scholarly journals Metagenome of SARS-Cov2 patients in Shenzhen with travel to Wuhan shows a wide range of species - Lautropia, Cutibacterium, Haemophilus being most abundant - and Campylobacter explaining diarrhea

2020 ◽  
Author(s):  
Sandeep Chakraborty
Keyword(s):  
Secondary Infection ◽  
Bacterial Species ◽  
Bacterial Load ◽  
San Diego County ◽  
Opportunistic Pathogens ◽  
Sequencing Data ◽  
Familial Cluster ◽  
Chinese Study ◽  
Wide Range ◽  
Initial Results

The metagenome of patients infected with SARS-Cov2 [1] has shown Prevotella to be a key player in immune response [2] in one Chinese study [3], just starting in another [4] and a host of other opportunistic pathogens in a study from San Diego county [5]. The metagenome can also be queried to find host response genes [5], as was done in monkey cells infected with SARS-Cov2 [6]Nanopore sequencing data from a familial cluster in ShenzhenThe patients were tested for 4 bacterial species - Bordetella pertussis, Bordetella parapertussis, Chlamydophila pneumoniae, and Mycoplasma pneumoniae. The sequencing data (Accid:SRR10948474, Nanopore) from five patients in a family cluster from Shenzhen who presented with unexplained pneumonia after returning from Wuhan (Table 1) shows a wide range of bacterial species - Lautropia, Cutibacterium, Haemophilus being most abundant. The presence of Campylobacter explains diarrhea seen in the patient [7,8]. Also, their tests should have detected Mycoplasma, since it is there in the data.Significant bacterial load with some bacterial species predominatingThe bacterial reads are about 20% (95K out of 500K reads). The viral load is also significant here (70K reads) [2]. They are in SI.familial/allsequences.fa. The number of bacterial species (with at least two reads) is 876 (SI.familial/list.allbacteria.txt). Thus, it is important to consider secondary infection, a possible reason why azithromycin (in addition to hydroxychloroquine) has given good initial results in a clinical trial [9].

scholarly journals Metagenome of SARS-Cov2 from a patient in Brazil shows a wide range of bacterial species - Lautropia, Prevotella, Haemophilus - overshadowing viral reads, which does not even add up to a full genome, explaining false negatives

2020 ◽  
Author(s):  
Sandeep Chakraborty
Keyword(s):  
Bacterial Species ◽  
Bacterial Load ◽  
San Diego County ◽  
Nasopharyngeal Swab ◽  
Suspected Case ◽  
Full Genome ◽  
Rt Pcr ◽  
False Negatives ◽  
Wide Range ◽  
Local Transmission

LetterHere, I analyze the metagenome from the nasopharyngeal swab of a suspected case of local transmission of Covid-19, in Brazil (Accid:PRJNA613951).Very little viral load, not covering the entire genomeThere are just 152 reads matching to SARS-Cov2 [1] (SIbrazil/SARS-Cov2.reads.fa), which adds up a total of 21190 bp, much lesser than the 30000bp SARS-Cov2 genome. This is a very plausible cause for false negatives, there is just not enough virus to detect.For eg, if the RT-PCR test was looking for a genomic fragment in the spike protein (3879bp) from 369– 1174, it would not find a match. Thus, it is important to use multiple primers spread across the genome, something which the CDC test does not do.Much more bacterial load - Lautropia, Prevotella, Haemophilus dominatingThere are a wide range of bacteria (SIbrazil/allbact.list.txt,n=117) - Lautropia, Prevotella, Haemophilus dominating (Table 1). These are the same bacteria found in China [2] and San Diego county [3]. There are 10851 reads matching to bacteria (SIbrazil/allbactsequences.fa). These bacterial co-infections form the basis of hydroxychloroquine and azithromycin working in clinical trials [4].

scholarly journals SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

scholarly journals Benchmarking topological accuracy of bacterial phylogenomic workflows using in silico evolution

2021 ◽  
Author(s):  
Boas CL van der Putten ◽  
Niek AH Huijsmans ◽  
Daniel R Mende ◽  
Constance Schultsz
Keyword(s):  
De Novo ◽  
Phylogenetic Analyses ◽  
Bacterial Species ◽  
Phylogenetic Reconstruction ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
De Novo Genome Assembly ◽  
Relevant Alternatives ◽  
Wide Range ◽  
Similar Accuracy

