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Background Human Adenoviruses (HAdVs) are highly contagious pathogens of clinical importance, especially among the pediatric population. Studies on comparative viral genomic analysis of cases associated with severe and mild infections due to HAdV are limited. Using whole-genome sequencing (WGS), we investigated whether there were any differences between circulating HAdV strains associated with severe infections (meningitis, sepsis, convulsion, sudden infant death syndrome, death, and hospitalization) and mild clinical presentations in pediatric patients hospitalized between the years 1998 and 2017 in a tertiary care hospital group in Bern, Switzerland covering a population base of approx. 2 million inhabitants. The HAdV species implicated in causing severe infections in this study included HAdV species C genotypes (HAdV1, HAdV2, and HAdV5). Clustering of the HAdV whole-genome sequences of the severe and mild cases did not show any differences except for one sample (isolated from a patient presenting with sepsis, meningitis, and hospitalization) that formed its own cluster with HAdV species C genotypes. This isolate showed intertypic recombination events involving four genotypes, had the highest homology to HAdV89 at complete genome level, but possessed the fiber gene of HAdV1, thereby representing a novel genotype of HAdV species C. The incidence of potential recombination events was higher in severe cases than in mild cases. Our findings confirm that recombination among HAdVs is important for molecular evolution and emergence of new strains. Therefore, further research on HAdVs, particularly among susceptible groups, is needed and continuous surveillance is required for public health preparedness including outbreak investigations.
Joyce Odeke Akello; Richard Kamgang; Maria Teresa Barbani; Franziska Suter-Riniker; Christoph Aebi; Christian Beuret; Daniel H. Paris; Stephen L Leib; Alban Ramette. Genomic analyses of human adenoviruses unravel novel recombinant genotypes associated with severe infections in pediatric patients. 2021, 1 .
AMA StyleJoyce Odeke Akello, Richard Kamgang, Maria Teresa Barbani, Franziska Suter-Riniker, Christoph Aebi, Christian Beuret, Daniel H. Paris, Stephen L Leib, Alban Ramette. Genomic analyses of human adenoviruses unravel novel recombinant genotypes associated with severe infections in pediatric patients. . 2021; ():1.
Chicago/Turabian StyleJoyce Odeke Akello; Richard Kamgang; Maria Teresa Barbani; Franziska Suter-Riniker; Christoph Aebi; Christian Beuret; Daniel H. Paris; Stephen L Leib; Alban Ramette. 2021. "Genomic analyses of human adenoviruses unravel novel recombinant genotypes associated with severe infections in pediatric patients." , no. : 1.
Background In Switzerland, HIV-1 transmission among men who have sex with men (MSM) has been dominated by subtype B, whilst non-B subtypes are commonly attributed to infections acquired abroad among heterosexuals. Here, we evaluated the temporal trends of non-B subtypes and the characteristics of molecular transmission clusters (MTCs) among MSM. Methods Sociodemographic and clinical data and partial pol sequences were obtained from participants enrolled in the Swiss HIV Cohort Study. For non-B subtypes, maximum likelihood trees were constructed, from which Swiss MTCs were identified and analyzed by transmission group. Results Non-B subtypes were identified in 8.1% (416/5116) of MSM participants. CRF01_AE was the most prevalent strain (3.5%), followed by subtype A (1.2%), F (1.1%), CRF02_AG (1.1%), C (0.9%), and G (0.3%). Between 1990 and 2019, an increase in the proportion of newly diagnosed individuals (0/123 [0%] to 11/32 [34%]) with non-B subtypes in MSM was found. Across all non-B subtypes, the majority of MSM MTCs were European. Larger MTCs were observed for MSM than heterosexuals. Conclusions We found a substantial increase in HIV-1 non-B subtypes among MSM in Switzerland and the occurrence of large MTCs, highlighting the importance of molecular surveillance in guiding public health strategies targeting the HIV-1 epidemic.
Jessy J Duran Ramirez; Tala Ballouz; Huyen Nguyen; Katharina Kusejko; Sandra E Chaudron; Michael Huber; Hans H Hirsch; Matthieu Perreau; Alban Ramette; Sabine Yerly; Matthias Cavassini; Marcel Stöckle; Hansjakob Furrer; Pietro Vernazza; Enos Bernasconi; Huldrych F Günthard; Roger D Kouyos; K Aebi-Popp; A Anagnostopoulos; M Battegay; J Böni; D L Braun; H C Bucher; A Calmy; A Ciuffi; G Dollenmaier; M Egger; L Elzi; J Fehr; J Fellay; C A Fux; D Haerry; B Hasse; M Hoffmann; I Hösli; C R Kahlert; L Kaiser; O Keiser; T Klimkait; H Kovari; B Ledergerber; G Martinetti; B Martinez de Tejada; C Marzolini; K J Metzner; N Müller; D Nicca; P Paioni; G Pantaleo; A Rauch; C Rudin; P Schmid; R Speck; P Tarr; A Trkola; G Wandeler; R Weber; Swiss HIV Cohort Study. Increasing Frequency and Transmission of HIV-1 Non-B Subtypes Among Men Who Have Sex With Men in the Swiss HIV Cohort Study. Journal of Infectious Diseases 2021, 1 .
AMA StyleJessy J Duran Ramirez, Tala Ballouz, Huyen Nguyen, Katharina Kusejko, Sandra E Chaudron, Michael Huber, Hans H Hirsch, Matthieu Perreau, Alban Ramette, Sabine Yerly, Matthias Cavassini, Marcel Stöckle, Hansjakob Furrer, Pietro Vernazza, Enos Bernasconi, Huldrych F Günthard, Roger D Kouyos, K Aebi-Popp, A Anagnostopoulos, M Battegay, J Böni, D L Braun, H C Bucher, A Calmy, A Ciuffi, G Dollenmaier, M Egger, L Elzi, J Fehr, J Fellay, C A Fux, D Haerry, B Hasse, M Hoffmann, I Hösli, C R Kahlert, L Kaiser, O Keiser, T Klimkait, H Kovari, B Ledergerber, G Martinetti, B Martinez de Tejada, C Marzolini, K J Metzner, N Müller, D Nicca, P Paioni, G Pantaleo, A Rauch, C Rudin, P Schmid, R Speck, P Tarr, A Trkola, G Wandeler, R Weber, Swiss HIV Cohort Study. Increasing Frequency and Transmission of HIV-1 Non-B Subtypes Among Men Who Have Sex With Men in the Swiss HIV Cohort Study. Journal of Infectious Diseases. 2021; ():1.
