FNSC3180 Food Microbiology, Chinese Univ of Hong Kong, by HS Kwan: June 2011

Thursday, June 30, 2011

Article: New salmonella-based 'clean vaccines' aid the fight against infectious disease

New salmonella-based 'clean vaccines' aid the fight against infectious disease - Physorg

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Article: EU investigating if Egypt seeds common link in E. coli outbreak in Germany and France

EU investigating if Egypt seeds common link in E. coli outbreak in Germany and France - The Washington Post

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Wednesday, June 29, 2011

Article: Decoding Genomes Of Microbe Ecosystems Could Deliver Untold Benefits

Decoding Genomes Of Microbe Ecosystems Could Deliver Untold Benefits - Fast Company

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Article from Science News: Mutated Bacteria Drives Scarle...

I thought you might be interested in this article from Science News:

Mutated Bacteria Drives Scarlet Fever Outbreak

http://news.sciencemag.org/scienceinsider/2011/06/mutated-bacteria-drives-scarlet.html?ref=wp

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Article: Alfalfa Sprouts Salmonella Risk Warning Issued By FDA

Alfalfa Sprouts Salmonella Risk Warning Issued By FDA - Medical News Today

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Article: Understanding the E. coli outbreak part four

Understanding the E. coli outbreak part four - Examiner

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Tuesday, June 28, 2011

Article: The long and winding road to a PhD [infographic] - Holy Kaw!

The long and winding road to a PhD [infographic] - Holy Kaw! - holykaw.alltop.com

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Article: Tyson Bribery Case Reveals Gaps in Meat Inspection Policy, White Collar Crime Law

Tyson Bribery Case Reveals Gaps in Meat Inspection Policy, White Collar Crime Law - The Huffington Post

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Article: Epidemiology and social media: conference fail : Aetiology

Epidemiology and social media: conference fail : Aetiology - scienceblogs.com

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Article: The E. coli O104:H4 Outbreak Gets More Confusing--and Potentially More Disturbing

The E. coli O104:H4 Outbreak Gets More Confusing--and Potentially More Disturbing - Scienceblogs

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Monday, June 27, 2011

Article: Understanding the E. coli outbreak part three

Understanding the E. coli outbreak part three - Examiner

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Article: French E.coli Strain Is The Same As Germany's

French E.coli Strain Is The Same As Germany's - The Huffington Post

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Article: Tips to Prevent Illness from Clostridium Perfringens

Tips to Prevent Illness from Clostridium Perfringens - FoodConsumer

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Sunday, June 26, 2011

Article: Spoonful of Medicine: As E. coli continues to claim lives, new approaches offer hope

Spoonful of Medicine: As E. coli continues to claim lives, new approaches offer hope - blogs.nature.com

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Article: E.coli: consumers advised not to eat raw bean sprouts

E.coli: consumers advised not to eat raw bean sprouts - The Daily Telegraph

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Saturday, June 25, 2011

Article: Science's 10 hottest fields

Science's 10 hottest fields - Financial Times

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Article: Will budget cuts spell the end for "Team D"?

Will budget cuts spell the end for "Team D"? - Consumer Reports

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Article: France halt sales of 3 seed types linked to British vendor after E. coli outbreak

France halt sales of 3 seed types linked to British vendor after E. coli outbreak - The Washington Post

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International Activities > Foreign Food Inspection Program Questions and Answers

FDA list of high risk food.

http://www.fda.gov/Food/InternationalActivities/ucm211823.htm#q2

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Article: Sickening Shopping Carts

Sickening Shopping Carts - Glamchic

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Article: E. coli: Some Answers, Many Questions Still

E. coli: Some Answers, Many Questions Still - Wired

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Article: MiSeq Aims for Ion Torrent

MiSeq Aims for Ion Torrent - Omics! Omics!

