Abstract
Escherichia coli is a predominant bacterium in the intestinal tracts of animals. Phylogenetically, strains have been classified into seven phylogroups, A, B1, B2, C, D, E, and F. Pathogenic strains have been categorized into several pathotypes such as Enteropathogenic (EPEC), Enterotoxigenic (ETEC), Enteroinvasive (EIEC), Enteroaggregative (EAEC), Diffusely adherent (DAEC), Uropathogenic (UPEC), Shiga-toxin producing (STEC) or Enterohemorrhagic (EHEC) and Extra-intestinal pathogenic E. coli (ExPEC). E. coli also survives as a commensal on the ocular surface. However, under conditions of trauma and immune-compromised states, E. coli causes conjunctivitis, keratitis, endopthalmitis, dacyrocystitis, etc. The phylogenetic affiliation and the pathotype status of these ocular E. coli strains is not known. For this purpose, the whole-genome sequencing of the 10 ocular E. coli strains was accomplished. Based on whole-genome SNP variation, the ocular E. coli strains were assigned to phylogenetic groups A (two isolates), B2 (seven isolates), and C (one isolate). Furthermore, results indicated that ocular E. coli originated either from feces (enteropathogenic and enterotoxigenic), urine (uropathogenic), or from extra-intestinal sources (extra-intestinal pathogenic). A high concordance was observed between the presence of AMR (Antimicrobial Resistance) genes and antibiotic resistance in the ocular E. coli strains. Furthermore, several virulent genes (fimB to fimI, papB to papX, etc.) and prophages (Enterobacteria phage HK97, Enterobacteria phage P1, Escherichia phage D108 etc.) were unique to ocular E. coli. This is the first report on a whole-genome analysis of ocular E. coli strains.
Highlights
The human eye is sterile prior to birth, but immediately after birth the ocular surface acquires several bacteria from the mother and the environment, and these survive on the ocular surface as commensals
The genomes of the 10 ocular strains were sequenced and compared with that of E. coli MG1655 with respect to several characteristics like genome coverage, completeness, the number of genes, the G+C% content of DNA, and number of tRNA genes (Table 1 and Table S1) which indicated a high degree of similarity and that majority of the genes were affiliated to E. coli MG1655
We detected chromosomal mutations inparE, gyrA, and parC that conferred resistance to fluoroquinolones like nalidixic acid and ciprofloxacin (Table 2B).We observed one or more of these three generalizations across all the antibiotic groups studied (Tables 2A,B and 3A). These results were in accordance with earlier results that demonstrated the presence of blaCTX-M-15 in E. coli strains from India [43,44] and from Europe, Asia, Canada, and United Kingdom [45,46,47,48]
Summary
The human eye is sterile prior to birth, but immediately after birth the ocular surface acquires several bacteria from the mother and the environment, and these survive on the ocular surface as commensals. Based on 16S rRNA gene sequencing, a greater bacterial diversity has been observed associated with the lid margin and lower conjunctival sac [1,2,3]. These bacteria are normally harmless and do not cause any infections. Virulence is enhanced by virulent factors [8], the presence of prophages, plasmids, ability to conjugate, etc. These studies suggested that transposons, plasmids and insertion sequences contribute to the plasticity of the E. coli genome, resulting in an extremely large pangenome [10]
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