Chicago/Turabian StyleJessy J Duran Ramirez; Tala Ballouz; Huyen Nguyen; Katharina Kusejko; Sandra E Chaudron; Michael Huber; Hans H Hirsch; Matthieu Perreau; Alban Ramette; Sabine Yerly; Matthias Cavassini; Marcel Stöckle; Hansjakob Furrer; Pietro Vernazza; Enos Bernasconi; Huldrych F Günthard; Roger D Kouyos; K Aebi-Popp; A Anagnostopoulos; M Battegay; J Böni; D L Braun; H C Bucher; A Calmy; A Ciuffi; G Dollenmaier; M Egger; L Elzi; J Fehr; J Fellay; C A Fux; D Haerry; B Hasse; M Hoffmann; I Hösli; C R Kahlert; L Kaiser; O Keiser; T Klimkait; H Kovari; B Ledergerber; G Martinetti; B Martinez de Tejada; C Marzolini; K J Metzner; N Müller; D Nicca; P Paioni; G Pantaleo; A Rauch; C Rudin; P Schmid; R Speck; P Tarr; A Trkola; G Wandeler; R Weber; Swiss HIV Cohort Study. 2021. "Increasing Frequency and Transmission of HIV-1 Non-B Subtypes Among Men Who Have Sex With Men in the Swiss HIV Cohort Study." Journal of Infectious Diseases , no. : 1.
The structure of the exopolysaccharide capsule of Streptococcus pneumoniae is defined by the genetic arrangement of the capsule operon allowing the unequivocal identification of the pneumococcal serotype. Here, we investigated the environment-dependent composition of the polysaccharide structure of S. pneumoniae serotype 6F. When grown in a chemically defined medium (CDM) with glucose versus galactose, the exopolysaccharide capsule of the serotype 6F strains reveals a ratio of 1/0.6 or 1/0.3 for galactose/glucose in the capsule by 1H-NMR analyses, respectively. Increased production of the capsule precursor UDP-glucose has been identified by 31P-NMR in CDM with glucose. Flow cytometric experiments using monoclonal antibodies showed decreased labelling of Hyp6AG4 (specific for serotype 6A) antibodies when 6F is grown in glucose as compared to galactose, which mirrors the 1H-NMR results. Whole-genome sequencing analyses of serotype 6F isolates suggested that the isolates evolved during two different events from serotype 6A during the time when the 13-valent pneumococcal conjugate vaccine (PCV-13) was introduced. In conclusion, this study shows differences in the capsular structure of serotype 6F strains using glucose as compared to galactose as the carbon source. Therefore, 6F strains may show slightly different polysaccharide composition while colonizing the human nasopharynx (galactose rich) as compared to invasive locations such as the blood (glucose rich).
Joel Werren; Lukas Troxler; Oluwaseun Oyewole; Alban Ramette; Silvio Brugger; Rémy Bruggmann; Mark van der Linden; Moon Nahm; Ilche Gjuroski; Carlo Casanova; Julien Furrer; Markus Hilty. Carbon Source-Dependent Changes of the Structure of Streptococcus pneumoniae Capsular Polysaccharide with Serotype 6F. International Journal of Molecular Sciences 2021, 22, 4580 .
AMA StyleJoel Werren, Lukas Troxler, Oluwaseun Oyewole, Alban Ramette, Silvio Brugger, Rémy Bruggmann, Mark van der Linden, Moon Nahm, Ilche Gjuroski, Carlo Casanova, Julien Furrer, Markus Hilty. Carbon Source-Dependent Changes of the Structure of Streptococcus pneumoniae Capsular Polysaccharide with Serotype 6F. International Journal of Molecular Sciences. 2021; 22 (9):4580.
Chicago/Turabian StyleJoel Werren; Lukas Troxler; Oluwaseun Oyewole; Alban Ramette; Silvio Brugger; Rémy Bruggmann; Mark van der Linden; Moon Nahm; Ilche Gjuroski; Carlo Casanova; Julien Furrer; Markus Hilty. 2021. "Carbon Source-Dependent Changes of the Structure of Streptococcus pneumoniae Capsular Polysaccharide with Serotype 6F." International Journal of Molecular Sciences 22, no. 9: 4580.
Introduction In contrast to countries where carbapenemase-producing Enterobacterales (CPE) are endemic, only sporadic cases were reported in Switzerland until 2013. An aggravation of the epidemiological situation in neighbouring European countries indicated the need for a surveillance study in Switzerland. Aim We aimed to describe CPE distributions in Switzerland and identify epidemiological factors associated with changes in incidence. Methods Data on all human CPE isolates from 2013 to 2018 were collected by the Swiss Centre for Antibiotic Resistance (ANRESIS) and analysed for temporal and regional trends by Generalised Poisson regression. Isolates associated with infection or colonisation were included in a primary analysis; a secondary analysis included invasive isolates only. Statistical detection of regional clusters was performed with WHONET/SaTScan. Results We analysed 731 CPE isolates, of which 325 (44.5%) were associated with screenings and 173 (23.7%) with infections. Yearly detection of CPE isolates increased considerably during the study period from 65 to 212. The most frequently isolated species were Klebsiella pneumoniae (54%) and Escherichia coli (28%). The most frequent genotypes were OXA-48 (43%), KPC (21%) and NDM (14%). In contrast to the French-speaking parts of Switzerland (West, Geneva) where OXA-48 were the predominant genotypes (around 60%), KPC was the most frequently detected genotype in the Italian-speaking region (63%). WHONET/SaTScan outbreak detection analysis identified seven clusters in five regions of Switzerland. Conclusions In a first continuous surveillance of CPE in Switzerland, we found that the epidemiological situation aggravated nationwide and that regional patterns of CPE genotypes mirrored the situation in neighbouring European countries.
Alban Ramette; Michael Gasser; Patrice Nordmann; Reinhard Zbinden; Jacques Schrenzel; Damir Perisa; Andreas Kronenberg. Temporal and regional incidence of carbapenemase-producing Enterobacterales, Switzerland, 2013 to 2018. Eurosurveillance 2021, 26, 1900760 .
