Identification of Source of Brucella suis Infection in Human by Using Whole-Genome Sequencing, United States and Tonga.
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ABSTRACT:
SUBMITTER: Quance C
PROVIDER: S-EPMC4696693 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:UnlabelledRecent breakthroughs in next-generation sequencing technologies have led to the identification of small noncoding RNAs (sRNAs) as a new important class of regulatory molecules. In prokaryotes, sRNAs are often bound to the chaperone protein Hfq, which allows them to interact with their partner mRNA(s). We screened the genome of the zoonotic and human pathogen Brucella suis 1330 for the presence of this class of RNAs. We designed a coimmunoprecipitation strategy that relies on the use of Hfq as a bait to enrich the sample with sRNAs and eventually their target mRNAs. By deep sequencing analysis of the Hfq-bound transcripts, we identified a number of mRNAs and 33 sRNA candidates associated with Hfq. The expression of 10 sRNAs in the early stationary growth phase was experimentally confirmed by Northern blotting and/or reverse transcriptase PCR.ImportanceBrucella organisms are facultative intracellular pathogens that use stealth strategies to avoid host defenses. Adaptation to the host environment requires tight control of gene expression. Recently, small noncoding RNAs (sRNAs) and the sRNA chaperone Hfq have been shown to play a role in the fine-tuning of gene expression. Here we have used RNA sequencing to identify RNAs associated with the B. suis Hfq protein. We have identified a novel list of 33 sRNAs and 62 Hfq-associated mRNAs for future studies aiming to understand the intracellular lifestyle of this pathogen.
| S-EPMC4719455 | biostudies-literature
Project description:We report the identification of new noncoding RNAs in Brucella suis 1330 and that are associated to the chaperone protein Hfq
2015-11-25 | GSE73621 | GEO
Project description:We report the identification of new noncoding RNAs in Brucella suis 1330 and that are associated to the chaperone protein Hfq Coimmunoprecipitation using Flag-tagged Hfq as bait
2015-11-25 | E-GEOD-73621 | biostudies-arrayexpress
Project description:We report the identification of RNAs in Streptococcus pneumoniae D39 that are associated to the KhpA/B proteins
2018-02-14 | GSE103735 | GEO
Project description:A butcher with chronic dermatitis presented with a second episode of Streptococcus suis meningitis, 8 years after the first episode. To distinguish between reinfection and persistent carriage, we compared the two S. suis isolates using whole genome sequencing. We investigated whole genome sequences of the S. suis isolates by means of substitution rates and population structure of closely related strains in addition to available clinical information. Genome-wide analyses revealed an inserted region consisting of 12 genes in the first isolate and the calculated substitution rate between the isolates suggested infections were caused by highly similar, but unrelated strains. Continuous occupational exposure likely resulted in reinfection with S. suis in a butcher.
| S-EPMC7379552 | biostudies-literature
Project description:Streptococcus suis is an important bacterial pathogen in pigs that may also cause zoonotic disease in humans. The aim of the study was to evaluate matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification of S. suis case isolates from diseased pigs and tonsil isolates from healthy pigs and wild boar using sequence analysis methods. Isolates (n = 348) that had been classified as S. suis by MALDI-TOF MS were whole-genome sequenced and investigated using analyses of (i) the 16S rRNA gene, (ii) the recN gene, and (iii) whole-genome average nucleotide identity (ANI). Analysis of the 16S rRNA gene indicated that 82.8% (288 out of 348) of the isolates were S. suis, while recN gene analysis indicated that 75.6% (263 out of 348) were S. suis. ANI analysis classified 44.3% (154 out of 348) as S. suis. In total, 44% (153 out of 348) of the investigated isolates were classified as S. suis by all of the species identification methods employed. The mean MALDI-TOF MS score was significantly higher for the S. suis case isolates than for the tonsil isolates; however, the difference is of limited practical use. The results show that species confirmation beyond MALDI-TOF MS is needed for S. suis isolates. Since the resolution of 16S rRNA gene analysis is too low for Streptococcus spp., ANI analysis with a slightly lowered cutoff of 94% may be used instead of, or in addition to, recN gene analysis. Supplementation of the MALDI-TOF MS reference library with mass spectra from S. orisratti, S. parasuis, S. ruminantium, and additional S. suis serotypes should be considered in order to produce more accurate classifications.
