Campylobacter jejuni isolates in Finnish patients differ according to the origin of infection

<p>Abstract</p> <p>Background</p> <p><it>Campylobacter jejuni </it>is a significant cause of bacterial enteritis worldwide. Very little is known about the pathogenicity mechanisms and virulence factors of this important enteropathogen. <it>C. jejuni </it>isolates from 166 Finnish patients, collected from July to December in 2006, were studied for the presence of putative virulence factors and susceptibility to antimicrobials. Isolates were tested for production of γ-glutamyltransferase (GGT) as well as the presence of genes <it>ceuE</it>, <it>cgtB</it>, <it>ciaB</it>, <it>cj0486</it>, <it>pldA</it>, <it>virB11</it>, <it>wlaN</it>, and the gene cluster <it>cdtABC</it>. Bacterial characteristics were compared to information on foreign travel history as well as information on the course and the symptoms of disease obtained from questionnaires returned by patients.</p> <p>Results</p> <p>Except for one domestic isolate, antimicrobial resistance was only detected in isolates of foreign origin. Univariate analyses showed association between bloody stools and both GGT production (p = 0.025) and the presence of <it>cgtB </it>(p = 0.034). Multivariate analysis verified that GGT production was more prevalent in domestic isolates (p < 0.0001), while the genes <it>cj0486 </it>(p < 0.0001) and <it>ceuE </it>(p < 0.0001) were associated with <it>C. jejuni </it>isolates of foreign origin.</p> <p>Conclusions</p> <p>The results indicate that imported and domestic <it>C. jejuni </it>isolates differ significantly in several aspects from each other.</p

Finnish Campylobacter jejuni Strains of Multilocus Sequence Type ST-22 Complex Have Two Lineages with Different Characteristics

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Campylobacter jejuni Colonization in Wild Birds: Results from an Infection Experiment

Campylobacter jejuni is a common cause of bacterial gastroenteritis in most parts of the world. The bacterium has a broad host range and has been isolated from many animals and environments. To investigate shedding patterns and putative effects on an avian host, we developed a colonization model in which a wild bird species, the European Robin Erithacus rubecula, was inoculated orally with C. jejuni from either a human patient or from another wild bird species, the Song Thrush Turdus philomelos. These two isolates were genetically distinct from each other and provoked very different host responses. The Song Thrush isolate colonized all challenged birds and colonization lasted 6.8 days on average. Birds infected with this isolate also showed a transient but significant decrease in body mass. The human isolate did not colonize the birds and could be detected only in the feces of the birds shortly after inoculation. European Robins infected with the wild bird isolate generated a specific antibody response to C. jejuni membrane proteins from the avian isolate, which also was cross-reactive to membrane proteins of the human isolate. In contrast, European Robins infected with the human isolate did not mount a significant response to bacterial membrane proteins from either of the two isolates. The difference in colonization ability could indicate host adaptations

SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing

From Springer Nature via Jisc Publications RouterHistory: received 2022-04-21, rev-recd 2022-09-08, accepted 2022-10-05, registration 2022-10-10, pub-electronic 2022-10-18, online 2022-10-18, collection 2022-12Acknowledgements: Acknowledgements: We are immensely grateful to all our co-workers at the Section for Clinical Microbiology and Hospital Hygiene at Uppsala University Hospital, who PCR tested all the COVID-19 samples and consequently extracted the viral RNA for us from the positive samples. Secondly, we are deeply thankful to Tor-Elesh Albrigtsen for the remarkable assistance with data science, analysis and programming in Python.Publication status: PublishedFunder: Science for Life Laboratory; doi: http://dx.doi.org/10.13039/501100009252; Grant(s): ZSC – National core facility for pandemic preparednessFunder: Scandinavian Society for Antimicrobial Chemotherapy Foundation; doi: http://dx.doi.org/10.13039/501100011777; Grant(s): SLS-961049Funder: Erik, Karin and Gösta Selander Foundation; Grant(s): 2022Funder: Regionala Forskningsrådet Uppsala/Örebro; doi: http://dx.doi.org/10.13039/100019032; Grant(s): RFR-930984Funder: Uppsala UniversityAbstract: Background: Since the beginning of the COVID-19 pandemic, new variants of significance to public health have emerged. Consequently, early detection of new mutations and variants through whole-genome sequencing remains crucial to assist health officials in employing appropriate public health measures. Methods: We utilized the ARTIC Network SARS-CoV-2 tiled amplicon approach and Nanopore sequencing to sequence 4,674 COVID-19 positive patient samples from Uppsala County, Sweden, between week 15 and 52 in 2021. Using this data, we mapped the circulating variants of concern (VOC) in the county over time and analysed the Spike (S) protein mutational dynamics in the Delta variant throughout 2021. Results: The distribution of the SARS-CoV-2 VOC matched the national VOC distribution in Sweden, in 2021. In the S protein of the Delta variant, we detected mutations attributable to variants under monitoring and variants of interest (e.g., E484Q, Q613H, Q677H, A222V and Y145H) and future VOC (e.g., T95I and Y144 deletion, which are signature mutations in the Omicron variant). We also frequently detected some less well-described S protein mutations in our Delta sequences, that might play a role in shaping future emerging variants. These include A262S, Q675K, I850L, Q1201H, V1228L and M1237I. Lastly, we observed that some of the Delta variant’s signature mutations were underrepresented in our study due to artifacts of the used bioinformatics tools, approach and sequencing method. We therefore discuss some pitfalls and considerations when sequencing SARS-CoV-2 genomes. Conclusion: Our results suggest that genomic surveillance in a small, representative cohort can be used to make predictions about the circulating variants nationally. Moreover, we show that detection of transient mutations in currently circulating variants can give valuable clues to signature mutations of future VOC. Here we suggest six such mutations, that we detected frequently in the Delta variant during 2021. Lastly, we report multiple systematic errors that occurred when following the ARTIC Network SARS-CoV-2 tiled amplicon approach using the V3 primers and Nanopore sequencing, which led to the masking of some of the important signature mutations in the Delta sequences

No colonization resistance to Campylobacter jejuni in broilers fed brown algal extract-supplemented diets

IntroductionCampylobacter jejuni gastroenteritis is the most commonly reported zoonosis within the EU, with poultry products regarded as the primary source of transmission to humans. Therefore, finding strategies to reduce Campylobacter colonization in broilers holds importance for public health. Recent studies suggest that supplementation of broiler feed with brown algal extracts, particularly laminarin, can provide beneficial effects on broiler gut health, growth performance, and gut microbiota. However, its effect on gut microbiota development and subsequent reduction of Campylobacter loads in broiler caeca during the later stages of the birds' lives remains unclear.MethodsExperimental colonization of Ross 308 broilers with two different strains of C. jejuni was conducted, with groups fed either a basal diet or the same basal diet supplemented with 725 ppm algal extract from Saccharina latissima to provide 290 ppm laminarin. Fecal samples were collected for bacterial enumeration, and caecal samples were obtained before and after the C. jejuni challenge for the determination of microbiota development.Results and discussionNo significant differences in fecal C. jejuni concentrations between the groups fed different diets or exposed to different C. jejuni strains were observed. This suggests that both strains colonized the birds equally well and that the laminarin rich algal extract did not have any inhibitory effect on C. jejuni colonization. Notably, 16S rRNA amplicon sequencing revealed detailed data on the caecal microbiota development, likely influenced by both bird age and C. jejuni colonization, which can be valuable for further development of broiler feed formulations aimed at promoting gut health

Prevalence of SARS-CoV-2 Omicron Sublineages and Spike Protein Mutations Conferring Resistance against Monoclonal Antibodies in a Swedish Cohort during 2022–2023