AMA StyleAlban Ramette, Michael Gasser, Patrice Nordmann, Reinhard Zbinden, Jacques Schrenzel, Damir Perisa, Andreas Kronenberg. Temporal and regional incidence of carbapenemase-producing Enterobacterales, Switzerland, 2013 to 2018. Eurosurveillance. 2021; 26 (15):1900760.
Chicago/Turabian StyleAlban Ramette; Michael Gasser; Patrice Nordmann; Reinhard Zbinden; Jacques Schrenzel; Damir Perisa; Andreas Kronenberg. 2021. "Temporal and regional incidence of carbapenemase-producing Enterobacterales, Switzerland, 2013 to 2018." Eurosurveillance 26, no. 15: 1900760.
The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants of concern (VoCs) and recommendations for lineage specific surveillance. In Switzerland, during the last weeks of December 2020, we established a nationwide screening protocol across multiple laboratories, focusing first on epidemiological and microbiological definitions. In January 2021, we validated and implemented an N501Y-specific PCR to rapidly screen for VoCs, which are then confirmed using amplicon sequencing or whole genome sequencing (WGS). A total of 13,387 VoCs have been identified since the detection of the first Swiss case in October 2020, with 4194 being B.1.1.7, 172 B.1.351, and 7 P.1. The remaining 9014 cases of VoCs have been described without further lineage specification. Overall, all diagnostic centers reported a rapid increase of the percentage of detected VOCs, with a range of 6 to 46% between 25 to 31 of January 2021 increasing towards 41 to 82% between 22 to 28 of February. A total of 739 N501Y positive genomes were analysed and show a broad range of introduction events to Switzerland. In this paper, we describe the nationwide coordination and implementation process across laboratories, public health institutions, and researchers, the first results of our N501Y-specific variant screening, and the phylogenetic analysis of all available WGS data in Switzerland, that together identified the early introduction events and subsequent community spreading of the VoCs.
Ana Goncalves Cabecinhas; Tim Roloff; Madlen Stange; Claire Bertelli; Michael Huber; Alban Ramette; Chaoran Chen; Sarah Nadeau; Yannick Gerth; Sabine Yerly; Onya Opota; Trestan Pillonel; Tobias Schuster; Cesar Metzger; Jonas Sieber; Michael Bel; Nadia Wohlwend; Christian Baumann; Michel Koch; Pascal Bittel; Karoline Leuzinger; Myrta Brunner; Franziska Suter-Riniker; Livia Berlinger; Kirstine Søgaard; Christiane Beckmann; Christoph Noppen; Maurice Redondo; Ingrid Steffen; Helena Seth-Smith; Alfredo Mari; Reto Lienhard; Martin Risch; Oliver Nolte; Isabella Eckerle; Gladys Martinetti Lucchini; Emma Hodcroft; Richard Neher; Tanja Stadler; Hans Hirsch; Stephen Leib; Lorenz Risch; Laurent Kaiser; Alexandra Trkola; Gilbert Greub; Adrian Egli. SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms 2021, 9, 677 .
AMA StyleAna Goncalves Cabecinhas, Tim Roloff, Madlen Stange, Claire Bertelli, Michael Huber, Alban Ramette, Chaoran Chen, Sarah Nadeau, Yannick Gerth, Sabine Yerly, Onya Opota, Trestan Pillonel, Tobias Schuster, Cesar Metzger, Jonas Sieber, Michael Bel, Nadia Wohlwend, Christian Baumann, Michel Koch, Pascal Bittel, Karoline Leuzinger, Myrta Brunner, Franziska Suter-Riniker, Livia Berlinger, Kirstine Søgaard, Christiane Beckmann, Christoph Noppen, Maurice Redondo, Ingrid Steffen, Helena Seth-Smith, Alfredo Mari, Reto Lienhard, Martin Risch, Oliver Nolte, Isabella Eckerle, Gladys Martinetti Lucchini, Emma Hodcroft, Richard Neher, Tanja Stadler, Hans Hirsch, Stephen Leib, Lorenz Risch, Laurent Kaiser, Alexandra Trkola, Gilbert Greub, Adrian Egli. SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing. Microorganisms. 2021; 9 (4):677.
Chicago/Turabian StyleAna Goncalves Cabecinhas; Tim Roloff; Madlen Stange; Claire Bertelli; Michael Huber; Alban Ramette; Chaoran Chen; Sarah Nadeau; Yannick Gerth; Sabine Yerly; Onya Opota; Trestan Pillonel; Tobias Schuster; Cesar Metzger; Jonas Sieber; Michael Bel; Nadia Wohlwend; Christian Baumann; Michel Koch; Pascal Bittel; Karoline Leuzinger; Myrta Brunner; Franziska Suter-Riniker; Livia Berlinger; Kirstine Søgaard; Christiane Beckmann; Christoph Noppen; Maurice Redondo; Ingrid Steffen; Helena Seth-Smith; Alfredo Mari; Reto Lienhard; Martin Risch; Oliver Nolte; Isabella Eckerle; Gladys Martinetti Lucchini; Emma Hodcroft; Richard Neher; Tanja Stadler; Hans Hirsch; Stephen Leib; Lorenz Risch; Laurent Kaiser; Alexandra Trkola; Gilbert Greub; Adrian Egli. 2021. "SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing." Microorganisms 9, no. 4: 677.
The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8–9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.
Franziska Hufsky; Niko Beerenwinkel; Irmtraud M. Meyer; Simon Roux; Georgia May Cook; Cormac M. Kinsella; Kevin Lamkiewicz; Mike Marquet; David F. Nieuwenhuijse; Ingrida Olendraite; Sofia Paraskevopoulou; Francesca Young; Ronald Dijkman; Bashar Ibrahim; Jenna Kelly; Philippe Le Mercier; Manja Marz; Alban Ramette; Volker Thiel. The International Virus Bioinformatics Meeting 2020. Viruses 2020, 12, 1398 .
