Posts Tagged ‘Antibiotic resistance’
June 27, 2011 Institute of Science in Society
Greatly assisted horizontal gene transfer and recombination turned previously harmless bacteria into dangerous pathogens Dr. Mae-Wan Ho
Rapid decoding in the new scientific commons
The E. coli O104:H4 genome was rapidly decoded within days of the initial outbreak in Germany by Beijing Genomics Institute (BGI)’s third generation technologies, and the raw data promptly uploaded to a public database (ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482) so geneticists all over the world could analyse and annotate the sequences and share their findings quickly in a new scientific commons on the internet.
It was clear that the outbreak E. coli O104:H4 is a new strain with a genome size of about 5.2 Mbp (million basepairs), which unusually, has both the properties of enteroaggregative E. coli (EAEC) that cause diarrhoea and enterohaemolytic E. coli (EHEC) that cause haemolytic uremic syndrome (HUS, or bloody urine), along with resistance to the widest range of antibiotics .
The outbreak strain is most similar to EAEC 55989, previously isolated in the Central African Republic from an HIV-positive adult, and since emerged as a major cause of diarrhoea in children and adults worldwide . EAEC carry small extra units of genetic material called plasmids; the German outbreak strain has the typical plasmid genes of EAEC bacteria, as well as the Shiga toxin genes of EHEC carried on prophage (genome of bacteria virus) integrated in the bacterial chromosome.
Rampant horizontal gene transfer
Preliminary analyses using an algorithm that searches for protein similarity to define genes based on known proteins in E. coli and other bacteria, detected 6327 genes in all, 6156 coding for proteins and 171 coding for ribosomal and tRNA.
Of the proteins identified, 33 genes are toxins, 3 suspected haemolysins (proteins causing haemolysis), a putative hemolysin expression modulating protein, and a channel protein of hemolysin III family. In addition, 31 predicted genes are related to specific antibiotic resistance: beta-lactamic, aminoglycoside, macrolide, polymyxin, tetracycline, fosfomycin and deoxycholate, novobiocin, chloramphenicol, bicyclomycin, norfloxacin and enoxacin and 6-mercaptopurine . The strain is also rich in adhesion, secretion systems, pathogenicity and virulence related proteins. It seems to have a restriction-modification system, many proteins involved in Fe transport and utilization (siderophores as aerobactin and enterobactin), lysozyme, one inhibitor of pancreatic serine proteases, proteins involved in anaerobic respiration, antimicrobial peptides, proteins involved in quorum sensing and biofilm formation that could confer competitive advantage to the strain. There are genes for tellurium resistance and resistance to other metals including mercury, nickel, copper, zinc and cobalt, and more than 170 phage proteins.
The proteins are from all major classes of E. coli, pathogenic and otherwise, and at least 21 bacteria of other genera. Most of the proteins (2810) are from E. coli O26:H11 (strain 11368/EHEC), while the second largest contribution (1166) are from E.coli O44:H18 (strain 042/EAEC). Only 51 proteins are recognizably from E. coli K12, the laboratory strain originating from the original ‘wild-type’ isolate, a harmless strain. Other bacteria with major contributions include Salmonella typhi (54 proteins), Yersinia pestis (29 proteins), Shigella dysenteriae (16 proteins) S. flexneri (20 proteins), S. boydii (9 proteins) and Bacillus cereus.
Judging from the fact that only 51 of 6156 proteins in the outbreak strain are identified with E. coli K12, the degree of divergence from the harmless ‘wild-type’ is more than 99 percent, and much of that could be due to horizontal gene transfer.
Do you know what is in your meat?
If you buy your meat at a supermarket in Canada, it is likely to be contaminated with multiple antibiotic-resistant superbugs like salmonella and E. coli. Researchers with CBC’s Marketplace bought 100 samples of chicken from major brands at large chain supermarkets in Montreal, Toronto and Vancouver and tested them for bacteria. Their findings: Two-thirds of the chicken samples tested had bacteria, which often happens with raw chicken, but all of that bacteria was resistant to at least one antibiotic. Some of the samples were resistant to between six and eight types of antibiotics.
Some of the brands included in this study were:
- Lilydale: resistant to 5 antibiotics.
- Maple Leaf Prime: resistant to 6 antibiotics.
- Rava: resistant to 7 antibiotics.
- Loblaws Club Pack: resistant to 8 antibiotics.
Some experts say that chicken in Canada get antibiotics every day as part of their feed, regardless of whether they are sick or not. The Chicken Farmers of Canada claim that there is only “judicious” use of antibiotics (and not simply routine use of it).
The Marketplace researchers even tested brands advertised as “antibiotic-free,” such as Loblaws “Free From” brand, as well as organic chicken brands. They were alamred to find that even these chickens had antibiotic-resistant bugs. One organic farmer in Quebec said that they do not use any antibiotics at all, but they do buy conventional chicks (which are then raised organic) and he says the only conceivable way his meat could have been exposed to antibiotics is if the eggs were injected with antibiotics before he takes the chicks.
H.R. 1549, the Preservation of Antibiotics For Medical Treatment Act of 2009 now under consideration by the House, would limit the amount of antibiotics that can be used on factory animal farms. “The farm lobby’s opposition makes its passage unlikely,” The New York Times reported Monday.
Industrial agriculture has adopted many practices that put public health at risk. Factory farms routinely feed animals antibiotics to off-set crowding and bad sanitation.