| 1. |
- Kaden, René, 1975-, et al.
(författare)
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A novel real-time PCR assay for specific detection of Brucella melitensis
- 2017
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Ingår i: BMC Infectious Diseases. - : BIOMED CENTRAL LTD. - 1471-2334. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background: Brucellosis is a zoonosis that occurs worldwide. The disease has been completely eradicated in livestock in Sweden in 1994, and all cases of confirmed human brucellosis are imported into Sweden from other countries. However, due to an increase in the number of refugees and asylum seekers from the middle-east to Sweden, there is a need to improve the current diagnostic methodology for Brucella melitensis. Whilst culture of Brucella species can be used as a diagnostic tool, real-time PCR approaches provide a much faster result. The aim of this study was to set up a species-specific real-time PCR for the detection of all biovars of Brucella melitensis, which could be used routinely in diagnostic laboratories. Methods: A Brucella melitensis real-time PCR assay was designed using all available genomes in the public database of Brucella (N=96) including all complete genomes of Brucella melitensis (N=17). The assay was validated with a collection of 37 Brucella species reference strains, 120 Brucella melitensis human clinical isolates, and 45 clinically relevant non-Brucella melitensis strains. Results: In this study we developed a single real-time PCR for the specific detection of all biovars of Brucella melitensis. Conclusions: This new real-time PCR method shows a high specificity (100%) and a high sensitivity ( 1.25 GE/mu l) and has been implemented in the laboratories of four governmental authorities across Sweden.
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| 2. |
- Kaden, Rene, 1975-, et al.
(författare)
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First case of human bacteraemia by Catabacter hongkongensis in Scandinavia
- 2017
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Ingår i: New Microbes and New Infections. - : Elsevier BV. - 2052-2975. ; 15, s. 6-8
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Tidskriftsartikel (refereegranskat)abstract
- Catabacter hongkongensis was isolated and cultured from human blood for the first time in Scandinavia. The patient, an 83 year old man from Dalarna, Sweden, recovered without antibiotic treatment while a high mortality rate associated with Catabacter hongkongensis infections was reported from China, Canada, and France. The genome of the strain ABBA15k was sequenced, assembled, and analyzed. In contrast to the type strain of the species HKU16T no antibiotic resistance was observed in Scandinavian strain ABBA15k. The strain was deposited as CCUG 68271 and the draft genome sequence is available from DDBJ/EMBL/GenBank under the accession number LLYX00000000.
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| 3. |
- Lytsy, Birgitta, 1968-, et al.
(författare)
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Time to review the gold standard for genotyping vancomycin-resistant enterococci in epidemiology : Comparing whole-genome sequencing with PFGE and MLST in three suspected outbreaks in Sweden during 2013–2015
- 2017
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Ingår i: Infection, Genetics and Evolution. - : Elsevier BV. - 1567-1348 .- 1567-7257. ; 54, s. 74-80
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Tidskriftsartikel (refereegranskat)abstract
- Vancomycin-resistant enterococci (VRE) are a challenge to the health-care system regarding transmission rate and treatment of infections. VRE outbreaks have to be controlled from the first cases which means that appropriate and sensitive genotyping methods are needed.The aim of this study was to investigate the applicability of whole genome sequencing based analysis compared to Pulsed-Field Gel Electrophoresis (PFGE) and Multi-Locus Sequence Typing (MLST) in epidemiological investigations as well as the development of a user friendly method for daily laboratory use.Out of 14,000 VRE - screening samples, a total of 60 isolates positive for either vanA or vanB gene were isolated of which 38 were from patients with epidemiological links from three suspected outbreaks at Uppsala University Hospital. The isolates were genotypically characterised with PFGE, MLST, and WGS based core genome Average Nucleotide Identity analysis (cgANI). PFGE was compared to WGS and MLST regarding reliability, resolution, and applicability capacity.The PFGE analysis of the 38 isolates confirmed the epidemiological investigation that three outbreaks had occurred but gave an unclear picture for the largest cluster. The WGS analysis could clearly distinguish six ANI clusters for those 38 isolates.As result of the comparison of the investigated methods, we recommend WGS-ANI analysis for epidemiological issues with VRE. The recommended threshold for Enterococcus faecium VRE outbreak strain delineation with core genome based ANI is 98.5%.All referred sequences of this study are available from the NCBI BioProject number PRJNA301929.
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| 4. |
- Nilsson, Anna, et al.