AMA StyleFranziska Hufsky, Niko Beerenwinkel, Irmtraud M. Meyer, Simon Roux, Georgia May Cook, Cormac M. Kinsella, Kevin Lamkiewicz, Mike Marquet, David F. Nieuwenhuijse, Ingrida Olendraite, Sofia Paraskevopoulou, Francesca Young, Ronald Dijkman, Bashar Ibrahim, Jenna Kelly, Philippe Le Mercier, Manja Marz, Alban Ramette, Volker Thiel. The International Virus Bioinformatics Meeting 2020. Viruses. 2020; 12 (12):1398.
Chicago/Turabian StyleFranziska Hufsky; Niko Beerenwinkel; Irmtraud M. Meyer; Simon Roux; Georgia May Cook; Cormac M. Kinsella; Kevin Lamkiewicz; Mike Marquet; David F. Nieuwenhuijse; Ingrida Olendraite; Sofia Paraskevopoulou; Francesca Young; Ronald Dijkman; Bashar Ibrahim; Jenna Kelly; Philippe Le Mercier; Manja Marz; Alban Ramette; Volker Thiel. 2020. "The International Virus Bioinformatics Meeting 2020." Viruses 12, no. 12: 1398.
Mycobacterium chelonae infections usually resolve with adequate therapy. We report the case of an adolescent with a chronic and progressive M chelonae infection refractory to combined antimicrobial and surgical therapy. Whole genome sequence analysis of consecutive isolates distinguished reinfection from recurrence and contributed to the diagnosis of a factitious disorder.
Sarah Flohr; Alban Ramette; Philipp K A Agyeman; Andrea Duppenthaler; Cordula Scherer; Peter M Keller; Christoph Aebi. Recurrent Mycobacterium chelonae Skin Infection Unmasked as Factitious Disorder Using Bacterial Whole Genome Sequence Analysis. Open Forum Infectious Diseases 2020, 7, 1 .
AMA StyleSarah Flohr, Alban Ramette, Philipp K A Agyeman, Andrea Duppenthaler, Cordula Scherer, Peter M Keller, Christoph Aebi. Recurrent Mycobacterium chelonae Skin Infection Unmasked as Factitious Disorder Using Bacterial Whole Genome Sequence Analysis. Open Forum Infectious Diseases. 2020; 7 (11):1.
Chicago/Turabian StyleSarah Flohr; Alban Ramette; Philipp K A Agyeman; Andrea Duppenthaler; Cordula Scherer; Peter M Keller; Christoph Aebi. 2020. "Recurrent Mycobacterium chelonae Skin Infection Unmasked as Factitious Disorder Using Bacterial Whole Genome Sequence Analysis." Open Forum Infectious Diseases 7, no. 11: 1.
Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. The approach was complemented by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. The identification of the enterovirus sequences in the samples was confirmed by short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94% and 97%. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains.
Carole Grädel; Miguel A. Terrazos Miani; Christian Baumann; Maria Teresa Barbani; Stefan Neuenschwander; Stephen L. Leib; Franziska Suter-Riniker; Alban Ramette. Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing. Viruses 2020, 12, 841 .
AMA StyleCarole Grädel, Miguel A. Terrazos Miani, Christian Baumann, Maria Teresa Barbani, Stefan Neuenschwander, Stephen L. Leib, Franziska Suter-Riniker, Alban Ramette. Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing. Viruses. 2020; 12 (8):841.
Chicago/Turabian StyleCarole Grädel; Miguel A. Terrazos Miani; Christian Baumann; Maria Teresa Barbani; Stefan Neuenschwander; Stephen L. Leib; Franziska Suter-Riniker; Alban Ramette. 2020. "Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing." Viruses 12, no. 8: 841.
The "One Health" framework emphasizes the ecological relationships between soil, plant, animal and human health. Microbiomes play important roles in these relationships, as they modify the health and performance of the different compartments and influence the transfer of energy, matter and chemicals between them. Standardized methods to characterize microbiomes along food chains are, however, currently lacking. To address this methodological gap, we evaluated the performance of DNA extraction kits and commonly recommended primer pairs targeting different hypervariable regions (V3‐V4, V4, V5‐V6, V5‐V6‐V7) of the 16S rRNA gene, on microbiome samples along a model food chain, including soils, maize roots, cattle rumen, and cattle and human faeces. We also included faeces from gnotobiotic mice colonized with defined bacterial taxa and mock communities to confirm the robustness of our molecular and bioinformatic approaches on these defined low microbial diversity samples. Based on Amplicon Sequence Variants, the primer pair 515F‐806R led to the highest estimates of species richness and diversity in all sample types and offered maximum diversity coverage of reference databases in in silico primer analysis. The influence of the DNA extraction kits was negligible compared to the influence of the choice of primer pairs. Comparing microbiomes using 515F‐806R revealed that soil and root samples have the highest estimates of species richness while lowest richness was observed in human faeces. Primer pair choice directly influenced the estimation of community changes within and across compartments and may give rise to preferential detection of specific taxa. This work demonstrates why a standardized approach is necessary to analyse microbiomes within and between source compartments along food chains in the context of the One Health framework.
Wasim. Uddin; Klaus Schlaeppi; Francesca Ronchi; Stephen L. Leib; Matthias Erb; Alban Ramette. Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework. Molecular Ecology Resources 2020, 20, 1558 -1571.
AMA StyleWasim. Uddin, Klaus Schlaeppi, Francesca Ronchi, Stephen L. Leib, Matthias Erb, Alban Ramette. Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework. Molecular Ecology Resources. 2020; 20 (6):1558-1571.
Chicago/Turabian StyleWasim. Uddin; Klaus Schlaeppi; Francesca Ronchi; Stephen L. Leib; Matthias Erb; Alban Ramette. 2020. "Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework." Molecular Ecology Resources 20, no. 6: 1558-1571.
Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, those viruses are identified by PCR based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. Results of the approach were complemented with those obtained by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% to 99.6 % of the best reference genomes. The identification of the enterovirus sequences in the sample was confirmed by the short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94-97%. Here we show that nanopore DRS can be used to correctly identify the genotypes of enteroviruses from patient stool samples with high viral load.
Carole Grädel; Miguel A Terrazos Miani; Christian Baumann; Maria Teresa Barbani; Stefan Neuenschwander; Stephen L Leib; Franziska Suter-Riniker; Alban Ramette. Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing. 2020, 1 .
