AT Homopolymer Strings in Salmonella enterica Subspecies I Contribute to Speciation and Serovar Diversity

Adenine and thymine homopolymer strings of at least 8 nucleotides (AT 8+mers) were characterized in Salmonella enterica subspecies I. The motif differed between other taxonomic classes but not between Salmonella enterica serovars. The motif in plasmids was possibly associated with serovar. Approximately 12.3% of the S. enterica motif loci had mutations. Mutability of AT 8+mers suggests that genomes undergo frequent repair to maintain optimal gene content, and that the motif facilitates self-recognition; in addition, serovar diversity is associated with plasmid content. A theory that genome regeneration accounts for both persistence of predominant Salmonella serovars and serovar diversity provides a new framework for investigating root causes of foodborne illness.

Horsing Around: Escherichia coli ST1250 of Equine Origin Harboring Epidemic IncHI1/ST9 Plasmid with blaCTX-M-1 and an Operon for Short-Chain Fructooligosaccharide Metabolism

ABSTRACT The relatedness of the equine-associated Escherichia coli strain ST1250 and its single- and double-locus variants (ST1250-SLV/DLV), obtained from horses in Europe, was studied by comparative genome analysis. A total of 54 isolates of E. coli ST1250 and ST1250-SLV/DLV from healthy and hospitalized horses across Europe (Czech Republic [n = 23], The Netherlands [n = 18], Germany [n = 9], Denmark [n = 3], and France [n = 1]) from 2008 to 2017 were subjected to whole-genome sequencing. An additional 25 draft genome assemblies of E. coli ST1250 and ST1250-SLV/DLV were obtained from the public databases. The isolates were compared for genomic features, virulence genes, clade structure, and plasmid content. The complete nucleotide sequences of eight IncHI1/ST9 plasmids and one IncHI1/ST2 plasmid were obtained using long-read sequencing by PacBio or MinION. In the collection of 79 isolates, only 10 were phylogenetically close (<8 single nucleotide polymorphisms [SNP]). The majority of isolates belonged to phylogroup B1 (73/79 [92.4%]) and carried blaCTX-M-1 (58/79 [73.4%]). The plasmid content of the isolates was dominated by IncHI1 of ST9 (56/62 [90.3%]) and ST2 (6/62 [9.7%]), while 84.5% (49/58) of the blaCTX-M-1 genes were associated with the presence of the IncHI1 replicon of ST9 and 6.9% (4/58) with the IncHI1 replicon of ST2 within the corresponding isolates. The operon for the utilization of short-chain fructooligosaccharides (the fos operon) was present in 55 of 79 (69.6%) isolates, and all of these carried IncHI1/ST9 plasmids. The eight complete IncHI1/ST9 plasmid sequences showed the presence of blaCTX-M-1 and the fos operon within the same molecule. Sequences of IncHI1/ST9 plasmids were highly conserved (>98% similarity) regardless of country of origin and differed only in the structure and integration site of the multidrug resistance (MDR) region. E. coli ST1250 and ST1250-SLV/DLV are phylogenetically diverse strains associated with horses. A strong linkage of E. coli ST1250 with the epidemic multidrug resistance plasmid lineage IncHI1/ST9 carrying blaCTX-M-1 and the fos operon was identified.

Comparison of Commensal and Clinical Isolates for Diversity of Plasmids in Escherichia coli and Klebsiella pneumoniae

ABSTRACT In this study, the plasmid content of clinical and commensal strains was analyzed and compared. The replicon profile was similar in both populations, except for L, M, A/C, and N (detected only in clinical strains) and HI1 (only in commensal strains). Although I1 and F were the most frequent replicons, only IncI1, sequence type 12 (ST12) was associated with blaCMY-2 in both populations. In contrast, the widespread resistant IncF plasmids were not linked to a single epidemic plasmid.

