Bifidobacterium longum Bacteremia in Preterm Infants Receiving Probiotics

Administration of probiotics to premature newborns has been shown to prevent necrotizing enterocolitis and reduce all-cause mortality. In our hospital, we documented 2 cases of Bifidobacterium longum subspecies infantis bacteremia in newborns receiving probiotics. By comparative genomics, we confirmed that the strains isolated from each patient originated from the probiotic

Distinct Genomic Features Characterize Two Clades of <i>Corynebacterium diphtheriae</i>: Proposal of <i>Corynebacterium diphtheriae</i> Subsp. <i>diphtheriae</i> Subsp. nov. and <i>Corynebacterium diphtheriae</i> Subsp. <i>lausannense</i> Subsp. nov.

&lt;i&gt;Corynebacterium diphtheriae&lt;/i&gt; is the etiological agent of diphtheria, a disease caused by the presence of the diphtheria toxin. However, an increasing number of records report non-toxigenic &lt;i&gt;C. diphtheriae&lt;/i&gt; infections. Here, a &lt;i&gt;C. diphtheriae&lt;/i&gt; strain was recovered from a patient with a past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi. Whole-genome sequencing (WGS), performed in parallel with PCR targeting the toxin gene and the Elek test, provided clinically relevant results in a short turnaround time, showing that the isolate was non-toxigenic. A comparative genomic analysis of the new strain (CHUV2995) with 56 other publicly available genomes of &lt;i&gt;C. diphtheriae&lt;/i&gt; revealed that the strains CHUV2995, CCUG 5865 and CMCNS703 share a lower average nucleotide identity (ANI) (95.24 to 95.39%) with the &lt;i&gt;C. diphtheriae&lt;/i&gt; NCTC 11397 &lt;sup&gt;T&lt;/sup&gt; reference genome than all other &lt;i&gt;C. diphtheriae&lt;/i&gt; genomes (&gt;98.15%). Core genome phylogeny confirmed the presence of two monophyletic clades. Based on these findings, we propose here two new &lt;i&gt;C. diphtheriae&lt;/i&gt; subspecies to replace the lineage denomination used in previous multilocus sequence typing studies: &lt;i&gt;C. diphtheriae&lt;/i&gt; subsp. &lt;i&gt;lausannense&lt;/i&gt; subsp. nov. (instead of lineage-2), regrouping strains CHUV2995, CCUG 5865, and CMCNS703, and &lt;i&gt;C. diphtheriae&lt;/i&gt; subsp. &lt;i&gt;diphtheriae&lt;/i&gt; subsp. nov, regrouping all other &lt;i&gt;C. diphtheriae&lt;/i&gt; in the dataset (instead of lineage-1). Interestingly, members of subspecies &lt;i&gt;lausannense&lt;/i&gt; displayed a larger genome size than subspecies &lt;i&gt;diphtheriae&lt;/i&gt; and were enriched in COG categories related to transport and metabolism of lipids (I) and inorganic ion (P). Conversely, they lacked all genes involved in the synthesis of pili (SpaA-type, SpaD-type and SpaH-type), molybdenum cofactor and of the nitrate reductase. Finally, the CHUV2995 genome is particularly enriched in mobility genes and harbors several prophages. The genome encodes a type II-C CRISPR-Cas locus with 2 spacers that lacks &lt;i&gt;csn2&lt;/i&gt; or &lt;i&gt;cas4&lt;/i&gt; , which could hamper the acquisition of new spacers and render strain CHUV2995 more susceptible to bacteriophage infections and gene acquisition through various mechanisms of horizontal gene transfer

Clinical bioinformatics for microbial genomics and metagenomics:an ESCMID Postgraduate Technical Workshop

The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) workshop on genomics and metagenomics was held in Lausanne from 9th to 12th September 2019. As many as 68 participants from 20 countries from all 5 continents participated to this postgraduate technical workshop. During 4 days, the participants shared their time between conferences on various topics related to the implementation of genomics and metagenomics in a clinical diagnostic laboratory. These included talks from the clinics and talks from bioinformatic experts. A significant time was also dedicated to practicals covering various aspects of the data analysis of NGS sequences (quality check, annotation of virulence and antibiotic resistance genes, taxonomic assignment of amplicons, strain typing, …). This ESCMID meeting co-organized by A Lebrand and G Greub, with the help of the European Study Group for Genomics ad Molecular Diagnostics (ESGMD) provided a unique opportunity to exchange knowledge and ideas on the most recent bioinformatic approaches, as well as how to report such NGS results in diagnostic laboratories. This meeting report summarizes the key messages of this meeting