AMA StyleCarole Grädel, Miguel A Terrazos Miani, Christian Baumann, Maria Teresa Barbani, Stefan Neuenschwander, Stephen L Leib, Franziska Suter-Riniker, Alban Ramette. Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing. . 2020; ():1.
Chicago/Turabian StyleCarole Grädel; Miguel A Terrazos Miani; Christian Baumann; Maria Teresa Barbani; Stefan Neuenschwander; Stephen L Leib; Franziska Suter-Riniker; Alban Ramette. 2020. "Whole genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing." , no. : 1.
Amplicon sequencing of the 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations, with the most significant being the inability to resolve mixed amplicons when closely related species are coamplified from a mixed culture. This often leads to either increased turnaround time or absence of usable sequence data. Short-read next-generation sequencing (NGS) technologies could solve the mixed amplicon issue but would lack both cost efficiency at low throughput and fast turnaround times.
Stefan Moritz Neuenschwander; Miguel Angel Terrazos Miani; Heiko Amlang; Carmen Perroulaz; Pascal Bittel; Carlo Casanova; Sara Droz; Jean-Pierre Flandrois; Stephen L. Leib; Franziska Suter-Riniker; Alban Ramette. A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing. Journal of Clinical Microbiology 2020, 58, 1 .
AMA StyleStefan Moritz Neuenschwander, Miguel Angel Terrazos Miani, Heiko Amlang, Carmen Perroulaz, Pascal Bittel, Carlo Casanova, Sara Droz, Jean-Pierre Flandrois, Stephen L. Leib, Franziska Suter-Riniker, Alban Ramette. A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing. Journal of Clinical Microbiology. 2020; 58 (6):1.
Chicago/Turabian StyleStefan Moritz Neuenschwander; Miguel Angel Terrazos Miani; Heiko Amlang; Carmen Perroulaz; Pascal Bittel; Carlo Casanova; Sara Droz; Jean-Pierre Flandrois; Stephen L. Leib; Franziska Suter-Riniker; Alban Ramette. 2020. "A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing." Journal of Clinical Microbiology 58, no. 6: 1.
Background Identifying local outbreaks and their drivers is a key step toward curbing human immunodeficiency virus (HIV) transmission and potentially achieving HIV elimination. Such outbreaks can be identified as transmission clusters extracted from phylogenetic trees constructed of densely sampled viral sequences. In this study, we combined phylogenetic transmission clusters with extensive data on virological suppression and behavioral risk of cluster members to quantify the drivers of ongoing transmission over 10 years. Methods Using the comprehensive Swiss HIV Cohort Study and its drug-resistance database, we reconstructed phylogenetic trees for each year between 2007 and 2017. We identified HIV transmission clusters dominated by men who have sex with men (MSM) and determined their annual growth. We used Poisson regression to assess if cluster growth was associated with a per-cluster infectivity and behavioral risk score. Results Both infectivity and behavioral risk scores were significantly higher in growing MSM transmission clusters compared to nongrowing clusters (P ≤ .01). The fraction of transmission clusters without infectious members acquiring new infections increased significantly over the study period. The infectivity score was significantly associated with per-capita incidence of MSM transmission clusters in 8 years, while the behavioral risk score was significantly associated with per-capita incidence of MSM transmission clusters in 3 years. Conclusions We present a phylogenetic method to identify hotspots of ongoing transmission among MSM. Our results demonstrate the effectiveness of treatment as prevention at the population level. However, the significantly increasing number of new infections among transmission clusters without infectious members highlights a relative shift from diagnosed to undiagnosed individuals as drivers of HIV transmission in Swiss MSM.
Nadine Bachmann; Katharina Kusejko; Huyen Nguyen; Sandra E Chaudron; Claus Kadelka; Teja Turk; Jürg Böni; Matthieu Perreau; Thomas Klimkait; Sabine Yerly; Manuel Battegay; Andri Rauch; Alban Ramette; Pietro Vernazza; Enos Bernasconi; Matthias Cavassini; Huldrych F Günthard; Roger D Kouyos; A Anagnostopoulos; D L Braun; H C Bucher; A Calmy; A Ciuffi; G Dollenmaier; M Egger; L Elzi; J Fehr; J Fellay; H Furrer; C A Fux; D Haerry; B Hasse; H H Hirsch; M Hoffmann; I Hösli; M Huber; C R Kahlert; L Kaiser; O Keiser; H Kovari; B Ledergerber; G Martinetti; B Martinez de Tejada; C Marzolini; K J Metzner; N Müller; D Nicca; P Paioni; G Pantaleo; C Rudin; A U Scherrer; P Schmid; R Speck; M Stöckle; P Tarr; A Trkola; G Wandeler; R Weber; Swiss HIV Cohort Study. Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of Human Immunodeficiency Virus Transmission in Men Who Have Sex With Men. Clinical Infectious Diseases 2020, 72, 2175 -2183.
AMA StyleNadine Bachmann, Katharina Kusejko, Huyen Nguyen, Sandra E Chaudron, Claus Kadelka, Teja Turk, Jürg Böni, Matthieu Perreau, Thomas Klimkait, Sabine Yerly, Manuel Battegay, Andri Rauch, Alban Ramette, Pietro Vernazza, Enos Bernasconi, Matthias Cavassini, Huldrych F Günthard, Roger D Kouyos, A Anagnostopoulos, D L Braun, H C Bucher, A Calmy, A Ciuffi, G Dollenmaier, M Egger, L Elzi, J Fehr, J Fellay, H Furrer, C A Fux, D Haerry, B Hasse, H H Hirsch, M Hoffmann, I Hösli, M Huber, C R Kahlert, L Kaiser, O Keiser, H Kovari, B Ledergerber, G Martinetti, B Martinez de Tejada, C Marzolini, K J Metzner, N Müller, D Nicca, P Paioni, G Pantaleo, C Rudin, A U Scherrer, P Schmid, R Speck, M Stöckle, P Tarr, A Trkola, G Wandeler, R Weber, Swiss HIV Cohort Study. Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of Human Immunodeficiency Virus Transmission in Men Who Have Sex With Men. Clinical Infectious Diseases. 2020; 72 (12):2175-2183.