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Friday, June 24, 2011

The Tree of Life: Fun with Ligercat: pubmed word clouds

http://phylogenomics.blogspot.com/2011/06/fun-with-ligercat-pubmed-word-clouds.html

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Article: Gangrenous Bowel Shows Deadly Risk of German Bug, Study Says

Gangrenous Bowel Shows Deadly Risk of German Bug, Study Says - Business Week

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From Foodborne Pathogen Team Kwan Lab CUHK--German outbreak strains: Alignment-free whole-genome phylogeny suggested that EAEC 55989 is a close relative but not a direct parent

German outbreak strains: Alignment-free whole-genome phylogeny suggested that EAEC 55989 is a close relative but not a direct parent

Introduction:

Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 9 outbreak isolates against existing E. coli genomes using the alignment-free feature frequency profile (FFP) method (Sims et al. 2009).

Datasets:

1. Genome sequences of 30 E. coli isolates from NCBI, and

2. Genome sequences of 9 outbreak isolates, TY2482 from BGI, LB226692 from Life Technologies, 5 isolates from HPA, and 2 isolates from Göttingen.

Method:

1. Genome sequences were converted into an RY (purine/pyrimidine)-coded form.

2. Overlapping features, l-mers of length 24, were counted over each of the whole genomes.

3. Forward and reverse complement features were considered equivalent.

4. Only core features which were present in all 39 isolates were extracted.

5. Features occurring more than 3 times in any of the isolates were removed.

6. Simple cumulative distances were calculated among all feature states in an unordered manner.

7. A neighbor-joining tree was plotted with the resulting distance matrix using MEGA5.

For details, please refer to Sims & Kim (2011).

Results:

The following is the phylogenetic tree produced using the current alignment-free method. Outbreak isolates were highlighted in red.

Our tree generally agrees with that reported by Konrad Paszkiewicz & Kat Holt built using a SNP-based approach, both revealing a high similarity among the outbreak isolates and 55989 being the most closely related isolate sequenced thus far. However, we should note that the genetic difference between 55989 and the outbreak isolates in our FFP tree is greater than that in the tree built based on SNPs.

Linear phylogenetic inference of bacteria might be problematic due to horizontally transferred elements. While Kat Holt tried to remove obviously horizontally transferred DNA by removing SNP calls in genes annotated with keywords like "phage" and "transposase", we removed features likely to be associated with mobile or repetitive DNA by filtering out features with high frequencies and used an unordered character state model to reduce the effect of lateral transfer signal. Both methods seem to work well.

Concluding remarks:
To sum up, using an alignment-free phylogenetic approach, we further confirm 55989 being the most closely related isolate to the outbreak isolates sequenced thus far, again showing an EAEC-origin of the outbreak isolates. However, the genetic difference suggested that 55989 is not a direct parent of the outbreak isolates.

References:

Sims GE, Jun S-R, Wu GA, Kim S-H (2009) Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. PNAS 106:2677-2682.

Sims GE, Kim S-H (2011) Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). PNAS 108:8329-8334.

Prepared by Simon CHEUNG, Wenyan NONG, Lei LI & H.S. KWAN

Eurosurveillance editorial on E. coli outbreak credits crowdsourcing « bacpathgenomics

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Article: Hog roast salmonella investigated

Hog roast salmonella investigated - BBC

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WHO/Europe | EHEC outbreak: Update 22

http://www.euro.who.int/en/what-we-do/health-topics/emergencies/international-health-regulations/news/news/2011/06/ehec-outbreak-update-22

Table copied from WHO report linked above:

"
The table shows the reported cases of and deaths from HUS and EHEC infection as of 22 June at 15:00 CET.

Country	HUS		EHEC		Comments
Country	Cases	Deaths	Cases	Deaths
Austria	1	0	3	0
Canada	0	0	1	0
Czech Republic	0	0	1	0	A tourist from the United States who had travelled in Germany
Denmark	9	0	13	0
France	0	0	2	0
Germany	823	29	2865	13
Greece	0	0	1	0	A German tourist
Luxembourg	1	0	1	0
Netherlands	4	0	5	0
Norway	0	0	1	0	Contact with a German in Norway
Poland	2	0	1	0
Spain	1	0	1	0
Sweden	17	1	33	0
Switzerland	0	0	5	0
United Kingdom	3	0	3	0
United States of America	3	0	2	0	3 HUS cases (all confirmed) and 2 EHEC cases (one confirmed and one suspected)
Total	864	30	2938	13

Note. There are 3802 HUS and EHEC cases in total, including 43 fatalities.