INFLUENCE OF YERSINIA PESTIS PLASMID CONTENT ON BIOFILM FORMATION IN FLEAS WITH DIFFERENT VECTOR ACTIVITY

Aim. Influence of the plague agent plasmid content on biofilm formation in vivo and death rate of fleas-vectors with different vector activity in experiment were analyzed. Materials and methods. Three Yersinia pestis strains: virulent I-3230 (pYT, pYV, pYP) and I-2638 (pYT, pYV, pYP, pTP 33), and its selected avirulent isogenic clone I-3480 lacking two plasmids (pYV, pYP) were used. Three species of fleas were artificially infected: 477 individuals of Xenopsylla cheopis (a highly active vector), 441 - Citellophilus tesquorum (an active vector), 519 - Frontopsylla lucu-lenta (a low-active vector). The peculiarities of Y. pestis biofilm formation in fleas were estimated by a portion of individuals with bacterial «conglomerates» and «blocks» for a feeding. Death rate of the insects was defined by the percent of the dead fleas at each feeding. Results. All three flea species infected by Y. pestis strains carrying an additional plasmid pTP33 (I-2638 and I-3480) demonstrated the increase of the individual number with various biofilm forms in comparison with the three-plasmid strain I-3230. In X. cheopis it occurred due to the blocked insects, in C. tesquo-rum - mainly due to the fleas containing «conglomerates», in F. luculenta it was completely connected with ectoparasites with «conglomerates». A share of X. cheopis and C. tesquorum died at a feeding was higher in ectoparasites infected with I-3230 strain and F. luculenta - infected by I-2638. Conclusion. Y. pestis strains possessing an additional replicon pTP33 formed a biofilm in the infected insects more often and larger size than a classical three-plasmid variant. Influence of the strain plasmid content on death rate of the infected fleas depended on a vector species.

Plasmid Profiler: Comparative Analysis of Plasmid Content in WGS Data

SummaryComparative analysis of bacterial plasmids from whole genome sequence (WGS) data generated from short read sequencing is challenging. This is due to the difficulty in identifying contigs harbouring plasmid sequence data, and further difficulty in assembling such contigs into a full plasmid. As such, few software programs and bioinformatics pipelines exist to perform comprehensive comparative analyses of plasmids within and amongst sequenced isolates. To address this gap, we have developed Plasmid Profiler, a pipeline to perform comparative plasmid content analysis without the need forde novoassembly. The pipeline is designed to rapidly identify plasmid sequences by mapping reads to a plasmid reference sequence database. Predicted plasmid sequences are then annotated with their incompatibility group, if known. The pipeline allows users to query plasmids for genes or regions of interest and visualize results as an interactive heat map.Availability and ImplementationPlasmid Profiler is freely available software released under the Apache 2.0 open source software license. A stand-alone version of the entire Plasmid Profiler pipeline is available as a Docker container athttps://hub.docker.com/r/phacnml/plasmidprofiler_0_1_6/.The conda recipe for the Plasmid R package is available at:https://anaconda.org/bioconda/r-plasmidprofilerThe custom Plasmid Profiler R package is also available as a CRAN package athttps://cran.r-project.org/web/packages/Plasmidprofiler/index.htmlGalaxy tools associated with the pipeline are available as a Galaxy tool suite athttps://toolshed.g2.bx.psu.edu/repository?repository_id=55e082200d16a504The source code is available at:https://github.com/phac-nml/plasmidprofilerThe Galaxy implementation is available at:https://github.com/phac-nml/plasmidprofiler-galaxyContactEmail:[email protected]: National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, CanadaSupplementary informationDocumentation:http://plasmid-profiler.readthedocs.io/en/latest/

Double Copies ofblaKPC-3::Tn4401aon an IncX3 Plasmid in Klebsiella pneumoniae Successful Clone ST512 from Italy

ABSTRACTA carbapenem-resistant sequence type 512 (ST512)Klebsiella pneumoniaecarbapenemase 3 (KPC-3)-producingK. pneumoniaestrain showing a novel variant plasmid content was isolated in Palermo, Italy, in 2014. ST512 is a worldwide successful clone associated with the spread ofblaKPCgenes located on the IncFIIk pKpQIL plasmid. In our ST512 strain, theblaKPC-3gene was unusually located on an IncX3 plasmid, whose complete sequence was determined. Two copies ofblaKPC-3::Tn4401acaused by intramolecular transposition events were detected in the plasmid.