NCTC86

EscherichSupplementary online material for:
From Escherich to the Escherichia coli genome:
how a commensal bacterium shaped the history of modern microbiology

Guillaume Méric1, Matthew D. Hitchings2, Ben Pascoe1,3, Samuel K. Sheppard1,3,4

1Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK; 2Swansea University Medical School, Institute of Life Science, Singleton Park, Swansea, UK; 3MRC Cloud Infrastructure for Microbial Bioinformatics (CLIMB) Consortium, UK; 4Department of Zoology, University of Oxford, Oxford, UK.

This companion webpage contains supplementary material to the study of the dissemination and genomics of Escherichia coli strain NCTC86, one of the very first isolates of Theodor Escherich from 1885, published in 2016 in The Lancet Infectious Diseases.

Supplementary methods and analyses (genomics):

From the original stock archived at the NCTC, we obtained the whole genome sequence of NCTC86 using an Illumina MiSeq. The assembly of raw reads was made using Velvet into 314 contiguous sequences for a total assembled length of 4,933,644 bp (N50=32,645bp, N90=9,133bp). The genome sequence was archived in a BIGSdb web-based platform which allowed the export of specific sequences using BLAST [1]. Contiguous sequences were automatically annotated using RAST [2], giving a list of 4,856 predicted coding sequences in NCTC86. A reference pan-genome [3] was created using 12 reference genomes and NCTC86 (Table S1), and the resulting list of 7,608 genes was examined in a gene-by-gene manner [4] in a total of 72 public reference genomes, including NCTC86. All genomes shared 2,600 core genes, from which a concatenated gene-by-gene [4,5] alignment and a neighbour-joining phylogenetic tree were created (Figure S2). Strain NCTC86 shared 4,142 genes (85.3% of its coding genome) with the pig E. coli strain B41 (NCBI accession: NZ_AFAH00000000.2), which was its closest relative from our comparison dataset on a phylogenetic tree (Figure S2). Of these shared genes, 2,688 alleles (64.8% of all shared genes) were identical. There were 35 genes that were found only in NCTC86, amongst which genes possibly involved in maltose/maltodextrin utilisation and mannitol metabolism (Table S2), and possibly contributing to the positive maltose fermentation test performed in 1952 on the strain (Figure S1). Also in the list are some fimbriae and fimbrial assembly precursors (Table S2) that could play a role in host colonisation.

NCTC86 belongs to the common ST-10 within phylogroup A, and its reported resistance to penicillin and erythromycin (Figure S2) was not reflected by the presence of any allele listed in the Comprehensive Antibiotic Resistance Database (CARD) [6] or from the Lahey Clinic comprehensive list (http://www.lahey.org/Studies/), suggesting that specific mutations or general efflux metabolisms could contribute to this reported resistance. In our study, no gene associated with resistance to synthetic antibiotics such as sulphonamides or quinolones was detected in NCTC86. The isolate did not harbour any gene encoding for Shiga toxin subunits. Moreover, using the pathogenicity-island (PAI) detection server PAIDB v2.0 [7], we found no obvious PAI in the genome NCTC86. Additionally, very few virulence/colonisation-associated factors were detected: (a) the hek outermembrane protein, which is an auto-aggregating adhesin and invasion [8], (b) sfaEFA, from the S-fimbriae biosynthesis cluster, which linked to the attachment of bacteria to the host tissues [9] and (c) the entire vpeRABC locus, responsible for the biosynthesis of a carbohydrate permease that has been linked to fitness and virulence of uropathogenic E. coli (UPEC) [10].

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Supplementary figures and tables:

Figure S1. Reproduction of the earliest Batch Records for strain NCTC86 at the National Culture Type Collections.

FigureS1 (1).jpg

Figure S2. Phylogenetic context of strain NCTC86. The tree has been constructed using a neighbour-joining algorithm, based on gene-by-gene whole-genome alignments of strain NCTC86 with 71 other publicly-available representative genomes. The scale indicates the number of substitutions per sites.

FigureS2.jpg

Table S1. Genomes used to construct a reference pan-genome used in this study.

TableS1.jpg

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  3. Crossman LC, Chaudhuri RR, Beatson SA, Wells TJ, Desvaux M, et al. (2010) A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407. J Bacteriol 192: 5822-5831.
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Table S2. Genes specifically detected in E. coli strain NCTC86 and not in 71 other reference E. coli genomes. Annotations and predicted functions are based on automatic annotations using the RAST server [18]. FIGfam codes are as inferred by RAST, and defined as predicted similar functions for the predicted encoded protein for genes having the same FIGfam code. RAST evidence codes are a summary of the functional groups of the predicted gene functions.

TableS2.jpg

Data deposition:
The genome sequence of E. coli NCTC86 is available on the NCBI repository (BioProject: PRJNA312020; Biosample: SAMN04492850).

Acknowledgements:
Work in the Sheppard laboratory is supported by grants from the Wellcome Trust and the Medical Research Council (MRC). Genome sequencing was supported by the A4B project funded by the Welsh Assembly. G.M. is supported by a NISCHR Health Research Fellowship (HF-14-13). We thank Trevor Hince and Naomi King at the Lister Institute for their very kind help and access to archives. We thank Julie Russell for discussions and access to the archives of the NCTC labs.

Complete list of references cited in the manuscript:

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  18. Blattner FR, Plunkett G, 3rd, Bloch CA, Perna NT, Burland V, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462.
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