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CIDRAP >> German E coli outbreak kills 3 more, reaches 3,800 cases

http://www.cidrap.umn.edu/cidrap/content/fs/food-disease/news/jun2311ehec.html

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Thursday, June 23, 2011

Article: Salmonella 'superbug' threat from intensive pig farms

Salmonella 'superbug' threat from intensive pig farms - Food & Beverage

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Article: Deadly New Salmonella Strain Can Spread from Hogs to Humans

Deadly New Salmonella Strain Can Spread from Hogs to Humans - Treehugger

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Article: New device promises quick testing for food-borne pathogens

New device promises quick testing for food-borne pathogens - Channel NewsAsia

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Article: E. coli's sticky secret revealed in medical journal

E. coli's sticky secret revealed in medical journal - Smh.au

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Article: Mutated scarlet fever kills second child in Hong Kong

Mutated scarlet fever kills second child in Hong Kong - San Jose Mercury News

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Article: Scarlet-fever scare

Scarlet-fever scare - MarketWatch

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Article: Unusual Traits Blended in Germany E. Coli Strain - NYTimes.com

Unusual Traits Blended in Germany E. Coli Strain - NYTimes.com - www.nytimes.com

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Wednesday, June 22, 2011

Article: Hemolytic uremic syndrome (HUS) in history--part 3

Hemolytic uremic syndrome (HUS) in history--part 3 - Aetiology

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Article: A New Way to Combat Antibiotic-Resistant Bacteria

A New Way to Combat Antibiotic-Resistant Bacteria - FOX News

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Article: Cornell researchers tackle containment of E. coli

Cornell researchers tackle containment of E. coli - Ithaca Journal

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Article: Omics! Omics!: E.coli Outbreak Genomics

Omics! Omics!: E.coli Outbreak Genomics - omicsomics.blogspot.com

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Article: Nature News Blog: The German E. coli outbreak: 40 lives and hours of crowdsourced sequence analysis later

German E. coli Crowdsourcing is reported in Nature News Blog.

Nature News Blog: The German E. coli outbreak: 40 lives and hours of crowdsourced sequence analysis later - blogs.nature.com

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Tuesday, June 21, 2011

Article: GMO Pundit a.k.a. David Tribe: Complete map of German E. coli O104 (Acronym STpEAEC) genome released

GMO Pundit a.k.a. David Tribe: Complete map of German E. coli O104 (Acronym STpEAEC) genome released - gmopundit.blogspot.com

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Article: Hemolytic uremic syndrome (HUS) in history--part 2

Hemolytic uremic syndrome (HUS) in history--part 2 - Aetiology

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Can Technology Rescue the Sprouts Industry?

http://www.foodsafetynews.com/2011/06/can-technology-rescue-the-sprouts-industry/

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Article: Hemolytic uremic syndrome (HUS) in history--part 1

Hemolytic uremic syndrome (HUS) in history--part 1 - Aetiology

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Article: Alexion Pharmaceuticals Inc. Initiates Clinical Trial of Eculizumab as a Potential Treatment for Patients with STEC-HUS in Expanded Response to EHEC Crisis in Germany

Alexion Pharmaceuticals Inc. Initiates Clinical Trial of Eculizumab as a Potential Treatment for Patients with STEC-HUS in Expanded Response to EHEC Crisis in Germany - BioSpace

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Article: Deadly E. coli outbreak in Germany should be a warning, expert says

Deadly E. coli outbreak in Germany should be a warning, expert says - PhysOrg

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Imported from Food Pathogen Team Kwan Lab CUHK: Proposed analytical Workflow in a bacterial pathogen outbreak investigation

H.S. Kwan

A. Introduction

The German Escherichia coli outbreak causing serious diseases, notably, Haemoragghic Uremic Syndrome started in early May. The conventional typing methods including serotypinc, MLST sequence typing and pulse-field gel electrophoresis seemed to yield only limited information about the strain. The situation was a little chaotic. The strain could not be typed definitively as EAEC or EHEC. It was suspected to be a hybrid of EAEC and EHEC. More detail analysis was needed.

