High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides

Characterization of the novel optrA-carrying pseudo-compound transposon Tn7363 and an Inc18 plasmid carrying cfr(D) in Vagococcus lutrae

OBJECTIVES

To investigate the genetic context and transferability of the oxazolidinone resistance genes cfr(D) and optrA in a porcine Vagococcus lutrae isolate.

METHODS

V. lutrae isolate BN31 was screened for the presence of known oxazolidinone resistance genes via PCR assays. Conjugation experiments were carried out to assess horizontal transferability of resistance genes. WGS was performed using a combination of Nanopore MinION and Illumina HiSeq platforms. Detection of a translocatable unit (TU) was conducted by PCR.

RESULTS

V. lutrae isolate BN31 harboured the oxazolidinone resistance genes cfr(D) and optrA. The optrA gene, together with the phenicol resistance gene fexA, was located on a novel pseudo-compound transposon, designated Tn7363. Tn7363 was bounded by two copies of the new insertion sequence ISVlu1, which represented a new member of the ISL3 family. A TU, comprising one copy of ISVlu1 and the segment between the two IS elements including the optrA gene, was detected. The cfr(D) gene and an erm(B) gene were identified on the broad-host-range Inc18 plasmid pBN31-cfrD, a pAMβ1-like plasmid. Similar to plasmid pAMβ1, plasmid pBN31-cfrD was conjugative.

CONCLUSIONS

To the best of our knowledge, we report the first identification of the cfr(D) and optrA in Vagococcus. Two novel oxazolidinone resistance gene-carrying mobile genetic elements, Tn7363 and pBN31-cfrD, were identified in V. lutrae BN31. Considering their transmission potential, attention should be paid to the risk of transfer of the optrA and cfr(D) genes from V. lutrae to clinically more important bacterial pathogens.

First reported human bloodstream infection with Vagococcus lutrae

Vagococcus lutrae belongs to the Vagococcus genus; it is possible to isolate vagococci from marine hosts, contaminated food and soil. To our knowledge, this is the first case of bloodstream infection with V. lutrae and only the second reported human infection in the literature. As in the first reported case of clinical infection with V. lutrae, this woman had several wounds. The clinical investigation showed no other foci for the bloodstream infection, so we hypothesize that the wounds were colonized, although they showed no signs of infection and skin swabs did not reveal V. lutrae.

Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management

The small octopus (Octopus variabilis) is a popular seafood in many countries including South Korea. Because it is often consumed uncooked, the microorganisms in it often cause food poisoning. Therefore, analyzing the microbiome of the small octopus can help to understand the risk of food poisoning and manage octopus products better. A total of 40 small octopuses were collected from four sites in November and August. The microbiota was analyzed using Illumina Miseq sequencing, and the amount of bacteria was quantified by real-time PCR. In addition, we analyzed the influence of Vibrio vulnificus infection on the microbiome of the small octopus through artificial infection experiments. Bacteroidetes was the predominant phylum in August, and Proteobacteria was predominant in November. The composition of the microbiota in octopus depended on sampling region and season. The potential risk of foodborne illness from small octopus consumption might be higher in August than in November due to the abundance of potential pathogens. In the infection experiment, the proportion of V. vulnificus increased only at 27°C. The composition and functional gene profiles of the microbiota varied in a similar manner between non-infected and infected samples over time at the same temperature. These results indicated that the indigenous microbiota in small octopus could inhibit colonization by V. vulnificus during storage. Although further studies are necessary to clarify these results, our results could help us better understand food poisoning through octopus ingestion and manage products.

Tracing the Enterococci from Paleozoic Origins to the Hospital

We examined the evolutionary history of leading multidrug resistant hospital pathogens, the enterococci, to their origin hundreds of millions of years ago. Our goal was to understand why, among the vast diversity of gut flora, enterococci are so well adapted to the modern hospital environment. Molecular clock estimation, together with analysis of their environmental distribution, phenotypic diversity, and concordance with host fossil records, place the origins of the enterococci around the time of animal terrestrialization, 425-500 mya. Speciation appears to parallel the diversification of hosts, including the rapid emergence of new enterococcal species following the End Permian Extinction. Major drivers of speciation include changing carbohydrate availability in the host gut. Life on land would have selected for the precise traits that now allow pathogenic enterococci to survive desiccation, starvation, and disinfection in the modern hospital, foreordaining their emergence as leading hospital pathogens.

Complete and Assembled Genome Sequence of Vagococcus teuberi DSM 21459T, a Novel Species Isolated from Fermented Cow Milk in Mali

The genome of Vagococcus teuberi DSM 21459^T, a strain isolated from Malian fermented milk, was sequenced using single-molecule real-time sequencing. The genome of V. teuberi DSM 21459^T is the first sequenced genome of this novel species and the second genome among the genus Vagococcus.

Report of the first Vagococcus lutrae human infection, Marseille, France

Vagococcus lutrae is a Gram-positive coccus initially isolated from the common otter (Lutra lutra) but that has never been reported as a human pathogen. We describe the first case of human infection due to Vagococcus lutrae in Marseille, France.