A hybrid DNA sequencing approach is needed to properly link genotype to phenotype in multi-drug resistant bacteria

Adeel Farooq, Jungman Kim, Shahbaz Raza, Jeonghwan Jang, Dukki Han, Michael J. Sadowsky, Tatsuya Unno

Research output: Contribution to journalArticlepeer-review

Abstract

Antibiotic resistance genes (ARGs) are now viewed as emerging contaminants posing a potential worldwide human health risk. The degree to which ARGs are transferred to other bacteria via mobile genetic elements (MGEs), including insertion sequences (ISs), plasmids, and phages, has a strong association with their likelihood to function as resistance transfer determinants. Consequently, understanding the structure and function of MGEs is paramount to assessing future health risks associated with ARGs in an environment subjected to strong antibiotic pressure. In this study we used whole genome sequencing, done using MinION and HiSeq platforms, to examine antibiotic resistance determinants among four multidrug resistant bacteria isolated from fish farm effluent in Jeju, South Korea. The combined data was used to ascertain the association between ARGs and MGEs. Hybrid assembly using HiSeq and MinION reads revealed the presence of IncFIB(K) and pVPH2 plasmids, whose sizes were verified using pulsed field gel electrophoresis. Twenty four ARGs and 95 MGEs were identified among the 955 coding sequences annotated on these plasmids. More importantly, 22 of 24 ARGs conferring resistance to various antibiotics were found to be located near MGEs, whereas about a half of the ARGs (11 out of 21) were so in chromosomes. Our results also suggest that the total phenotypic resistance exhibited by the isolates was mainly contributed by these putatively mobilizable ARGs. The study gives genomic insights into the origins of putatively mobilizable ARGs in bacteria subjected to selection pressure.

Original languageEnglish (US)
Article number117856
JournalEnvironmental Pollution
Volume289
Early online dateJul 26 2021
DOIs
StateE-pub ahead of print - Jul 26 2021

Bibliographical note

Funding Information:
This work was supported by the research program funded by the Korea Disease Control and Prevention Agency ( 2020-ER5408-00 ). This research was also supported by the Collaborative Genome Program of the Korea Institute of Marine Science and Technology Promotion ( KIMST ) funded by the Ministry of Oceans and Fisheries (MOF) (No. 20180430 ), the Basic Science Research Program to Research Institute for Basic Sciences (RIBS) of Jeju National University through the National Research Foundation of Korea (NRF) funded by the Ministry of Education ( 2019R1A6A1A10072987 ), and by the Minnesota Agricultural Experiment Station .

Publisher Copyright:
© 2021 Elsevier Ltd

Keywords

  • Hybrid assembly
  • Mobile genetic elements
  • Mobilizable ARGs
  • Multidrug resistance

PubMed: MeSH publication types

  • Journal Article

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