A clinical metagenomic study of biopsies from Mexican endophthalmitis patients reveals the presence of complex bacterial communities and a diversity of resistance genes

Abstract

Infectious endophthalmitis is a severe ophthalmic emergency. This infection can be caused by bacteria and fungi. For efficient treatment, the administration of antimicrobial drugs to which the microbes are susceptible is essential. The aim of this study was to identify micro-organisms in biopsies of Mexican endophthalmitis patients using metagenomic next-generation sequencing and determine which antibiotic resistance genes were present in the biopsy samples. In this prospective case study, 19 endophthalmitis patients were recruited. Samples of vitreous or aqueous humour were extracted for DNA extraction for metagenomic next-generation sequencing. Analysis of the sequencing results revealed the presence of a wide variety of bacteria in the biopsies. Resistome analysis showed that homologues of antibiotic resistance genes were present in several biopsy samples. Genes possibly conferring resistance to ceftazidime and vancomycin were detected in addition to various genes encoding efflux pumps. Our findings contrast with the widespread opinion that only one or a few bacterial strains are present in the infected tissues of endophthalmitis patients. These diverse communities might host many of the resistance genes that were detected, which can further complicate the infections.

Keywords: endophthalmitis; moxifloxacin; resistome; shotgun metagenomics.

Fig. 1.. Relative abundance of sequencing reads assigned to taxonomic classes. Samples from left to right: META2, META3, META6, META7, META8, C15, C16, C17 and C19.

Fig. 2.. Heatmaps showing the 25 most abundant micro-organisms and virus per sample. (a) Samples META2, 3, 6, 7 and 8. (b) Samples C15, 16, 17 and 19. The top bar in both panels represents the mapping of the numerical values to a colour scale.

Fig. 3.. Heatmap of antibiotic resistance genes present in the samples.