Natural GMOs Part 86: The parents of the German E. coli germ engaged in horizontal gene transfer

STEC/EHEC outbreak – horizontally transferred genes « bacpathgenomics: “STEC/EHEC outbreak – horizontally transferred genes”

Kat Holt has produced a fantastic visual presentation of the family tree of the German disease causing E. coli EHEC/EAEC/STEC germ.

The Pundit won’t spoil her story with too much comment:
In the German outbreak bacteria, as in most E. coli, plenty of horizontal transfer has gone on to create the genome we are now looking at.
I’ve done about all I’m going to on this analysis, at least until some more complete data is released… but I did generate a summary plot and have a quick look at the origins of the stx, ter and other acquired genes.
This is a quick look at what the outbreak strain’s genome looks like:

Parentage of the German EAEC / EHEC / STEC E. coli strain

What is this showing us? Firstly, as established by other’s work mapping reads and contigs to the available E. coli reference genome sequences, the chromosome of the outbreak strain is most similar to strain Ec55989, an enteroaggregative E. coli (EAEC) isolated in Africa over a decade ago [central circle in figure]. It shares with this strain part of the EAEC plasmid [55989p, top right] carrying aggregative adhesion operons aat, the regulator aggR and some other bits, but it has a different aggregative adhesion fimbrial complement (AAF/I) from Ec55989. It has also acquired the stx2 phage carrying shiga-toxin 2 genes stx2A, stx2B [top left]; a plasmid sharing high similarity with the IncI plasmid pEC_Bactec, including blaCTX-M and blaTEM-1 beta-lactamase (antibiotic resistance) genes [bottom left] and a lot of sequence similar to plasmid pCVM29188_101 from Salmonella entericaKentucky [bottom left]. The circles represent the sequence of the plasmids and phage (previously sequenced and deposited in GenBank) that are most similar to sequences in the novel strain. The green rings indicate which parts of these references sequences are also present in the novel German strain (via BLAST comparison with TY2482/MIRA contigs)….so nearly all of the Ec55989 chromosome and pEC_Bactec plasmid, and not quite all of the other phage and plasmid sequences.

Kat also provides a reliable commentary of how several virulence genes were added to the outbreak strain’s disease-ability armoury from various bacterial viruses and plasmids. What’s interesting is how the parental chromosomes to the German beast are already studied several years back in other disease germs, and that their connection to the current outbreak can be deduced incredibly speedily by a really well trained mind assisted with good computer tools. Go to her site for further details.

Update

Kat also provides a reliable commentary of how several virulence genes were added to the outbreak strain’s disease-ability armoury from various bacterial viruses and plasmids (virus like optional extra chromosomes). What’s interesting is how the parental chromosomes to the German beast are already studied several years back in other disease germs, and that their connection to the current outbreak can be deduced incredibly speedily by a really well trained mind assisted with good computer tools. Go to her site for further details.

One germ parent fingered by Kat  is a plasmid related to that named pCVM29188_101  that has previously  found in the different species bacterial Salmonella enterica Kentucky. Another is the source of the new surface attachment genes carried on another plasmid related to that found previously in an African strain EAEC E. coli 55989, but this changed during the last few years of evolution by gaining new surface attachment genes. A third parent is the donor of the shigatoxin gene (stx2), which is likely to be the common food poisoning germ E.coli O157:H7 EHEC strain, which itself carries the gene stx2 within a mobile virus cassette that appears as an identical DNA that is in a somewhat  shortened version in the German germ. Another plasmid present in the German germ  is pEC_Bactec carrying antibiotic resistance gene — a plasmid widely distributed in other gut bacteria like Salmonella. Germ HUSEC041 O104:H4 also has new genes for tellurite chemical resistance not possessed by its distant African relative E. coli 55989, and these likely came from EHEC E. coli O157:H7 or its sisters.

Genome sequence provides another important clue on how to prevent E. coli food-borne disease outbreaks. The answer is 43.

Kat has, in another post,  made a very telling comment:

One thing that still remains is the question of whether, and how, this strain sticks to vegetables, which appears to be a significant factor in its successful transmission. Being an agreggative E. coli, this strain (like its sister strain Ec55989) carries the Ag-43 gene which is involved in biofilm formation and autoaggregation, which may turn out to be relevant.

Biofilms enable the persistence of germs on surfaces. The Ag-43 (Ag43)  gene mentioned by Kat codes for a surface protein called Antigen 43 that has been intensively studied for its role in enabling survival of E. coli on surfaces (see examples below). The surface proteindoes not seem to be involved in attachment to gut surfaces, and thus may have an important role in transmission from human to human by clinging to food surfaces. This may make uncooked vegetables a particularly potent means of disease transmission if indeed the German germ does have special abilities to attach persistently to leaf surfaces or even to the  internal cavities of plant material.

What a nasty menagerie of genes!

