Abstract:
Karst forests comprise 11.7% of the total land surface of the Philippines. Limited
research has been conducted to study this ecosystem since local research is chiefly
focused on its economic value, and not on the public health threats these unexplored
forests may impose. The possible relationship between resistomes and the soil microbial
communities (SMCs) of these landscapes are still poorly understood. As of the writing of
the current study, none of the karst forest soils have had their resistomes profiled. This
objective of the study is to provide a resistome profile of the metagenomic datasets from
unexplored karst forest soils in Guiuan, Samar. This includes the identification and
quantification of resistome types and gene groups in relation to SMCs. An efficient and
novel resistome pipeline, DugesiaAMR, was used for the descriptive and quantitative
analysis of putative resistome types and gene groups found within existing metagenomic
datasets. The datasets used were received from the Project 3 Team of CON-Kaigangan, a
program dedicated to the assessment and conservation of the karst landscapes found in
selected municipalities of Samar. Three resistome types were identified: drugs, metals,
and multi-compound. There were 26 resistome gene groups under drugs, 3 under metals,
and 2 under multi-compound. The findings showed the prevalence of drug resistance,
namely Macrolide-Lincosamide-Streptogramin (MLS), Aminoglycoside, and
Oxazolidinone resistance. DugesiaAMR was able to complete analysis of the datasets
(average of 168 million reads each) in 27 minutes on the 88-core high-performance
computing (HPC) machine and 81 minutes on the 4-core home computer, owing to the
high scalability of the programs used in the pipeline. The resistome types identified by
DugesiaAMR can spearhead further research on the resistome and SMCs of the
environmental samples and can subsequently enhance resistome surveillance in the
country.
