.stanford.edu/get/page/magaz… "It may be shit to you, but it's my bread and butter"

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#AAMTHI Young exploring probiotic potential of various spp from healthy CD-infected mice, but not naming them in this talk :-)

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#AAMTHI key paper on growing uncultured ncbi.nlm.nih.gov/pubmed/15294811 New strategies for cultivation and detection of previously uncultured microbes

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#AAMTHI need to go beyond 16S; short chain fatty acids levels go down in susceptibles

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#AAMTHI C diff becomes major component of microbiota in sick mice with CDI as measured by 16S cefaperazone model high mortality

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#AAMTHI preconditioning ABx, then clinda and C diff needed to cause colitis but lots of variability why some did not succumb?

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#AAMTHI mouse originally not good ncbi.nlm.nih.gov/pubmed/3533778 hamster popular mouse back in favour ncbi.nlm.nih.gov/pubmed?term=ke…

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#AAMTHI Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation ncbi.nlm.nih.gov/pubmed/19307217

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#AAMTHI Joke: Robert Koch one of few microbiologists not influenced by Falkow

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#AAMTHI traditional view CDI is ecological disease Koch's postulates; clindamycin colitis

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#AAMTHI dapper dresser Vincent Young takes the stage to talk about C diff and microbiota. sitemaker.umich.edu/younglab/home

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#AAMTHI Does the nose know? The odiferous diagnosis of Clostridium difficile-associated diarrhea ncbi.nlm.nih.gov/pubmed/17366472

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#AAMTHI cannot find any pubs on dogs smelling infection, but lots on cancer ncbi.nlm.nih.gov/pubmed/21790506

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#AAMTHI Beagle can sniff out smell of C. difficle; cheaper and quicker than PCR or genomics; nurses claim they can smell it

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#AAMTHI prediction of CDI recurrence possible ncbi.nlm.nih.gov/pubmed/19162027 may allow targeting of new treatments

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#AAMTHI “Archive of Live Tweets from Applying Advanced Molecular Techniques to Healthcare Infection Days 1-2 pathogenomics.bham.ac.uk/blog/2011/10/l…”

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#AAMTHI most recent study worked! Treatment with monoclonal antibodies against Clostridium difficile toxins ncbi.nlm.nih.gov/pubmed/20089970

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#AAMTHI oral and IVIG and hyperimmune Ig tried, but best is HuMab But in phase 2 HuMab antitoxin A alone failed

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#AAMTHI relations between Abies and CDI ncbi.nlm.nih.gov/pubmed/1066642… anti-toxin abies are protective against recurrence; interest in immune rx

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#AAMTHI IL-8 promoter -251 SNP ncbi.nlm.nih.gov/pubmed/21058913 African Americans get less CDI, have higher incidence of protective genotype

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#AAMTHI review from Kelly ncbi.nlm.nih.gov/pubmed/21415200 WBC counts predict bad outcome anti-CD18 ab prevents intestinal injury

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#AAMTHI Ciaran Kelly on C. difficile innate immunity colitis, pseudomembranes, PMNs, IL-8 promoter polymorphism tied to risk for CDI

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#AAMTHI storming talk just finished from Scott Hultgren too densely packed for tweeting; mannosides promising treatment ncbi.nlm.nih.gov/pubmed/20507142

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#AAMTHI more on UTI from Hultgren ncbi.nlm.nih.gov/pubmed/1809288…

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#AAMTHI complex dynamics in UTI ncbi.nlm.nih.gov/pubmed/21807904

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#AAMTHI also ncbi.nlm.nih.gov/pubmed/2129763…

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#AAMTHI talk on genetics of IBD to cut a long story short: ncbi.nlm.nih.gov/pubmed/21102463

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#AAMTHI clumping in plasma requires ClfA and coagulases; triple mutant cannot cause septic death direct thrombin inhibition delays death

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#AAMTHI two coagulases: Coa and vWBp; redundancy; double mutant delays time to death in sepsis model; coagulase gene very variable

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#AAMTHI Identifying protective antigens of Staphylococcus aureus, a pathogen that suppresses host immune responses. ncbi.nlm.nih.gov/pubmed/21753082

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#AAMTHI protein A vaccine reduces load in mice and abscess numbers sepsis model is different from abscess model; far more severe

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#AAMTHI isd system involved in haem transport; IsdB vaccine has just failed in human trial :-) protein A promising candidate

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#AAMTHI sortase (strA) mutants cannot form abscesses; cleared slowly by day 15; LPXTG proteins important; 23 in genome; sdrD, isdAB, coa,cWb

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#AAMTHI small number of conserved core proteins in S. aureus; in mice bloodstream infection clears but kidney infection endures; abscesses

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#AAMTHI the legendary Olaf Schneewind takes the podium; a man who confessed yesterday that he did not know what Twitter was is being tweeted

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Live Tweets from Applying Advanced Molecular Techniques to Healthcare Infection Days 1-2

25 Oct 2011

Here 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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Great Read at Birmingham: Captain Kirkup and Chris Stringer

01 Oct 2011

AV material associated with this week's Great Read at Birmingham events.

Captain Kirkup on Evolution and Game Theory

Video of the talk and subsequent Q&A : http://www.youtube.com/watch?v=15gxMlQQ6AA

Slides to go with this: http://www.youtube.com/watch?v=RTk9_DlOpcQ
(Open these in a separate window as they will need to be manually paused and progressed forward: sorry no synchronised slidecast available)

Chris Stringer on The Origin of Our Species
Podcast of the talk via YouTube (publicly available): http://www.youtube.com/watch?v=QryLIaRORlU

Open Education and Bio380 lecture on Neanderthals

01 Oct 2011

This academic year I have set myself the goal of making all my lecture available for all, in the public domain, via YouTube and maybe also Slideshare. The technical side of doing this is fairly straightforward (capture a screen movie via QuickTime), but the major hassle is ensuring and documenting permissions for all images. In my first attempt, I quickly realised that putting this information on the same slides as the images led to cluttered chaos, so I have piled them all up at the end of the talk.

Slidecast via YouTube

http://www.youtube.com/watch?v=LdYURwBW7L4

Slides via Slideshare

Bio380 Human Evolution: Waking the dead </p>

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