Discovery of novel shiga toxin-producing Escherichia coli (STEC)- specific bacteriophages from non-fecal composts using genomic characterization

Authors: Liao, Yen-Te; SUN, XINCHENG - Zhengzhou University; Quintela, Irwin; Bridges, David; LIU, FANG - Ocean University Of China; ZHANG, YUJIE - Shanghai Ocean University; Salvador, Alexandra; Wu, Vivian

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/12/2019
Publication Date: 4/2/2019
Citation: Liao, Y., Sun, X., Quintela, I.A., Bridges, D.F., Liu, F., Zhang, Y., Salvador, A., Wu, V.C. 2019. Discovery of novel shiga toxin-producing Escherichia coli (STEC)- specific bacteriophages from non-fecal composts using genomic characterization. Frontiers in Microbiology. 10:627. https://doi.org/10.3389/fmicb.2019.00627.
DOI: https://doi.org/10.3389/fmicb.2019.00627

Interpretive Summary: Composting is a complex process to degrade waste organic materials and to produce the finished products that can be used as soil amendments to improve crop yields. Manure-based composts have been widely researched for the presence of enteric pathogens, such STEC, because animal gastrointestinal tracts are the reservoir for these pathogens. In addition, STEC-specific phages are commonly isolated from feces or fecal-contaminated environments potentially due to high prevalence of STEC in the environment. However, not much research is focusing on the presence of STEC-specific bacteriophages in the composts free of fecal origin. Thus, the objectives of this study were to isolate and genomically characterize free STEC-specific bacteriophages, and to evaluate its association with STEC strains in the non-fecal composts. We isolated various STEC-specific phages against O111, O121, O145 and O157 STEC strains from the composts of yard trimmings and food scraps and further genomically characterized 4 phages, including vB_EcoM Ro111lw, vB_EcoM Ro121lw, vB_EcoS Ro145lw and vB_EcoM Ro157lw. These phages were named after the host range, phage morphology and the serotype of primary STEC strain. Most phages except for vB_EcoS Ro145lw (family Siphoviridae with long noncontractile tail) belonged to family Myoviridae with long contractile tail. The genomic analyses indicated that these phages were diverse at genetic level and no virulence genes, such stx, were found. The findings of this study provide valuable information regarding various novel STEC-specific phages isolated from non-fecal environment.

Technical Abstract: Composting is a complex process of degrading organic materials used for soil amendments to improve crop yields. A proper composting process can confer bactericidal effects due to the change of pH and temperature. Manure-based composts have been widely researched for the presence of enteric pathogens, such as STEC, because animal gastrointestinal tracts are the reservoir for these pathogens. Additionally, bacteriophages specific to Shiga toxin-producing E. coli (STEC) are commonly isolated from feces or fecal-contaminated environment. However, little is known regarding the presence of STEC-specific bacteriophages in the composts free of fecal origin. Thus, the objectives of this study were to isolate and genomically characterize free STEC-specific bacteriophages, and to evaluate its association with STEC strains in the non-fecal composts. For bacteriophage isolation, two compost samples of brush trimmings and food scraps were enriched with non-pathogenic E. coli (3 strains) and STEC strains (14 strains) cocktails, respectively. After purification, host range, plaque size, and phage morphology were obtained. Phage genomes were sequenced using Miseq sequencer with approximately 5 million paired-end (250-bp) sequence reads. Isolation of O157 and top six non-O157 STEC strains by use of culture methods combined with PCR-based confirmation was also conducted. Results showed that four novel STEC-infecting phages, including vB_EcoM Ro111lw, vB_EcoM Ro121lw, vB_EcoS Ro145lw and vB_EcoM Ro157lw, were isolated; however, no STEC strains were found. Although most phages except for vB_EcoS Ro145lw (family Siphoviridae) belonged to family Myoviridae, the plaque size and host range among all these phages varied. The phages were diverse in genetic levels but none was positive of stx or other virulence genes. Furthermore, phage vB_EcoM Ro111lw was the only one classified at species level as Felix 01-like phage. The findings of this study provide valuable insight of various novel STEC-specific phages isolated from non-fecal environment; furthermore, no STEC found in the samples and no virulence genes encoded in the phages likely indicate these phages are potential candidates to control STEC strains.