Monoclonal antibodies (mAbs) are an important treatment option for COVID-19 caused by SARS-CoV-2, especially in immunosuppressed patients. However, this treatment option can become ineffective due to mutations in the SARS-CoV-2 genome, mainly in the receptor binding domain (RBD) of the spike (S) protein. In the present study, 7950 SARS-CoV-2 positive samples from the Uppsala and Örebro regions of central Sweden, collected between March 2022 and May 2023, were whole-genome sequenced using amplicon-based sequencing methods on Oxford Nanopore GridION, Illumina MiSeq, Illumina HiSeq, or MGI DNBSEQ-G400 instruments. Pango lineages were determined and all single nucleotide polymorphism (SNP) mutations that occurred in these samples were identified. We found that the dominant sublineages changed over time, and mutations conferring resistance to currently available mAbs became common. Notable ones are R346T and K444T mutations in the RBD that confer significant resistance against tixagevimab and cilgavimab mAbs. Further, mutations conferring a high-fold resistance to bebtelovimab, such as the K444T and V445P mutations, were also observed in the samples. This study highlights that resistance mutations have over time rendered currently available mAbs ineffective against SARS-CoV-2 in most patients. Therefore, there is a need for continued surveillance of resistance mutations and the development of new mAbs that target more conserved regions of the RBD.Acknowledgements: We would like to thank the personnel at Clinical Microbiology and Hospital Hygiene, Uppsala University Hospital for their help with handling samples, RNA extraction, PCR, and whole-genome sequencing.Funder: Regional Research Council Mid Sweden; Grant(s): RFR-98011

The pattern of influenza virus attachment varies among wild bird species

The ability to attach to host cells is one of the main determinants of the host range of influenza A viruses. By using virus histochemistry, we investigate the pattern of virus attachment of both a human and an avian influenza virus in colon and trachea sections from 12 wild bird species. We show that significant variations exist, even between closely related avian species, which suggests that the ability of wild birds to serve as hosts for influenza viruses strongly varies among species. These results will prove valuable to assess the possibilities of interspecies transmission of influenza viruses in natural environments and better understand the ecology of influenza

A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

Background: The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. Findings: This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families. Conclusions: This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long -read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses

Predicting risk habitats for the transmission of the small liver fluke, Dicrocoelium dendriticum to grazing ruminants

Abstract. A multiple regression model was used to analyse if the structure of vegetation and soil patches in grazed units (pastures) can be used as explanatory variables to predict the prevalence of Dicrocoelium dendriticum, a common parasite of cattle and sheep, in grazing cattle stocks on the Baltic island of Öland in southern Sweden. The scale dependency was evaluated by comparing three levels of spatial resolution of patches. Prevalence data were obtained from slaughtered animals. Our models predict that the prevalence of D. dendriticum increases in grazed areas with woody vegetation, whereas moist and wet areas decrease parasite prevalence. The predictive power of the statistical models increased with increasing level of patch resolution. Approximately 42 % of the variation in parasite prevalence (angular transformation) was explained by the areal proportion of vegetation types (4 th-root-transformed). Based on the results obtained, we believe that our model strategy provides a rational and systematic tool to identify habitats that carry risk for D. dendriticum infection of ruminants, and that it can be applied to other parasites with similar life cycles such as Fasciola hepatica

rprimer : an R/bioconductor package for design of degenerate oligos for sequence variable viruses

Background This paper presents a new R/Bioconductor package, rprimer, for design of degenerate oligos and PCR assays for sequence variable viruses. A multiple DNA sequence alignment is used as input data, while the outputs consist of comprehensive tables (data frames) and dashboard-like plots. The workflow can be run directly from the R console or through a graphical user interface (Shiny application). Here, rprimer is demonstrated and evaluated by using it to design two norovirus genogroup I (GI) assays: one RT-qPCR assay for quantitative detection and one RT-PCR assay for Sanger sequencing and polymerase-capsid based genotyping. Results The assays generated were evaluated using stool samples testing positive for norovirus GI. The RT-qPCR assay accurately amplified and quantified all samples and showed comparable performance to a widely-used standardised assay, while the RT-PCR assay resulted in successful sequencing and genotyping of all samples. Merits and limitations of the package were identified through comparison with three similar freely available software packages. Several features were comparable across the different tools, but important advantages of rprimer were its speed, flexibility in oligo design and capacity for visualisation. Conclusions An R/Bioconductor package, rprimer, was developed and shown to be successful in designing primers and probes for quantitative detection and genotyping of a sequence-variable virus. The package provides an efficient, flexible and visual approach to degenerate oligo design, and can therefore assist in virus research and method development