Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2022

Cyanobacteria as a critical reservoir of the environmental antimicrobial resistome (82538)

Verlaine J Timms 1 , Sean Bentsen 1 , Brett A Neilan 1
  1. School of Environmental and Life Sciences, University of Newcastle, Newcastle, NSW, Australia

Antimicrobial resistance (AMR) is predicted to cause a staggering 10 million deaths worldwide by 20501. This looming public health threat is thought to be a result of antibiotic over-use and the flux of antibiotic pollution from human activity. For example, 80% of antibiotics used in aquaculture end up in the environment2. This is thought to maintain environmental AMR gene prevalence that is potentially passed to pathogens of concern. The importance of the environmental resistome in maintaining and disseminating AMR genes is little understood. One dominant environmental bacterial species, the cyanobacteria, can harbour AMR genes, however little is known of the distribution and diversity of AMR genes in this group.

 

Cyanobacterial genomes (n=873) were downloaded from NCBI datasets https://www.ncbi.nlm.nih.gov/datasets/genomes/ in July 2021. Genomes were annotated (Prokka version 1.14.6) and AMR gene alleles predicted using ABRicate (version 0.9.8) with AMRFinder, NCBI, Card, Argannot and ResFinder databases. Genes with an identity > 75% were included for further analysis.

 

A total of 112 AMR genes with an average identity of 82% were found across 86 genomes. The predicted antibiotic resistance phenotypes (with number of genes) were: aminoglycoside (n = 6), beta-lactam (n = 9), chloramphenicol (n = 7), macrolide/ macrolide-lincosamide-streptogramin (n = 2), rifamycin (n =73), streptogramin (n = 7), tetracycline (n = 8). AMR genes were found in a range of environments across freshwater (n=23), terrestrial (n=29), host-associated (n=14), marine (n=7), thermal springs (n= 7) and unknown (n=9).

 

AMR genes to a range of antibiotic classes were present across all species of cyanobacteria with the potential to spread to other bacteria. AMR genes predicting rifamycin resistance dominated and these were found in genomes from a range of environments. Significantly, screening for rifamycin resistance genes has not been performed in studies employing PCR methods on environmental samples. This large genomic analysis can be used to inform future studies on which AMR genes should be targeted when assessing the burden of AMR in the environment.

  1. 1. Murray, C. L. J. et al. doi.org/10.1016/S0140-6736(21)02724-0 (2022).
  2. 2. Cabello, F. C. et. al. doi:10.1111/1462-2920.14891 (2020).