Identification of novel prophages and variants of integrative and conjugative elements in Elizabethkingia anophelis clinical isolates from Seremban, Malaysia.

Elizabethkingia anophelis is an emerging multidrug-resistant pathogen with scarce data from Malaysia. Here we present the complete genome sequences of seven E. anophelis clinical isolates from a tertiary hospital in Seremban, Malaysia. These sequences were analysed alongside over 400 publicly available E. anophelis genomes worldwide. Three of the seven E. anophelis isolates, Eli4, Eli5, and Eli6, were almost identical and their isolation over a six-weeks period from the same hospital was suggestive of nosocomial transmission. The other four E. anophelis isolates were genetically diverse. No plasmids were found in all seven E. anophelis isolates. A novel 39,686 bp prophage was identified in the E. anophelis Eli4 genome while a presumptive incomplete prophage was found in the genomes of Eli2, Eli4, Eli5 and Eli6. E. anophelis genomes are notable for possessing integrative and conjugative elements (ICEs), which enable the bacterium to acquire genes including those encoding antimicrobial resistance or virulence. Novel ICE sequences were discovered in the Seremban E. anophelis genomes, and this includes an ICE found in Eli8 designated Eli8_ICE1, which encodes phage defence genes such as type I restriction-modification systems, a bacterial cyclic oligonucleotide-based anti-phage signalling system (CBASS) and prokaryotic argonaute systems. The latter two phage defence genes have so far not been reported in the E. anophelis genome. This study demonstrates the diversity and plasticity of E. anophelis genomes and emphasises further research into the role of ICEs in phage defence systems and their potential impact on antimicrobial treatment and phage therapy.