Chicago/Turabian StyleNadine Bachmann; Katharina Kusejko; Huyen Nguyen; Sandra E Chaudron; Claus Kadelka; Teja Turk; Jürg Böni; Matthieu Perreau; Thomas Klimkait; Sabine Yerly; Manuel Battegay; Andri Rauch; Alban Ramette; Pietro Vernazza; Enos Bernasconi; Matthias Cavassini; Huldrych F Günthard; Roger D Kouyos; A Anagnostopoulos; D L Braun; H C Bucher; A Calmy; A Ciuffi; G Dollenmaier; M Egger; L Elzi; J Fehr; J Fellay; H Furrer; C A Fux; D Haerry; B Hasse; H H Hirsch; M Hoffmann; I Hösli; M Huber; C R Kahlert; L Kaiser; O Keiser; H Kovari; B Ledergerber; G Martinetti; B Martinez de Tejada; C Marzolini; K J Metzner; N Müller; D Nicca; P Paioni; G Pantaleo; C Rudin; A U Scherrer; P Schmid; R Speck; M Stöckle; P Tarr; A Trkola; G Wandeler; R Weber; Swiss HIV Cohort Study. 2020. "Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of Human Immunodeficiency Virus Transmission in Men Who Have Sex With Men." Clinical Infectious Diseases 72, no. 12: 2175-2183.
Background: Human adenovirus (HAdV) is an important pathogen seen in clinical practice. Long-term studies may help better understand epidemiological trends and changes in circulating genotypes over time. Purpose: Using a large biobank of samples from hospitalized, adenovirus-positive patients over a 20-year period, we aimed to analyze long-term epidemiological trends and genotypic relatedness among circulating HAdV strains. Methods: Based on samples from hospitalized patients confirmed to be HAdV positive in Bern, Switzerland, from 1998 to 2017, and on their associated demographic and clinical data, we identified epidemiological trends and risk factors associated with HAdV infection. HAdV genotyping was performed by PCR amplification and sequencing of the hypervariable hexon gene. The obtained sequences were phylogenetically compared with sequences from international HAdV strains. Results: HAdV was identified in 1302 samples tested. Cases of HAdV infection were reported throughout the years with no clear seasonality. Upper respiratory tract samples, conjunctivitis swabs, and stool had the highest positivity rate (56.2%, 18.7%, and 14.2% of the cases, respectively). HAdV infection was highest among children ≤ 4 years old. Increased number of HAdV cases were observed in years 2009 (n = 110) and 2010 (n =112). HAdV8 was the predominant genotype among patients older than 20 years, and was mostly associated with ophthalmic infection. Predominant genotypes among children ≤ 4 years old were HAdV1, HAdV2, and HAdV3, which were mostly associated with respiratory tract infections. Recurring peaks of increased HAdV cases were evidenced every 4 years among children ≤ 4 years old. Conclusion: Our study gives novel insights on long-term epidemiological trends and phylogenetic relatedness among circulating HAdV strains in Switzerland, country in which little data on HAdV prevalence and diversity was so far available.
Joyce Odeke Akello; Richard Kamgang; Maria Teresa Barbani; Franziska Suter-Riniker; Stephen L Leib; Alban Ramette. Epidemiology of Human Adenoviruses: A 20-Year Retrospective Observational Study in Hospitalized Patients in Bern, Switzerland. Clinical Epidemiology 2020, ume 12, 353 -366.
AMA StyleJoyce Odeke Akello, Richard Kamgang, Maria Teresa Barbani, Franziska Suter-Riniker, Stephen L Leib, Alban Ramette. Epidemiology of Human Adenoviruses: A 20-Year Retrospective Observational Study in Hospitalized Patients in Bern, Switzerland. Clinical Epidemiology. 2020; ume 12 ():353-366.
Chicago/Turabian StyleJoyce Odeke Akello; Richard Kamgang; Maria Teresa Barbani; Franziska Suter-Riniker; Stephen L Leib; Alban Ramette. 2020. "Epidemiology of Human Adenoviruses: A 20-Year Retrospective Observational Study in Hospitalized Patients in Bern, Switzerland." Clinical Epidemiology ume 12, no. : 353-366.
The “One Health” framework emphasizes the ecological relationships between soil, plant, animal and human health. Microbiomes play important roles in these relationships, as they modify the health and performance of the different compartments and influence the transfer of energy, matter and chemicals between them. Standardized methods to characterize microbiomes along food chains are, however, currently lacking. To address this methodological gap, we evaluated the performance of DNA extractions kits and commonly recommended primer pairs targeting different hypervariable regions (V3-V4, V4, V5-V6, V5-V6-V7) of the 16S rRNA gene, on microbiome samples along a model food chain, including soils, maize roots, cattle rumen, and cattle and human faeces. We also included faeces from gnotobiotic mice colonized with defined bacterial taxa and mock communities to confirm the robustness of our molecular and bioinformatic approaches on these defined low microbial diversity samples. Based on Amplicon Sequence Variants, the primer pair 515F-806R led to the highest estimates of species richness and diversity in all sample types and offered maximum diversity coverage of reference databases in in silico primer analysis. The influence of the DNA extraction kits was negligible compared to the influence of the choice of primer pairs. Comparing microbiomes using 515F-806R revealed that soil and root samples have the highest estimates of species richness and inter-sample variation. Species richness decreased gradually along the food chain, with the lowest richness observed in human faeces. Primer pair choice directly influenced the estimation of community changes (beta diversity) within and across compartments and may give rise to preferential detection of specific taxa. This work demonstrates why a standardized approach is necessary to analyse microbiomes within and between source compartments along food chains in the context of the One Health framework.
Wasimuddin Wasimuddin; Klaus Schlaeppi; Francesca Ronchi; Stephen L Leib; Matthias Erb; Alban Ramette. Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework. 2019, 843144 .
AMA StyleWasimuddin Wasimuddin, Klaus Schlaeppi, Francesca Ronchi, Stephen L Leib, Matthias Erb, Alban Ramette. Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework. . 2019; ():843144.
Chicago/Turabian StyleWasimuddin Wasimuddin; Klaus Schlaeppi; Francesca Ronchi; Stephen L Leib; Matthias Erb; Alban Ramette. 2019. "Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework." , no. : 843144.