Phylogenetic analyses are widely used in microbiological research, for example to trace the progression of bacterial outbreaks based on whole-genome sequencing data. In practice, multiple analysis steps such as de novo assembly, alignment and phylogenetic inference are combined to form phylogenetic workflows. Comprehensive benchmarking of the accuracy of complete phylogenetic workflows is lacking. To benchmark different phylogenetic workflows, we simulated bacterial evolution under a wide range of evolutionary models, varying the relative rates of substitution, insertion, deletion, gene duplication, gene loss and lateral gene transfer events. The generated datasets corresponded to a genetic diversity usually observed within bacterial species (≥95% average nucleotide identity). We replicated each simulation three times to assess replicability. In total, we benchmarked seventeen distinct phylogenetic workflows using 8 different simulated datasets. We found that recently developed k-mer alignment methods such as kSNP and SKA achieve similar accuracy as reference mapping. The high accuracy of k-mer alignment methods can be explained by the large fractions of genomes these methods can align, relative to other approaches. We also found that the choice of de novo assembly algorithm influences the accuracy of phylogenetic reconstruction, with workflows employing SPAdes or SKESA outperforming those employing Velvet. Finally, we found that the results of phylogenetic benchmarking are highly variable between replicates. We conclude that for phylogenomic reconstruction k-mer alignment methods are relevant alternatives to reference mapping at species level, especially in the absence of suitable reference genomes. We show de novo genome assembly accuracy to be an underappreciated parameter required for accurate phylogenomic reconstruction.

scholarly journals SCAPP: An algorithm for improved plasmid assembly in metagenomes

2020 ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Background: Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results: We developed SCAPP (Sequence Contents-Aware Plasmid Peeler) - an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions: SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases, and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

scholarly journals ‘Five patients at the early stage of the Wuhan seafood market pneumonia virus outbreak’ - bacterial load is much higher than SARS-Cov2 load, Pseudomonas is a definite problem in one patient, and Prevotella is abundant in all patients

2020 ◽  
Author(s):  
Sandeep Chakraborty
Keyword(s):  
Bronchoalveolar Lavage Fluid ◽  
Early Stage ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Pcr Primers ◽  
Lavage Fluid ◽  
Large Set ◽  
Wide Range ◽  
Metagenomic Study ◽  
Definite Problem

Here, I analyze the metagenome from the bronchoalveolar lavage fluid of 5 Covid19 [1–3] patients from Wuhan (Accid:PRJNA605983, Table 1). There is no published study on this dataset yet.Very little viral loadThere is very little viral load (in the tens per million reads), similar to the metagenomic study in Brazil [4]. This is a very plausible cause for false negatives, as there is just not enough virus to detect. Thus, it is important to have a large set of RT-PCR primers to cover more of the genome.Much more bacterial loadWhile there are a wide range of bacteria, Pseudomonas has definitely colonized patient1, while patient5 seems to have have the least bacterial load. Pseudomonas is associated with several diseases, several of which (pneu- monia and septicemia) are relevant in Covid19 [5]. The bacterial species and their sequences are submitted in SI5patients on a per patient basis. These bacterial co-infections form the basis of hydroxychloroquine [6] and azithromycin working in clinical trials [7].

scholarly journals Tatajuba ― Exploring the distribution of homopolymer tracts

2021 ◽  
Author(s):  
Leonardo de Oliveira Martins ◽  
Samuel Bloomfield ◽  
Emily Stoakes ◽  
Andrew J Grant ◽  
Andrew J Page ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Bacterial Species ◽  
Phase Variation ◽  
Length Variation ◽  
Sequencing Data ◽  
Regulate Gene Expression ◽  
Wide Range ◽  
Bioinformatics Software ◽  
Homopolymer Tract ◽  
Regulate Gene

Length variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialised bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivial as sequencing and bioinformatics methods are prone to introducing artefacts when presented with homopolymeric tracts due to the decreased base diversity. We present tatajuba, which can automatically identify potential homopolymeric tracts and their putative phenotypic impact, allowing for rapid investigation. We use it to detect all tracts in two separate datasets, one of Campylobacter jejuni and one of three Bordetella species, and to highlight those tracts that are polymorphic across samples. With this we confirm homopolymer tract variation with phenotypic impact found in previous studies and additionally find many more with potential variability. The software is written in C and is available under the open source license GNU GPL version 3 from https://github.com/quadram-institute-bioscience/tatajuba.

Biscogniauxia (Hypoxylon) Canker or Dieback in Trees

EDIS ◽  
2017 ◽  
Vol 2017 (6) ◽  
Author(s):  
Claudia Paez ◽  
Jason A. Smith
Keyword(s):  
Water Stress ◽  
Tree Species ◽  
Soil Compaction ◽  
Urban Areas ◽  
Root Disease ◽  
Poor Health ◽  
Green Spaces ◽  
Opportunistic Pathogens ◽  
Wide Range ◽  
Quercus Spp

Biscogniauxia canker or dieback (formerly called Hypoxylon canker or dieback) is a common contributor to poor health and decay in a wide range of tree species (Balbalian & Henn 2014). This disease is caused by several species of fungi in the genus Biscogniauxia (formerly Hypoxylon). B. atropunctata or B. mediterranea are usually the species found on Quercus spp. and other hosts in Florida, affecting trees growing in many different habitats, such as forests, parks, green spaces and urban areas (McBride & Appel, 2009).  Typically, species of Biscogniauxia are opportunistic pathogens that do not affect healthy and vigorous trees; some species are more virulent than others. However, once they infect trees under stress (water stress, root disease, soil compaction, construction damage etc.) they can quickly colonize the host. Once a tree is infected and fruiting structures of the fungus are evident, the tree is not likely to survive especially if the infection is in the tree's trunk (Anderson et al., 1995).