Nick Loman started a very interesting “Crowdsourcing” genomic analysis of the German Escherichia coli outbreak strain. The first set of analyses was based on the BGI genome sequencing reads. The first 2 sets of reads were provided by BGI and Life Technologies, both used the Ion Torrent Personal Genome Machine. Ion Torrent PGM was the machine of choice for its quick operation time. It seemed that The draft sequences were completed in only 3 days albeit the coverage was low. The quick turn around time allowed “Crowdsourcing” to start very early after the strains were given to BGI and Life Technologies to sequence. The speed of sequencing was important to give an initial quick analysis of the outbreak strain to show its major characteristics. Treatment could be chosen with this information. For deadly diseases, timing is always very important. Certainly, a few days later, the more powerful machines, Illumina HiSeq and Roche 454 Titanium, provided higher coverage for better assembly which was important for high resolution analyses.

My laboratory, Kwan Lab, CUHK, has noted the progress very early in the outbreak. For the last 2 and a half years, we have been constructing a Foodborne Pathogen Genome Sequence Database and sequencing the genomes of Hong Kong isolates of Salmonella Typhimurium and Vibrio parahaemolyticus. We have been asking ourselves how we can use the database for outbreak investigation. The “Crowdsourcing” activity has provided us first-hand experience of how genome sequences are used in a real outbreak investigation.

B. Questions and approaches to answer them

My understanding from the “Crowdsourcing” experience is that we have been asking several important questions about the strain responsible for the outbreak and using genome analysis to find the answers.

The questions are:

1. Is the outbreak strain isolated previously? That is, is it a known strain?

2. If not known, is it related to known strains?

3. If answer is no to above, then it is novel?

4. What are the pathogenicity features of the strain?

5. Is a typing scheme available to follow further cases?

6. If not, can we develop a typing scheme?

Answering these questions would allow us to understand the strain better and help us to

1. trace the outbreak strain,

2. find appropriate treatment for the disease,

3. understand the pathogenicity of the outbreak strain,

4. develop preventive measures for further and future outbreaks.

The genome sequencing combined with “Crowdsourcing” seemed to work well. We could answer the questions and further use the answers for treatment and control of the outbreak. Amazed by the efficiency and effectiveness of the process, I analyzed the genome analyses reported by the laboratories contributing to “Crowdsourcing” to find out which analysis is for answering each question.

C. Synthesis: Analytical workflow in a pathogenic bacteria outbreak

My synthesis from the genome sequencing-crowdsourcing experience is shown in Figure 1. The advantages of Genome sequencing approach are apparent comparing to conventional methods:

1. Genomic approach is definitive with little uncertainty

2. Genomic approach reveals whether the outbreak strain is known, related, or novel

3. Genomic analysis provides comprehensive information on pathogenicity of the outbreak strain

4. Comparative Genomics provide information to develop typing schemes for diagnosis of the outbreak strain in patients and food, important for management of the outbreak

5. Genomics provide lots of data for further comprehensive understanding of the outbreak strain, important for prevention of further and future outbreaks

Figure 1. Putative analytical workflow in a bacterial outbreak.

Top group, conventional workflow: after typing and analysis, there is still great uncertainty about its relationship to previously isolated and analysed strains. It is uncertain whether it is novel. Not much is known about the pathogenicity feature of the strain. The data cannot be used to generate a typing scheme.
Bottom group, genome sequencing and genomic analysis: after the analysis, the strain can be shown to be a known strain, or related to a known strain, or a novel strain. The pathogenicity is well studied at the genomic/gene level, providing knowledge for furhter analysis.
The right columns of boxes show the questions and whether they can be answered. The ? marks indicate much uncertainties. The ✓ marks indicate answers can be provided. The ✓ mark in the box means some information can be obtained for further analysis.

D. Concluding remarks

Genome sequencing and analyses with an appropriate workflow would be the new paradigm in bacterial outbreak investigation. It is important to have a fast genome sequencing turn-around time and later a high coverage sequencing for further detail analyses. This approach still costs dearly and can be prohibitive. When we can perform inexpensive, fast, and high-throughput genome sequencing, the genomic analysis paradigm will be established.