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020 - the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrasted these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland's border closures de-coupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86-98% reduction in introductions during Switzerland's strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Last, we quantified local transmission dynamics once introductions into Switzerland occurred, using a phylodynamic model. We found that transmission slowed 35-63% upon outbreak detection in summer 2020, but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics

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

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

Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum.

Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting &gt;100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold. Minimal target (Euo) boxes were found in conserved developmentally-regulated genes governing vertical genome transmission (cytokinesis and DNA replication) and genome plasticity (transposases). Our ChIP-Seq analysis with intracellular bacteria not only reveals that global TF regulation is maintained in the reduced regulatory genomes of Chlamydiae, but also predicts that master TFs interpret genomic information in the obligate intracellular α-proteobacteria, including the rickettsiae, from which modern day mitochondria evolved

Comparative genomics of the Chlamydiae

Les bactéries du phylum Chlamydiae sont des intracellulaires obliga¬toires qui comprennent d'important pathogènes tels que Chlamydia tra- chomatis et Chlamydia psittaci. De récentes analyses métagénomiques ont démontré la grande diversité et l'ubiquité de ces organismes. Ces bac¬téries peuvent infecter un large panel d'hôtes: des mammifères, des oiseaux, des arthropodes ou encore des eucaryotes unicellulaires. Ces bactéries intracellulaires sont difficiles à cultiver, et l'absence de système permettant de transformer la majorité des Chlamydiae freine les efforts de recherche. Cependant, une quantité croissante de données génomiques est rendue publique, permettant d'étudier certains aspects de la biolo¬gie et de l'évolution d'espèces non-cultivées par l'étude de leur génome. Dans cette thèse, une étude comparative à large échelle de l'ensemble des Chlamydiae connues a été entreprise afin de d'étudier la diversité, la biologie et l'évolution du phylum dans son ensemble. Une étude phylogénétique approfondie a tout d'abord été entreprise afin de clarifier les liens de parenté entre les espèces dont la séquence du génome est disponible, et afin de développer une approche permettant la classification de nouvelles souches. Le séquençage du génome d'une nouvelle espèce identifiée dans des tiques (Ixodes ricinus) a également été entrepris. De récentes études de la prévalence des Chlamydiae dans les tiques ont révélé la présence de nombreuses séquences de Chlamydiae. La plupart étaient très similaires à des séquences de la famille des Rhab- dochlamydiaceae. Un génome pratiquement complet a pu être séquencé et assemblé suite à l'extraction de l'ADN de l'un des échantillons de tiques. Une base de données a été mise en place, permettant d'effectuer des anal¬yses comparatives à l'échelle du phylum, ainsi que le transfert d'annotati¬ons d'organismes modèles et de bases de données de référence. Nos anal¬yses ont montré une grande diversité génétique et métabolique au sein du phylum. Les génomes des Chlamydiae du mérou semblent notam¬ment ne pas encoder de nombreuses protéines essentielles à la division des autres Chlamydiae. D'autres clades montrent des signes de dégrada- tion de certains gènes qui pourraient être en lien avec un changement récent de leur niche écologique. Ces analyses ont également permis l'identification de multiple protéines non caractérisées qui pourraient être impliquées i) dans des fonctions essentielles en lien avec le cycle de vie et la niche intracellulaire des Chlamydiae, y compris des protéines de la division et des protéines interagissant directement avec l'hôte (pro¬téines effectrices). ii) Des protéines spécifiques à chaque espèce. Ces protéines pourraient être impliquées dans la spécificité des différentes Chlamydiae pour leur (s) hôte(s). Toutes les données génomiques générées au cours de ce travail seront rendues publiques sous la forme d'un site web interactif afin de fournir une ressource de haute qualité à la commu¬nauté scientifique. -- Members of the Chlamydiae phylum are obligate intracellular bacte- ria, and include important pathogens such as Chlamydia trachomatis and Chlamydia psittaci. Analyses of metagenomic data show that Chlamydiae are highly diverse and ubiquitous. Known species infect a large range of eukaryotes including mammals, birds, fishes, arthropods and free-living amoeba. An increasing number of chlamydial species are progressively described, but most research efforts focus on only few species. Indeed, the difficulty to culture obligate intracellular bacteria and the lack of genetic transformation system complicate the study of Chlamydiae. Nev- ertheless, genomics data is accumulating at an increasing pace, allowing the study of the biology of uncultured organisms. We performed a lare scale comparative analysis of ail known Chlamydiae in order to investi- gate the diversity, biology and évolution of the phylum Chlamydiae. First, in depth phylogenetic analyses were performed in order to clarify the relationship between sequenced chlamydial genomes and to investi- gate new approaches for the classification of new strains. In addition, genome sequencing of a représentative strain of a new species infect- ing ticks (Ixodes ricinus) was undertaken. Recent investigations of the prevalence of Chlamydiae in ticks revealed numerous chlamydial rRNA se¬quences. They were mainly phylogenetically related to the Rhabdochlamy- diaceae family. A nearly complété chlamydial genome could be sequenced and assembled from a heavily infected tick sample. A database was developed, allowing comparative genomic analyses at the scale of the entire phylum and annotation transfer from model or¬ganisms and reference databases. Comparative analyses showed a high genetic and metabolic diversity. Chlamydiae infecting Orange-spotted grouper lack essential division proteins, while other clades exhibit clear evidences of gene decay that might relate to recent shifts in their ecolog- ical niche. Detailed analyses allowed the identification multiple unchar- acterized proteins that may be involved in: i) core functionalities related to the conserved life-cycle and intracellular niche of the Chlamydiae, in- cludirig proteins involved in division and conserved mechanisms of in¬teraction with the eukaryotic host cell (e.g. effector proteins), ii) Species specific proteins that might be involved in host-specific interactions. Ail data produced will be made public as part of an online database in order to provide a high quality resource for the chlamydia research community