Update

(9/06/2011) From Kat Holt’s blog again:
Scott Weissman at the Seattle Children’s Hospital. He has done some analysis of the wide-spectrum penicillin resistance (beta-lactamase CTX-M)  mini-chromosome plasmid from the German outbreak strain . It can be classified as a pST31 plasmid using http://pubmlst.org/plasmid/ plasmid classification database. At least 15 occurences of the pST31 plasmid have been documented including one called pBactec (Smet et al, PLoS One, 2011;5:e11202 )  that carries wide spectrum penincillin resistance gene. The ability on these plasmids to undergo radical evolution is discussed by Annemieke Smet and her colleadues. They have been found in various E coli and Shigella germs found from humans and animals

FRIDAY, JULY 8, 2011 Hong Kong Genomics lab.

German E. coli outbreak strain: Prophage analysis of close-assembled TY2482 against 55989 using PHAST [virus DNA detecting software]

Concluding remarks:
Using PHAST, 7 potential prophages have been identified in the close-assembled outbreak isolate TY2482, of which 2 seem to be missing / distantly-related to those in the most closely related strain 55989. The 2 additional phages were found to be of Stx2 converting phage origin but only one of them carries the Stx genes.
Prepared by Simon M.K. CHEUNG, Lei LI, Wenyan NONG and H.S. KWAN.

Some papers about Antigen 43

1: de Luna MG, Scott-Tucker A, Desvaux M, Ferguson P, Morin NP, Dudley EG, Turner S, Nataro JP, Owen P, Henderson IR. The Escherichia coli biofilm-promoting protein Antigen 43 does not contribute to intestinal colonization. FEMS Microbiol Lett. 2008 Jul;284(2):237-46. Epub 2008 May 27. PubMed PMID: 18507683.
2: Klemm P, Hjerrild L, Gjermansen M, Schembri MA. Structure-function analysis of the self-recognizing Antigen 43 autotransporter protein from Escherichia coli. Mol Microbiol. 2004 Jan;51(1):283-96. PubMed PMID: 14651628.
3: Wegrzyn G, Thomas MS. Modulation of the susceptibility of intestinal bacteria to bacteriophages in response to Ag43 phase variation — a hypothesis. Med Sci Monit. 2002 Jun;8(6):HY15-8. PubMed PMID: 12070443.
4: Kjaergaard K, Schembri MA, Ramos C, Molin S, Klemm P. Antigen 43 facilitates formation of multispecies biofilms. Environ Microbiol. 2000 Dec;2(6):695-702. PubMed PMID: 11214802.
5: Kjaergaard K, Schembri MA, Hasman H, Klemm P. Antigen 43 from Escherichia coli induces inter- and intraspecies cell aggregation and changes in colony morphology of Pseudomonas fluorescens. J Bacteriol. 2000 Sep;182(17):4789-96. PubMed PMID: 10940019; PubMed Central PMCID: PMC111355.
6: Danese PN, Pratt LA, Dove SL, Kolter R. The outer membrane protein, antigen 43, mediates cell-to-cell interactions within Escherichia coli biofilms. Mol Microbiol. 2000 Jul;37(2):424-32. PubMed PMID: 10931336.
7: Hasman H, Chakraborty T, Klemm P. Antigen-43-mediated autoaggregation of Escherichia coli is blocked by fimbriation. J Bacteriol. 1999 Aug;181(16):4834-41. PubMed PMID: 10438752; PubMed Central PMCID: PMC93969

David Tribe is an applied geneticist, teaching graduate/undergrad courses in food science, food safety, biotechnology and microbiology at the University of Melbourne.


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13 comments to Natural GMOs Part 86: The parents of the German E. coli germ engaged in horizontal gene transfer

  • Michelle

    I am just wondering if this has all been naturally transferred to this present strain of E coli, or has it been specifically bred into it?

    • There is no reason to suppose gene rearrangement hasn’t happened away from the laboratory in a natural setting, in guts of people and animals, or other environments such as water and soil, or surfaces on plants (or biogas plants, or sewage processing plants). The mechanisms for this to happen in nature are all observed by microbiologists. They are diverse, and have great flexibility. In addition to movement between species, natural movement to new chromosomal locations has been detected. Use of antibiotics in medicine and animal husbandry has contributed to E. coli evolution– as seen by the plasmids bearing genes for antibiotic resistance found in the German E. coli germ.

      We also know a lot of evolution like we see with the German E. coli strain happened long before deliberate genetic engineering was invented by humans. The DNA sequence analysis of the German outbreak EHEC strain shows no trace of any standard lab DNA remains. This is evidence against deliberate lab creation of the strain.