Methicillin-resistant Staphylococcus aureus (MRSA) strain AW7 is a commonly used challenge strain in experimental models of MRSA infection. Here, we report its draft genome sequence.
David Cameron; Alban Ramette; Josef Prazak; José Entenza; Matthias Haenggi; Yok-Ai Que; Gregory Resch. Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain AW7, Isolated from a Patient with Bacteremia. Microbiology Resource Announcements 2019, 8, 1 .
AMA StyleDavid Cameron, Alban Ramette, Josef Prazak, José Entenza, Matthias Haenggi, Yok-Ai Que, Gregory Resch. Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain AW7, Isolated from a Patient with Bacteremia. Microbiology Resource Announcements. 2019; 8 (40):1.
Chicago/Turabian StyleDavid Cameron; Alban Ramette; Josef Prazak; José Entenza; Matthias Haenggi; Yok-Ai Que; Gregory Resch. 2019. "Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus Strain AW7, Isolated from a Patient with Bacteremia." Microbiology Resource Announcements 8, no. 40: 1.
Amplicon sequencing of 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories, and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations with the most significant being the inability to resolve mixed amplicons when closely related species are co-amplified from a mixed culture. This often leads to either increased turnover time or absence of usable sequence data. Short-read NGS technologies could address the mixed amplicon issue, but would lack both cost efficiency at low throughput and fast turnaround times. Nanopore sequencing developed by Oxford Nanopore Technologies (ONT) could solve those issues by enabling flexible number of samples per run and adjustable sequencing time. Here we report on the development of a standardized laboratory workflow combined with a fully automated analysis pipelineLORCAN(Long Read Consensus ANalysis), which together provide a sample-to-report solution for amplicon sequencing and taxonomic identification of the resulting consensus sequences. Validation of the approach was conducted on a panel of reference strains and on clinical samples consisting of single or mixed rRNA amplicons associated with various bacterial genera by direct comparison to the corresponding Sanger sequences. Additionally, artificial read mixtures of closely related species were used to assessLORCAN’s behaviour when dealing with samples with known cross-contamination level. We demonstrate that by combining ONT amplicon sequencing results withLORCAN, the accuracy of Sanger sequencing can be closely matched (>99.6% sequence identity) and that mixed samples can be resolved at the single base resolution level. The presented approach has the potential to significantly improve the flexibility, reliability and availability of amplicon sequencing in diagnostic settings.
Stefan Moritz Neuenschwander; Miguel Angel Terrazos Miani; Heiko Amlang; Carmen Perroulaz; Pascal Bittel; Carlo Casanova; Sara Droz; Jean-Pierre Flandrois; Stephen L. Leib; Franziska Suter-Riniker; Alban Ramette. A sample-to-report solution for taxonomic identification of cultured bacteria in the clinical setting based on nanopore sequencing. 2019, 752774 .
AMA StyleStefan Moritz Neuenschwander, Miguel Angel Terrazos Miani, Heiko Amlang, Carmen Perroulaz, Pascal Bittel, Carlo Casanova, Sara Droz, Jean-Pierre Flandrois, Stephen L. Leib, Franziska Suter-Riniker, Alban Ramette. A sample-to-report solution for taxonomic identification of cultured bacteria in the clinical setting based on nanopore sequencing. . 2019; ():752774.
Chicago/Turabian StyleStefan Moritz Neuenschwander; Miguel Angel Terrazos Miani; Heiko Amlang; Carmen Perroulaz; Pascal Bittel; Carlo Casanova; Sara Droz; Jean-Pierre Flandrois; Stephen L. Leib; Franziska Suter-Riniker; Alban Ramette. 2019. "A sample-to-report solution for taxonomic identification of cultured bacteria in the clinical setting based on nanopore sequencing." , no. : 752774.
Enteroviruses affect millions of people worldwide and are of significant clinical importance. The standard method for enterovirus identification and genotyping still relies on Sanger sequencing of short diagnostic amplicons. In this study, we assessed the feasibility of nanopore sequencing using the new flow cell “Flongle” for fast, cost-effective, and accurate genotyping of human enteroviruses from clinical samples. PCR amplification of partial VP1 gene was performed from multiple patient samples, which were multiplexed together after barcoding PCR and sequenced multiple times on Flongle flow cells. The nanopore consensus sequences obtained from mapping reads to a reference database were compared to their Sanger sequence counterparts. Using clinical specimens sampled over different years, we were able to correctly identify enterovirus species and genotypes for all tested samples, even when doubling the number of barcoded samples on one flow cell. Average sequence identity across sequencing runs was >99.7%. Phylogenetic analysis showed that the consensus sequences achieved with Flongle delivered accurate genotyping. We conclude that the new Flongle-based assay with its fast turnover time, low cost investment, and low cost per sample represents an accurate, reproducible, and cost-effective platform for enterovirus identification and genotyping.
Carole Grädel; Miguel Angel Terrazos Miani; Maria Teresa Barbani; Stephen L Leib; Franziska Suter-Riniker; Alban Ramette. Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells. Genes 2019, 10, 659 .
AMA StyleCarole Grädel, Miguel Angel Terrazos Miani, Maria Teresa Barbani, Stephen L Leib, Franziska Suter-Riniker, Alban Ramette. Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells. Genes. 2019; 10 (9):659.
Chicago/Turabian StyleCarole Grädel; Miguel Angel Terrazos Miani; Maria Teresa Barbani; Stephen L Leib; Franziska Suter-Riniker; Alban Ramette. 2019. "Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells." Genes 10, no. 9: 659.
Shotgun metagenomics using next generation sequencing (NGS) is a promising technique to analyze both DNA and RNA microbial material from patient samples. Mostly used in a research setting, it is now increasingly being used in the clinical realm as well, notably to support diagnosis of viral infections, thereby calling for quality control and the implementation of ring trials (RT) to benchmark pipelines and ensure comparable results. The Swiss NGS clinical virology community therefore decided to conduct a RT in 2018, in order to benchmark current metagenomic workflows used at Swiss clinical virology laboratories, and thereby contribute to the definition of common best practices. The RT consisted of two parts (increments), in order to disentangle the variability arising from the experimental compared to the bioinformatics parts of the laboratory pipeline. In addition, the RT was also designed to assess the impact of databases compared to bioinformatics algorithms on the final results, by asking participants to perform the bioinformatics analysis with a common database, in addition to using their own in-house database. Five laboratories participated in the RT (seven pipelines were tested). We observed that the algorithms had a stronger impact on the overall performance than the choice of the reference database. Our results also suggest that differences in sample preparation can lead to significant differences in the performance, and that laboratories should aim for at least 5–10 Mio reads per sample and use depth of coverage in addition to other interpretation metrics such as the percent of coverage. Performance was generally lower when increasing the number of viruses per sample. The lessons learned from this pilot study will be useful for the development of larger-scale RTs to serve as regular quality control tests for laboratories performing NGS analyses of viruses in a clinical setting.
