Distribution of Phylogenetic Groups in Human Commensal Escherichia coli. Jannine K. Bailey, Jeremy L. Pinyon, Sashindran Anantham and Ruth M.

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1 JCM Accepts, published online ahead of print on 7 July 2010 J. Clin. Microbiol. doi: /jcm Copyright 2010, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved Distribution of Phylogenetic Groups in Human Commensal Escherichia coli Jannine K. Bailey, Jeremy L. Pinyon, Sashindran Anantham and Ruth M. Hall School of Molecular Bioscience, The University of Sydney, NSW 2006 Running title: Phylogenetic group and commensal E. coli Text word count: 518 Corresponding Author: Ruth M. Hall Mailing address: School of Molecular Bioscience, Biochemistry and Microbiology Building G08, The University of Sydney, NSW 2006, Australia. Phone: Fax: ruth.hall@mmb.usyd.edu.au

2 Most Escherichia coli infections other than gastrointestinal infections are believed to originate from human fecal flora and the term extra-intestinal pathogenic Escherichia coli (ExPEC) was introduced to describe these E. coli [13]. However, there is an enormous diversity of strains within the species E. coli, making it difficult to clearly identify the potential ExPEC strains amongst the gut E. coli from healthy people by any simple measure. One categorisation of E. coli isolates that is frequently determined is the phylogenetic group. E. coli generally fall into one of four phylogenetic groups: A, B1, B2, and D and early studies using MLEE, multilocus enzyme electrophoresis, indicated that isolates from human feces are not equally distributed between the groups, with group A predominant, whereas amongst ExPEC strains groups B2 and D predominate [see 13 and references therein]. A subsequent study using a triplex PCR to determine phylogenetic group [1] found a predominance of groups A and B1 [2] and it has become common for authors to state that phylogenetic groups A and B1 predominate amongst commensal E. coli. We have used the same multiplex assay to test 68 distinct E. coli strains recovered from the feces of healthy adults who had not taken antibiotics in the preceding 6 months and found a substantial under-representation of the B1 type at 7.4% of isolates (Table). This led us to re-examine published data on the distribution of phylogenetic groups amongst human commensal E. coli. Only data sets that used either a single isolate per individual, or a single representative of strains identified by extensive characterization of multiple isolates from the same sample, were included, and the total isolates listed is Specific features of the populations from which samples were collected are listed as footnotes. Comparison of the results of different studies reveals considerable variation in which phylogenetic group is most often encountered, and no clear trend to an excess abundance of groups A and B1 relative to B2 and D. Indeed, B1 is over-represented, measured as greater than 25% of isolates, in only 5 of the 25 studies listed, and is under-represented in the total at 17.9%. Phylogenetic group A, 2

3 which currently includes isolates that give no signal with the triplex PCR and may represent distinct types [17], is over-represented in 16 of 25 studies, and in the global total (32.0%). However, phylogenetic group B2 is also over-represented in 11 studies, including the largest which examined 530 isolates. Overall, 29.4% of the total isolates were from group B2. The combined data from these 1889 strains thus reveal that groups A and B2 are both somewhat more abundant (32.0% and 29.4% of total, respectively) than B1 or D (17.9% and 20.7% of total, respectively) in human feces, and a similar conclusion has recently been drawn by others [16]. While both geographic and temporal variation as well as specific features of the populations used may have influenced the outcome of the various studies, the differences could also simply be a reflection of the enormous overall diversity in the E. coli species pool. ACKNOWLEDGEMENTS The work, J. L. P and J. K. B. are supported by National Health and Medical Research Council (NHMRC) project grant ; R. M. H. is supported by an NHMRC Research Fellowship Grant S. A. is supported by an Australian Postgraduate Award. We thank all the participants from whom informed consent was obtained in accordance with the requirements of the Human Ethics Committee approval ( /10778) for the study. REFERENCES 1. Clermont, O., S. Bonacorsi, and E. Bingen Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66: Duriez, P., O. Clermont, S. Bonacorsi, E. Bingen, A. Chaventre, J. Elion, B. Picard, and E. Denamur Commensal Escherichia coli isolates are phylogenetically 3

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7 132 Table 1. Distribution of phylogenetic groups in commensal E. coli from human faeces Location Number Phylogenetic group Reference of Isolates Incidence Percentage Analysed a A B1 B2 D A B1 B2 D USA, Sweden [1] Paris, France [2] Olib & Silba, Croatia [2] Dogon, Mali [2] Michigan, USA [19] France b [7] Tokyo, Japan c [12] France d [18] Paris, France [3] Brest, France [3] Brittany, France e [3] Brittany, France f [3] French Guyana [3] Cotonou, Benin [3] Bogota, Colombia [3] Minnesota, USA g [15] Canberra, Australia [4] Madrid, Spain [6] Sweden h [11] Sweden i [10] Spain [14] USA j [5] Spain k [8] Spain [9] Sydney, Australia this study GLOBAL TOTAL a Where > 1 isolate per subject was used, prior identification of strains had been undertaken. b Hospital staff. 7

8 c Hospital food court staff. d Pregnant women. e Bank and insurance workers. f Pig farmers. g Newly admitted inpatients with no evidence of acute infection. h Infants 0-12 months old. i Schoolgirls aged 7-16 years. j 622 subjects were newly admitted hospital patients, disease status is unknown; the remaining 100 subjects were vegetarians; all from Minnesota & Wisconsin. k Subjects had suspected acute cystitis. Downloaded from on July 5, 2018 by guest 8