Contributors to this proposal: Billy CHENG, Lei LI, Qianli HUANG, Tommy AU, Jackie WONG, Wenyan NONG and Simon CHEUNG.

Monday, June 20, 2011

Article: Genetic family trees show the German outbreak of E coli is a member of small family of germs called EAEC — that includes an African germ — and is distinct from EHECs « Biofortified

Genetic family trees show the German outbreak of E coli is a member of small family of germs called EAEC — that includes an African germ — and is distinct from EHECs « Biofortified - www.biofortified.org

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Article: Germany confirms human E. coli transmission - Europe - Al Jazeera English

Germany confirms human E. coli transmission - Europe - Al Jazeera English - english.aljazeera.net

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Article: VIDEO: E. coli 'passed from human to human'

VIDEO: E. coli 'passed from human to human' - BBC

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Sunday, June 19, 2011

Germany's E. coli Outbreak: A Global Lesson

I recommend this report which has insightful information.

http://www.foodsafetynews.com/2011/06/germanys-e-coli-outbreak-a-global-lesson/

Quoting from the report:

".....the biggest shift should be instituting safer growing practices, particularly for fruits and vegetables because fresh produce does not receive enough attention under the current food safety system.

Indeed other harmful, Shiga toxin-producing strains of E. coli have been detected on vegetables other than sprouts over the course of the current outbreak investigation, raising questions about the prevalence of E. coli contamination in European produce.

"They found an EHEC (enterohemorrhagic E. coli) in the Spanish cucumbers and they alerted the public, but the cucumbers were subsequently deemed 'innocent,' " said Wall, adding "but you don't want EHEC on your cucumbers."

In recent days, E. coli was also found on lettuce from Bavaria, Dutch beet sprouts and on lettuce from Frankfurt, although none of the pathogens was the O104:H4 outbreak strain that has been wreaking havoc in Germany since May 1.

"I think we're going to have to rewrite the whole script on produce," Wall said.

In both the United States and Europe, meat undergoes testing for pathogens (albeit not for E. coli O104, the serotype causing this outbreak). "We are paranoid about microbial quality and testing of cooked meats [in Europe]," says Wall.

But produce on the continent is monitored less frequently.

And while all meat sold in Europe must meet certain microbial standards, meaning that pathogen levels must be kept below a specified limit, these thresholds are imposed for only two types of produce: pre-washed lettuce and, ironically, bean sprouts..............."

".............Wall notes, there is "no time to fix [food safety problems] when the event is happening."

This is why he says it's important to use "peace time," when a major outbreak is not taking place, to implement measures necessary to cope with the next outbreak.

The problem with "peace time," is that during these periods, foodborne illness does not appear as threatening............"

We need to pay more attention to the microbial food safety of our fresh produce, especially now we are having food from all over the globe.

Tennessee E. coli Investigation Continues as More Cases are Confirmed | Ecoli Lawyer

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Article: Human waste danger

Human waste danger - NEWS.com.au

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I thought you should see this story

E. coli outbreak is traced everywhere from hospital beds to farm fields http://m.examiner.com/exToronto/pm_98394/contentdetail.htm?contentguid=JqWZm9TI

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Saturday, June 18, 2011

Article: Incidence of Foodborne Illness, 2010

Incidence of Foodborne Illness, 2010 - FoodConsumer

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news.gov.hk - Categories - Health & Community - Restaurant closed after Vibrio cholerae found

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香港政府新聞網 - 類別 - 社區與健康 - 中環食肆發現霍亂弧菌須封閉

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Friday, June 17, 2011

Article: E. Coli outbreak prompts public health reforms

E. Coli outbreak prompts public health reforms - The Local

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Article: Kristof: When food kills, blame the broken system

Kristof: When food kills, blame the broken system - Austin American Statesman

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ScienceDirect - International Journal of Food Microbiology : Antibiotic resistance in bacteria isolated from vegetables with regards to the marketing stage (farm vs. supermarket)

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Article: E coli in France: seven children in hospital as beefburgers blamed

E coli in France: seven children in hospital as beefburgers blamed - The Guardian

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Article: Listeria found at US Kellogg bakery

