Combining sequencing approaches to fully resolve a carbapenemase-encoding 
megaplasmid in a Pseudomonas shirazica clinical strain

Botelho, João; Lood, Cédric; Partridge, Sally R.; van Noort, Vera; Lavigne, Rob; Grosso, Filipa; Peixe, Luísa

doi:10.1080/22221751.2019.1648182

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Journal Article

Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain

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Botelho, João
Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Max Planck Society;

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Citation

Botelho, J., Lood, C., Partridge, S. R., van Noort, V., Lavigne, R., Grosso, F., et al. (2019). Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain. Emerging Microbes & Infections, 8(1), 1186-1194. doi:10.1080/22221751.2019.1648182.

Cite as: https://hdl.handle.net/21.11116/0000-0004-C180-0

Abstract

ABSTRACTHorizontal transfer of plasmids plays a pivotal role in dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Plasmid sequencing is thus paramount for accurate epidemiological tracking in hospitals and routine surveillance. Combining Nanopore and Illumina sequencing allowed full assembly of a carbapenemase-encoding megaplasmid carried by multidrug-resistant clinical isolate FFUP\_PS\_41. Average nucleotide identity analyses revealed that FFUP\_PS\_41 belongs to the recently proposed new species Pseudomonas shirazica, related to the P. putida phylogenetic group. FFUP\_PS\_41 harbours a 498,516-bp megaplasmid (pJBCL41) with limited similarity to publicly-available plasmids. pJBCL41 contains genes predicted to encode replication, conjugation, partitioning and maintenance functions and heavy metal resistance. The |aacA7|blaVIM-2|aacA4| cassette array (resistance to carbapenems and aminoglycosides) is located within a class 1 integron that is a defective Tn402 derivative. This transposon lies within a 50,273-bp region bound by Tn3-family 38-bp inverted repeats and flanked by 5-bp direct repeats (DR) that composes additional transposon fragments, five insertion sequences and a Tn3-Derived Inverted-Repeat Miniature Element. The hybrid Nanopore/Illumina approach allowed full resolution of a carbapenemase-encoding megaplasmid from P. shirazica. Identification of novel megaplasmids sheds new light on the evolutionary effects of gene transfer and the selective forces driving antibiotic resistance.