      • Tomas Fix

        We got over 6800 bioplants in Germany with heavy emphasize on the North for time beeing. A lot of more are in process of building. My first idea was when I heard about the EHEC infections was the following: The spring has been warm and dry. The bioplant sediments are dispersed before plant growth i.e. February/March. But the regular rain did not occur we observed duststorms even lethal consequences for traffic. So aerosols of bioplant sediments infested vegetable plantation. Then the problem started. So far it is only hypothetic but at least one medical microbiologist Mr schottdorf owner of a high end laboratory facility was also mentioning this possibility (http://www.schottdorf.de).

  • living in a rural area in germany we observed an exlosion of Biogas(Biofermentation) plants. Is a biofermentation not a formidable environment for gentransfer?
    The biofermentation sediments do not exceed 42C
    Sincerly from Germany
    TF

  • Yes very likely this is an environment in which gene transfer will occur. But bacteria are everywhere. In the soil, for example, many natural antibiotics are produced, and each producer organism has mechanisms for antibiotic self-protection, the gene for which can transfer to other microbes and thus render them antibiotic resistant. This is all part of natural evolution. Similarly, copper salts used in some farms as a fungicide select for bacteria with genes giving copper salt tolerance. See
    http://gmopundit.blogspot.com/2005/11/copper-fungicide-use-in-farms-can.html

    Plasmids exist which carry both copper resistance and anti-biotic resistance genes on the same mobile mini-chromosome, so use of inorganic copper fungicide promotes antibiotic resistance.

  • Tomas Fix

    Copper salts and arsenic components are used in biological farming in Germany. This would be an argument against it. On the other hand antibiotic use in cattle and poultry farmin especially are common.

  • The EHEC Cluster in Germany.All EHEC Counties have mor than 10% of infections.
    http://www.rki.de/cln_178/nn_205760/DE/Content/InfAZ/E/EHEC/ehec__Tabelle-Erkrankung-Tod__BuLae,lv3=2099582.html#LkE3Erklaerung
    One sprout produce should be the culprit and the place of genetransfer??

    • The table you link shows that 4 counties (which if my memory serves (it often doesn’t – if only I had access to some sort of electronic repository of knowledge I could go to to check this >< – are geographically contiguous) have 75% of EHEC infections – 12 counties have less than 10% of infections – which appears to be in line with a point source in that region being the issue.

      As to whether this was the place of the gene transfer – I don't think that question is pertinent – David states above that the evolution of this strain occured before deliberate genetic engineering by humans was being done, so this puts the time of the transfer decades ago at the very minimum (I'm thinking David has the numbers elsewhere and that they're significantly bigger than decades) so spatially the transfer could have occured practically anywhere.

      • I agree. The trend of scientific discussion seems to be leaning towars this organism being just one of many similar organisms that have been around with perhaps a few extra genes, and in about a week we should know exactly how it differes from the one circulating about 10 years back. The German scientists at U Muenster analysing this are probably working it out as we “speak”. It’s very likely it changed by just addition of one or two new mini-chromosomes and this is routine in germ evolution. The events require no special conditions, but they would be promoted by large organism numbers and especially selective pressure like copper and antibiotics. A later post refers to
        http://www.nature.com/news/2011/110609/full/news.2011.360.html which discusses the possible role of antibiotics in promoting the spread of toxin genes among different E. coli pathogens. One other factor not fully discussed yet is that bacteria like to exchange genes on surfaces. This germ has a surface coat called Antigen 43 that is predicted to help it attach to surfaces (vegetable leaves, rocks in streams). These would provide the opportunities for gene transfer too. There is a huge scientific literature on this topic. It has been “hot” microbiology for about ten years.

  • My collegue who is physician almost lost his daughter tu HUS by EHEC 2006. The child survived fortunately. As the microbiologist approach the phenomen of EHEC in Germnany sucessfully the epidemologists have no clue. The scientifiv community is bullied by the rentseekers in the biogas business and the strong organic farming lobby in Germany.
    Thanks for all remarks which helped to make up my mind.

    • Oh how horrible for your Colleague and his family.

      Bullying is unfortunately not an isolated event in the organic sector and from the anti-GMO lobby groups. On 2 occasions when I have raised the issue of risks due to E. coli in organic produce in public discussions about possible risks from genetically engineered foods, the same leader of a major organic farming group has threatened me with legal action if I say any more about this issue. On another occasion another member of this lobby sector has threatened my employer with legal action over some fair public communication of benefits of Bt-maize in preventing fumonisin toxin formation, a serious issue with “organic maize meal” (cornflour). See also what happened in Italy on fumonisins.

      Given the harm caused by this bullying and the issues raised by the truly horrible foodborne disease outbreak now happening in Northern Europe it is crucial to have direct debate on these matters. Unfortunately, most scientists don’t have the time nor the backbone to get their views over in public in the face of the behaviour. The rent-seeking by the biofuel sector also is a major moral scandal, and is a significant contribution to high global food prices. Both these issues and the politics that surround them need public discussion but until now most newspapers have stayed away. This satire item is a good start.

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