Listeria found at US Kellogg bakery - Australian Food News

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Article: E. Coli Bacteria More Likely to Develop Resistance After Exposure to Low Levels of Antibiotics, Study Published in

E. Coli Bacteria More Likely to Develop Resistance After Exposure to Low Levels of Antibiotics, Study Published in - BioSpace

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Germany's E. coli Outbreak Most Costly In History

http://www.foodsafetynews.com/2011/06/europes-o104-outbreak---most-costly-in-history/

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BGI

http://www.genomics.cn/en/news_show.php?type=show&id=660

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Thursday, June 16, 2011

Article: Safety Rules For Sewage Sludge May Be Outdated

Safety Rules For Sewage Sludge May Be Outdated - Chemical & Engineering News

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Article: France Recalls 10 Tons of Hamburgers Over E. Coli Scare

France Recalls 10 Tons of Hamburgers Over E. Coli Scare - The Huffington Post

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Göttingen Genomics Laboratory

http://www.g2l.bio.uni-goettingen.de/

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Article from Science News: The Dirty 11: Panel Names Path...

I thought you might be interested in this article from Science News:

The Dirty 11: Panel Names Pathogens That Pose Biggest Security Risk for Research

http://news.sciencemag.org/scienceinsider/2011/06/the-dirty-11-panel-names-pathogens.html?ref=wp

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Landes Bioscience Journals: Bioengineered Bugs

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E. coli data released under Creative Commons 0 license

http://wp.me/p1sxjJ-4y

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German E. Coli Outbreak May Trigger New Food Regulations, Predicts Researcher - FoodIngredientsFirst

http://www.foodingredientsfirst.com/news/German-E-Coli-Outbreak-May-Trigger-New-Food-Regulations-Predicts-Researcher.html

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Article: Meridian Tests For Killer E. Coli

Meridian Tests For Killer E. Coli - Daily Markets

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Article: Bean sprouts and E. coli O104:H4

Bean sprouts and E. coli O104:H4 - Bio Job Blog

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Article: Chemist develops nanomaterials and polymers to detect, repel E. coli

Chemist develops nanomaterials and polymers to detect, repel E. coli - Nanowerk

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Wednesday, June 15, 2011

Article: Our medicines are failing

Our medicines are failing - The Washington Post

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Article: Barbecue season is here

Barbecue season is here - Wetaskiwin Times

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Article: City Room: The War on Food-Borne Pathogens

City Room: The War on Food-Borne Pathogens - The New York Times

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Article: VIDEO: Berlin's cucumber eating contest

VIDEO: Berlin's cucumber eating contest - BBC

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Scientists Shed Light on Germany's Deadly Pathogen

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Fwd: Eurosurveillance - View Article

Characteristics of the enteroaggregative Shiga toxin/verotoxin-producing Escherichia coli O104:H4 strain causing the outbreak of haemolytic uraemic syndrome in Germany, May to June 2011

http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19889

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Fwd: Eurosurveillance - View Article

Eurosurveillance, Volume 16, Issue 24, 16 June 2011

Editorials

Enteroaggregative, Shiga toxin-producing Escherichia coli O104:H4 outbreak: new microbiological findings boost coordinated investigations by European public health laboratories

M J Struelens (

)¹, D Palm¹, J Takkinen²

http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19890

Exerted from the editorial:

".............fascinating development stems from comparative genomics, available in real time, to elucidate the ancestral origin of the 2011 outbreak strain. On 2 June, further information on the nature of the hybrid EAggEC STEC/VTEC pathotype of this strain came from whole genome sequence information generated by two groups of German academic investigators [11]. Sequence information from a third isolate from a patient was subsequently generated at the Health Protection Agency, United Kingdom. The data sets from these sequencing initiatives were instantly released for public access, resulting in data analysis among bioinformaticians and other researchers around the world..........."

My laboratory "Kwan Lab" has been participating in the data analysis of the sequences.