| S-EPMC8525557 | biostudies-literature
Project description:Brucella species are the most important zoonotic pathogens worldwide and cause considerable harm to humans and animals. In this study, we presented the complete genome of B. suis 019 isolated from sheep (ovine) with epididymitis. B. suis 019 has a rough phenotype and can infect sheep, rhesus monkeys and possibly humans. The comparative genome analysis demonstrated that B. suis 019 is closest to the vaccine strain B. suis bv. 1 str. S2. Further analysis associated the rsh gene to the pathogenicity of B. suis 019, and the WbkA gene to the rough phenotype of B. suis 019. The 019 complete genome data was deposited in the GenBank database with ID PRJNA308608.
| S-EPMC4773751 | biostudies-literature
Project description:Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen capable of causing severe disease in humans. Rapid and accurate identification and characterization techniques are essential during outbreak investigations. Current methods for characterization of STEC are expensive and time-consuming. With the advent of rapid and cheap whole genome sequencing (WGS) benchtop sequencers, the potential exists to replace traditional workflows with WGS. The aim of this study was to validate tools to do reference identification and characterization from WGS for STEC in a single workflow within an easy to use commercially available software platform. Publically available serotype, virulence, and antimicrobial resistance databases were downloaded from the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org) and integrated into a genotyping plug-in with in silico PCR tools to confirm some of the virulence genes detected from WGS data. Additionally, down sampling experiments on the WGS sequence data were performed to determine a threshold for sequence coverage needed to accurately predict serotype and virulence genes using the established workflow. The serotype database was tested on a total of 228 genomes and correctly predicted from WGS for 96.1% of O serogroups and 96.5% of H serogroups identified by conventional testing techniques. A total of 59 genomes were evaluated to determine the threshold of coverage to detect the different WGS targets, 40 were evaluated for serotype and virulence gene detection and 19 for the stx gene subtypes. For serotype, 95% of the O and 100% of the H serogroups were detected at > 40x and ? 30x coverage, respectively. For virulence targets and stx gene subtypes, nearly all genes were detected at > 40x, though some targets were 100% detectable from genomes with coverage ?20x. The resistance detection tool was 97% concordant with phenotypic testing results. With isolates sequenced to > 40x coverage, the different databases accurately predicted serotype, virulence, and resistance from WGS data, providing a fast and cheaper alternative to conventional typing techniques.
| S-EPMC4876609 | biostudies-literature
Project description:BackgroundBrucellosis is a bacterial disease caused by Brucella infection. In the late fifties, Brucella suis vaccine strain S2 with reduced virulence was obtained by serial transfer of a virulent B. suis biovar 1 strain in China. It has been widely used for vaccination in China since 1971. Until now, the mechanisms underlie virulence attenuation of S2 are still unknown.ResultsIn this paper, the whole genome sequencing of S2 was carried out by Illumina Hiseq2000 sequencing method. We further performed the comparative genomic analysis to find out the differences between S2 and the virulent Brucella suis strain 1330. We found premature stops in outer membrane autotransporter omaA and eryD genes. Single mutations were found in phosphatidylcholine synthase, phosphorglucosamine mutase, pyruvate kinase and FliF, which have been reported to be related to the virulence of Brucella or other bacteria. Of the other different proteins between S2 and 1330, such as Omp2b, periplasmic sugar-binding protein, and oligopeptide ABC transporter, no definitive implications related to bacterial virulence were found, which await further investigation.ConclusionsThe data presented here provided the rational basis for designing Brucella vaccines that could be used in other strains.
| S-EPMC5029015 | biostudies-literature
Project description:In 2021, a case of canine brucellosis diagnosed in a dog with orchitis was presented to a veterinary practice in Germany. Serological testing excluded Brucella (B.) canis as a causative agent, but molecular analysis revealed the presence of B. suis biovar 1. Since biovar 1 is not endemic in Europe and the dog had no history of travel to endemic areas, a comprehensive epidemiological investigation was conducted using whole genome sequence data to determine the source of infection. We describe the clinical progress of the animal and the potential infection of a veterinary clinic employee. The findings highlight the importance of considering less common Brucella species as possible causes of canine brucellosis. The data also emphasize that it is quite challenging to identify Brucella species in a routine diagnostic laboratory and to conduct epidemiological investigations to unveil possible transmission routes.
| S-EPMC10435866 | biostudies-literature