pubmed.ncbi.nlm.nih.gov

Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems - PubMed

️Sat Jan 01 2022

Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems

Manita Guragain et al. Sci Rep. 2022.

Abstract

Certain strains of Escherichia coli possess and express the toxin colibactin (Clb) which induces host mutations identical to the signature mutations of colorectal cancer (CRC) that lead to tumorigenic lesions. Since cattle are a known reservoir of several Enterobacteriaceae including E. coli, this study screened for clb amongst E. coli isolated from colons of cattle-at-harvest (entering beef processing facility; n = 1430), across the beef processing continuum (feedlot to finished subprimal beef; n = 232), and in ground beef (n = 1074). Results demonstrated that clb⁺ E. coli were present in cattle and beef. Prevalence of clb⁺ E. coli from colonic contents of cattle and ground beef was 18.3% and 5.5%, respectively. clb⁺ E. coli were found susceptible to commonly used meat processing interventions. Whole genome sequencing of 54 bovine and beef clb⁺ isolates showed clb occurred in diverse genetic backgrounds, most frequently in phylogroup B1 (70.4%), MLST 1079 (42.6%), and serogroup O49 (40.7%).

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

**Figure 1**
*clb*⁺ *E. coli* among cattle-at-harvest. (a) Percentage prevalence of *clb*⁺ *E. coli* among all generic *E. coli* isolated from cattle (b) Number of animals carrying *clb*⁺ *E. coli*. (c) Number of cattle lots carrying *clb*⁺ *E. coli.* Statistical significance was calculated by Fisher’s exact test. *, significant (p < 0.05); ***, extremely significant (p < 0.001). CONV, conventionally raised; RWA, Raised without antibiotics.

**Figure 2**
*clb*⁺ *E. coli* occurring in ground beef. (a) Percentage prevalence of *clb*⁺ *E. coli* in ground beef among all generic *E. coli* isolated; (b) Percentage of ground beef samples carrying *clb*⁺ *E. coli.* Statistical significance was calculated by Fisher’s exact test. *, significant (p < 0.05). CONV: ground beef produced from conventionally raised cattle; RWA: ground beef produced with label claim of “from beef raised without antibiotics”.

**Figure 3**
Beef flank inoculation assay. LA, 2% lactic acid (1 min). PAA, 200 ppm peroxyacetic acid (1 min). Brom, 300 ppm BoviBromine (1 min). Steam, flank surface temperature achieved 82 °C with dry steam (15 s). Statistical significance between *clb*⁺ *E. coli* and reference *E. coli* O157:H7 was calculated by Fisher’s exact test (p ≥ 0.05, not significant). Data presented represents average of 2 biological replicates, 12 technical replicates each on individual beef flanks. *clb*⁺ *E. coli*, *E. coli* O157:H7.

formula image — **Figure 3**
Beef flank inoculation assay. LA, 2% lactic acid (1 min). PAA, 200 ppm peroxyacetic acid (1 min). Brom, 300 ppm BoviBromine (1 min). Steam, flank surface temperature achieved 82 °C with dry steam (15 s). Statistical significance between *clb*⁺ *E. coli* and reference *E. coli* O157:H7 was calculated by Fisher’s exact test (p ≥ 0.05, not significant). Data presented represents average of 2 biological replicates, 12 technical replicates each on individual beef flanks. *clb*⁺ *E. coli*, *E. coli* O157:H7.

**Figure 4**
Maximum likelihood phylogenetic tree of (a) 54 core genomes of *clb*⁺ *E. coli* isolated from beef production and processing continuum, and (b) 39 *pks* island sequences extracted from the contigs carrying full length *pks* island (*clbA*-*clbS*). Phylogenetic trees were constructed using IQ-tree and visualized with iTOL v6. Numbers on the outermost column represent multilocus sequence types (MLST).

**Figure 5**
Distribution of acquired antibiotic resistance genes in *clb*⁺ *E. coli*. Heat map was created and visualized using ggplot2 package of R. Column represents *E. coli* isolates and row represents acquired antibiotic resistance genes. *, Phylogroup B2; # Phylogroup A.

**Figure 6**
Distribution of acquired virulence genes in *clb*⁺ *E. coli*. Heat map was created and visualized using ggplot2 package of R. Column represents *E. coli* isolates and row represents acquired virulence genes. *, Phylogroup B2; # Phylogroup A.

Cited by

The GEA pipeline for characterizing Escherichia coli and Salmonella genomes.
Dickey AM, Schmidt JW, Bono JL, Guragain M. Dickey AM, et al. Sci Rep. 2024 Jun 10;14(1):13257. doi: 10.1038/s41598-024-63832-z. Sci Rep. 2024. PMID: 38858528 Free PMC article.

References

1. U.S Cancer Statistics Working group. U.S. Cancer statistics data visualizations tool, baed on 2020 submission data (1998–2018) (2021). www.cdc.gov/cancer/dataviz
1. Dekker E, Tanis PJ, Vleugels JLA, Kasi PM, Wallace MB. Colorectal cancer. Lancet. 2019;394:1467–1480. doi: 10.1016/S0140-6736(19)32319-0. - DOI - PubMed
1. Bouvard V, et al. Carcinogenicity of consumption of red and processed meat. Lancet Oncol. 2015;16:1599–1600. doi: 10.1016/S1470-2045(15)00444-1. - DOI - PubMed
1. Domingo JL, Nadal M. Carcinogenicity of consumption of red meat and processed meat: A review of scientific news since the IARC decision. Food Chem. Toxicol. 2017;105:256–261. doi: 10.1016/j.fct.2017.04.028. - DOI - PubMed
1. Buc E, et al. High prevalence of mucosa-associated E. coli producing cyclomodulin and genotoxin in colon cancer. PLoS ONE. 2013;8:e56964. doi: 10.1371/journal.pone.0056964. - DOI - PMC - PubMed

Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems - PubMed