Thomas Junier; Michael Huber; Stefan Schmutz; Verena Kufner; Osvaldo Zagordi; Stefan Neuenschwander; Alban Ramette; Jakub Kubacki; Claudia Bachofen; Weihong Qi; Florian Laubscher; Samuel Cordey; Laurent Kaiser; Christian Beuret; Valérie Barbié; Jacques Fellay; Aitana Lebrand. Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial. Genes 2019, 10, 655 .
AMA StyleThomas Junier, Michael Huber, Stefan Schmutz, Verena Kufner, Osvaldo Zagordi, Stefan Neuenschwander, Alban Ramette, Jakub Kubacki, Claudia Bachofen, Weihong Qi, Florian Laubscher, Samuel Cordey, Laurent Kaiser, Christian Beuret, Valérie Barbié, Jacques Fellay, Aitana Lebrand. Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial. Genes. 2019; 10 (9):655.
Chicago/Turabian StyleThomas Junier; Michael Huber; Stefan Schmutz; Verena Kufner; Osvaldo Zagordi; Stefan Neuenschwander; Alban Ramette; Jakub Kubacki; Claudia Bachofen; Weihong Qi; Florian Laubscher; Samuel Cordey; Laurent Kaiser; Christian Beuret; Valérie Barbié; Jacques Fellay; Aitana Lebrand. 2019. "Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial." Genes 10, no. 9: 655.
Polymicrobial infections of the respiratory tract due to antibiotic resistant bacteria are a great concern in patients with cystic fibrosis (CF). We therefore aimed at establishing a functional metagenomic method to analyze the nasal resistome in infants with CF within the first year of life. We included samples from patients before antibiotic treatment, which allowed obtaining information regarding natural status of the resistome. In total, we analyzed 130 nasal swabs from 26 infants with CF and screened for β-lactams (ampicillin, amoxicillin-clavulanic acid, and cefuroxime) and other classes of antibiotic resistances (tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole). For 69 swabs (53% of total), we found at least one non-susceptible phenotype. Analyses of the inserts recovered from non-susceptible clones by nanopore MinION sequencing revealed a large reservoir of resistance genes including mobile elements within the antibiotic naïve samples. Comparing the data of the resistome with the microbiota composition showed that the bacterial phyla and operational taxonomic units (OTUs) of the microbiota rather than the antibiotic treatment were associated with the majority of non-susceptible phenotypes in the resistome. Future studies will reveal if characterization of the resistome can help in clinical decision-making in patients with CF.
Aurélie Allemann; Julia G. Kraemer; Insa Korten; Kathryn Ramsey; Carmen Casaulta; Daniel Wüthrich; Alban Ramette; Andrea Endimiani; Philipp Latzin; Markus Hilty; on Behalf of SCILD Study Group. Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life. Frontiers in Microbiology 2019, 10, 212 .
AMA StyleAurélie Allemann, Julia G. Kraemer, Insa Korten, Kathryn Ramsey, Carmen Casaulta, Daniel Wüthrich, Alban Ramette, Andrea Endimiani, Philipp Latzin, Markus Hilty, on Behalf of SCILD Study Group. Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life. Frontiers in Microbiology. 2019; 10 ():212.
Chicago/Turabian StyleAurélie Allemann; Julia G. Kraemer; Insa Korten; Kathryn Ramsey; Carmen Casaulta; Daniel Wüthrich; Alban Ramette; Andrea Endimiani; Philipp Latzin; Markus Hilty; on Behalf of SCILD Study Group. 2019. "Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life." Frontiers in Microbiology 10, no. : 212.
One of the options to mitigate atmospheric CO2 increase is CO2 Capture and Storage in sub-seabed geological formations. Since predicting long-term storage security is difficult, different CO2 leakage scenarios and impacts on marine ecosystems require evaluation. Submarine CO2 vents may serve as natural analogues and allow studying the effects of CO2 leakage in a holistic approach. At the study site east of Basiluzzo Islet off Panarea Island (Italy), gas emissions (90–99% CO2) occur at moderate flows (80–120 L m−2 h−1). We investigated the effects of acidified porewater conditions (pHT range: 5.5–7.7) on the diversity of benthic bacteria and invertebrates by sampling natural sediments in three subsequent years and by performing a transplantation experiment with a duration of one year, respectively. Both multiple years and one year of exposure to acidified porewater conditions reduced the number of benthic bacterial operational taxonomic units and invertebrate species diversity by 30–80%. Reduced biodiversity at the vent sites increased the temporal variability in bacterial and nematode community biomass, abundance and composition. While the release from CO2 exposure resulted in a full recovery of nematode species diversity within one year, bacterial diversity remained affected. Overall our findings showed that seawater acidification, induced by seafloor CO2 emissions, was responsible for loss of diversity across different size-classes of benthic organisms, which reduced community stability with potential relapses on ecosystem resilience.
Massimiliano Molari; Katja Guilini; Lidia Lins; Alban Ramette; Ann Vanreusel. CO2 leakage can cause loss of benthic biodiversity in submarine sands. Marine Environmental Research 2019, 144, 213 -229.
AMA StyleMassimiliano Molari, Katja Guilini, Lidia Lins, Alban Ramette, Ann Vanreusel. CO2 leakage can cause loss of benthic biodiversity in submarine sands. Marine Environmental Research. 2019; 144 ():213-229.
Chicago/Turabian StyleMassimiliano Molari; Katja Guilini; Lidia Lins; Alban Ramette; Ann Vanreusel. 2019. "CO2 leakage can cause loss of benthic biodiversity in submarine sands." Marine Environmental Research 144, no. : 213-229.