Stereospecific, Palladium-catalyzed C(sp3)–H Alkenylation and Alkynylation of a Proline Derivative Enabled by 8-Aminoquinoline as a Directing Group

2020 ◽  
Author(s):  
Aleksandra Balliu ◽  
Aaltje Roelofje Femmigje Strijker ◽  
Michael Oschmann ◽  
Monireh Pourghasemi Lati ◽  
Oscar Verho
Keyword(s):  
Carboxylic Acid ◽  
Building Blocks ◽  
Wide Range ◽  
Palladium Catalyzed ◽  
Directing Group ◽  
High Yields ◽  
Vinyl Iodides ◽  
Initial Results

<p>In this preprint, we present our initial results concerning a stereospecific Pd-catalyzed protocol for the C3 alkenylation and alkynylation of a proline derivative carrying the well utilized 8‑aminoquinoline directing group. Efficient C–H alkenylation was achieved with a wide range of vinyl iodides bearing different aliphatic, aromatic and heteroaromatic substituents, to furnish the corresponding C3 alkenylated products in good to high yields. In addition, we were able show that this protocol can also be used to install an alkynyl group into the pyrrolidine scaffold, when a TIPS-protected alkynyl bromide was used as the reaction partner. Furthermore, two different methods for the removal of the 8-aminoquinoline auxiliary are reported, which can enable access to both <i>cis</i>- and <i>trans</i>-configured carboxylic acid building blocks from the C–H alkenylation products.</p>

scholarly journals Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas

2021 ◽  
Vol 9 (4) ◽  
pp. 862
Author(s):  
Vittoria Catara ◽  
Jaime Cubero ◽  
Joël F. Pothier ◽  
Eran Bosis ◽  
Claude Bragard ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Bacterial Species ◽  
Management Strategies ◽  
Diagnostic Methods ◽  
Plant Diseases ◽  
Wild Plants ◽  
Future Climate Change ◽  
Climate Change Scenarios ◽  
Wide Range ◽  
Diversity Studies

Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.

scholarly journals Effectiveness of 0.66% Povidone-Iodine Eye Drops on Ocular Surface Flora before Cataract Surgery: A Nationwide Microbiological Study

2021 ◽  
Vol 10 (10) ◽  
pp. 2198
Author(s):  
Rosario Musumeci ◽  
Pasquale Troiano ◽  
Marianna Martinelli ◽  
Matteo Piovella ◽  
Claudio Carbonara ◽  
...  
Keyword(s):  
Cataract Surgery ◽  
Ocular Surface ◽  
Povidone Iodine ◽  
Bacterial Species ◽  
Bacterial Flora ◽  
Bacterial Load ◽  
Controlled Study ◽  
Eye Drops ◽  
Microbiological Analysis ◽  
Contralateral Eye

A multicenter, nonrandomized, prospective, controlled study was conducted to evaluate, as perioperative prophylactic treatment, the anti-infective effectiveness of 0.66% povidone-iodine eye drops (IODIM®) against the bacterial flora of the conjunctival surface of patients who undergo cataract surgery. Eye drops containing 0.66% povidone-iodine were applied to the eye undergoing cataract surgery; the untreated contralateral eye was used as control. One hundred and twenty patients set to receive unilateral cataract surgery were enrolled in 5 Italian Ophthalmology Centers and pretreated for three days with 0.66% povidone-iodine eye drops. The contralateral eye, used as control, was left untreated. Conjunctival swabs of both eyes were collected at the baseline visit and after three days of treatment, just before the cataract surgery. A qualitative and quantitative microbiological analysis of bacterial presence was evaluated by means of bacterial culture, followed by identification. Methicillin resistance determination was also performed on staphylococci isolates. Bacterial load before and after treatment of the eye candidate for cataract surgery was evaluated and compared to the untreated eye. A reduction or no regrowth on the culture media of the bacterial load was observed in 100% of the study subjects. A great heterogenicity of bacterial species was found. The 0.66% povidone-iodine eye drops, used for three days prior to cataract surgery, were effective in reducing the conjunctival bacterial load. The 0.66% povidone-iodine eye drops (IODIM®) might represent a valid perioperative prophylactic antiseptic adjuvant treatment to protect the ocular surface from microbial contamination in preparation of the surgical procedure.

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