(författare)
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Genomic and phenotypic characteristics of Swedish C. jejuni water isolates
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12:12
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Tidskriftsartikel (refereegranskat)abstract
- Campylobacter jejuni is the most common cause of bacterial gastroenteritis. Major reservoirs are warm-blooded animals, poultry in particular, but Campylobacter can also be transmitted via water. In this paper, we have taken a closer look at the biology and potential virulence of C. jejuni water isolates. Seven C. jejuni isolates from incoming surface water at water plants in Sweden were characterized with whole genome sequencing and phenotypical testing. Multi locus sequence typing analysis revealed that these isolates belonged to groups known to include both common (ST48CC) and uncommon (ST1275CC, ST683, ST793 and ST8853) human pathogens. Further genomic characterization revealed that these isolates had potential for arsenic resistance (due to presence of arsB gene in all isolates), an anaerobic dimethyl sulfoxide oxidoreductase (in three isolates) and lacked the MarR-type transcriptional regulator gene rrpB (in all but one isolate) earlier shown to be involved in better survival under oxidative and aerobic stress. As putative virulence factors were concerned, there were differences between the water isolates in the presence of genes coding for cytolethal distending toxin (cdtABC), Type VI secretion system and sialylated LOS, as well as in biofilm formation. However, all isolates were motile and could adhere to and invade the human HT-29 colon cancer cell line in vitro and induce IL-8 secretion suggesting potential to infect humans. This is, to the best of our knowledge, the first study where C. jejuni water isolates have been characterized using whole genome sequencing and phenotypical assays. We found differences and shared traits among the isolates but also potential to infect humans.
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| 5. |
- Skarp, Astrid, et al.
(författare)
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Accessory genetic content in Campylobacter jejuni ST21CC isolates from feces and blood
- 2017
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Ingår i: International Journal of Medical Microbiology. - : Elsevier BV. - 1438-4221 .- 1618-0607. ; 307:4-5, s. 233-240
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Tidskriftsartikel (refereegranskat)abstract
- Campylobacter jejuni is an important foodborne pathogen and the most commonly reported bacterial cause of gastroenteritis. C. jejuni is occasionally found in blood, although mechanisms important for invasiveness have remained unclear. C. jejuni is divided into many different lineages, of which the ST21 clonal complex (CC) is widely distributed. Here, we performed comparative genomic and in vitro analyses on 17C. jejuni ST21CC strains derived from human blood and feces in order to identify features associated with isolation site. The ST21CC lineage is divided into two large groups; centered around ST-21 and ST-50. Our clinical strains, typed as ST-50, showed further microevolution into two distinct clusters. These clusters were distinguished by major differences in their capsule loci and the distribution of accessory genetic content, including C. jejuni integrated elements (CJIEs) and plasmids. Accessory genetic content was more common among fecal than blood strains, whereas blood strains contained a hybrid capsule locus which partially consisted of C. jejuni subsp. doylei-like content. In vitro infection assays with human colon cell lines did not show significant differences in adherence and invasion between the blood and fecal strains. Our results showed that CJIEs and plasmid derived genetic material were less common among blood isolates than fecal isolates; in contrast, hybrid capsule loci, especially those containing C. jejuni subsp. doylei-like gene content, were found among many isolates derived from blood. The role of these findings requires more detailed investigation.
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| 6. |
- Wahab, Tara, et al.
(författare)
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GIFeGSH : A New Genomic Island Might Explain the Differences in Brucella Virulence
- 2017
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Ingår i: Open Journal of Animal Sciences. - : Scientific Research Publishing, Inc.. - 2161-7597 .- 2161-7627. ; 7, s. 141-148
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Tidskriftsartikel (refereegranskat)abstract
- An imported dog was confirmed to be positive with canine brucellosis in Sweden in 2010. The whole genome of Brucella canis SVA10 was subjected to phage analysis (WGS-PA) and was assigned to the Asian B. canis cluster. Further analysis indicated that the genome of B. canis SVA10 is smaller compared to genomes of the same species. A 35,781 bp genomic island (GI) was found to be absent in strain SVA10 which was detected by read mapping the paired reads to the genome of B. canisATCC 23,365T. The lacking genes of genomic island GIFeGSH are mainly coding for iron uptake enzymes and parts of the glutathione pathway. A screening of all available whole genome sequences of Brucella strains confirmed that GIFeGSH is also missing in four more strains of B. canis but present in several strains of B. abortus, B. melitensis, B. suis, B. ovis, B. microti, B. pinnipedialis, and B. ceti. Parts of the GI were present, but scattered in two other B. canis strains. The aim of this study was to find differences in the genomes of Brucella which might explain former described differences in virulence. The analysis was extended to all available Brucella genomes after the detection of a genomic island in strain SVA10.
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