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Article: Bad News Birds: 80% of Seattle-Area Chicken Contaminated

Bad News Birds: 80% of Seattle-Area Chicken Contaminated - Seattlest

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Article: Some Thoughts About EAEC, Reservoirs, and Pathogenicity

Some Thoughts About EAEC, Reservoirs, and Pathogenicity - Scienceblogs

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Article: Intralytix Completes Regulatory Clearance for Phage-Based E. coli Food Safety Technology

Intralytix Completes Regulatory Clearance for Phage-Based E. coli Food Safety Technology - Centre Daily Times

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Tuesday, June 14, 2011

Article: German two-year-old dies from E. coli

German two-year-old dies from E. coli - Canada.com

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Article: New Germany E. Coli Cases Decline

New Germany E. Coli Cases Decline - www.huffingtonpost.com

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Article: Eat Your Fruits, Veggies, Pesticides: Health Risk?

Eat Your Fruits, Veggies, Pesticides: Health Risk? - ABC News

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Article: Researchers, companies quick to crack E. coli case

Researchers, companies quick to crack E. coli case - FierceBioResearcher

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Article: Multilocus Sequence Typing and How to Make a Mad Biologist Cranky

Multilocus Sequence Typing and How to Make a Mad Biologist Cranky - Scienceblogs

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Monday, June 13, 2011

Article: Optical Mapping First to Definitively Determine Deadly E. coli Strains in German Outbreak Are From a Single Source and Related to Earlier Outbreaks

Optical Mapping First to Definitively Determine Deadly E. coli Strains in German Outbreak Are From a Single Source and Related to Earlier Outbreaks - Centre Daily Times

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Imported from Food Pathogen Team Kwan Lab CUHK: Outbreak strains have EAEC secreted proteins but not EHEC secreted proteins

Introduction:

In our first blog, we find the outbreak strains actually have the similarity pathogenicity as EAEC E.coli Ec55989 strain based on alignment with virulence factors from VFDB.

Two questions remain:

Whether the outbreak strains are really "EAEC" intrinsically, and only acquiring Stx2 gene to become a EAEC/EHEC hybrid?
Whether these outbreak strains also maintain other EHEC features such as secretion systems?

Methods:

We used datasets of genome sequences of the three outbreak strains (TY2482, LB226692 and H112180280), the EAEC strain 55989, and the EHEC strain O157:H7 Sakai. We use EHEC strain O157:H7 and EAEC strain 55989 as central reference sequences to align with the three outbreak strain genome sequences to identify the presence or absence of EHEC-specific and EAEC-specific secretary proteins using BRIG.

Results:

1. The Type III secretion system (T3SS) and related translocated proteins of EHEC are missing in all outbreak strains. Figure 1 shows general features of EHEC E.coli O157:H7 strain and its homology to HPA strain (H112180280), BGI TY2482 strain, Life technology (LB226692), and E.coli 55989 strain, ordered from inner to outside rings. The three inner rings showed high sequence similarities among the outbreak strains. The two EHEC-specific gene clusters encoding T3SS (shown in left and colored in red), are missing in the outbreak strains and EAEC 55989 strains.

Figure 1

2. The outbreak strains harbor the EAEC secretion system and its translocated proteins. Figure 2 is a plot of EAEC strain 55989 strain and its homology to HPA sequence (H112180280), BGI sequence (TY2482), Life technology seqeuence (LB226692), and E.coli O157:H7 sequence, respectively.
All the EAEC-specific secretory genes (shown in the outside ring and colored in black) are present in the outbreak strains as well as in EAEC 55989 strain.

Figure 2

Analysed by Lei Li, edited by Billy Cheng and HS Kwan

Article: Keeping American food supply safe

A summary worth reading.

- www.epi.ufl.edu

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Article: Report: The 10 Pathogen-Food Combinations That Most Hurt Public Health - Health Blog - WSJ

Report: The 10 Pathogen-Food Combinations That Most Hurt Public Health - Health Blog - WSJ - blogs.wsj.com

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Article: Why E. coli and Salmonella Love Sprouts

Why E. coli and Salmonella Love Sprouts - WSJ: Health Blog

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Article: E.coli patients may need kidney transplants

