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

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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

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