Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids

Abstract

Plasmid typing can provide insights into the epidemiology and transmission of plasmid-mediated antibiotic resistance. The principal plasmid typing schemes are replicon typing and MOB typing, which utilize variation in replication loci and relaxase proteins respectively. Previous studies investigating the proportion of plasmids assigned a type by these schemes (‘typeability’) have yielded conflicting results; moreover, thousands of plasmid sequences have been added to NCBI in recent years, without consistent annotation to indicate which sequences represent complete plasmids. Here, a curated dataset of complete Enterobacteriaceae plasmids from NCBI was compiled, and used to assess the typeability and concordance of in silico replicon and MOB typing schemes. Concordance was assessed at hierarchical replicon type resolutions, from replicon family-level to plasmid multilocus sequence type (pMLST)-level, where available. We found that 85% and 65% of the curated plasmids could be replicon and MOB typed, respectively. Overall, plasmid size and the number of resistance genes were significant independent predictors of replicon and MOB typing success. We found some degree of non-concordance between replicon families and MOB types, which was only partly resolved when partitioning plasmids into finer-resolution groups (replicon and pMLST types). In some cases, non-concordance was attributed to ambiguous boundaries between MOBP and MOBQ types; in other cases, backbone mosaicism was considered a more plausible explanation. β-lactamase resistance genes tended not to show fidelity to a particular plasmid type, though some previously reported associations were supported. Overall, replicon and MOB typing schemes are likely to continue playing an important role in plasmid analysis, but their performance is constrained by the diverse and dynamic nature of plasmid genomes.

Plasmid evolution in carbapenemase‐producing Enterobacteriaceae: a review

“…This method was labor‐intensive and almost impossible on large sample sizes. To overcome these limitations, new typing schemes were introduced to facilitate the characterization and epidemiological analysis of resistance plasmids …”

“…The MOB typing overcomes replicon typing limitations in that it targets relaxases, of which only one can be encoded in a plasmid. Unlike the PBRT, which detects plasmids at higher resolution, the MOB typing uses lower resolution to classify plasmids . However, PBRT and DPMT have been combined to successfully classify plasmids in clinically relevant pathogens …”

“…However, these typing schemes have a relatively lower discriminatory power than recent techniques, such as plasmid multilocus sequence typing (pMLST), whole‐plasmid sequencing (WPS), and whole‐genome sequencing (WGS) . The PBRT methods have drawbacks, including (1) the presence of multiple replicons in a single plasmid, which complicates plasmid classification; (2) rapid evolution of plasmid replicons; and (3) the presence of hybrid replication regions that make plasmid classification complicated . Nevertheless, PCR‐based typing methods may be used preliminarily for screening plasmids prior to using higher resolution techniques.…”

“…In cases where pMLST is not available and plasmid subtyping is needed, the conventional technique restriction fragment length polymorphism (RFLP) can be used. However, the results produced by RFLP method can be difficult to interpret and subjective …”

A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database

“…Value of the data To our knowledge, this is currently the only large curated dataset of complete plasmids, compiled according to well-defined, and transparently validated, inclusion and exclusion criteria.The data could be used to benchmark the performance of plasmid typing schemes [1].The data could be used for reference-based plasmid analyses [2]; for example, contigs could be queried against the curated plasmid sequences with the aim of distinguishing plasmid from chromosomal contigs [3] or assessing plasmid genetic content [4].The protein dataset is a useful resource for MOB typing [5]. Information about sequence conservation from aligned protein database sequences can be harnessed using more powerful profile-based homology searching [6], enabling improved MOB typing compared with standard protein BLAST.…”