E.coli patients may need kidney transplants - The Local

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German E coli outbreak news - Google News

http://news.google.co.uk/news/search?pz=1&cf=all&ned=uk&hl=en&as_q=German+E+coli+outbreak+news&as_epq=&as_oq=&as_eq=&as_scoring=n&btnG=Search&as_drrb=q&as_qdr=a&as_minm=5&as_mind=13&as_maxm=6&as_maxd=12&as_nsrc=&as_nloc=&geo=&as_author=&as_occt=any

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German E. coli outbreak - Google Search

http://www.google.co.uk/search?tbm=isch&hl=en&source=hp&biw=980&bih=1208&q=german+coli+outbreak&btnG=Search+Images&gbv=2&aq=f&aqi=&aql=&oq=

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Article: Sprouts, Poster Plant of Health Food, Can Pack Risks - NYTimes.com

Sprouts, Poster Plant of Health Food, Can Pack Risks - NYTimes.com - www.nytimes.com

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Article: E. Coli Fallout - My Salad, My Health - NYTimes.com

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Sunday, June 12, 2011

Article: Scientists Provide Free Access To The E. coli's Genetic Regulation Data

Scientists Provide Free Access To The E. coli's Genetic Regulation Data - Medical News Today

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I thought you should see this story

Scientists probe DNA of E. coli for outbreak clues http://m.timesunion.com/tu/db_40479/contentdetail.htm?contentguid=Zt7HmZIC&storycount=14&detailindex=0&pn=&ps=

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Germany pledges 'immediate' review after E.coli crisis contained

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Whole-genome phylogeny of Escherichia coli/Shigell... [Proc Natl Acad Sci U S A. 2011] - PubMed result

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Article: EU Confirms Sprouts as E. Coli Source

This report seems to be credible!

EU Confirms Sprouts as E. Coli Source - The Wall Street Journal

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Article: German officials see no E. coli fault at organic farm

German officials see no E. coli fault at organic farm - Mail&Gurdianonline

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Imported from Food Pathogen Team Kwan Lab CUHK: The outbreak strains have similar pathogencity as Ecoli EAEC strain 55989: Alignment of virulence factors from VFDB

LINK: http://hskwanfptcuhk.blogspot.com/2011/06/outbreak-strains-have-similar.html

Introduction: We are curious about whether the two outbreak strains with genome sequenced, TY2482 and LB226692 are using a combination of EAEC and EHEC pathogenic mechanisms or mainly use either EAEC or EHEC mechanism for infection.

Method: We extracted all the E. coli virulence factors from VFDB, and aligned them against genome sequences of the two outbreak strains, TY2482 and LB226692, the EAEC strain 55989 and its plasmid, and the EHEC strain O157:H7 Sakai and its two plasmids, using BLASTN.

Results:

A. Adherence to host cell surfaces is crucial to pathogenic E. coli to initiate infection, we found that:

Both TY2482 and LB226692 harbor the E. coli common pilus (ECP) genes, as in 55989 and O157:H7, for mimicking commensal E. coli to evade the host immune system.
BothTY2482 and LB226692 lack the EHEC-specific adherence genes including efa1 and intimin, which inhibits lymphocyte activation and binds Tir to cause dramatic intracellular changes respectively.
Both TY2482 and LB22692 retain most of the set of adherence genes of typical EAEC, though there are some variations, for example, aag3B, an invasive protein, is missing.

Figure 1
The first and second column is VF id and corresponding length, the numbers in the other columns are the alignment length outputed by blast .

B. Virulence Factors: More evidence suggests that the pathogenic mechanism of TY2482 and LB226692 may be more similar to that of typical EAEC.
We show that except Stx2 and espP, virulence factors coding for EHEC toxin, EHEC iron uptake, EHEC protease, EHEC regulation are mostly missing in TY2482 and LB226692, while VFs encoding EAEC toxin are present.

Figure 2

We also found that EHEC Type III secretion system (T3SS) and related translocated proteins are missing in TY2482 and LB226692. T3SS is crucial in EHEC pathogenesis for injecting Tir and other effectors directly into the host cell, and subsequently activating cell-signalling pathways to cause changes in cytoskeleton.

What secretion system(s) are employed by TY2482 and LB226692?

Prepared by Li Lei, Billy Cheng, and HS Kwan