Pathogenicity Classification using Phylogenetic Analysis of Escherichia coli Strains
Authors: Mohamed Ibrahim Ahmed Farah , Yusof Nik Yusnoraini , Mat-Sharani Shuhaila 
Published: November 2022

Escherichia coli (E. coli) is an adaptable gram-negative bacillus facultative an aerobic bacterium that belongs to the family of Enterobacteriaceae. It is well known to be a commensal of the human and animal gastrointestinal tract and environments unrelated to the host, such as water, soil, manure, and food.  This study was focused on identifying the pathogenicity of three local isolated E. coli strains (Malaysia) compared to the other 22 completed genome strains from the available database. The local strains are INF13/18/A [1], INF32/16/A [2], and INF191/17/A [3]. which are identified as extended-spectrum beta-lactamase types. 16S rRNA was used to build a phylogenetic tree by using MUSCLE for alignment and MEGA with 1000 bootstraps to build a tree (Figure 1), and then Figtree was used for visualisation. The outlier in this phylogenetic analysis is H3RV (a mycobacterium strain).

 

The analysis revealed that the 22 completed genome strains can be divided into two main clusters with one cluster mainly more pathogen and least pathogen. Based on previous pathogenicity studies revealed that Shiga-toxin-producing E. coli are pathogens that are ER strains that cause diarrheal disease in humans and are of a public health concern due to their ability to cause outbreaks and severe diseases such as haemorrhagic colitis or haemolytic-uremic syndrome [4].

 

Furthermore, CVM strains also reported as pathogen (GCA_008385405.1, GCA_008386375.1, GCA_004281435.2, GCA_008385205.1, and GCA_008383145.1). Therefore, the first cluster containing all ER strains and CVM is pathogenic. The second cluster included all local strains, two of the local strains (INF13/18/A and INF191/17/A) closely with Al Ain [5] and AR-0427 (GCF_008727195.1) which both are known to be Shiga-toxin producing strains (0157). This suggested that these two local strains are true pathogens. While one of the other local strains INF32/16/A shares a recent common ancestor with a non-pathogenic laboratory strain K-12 substr. MG1655 [6], which could be probably suggested that this local strain is non-pathogenic.

 

In addition to that the second clusters, JME strains were clustered together with ecMN1F (GCA_008824125.1). The distribution of lineage is also not related to sampling locations because the first cluster has CVM strains and ER strains from the USA and New Zealand, respectively. While the two local strains from Malaysian strains were also found close to the United States of America (K-12 substr. MG1655) [6].

 

In conclusion, this study shows the pathogenicity group classification of E. coli strains and requires further investigation to determine the level of pathogenicity of these organisms.

A phylogenetic of E. coli used 16S rRNA, shows dividing into two common ancestors and the outlier, the strains of the above common ancestor such as CVM and ER [7] strains are true pathogenic, while the strains of the second common ancestor are showing some pathogenic and some non-pathogenic which closely related with the local sample.