Alpha and Omicron SARS-CoV-2 Adaptation in an Upper Respiratory Tract Model

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing an unprecedented pandemic. Although vaccines and antivirals are limiting the spread, SARS-CoV-2 is still under selective pressure in human and animal populations, as demonstrated by the emergence of variants of concern. To better understand the driving forces leading to new subtypes of SARS-CoV-2, we infected an ex vivo cell model of the human upper respiratory tract with Alpha and Omicron BA.1 variants for one month. Although viral RNA was detected during the entire course of the infection, infectious virus production decreased over time. Sequencing analysis did not show any adaptation in the spike protein, suggesting a key role for the adaptive immune response or adaptation to other anatomical sites for the evolution of SARS-CoV-2

Table1.XLSX

<p>The Chlamydiae phylum exclusively encompasses bacteria sharing a similar obligate intracellular life cycle. Existing 16S rDNA data support a high diversity within the phylum, however genomic data remain scarce owing to the difficulty in isolating strains using culture systems with eukaryotic cells. Yet, Chlamydiae genome data extracted from large scale metagenomic studies might help fill this gap. This work compares 33 cultured and 27 environmental, uncultured chlamydial genomes, in order to clarify the phylogenetic relatedness of the new chlamydial clades and to investigate the genetic diversity of the Chlamydiae phylum. The analysis of published chlamydial genomes from metagenomics bins and single cell sequencing allowed the identification of seven new deeply branching chlamydial clades sharing genetic hallmarks of parasitic Chlamydiae. Comparative genomics suggests important biological differences between those clades, including loss of many proteins involved in cell division in the genus Similichlamydia, and loss of respiratory chain and tricarboxylic acid cycle in several species. Comparative analyses of chlamydial genomes with two proteobacterial orders, the Rhizobiales and the Rickettsiales showed that genomes of different Rhizobiales families are much more similar than genomes of different Rickettsiales families. On the other hand, the chlamydial 16S rRNAs exhibit a higher sequence conservation than their Rickettsiales counterparts, while chlamydial proteins exhibit increased sequence divergence. Studying the diversity and genome plasticity of the entire Chlamydiae phylum is of major interest to better understand the emergence and evolution of this ubiquitous and ancient clade of obligate intracellular bacteria.</p