Plasmids of Distinct IncK Lineages Show Compatible Phenotypes

Rozwandowicz, Marta; Brouwer, Michael S. M.; Zomer, Aldert; Bossers, Alex; Harders, Frank; Mevius, Dik; Wagenaar, Jaap A.; Hordijk, Joost

doi:10.1128/aac.01954-16

Cited by 22 publications

(25 citation statements)

References 21 publications

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“…Replicon typing is dependent on the availability of prior experimental evidence and remains restricted to culturable bacteria from the family Enterobacteriaceae and several well-studied genera of gram-positive bacteria 1,10–12 . Furthermore, this approach can lead to ambiguous classification, even for experimentally validated replicons, as recently demonstrated by the discovery of compatible plasmids assigned to the same replicon type, which led to the further subdivision of the IncK type into IncK1 and IncK2 13 , and IncA/C type into IncA and IncC 14 . In addition, plasmids can carry genes from more than one replication machinery and are thus assigned to multiple replicon types, further reducing interpretability 7,8 .…”

Section: Introductionmentioning

confidence: 99%

Large-scale network analysis captures biological features of bacterial plasmids

Acman

Dorp

Santini

et al. 2019

Preprint

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11Most bacteria exchange genetic material through Horizontal Gene Transfer (HGT). The primary vehicles for HGT 12 are plasmids and plasmid-borne transposable elements, though their population structure and dynamics remain 13 poorly understood. Here, we quantified genetic similarity between more than 10,000 bacterial plasmids and 14 reconstructed a network based on their shared k-mer content. Using a community detection algorithm, we assigned 15 plasmids into cliques which are highly correlated with plasmid gene content, bacterial host range, GC content, as 16 well as replicon and mobility (MOB) type classifications. Resolving the plasmid population structure further 17 allowed identification of candidates for yet-undescribed replicon genes. Our work provides biological insights 18 into the dynamics of plasmids and plasmid-borne mobile elements, with the latter representing the main drivers 19 of HGT at broad phylogenetic scales. Our results illustrate the potential of network-based analyses for the bacterial 20 'mobilome' and open up the prospect of a natural, exhaustive classification framework for bacterial plasmids. 21 48 assignments and can cover a potentially wider taxonomic range, however they are not applicable to the 49 classification of non-mobilizable plasmids. These two typing schemes have inspired several in silico classification 50 tools, such as PlasmidFinder 12 , the plasmid MultiLocus Sequence Typing (MLST) database, and MOB-suite 15 . 51However, all of these tools intrinsically rely on the completeness of their reference sequence databases, which 52 typically lack representatives from understudied and/or unculturable bacterial hosts. 53As bacterial plasmids undergo extensive recombination and HGT, their evolutionary history is not well captured 54 by phylogenetic trees, which are designed for the analysis of point mutation in sequence alignments 16,17 . Network 55 models offer an attractive alternative given they can incorporate both horizontal and vertical inheritance 18 , and 56 can deal with point mutations as well as structural variants. Networks have gained much attention in the past 57 decade as an alternative method for studying prokaryotic evolution, including plasmids 3,8,18,19 . Plasmid gene-58 sharing networks have proven a useful means to track AMR and virulence dissemination yielding deeper insights 59 Results 76 A dataset of complete bacterial plasmids 77A dataset of complete bacterial plasmids was assembled comprising 10,696 sequences found in bacteria from 22 78 phyla and over 400 genera ( Supplementary Table 1, Figure 1A, and Supplementary Figure 1). The composition 79 of plasmid hosts reflects current research interests, with the Proteobacteria and Firmicutes phyla together 80 representing over 84% of plasmid sequences. In total, 510,463 different Coding Sequences (CDSs) were identified 81 in the plasmid dataset. 66.01% of the CDSs were predicted to encode a hypothetical protein, 27.9% had a known 82 product with Gene Ontology (GO) biological process annotation, with the remai...

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Section: Introductionmentioning

confidence: 99%

Large-scale network analysis captures biological features of bacterial plasmids

Acman

Dorp

Santini

et al. 2019

Preprint

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“…Furthermore, the conjugal transfer system (tra locus) of IncI1 plasmids was found in pET20160881. These results indicate that pET20160881 differs from the recently described IncK1 and IncK2 plasmids (12,16) and may be a variant of the IncK plasmid.…”

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confidence: 48%

“…Plasmid pET20160881 is 97,940 bp in size, with an average GC content of 51.0%, and harbors 128 predicted open reading frames (ORFs). Based on comparative analysis of IncK plasmids, pET20160881 contains an IncK replicon detected in the PBRT scheme (11) and a conserved plasmid backbone of IncK responsible for plasmid replication, stability, and partitioning (12,15,16). However, this plasmid was untypeable with new sets of primers for IncK sequence typing (12) and showed 46.6 and 47.5% overall nucleotide identity with the plasmid pCT (IncK1, GenBank accession no.…”

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confidence: 99%

“…Antimicrobial susceptibilities were tested via the broth microdilution method using a customized KRCDCF panel with 16 antimicrobials and a commercial ESB1F plate (Sensititre, TREK Diagnostic Systems, OH, USA) according to CLSI guidelines (9); for cefotaxime-resistant strains, extended-spectrum betalactamase (ESBL) genes were analyzed using multiplex PCR and sequencing (10). From one selected isolate, the plasmid harboring the bla gene was transferred into azideresistant E. coli strain J53 by transconjugation and was characterized by PCR-based Inc/rep typing (PBRT) (11,12). The number and size of the plasmid in the donor and transconjugant strains were verified by PFGE with S1-nuclease digestion of whole-cell DNA (S1-PFGE) (13).…”

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confidence: 99%

“…The sequencing reads were assembled as described previously (12), and annotations were performed using Rapid Annotation Subsystem Technology (RAST) (http://rast.nmpdr.org/). Plasmid pET20160881 is 97,940 bp in size, with an average GC content of 51.0%, and harbors 128 predicted open reading frames (ORFs).…”

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confidence: 99%

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Outbreak of CTX-M-15-Producing Enterotoxigenic Escherichia coli O159:H20 in the Republic of Korea in 2016

Kim

Park

Shin

et al. 2017

Antimicrob Agents Chemother

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We investigated an outbreak of enterotoxigenic Escherichia coli (ETEC) O159:H20 associated with the consumption of a tossed-noodle dish in a high school in 2016. Thirty-three ETEC strains isolated from clinical and food samples were genetically indistinguishable. The outbreak strains were resistant to third-generation cephalosporins and harbored a bla CTX-M-15 gene on a 97-kb self-transferable IncK plasmid. This is the first outbreak caused by CTX-M-15-producing ETEC strains.

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Plasmids and Their Hosts

Shintani

Suzuki

2019

DNA Traffic in the Environment

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Plasmids of Distinct IncK Lineages Show Compatible Phenotypes

Cited by 22 publications

References 21 publications

Large-scale network analysis captures biological features of bacterial plasmids

Large-scale network analysis captures biological features of bacterial plasmids

Outbreak of CTX-M-15-Producing Enterotoxigenic Escherichia coli O159:H20 in the Republic of Korea in 2016

Plasmids and Their Hosts

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