Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae

Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae

► We perform comparative genomics of IncX plasmids from humans and animals. ► We develop a refined definition of the IncX subgroups. ► We develop a PCR-based replicon typing procedure for the IncX subgroups. IncX plasmids are narrow host range plasmids of Enterobactericeae that have been isolated fo...

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Bibliographic Details
Published in:Plasmid Vol. 68; no. 1; pp. 43 - 50
Main Authors: Johnson, Timothy J., Bielak, Eliza M., Fortini, Daniela, Hansen, Lars Hestbjerg, Hasman, Henrik, Debroy, Chitrita, Nolan, Lisa K, Carattoli, Alessandra
Format: Journal Article
Language:English
Published: United States Elsevier Inc 01-07-2012
Subjects:
Amino acids
Antimicrobial agents
Bacterial Typing Techniques
Biofilms
Drug resistance
Drug Resistance, Bacterial - genetics
Enterobacteriaceae
Enterobacteriaceae - classification
Enterobacteriaceae - genetics
Genomes
Genomics
Host range
IncX
Molecular Sequence Data
Nucleotides
Phylogeny
Pili
Plasmid
Plasmids
Plasmids - genetics
Polymerase Chain Reaction - methods
Replicon
Replicon typing
Resistance
Synteny
Typing
Plasmid
Resistance
IncX
Replicon typing
Genomics
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Summary:► We perform comparative genomics of IncX plasmids from humans and animals. ► We develop a refined definition of the IncX subgroups. ► We develop a PCR-based replicon typing procedure for the IncX subgroups. IncX plasmids are narrow host range plasmids of Enterobactericeae that have been isolated for over 50years. They are known to encode type IV fimbriae enabling their own conjugative transfer, and to provide accessory functions to their host bacteria such as resistance towards antimicrobial agents and biofilm formation. Previous plasmid-based replicon typing procedures have indicated that the prevalence of IncX plasmids is low among members of the Enterobacteriaceae. However, examination of a number of IncX-like plasmid sequences and their occurrence in various organisms suggests that IncX plasmid diversity and prevalence is underappreciated. To address these possible shortcomings, we generated additional plasmid sequences of IncX plasmids of interest and compared them to the genomes of all sequenced IncX-like plasmids. These comparisons revealed that IncX plasmids possess a highly syntenic plasmid backbone, but that they are quite divergent with respect to nucleotide and amino acid similarity. Based on phylogenetic comparisons of the sequenced IncX plasmids, the IncX plasmid group has been expanded to include at least four subtypes, IncX1-IncX4. A revised IncX plasmid replicon typing procedure, based upon these sequences and subtypes, was then developed. Use of this revised typing procedure revealed that IncX plasmid occurrence among bacterial populations is much more common than had previously been acknowledged. Thus, this revised procedure can be used to better discern the occurrence of IncX type plasmids among enterobacterial populations.
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ISSN:0147-619X
1095-9890
DOI:10.1016/j.plasmid.2012.03.001