scholarly journals Pan-genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia

2019 ◽  
Author(s):  
Bryan Naidenov ◽  
Karyn Willyerd ◽  
Alexander Lim ◽  
Nathanial J Torres ◽  
William L. Johnson ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
De Novo ◽  
Binary Classification ◽  
Genomic Analysis ◽  
Machine Learning Algorithms ◽  
Emerging Pathogens ◽  
Phenotypic Resistance ◽  
Elizabethkingia Meningoseptica ◽  
Long Read ◽  
Or Gene

AbstractThe Elizabethkingia are a genetically diverse genus of emerging pathogens that exhibit multidrug resistance to a range of common antibiotics. Two representative species, Elizabethkingia bruuniana and Elizabethkingia meningoseptica, were phenotypically tested to determine minimum inhibitory concentrations for five antibiotics. Ultra-long read sequencing with Oxford Nanopore Technologies and subsequent de novo assembly produced complete, gapless circular genomes for each strain. Alignment based annotation with Prokka identified 5,480 features in E. bruuniana and 5,203 features in E. meningoseptica, where none of these identified genes or gene combinations corresponded to observed phenotypic resistance values. Pan-genomic analysis, performed with an additional 19 Elizabethkingia strains, identified a core-genome size of 2,658,537 bp, 32 uniquely identifiable intrinsic chromosomal antibiotic resistance core-genes and 77 antibiotic resistance pan-genes. Using core-SNPs and pan-genes in combination with six machine learning algorithms, binary classification of clindamycin and vancomycin resistance achieved f1 scores of 0.94 and 0.84 respectively. Performance on the more challenging multiclass problem for fusidic acid, rifampin and ciprofloxacin resulted in f1 scores of 0.70, 0.75 and 0.54 respectively.

scholarly journals Long-read genome sequencing for the diagnosis of neurodevelopmental disorders

2020 ◽  
Author(s):  
Susan M. Hiatt ◽  
James M.J. Lawlor ◽  
Lori H. Handley ◽  
Ryne C. Ramaker ◽  
Brianne B. Rogers ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Neurodevelopmental Disorders ◽  
De Novo ◽  
Genomic Analysis ◽  
Data Sets ◽  
Short Read ◽  
Long Read ◽  
Variant Detection ◽  
Circular Consensus Sequencing

AbstractPurposeExome and genome sequencing have proven to be effective tools for the diagnosis of neurodevelopmental disorders (NDDs), but large fractions of NDDs cannot be attributed to currently detectable genetic variation. This is likely, at least in part, a result of the fact that many genetic variants are difficult or impossible to detect through typical short-read sequencing approaches.MethodsHere, we describe a genomic analysis using Pacific Biosciences circular consensus sequencing (CCS) reads, which are both long (>10 kb) and accurate (>99% bp accuracy). We used CCS on six proband-parent trios with NDDs that were unexplained despite extensive testing, including genome sequencing with short reads.ResultsWe identified variants and created de novo assemblies in each trio, with global metrics indicating these data sets are more accurate and comprehensive than those provided by short-read data. In one proband, we identified a likely pathogenic (LP), de novo L1-mediated insertion in CDKL5 that results in duplication of exon 3, leading to a frameshift. In a second proband, we identified multiple large de novo structural variants, including insertion-translocations affecting DGKB and MLLT3, which we show disrupt MLLT3 transcript levels. We consider this extensive structural variation likely pathogenic.ConclusionThe breadth and quality of variant detection, coupled to finding variants of clinical and research interest in two of six probands with unexplained NDDs strongly support the value of long-read genome sequencing for understanding rare disease.

scholarly journals Antimicrobial Resistance Profiles of Adherent Invasive Escherichia coli Show Increased Resistance to β-Lactams

Antibiotics ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 251 ◽  
Author(s):  
Margarita Martinez-Medina ◽  
Francesco Strozzi ◽  
Belén Ruiz Del Castillo ◽  
Natalia Serrano-Morillas ◽  
Nuria Ferrer Bustins ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Antimicrobial Therapy ◽  
De Novo ◽  
Genomic Analysis ◽  
The Other ◽  
Phenotypic Resistance ◽  
E Coli ◽  
Gut Mucosa

The adherent invasive Escherichia coli (AIEC) pathotype has been associated with the aetiology of Crohn’s disease (CD). Scarce reports have shown the antimicrobial resistance (AMR) profiles of AIEC. Despite antibiotics not being recommended to treat CD, antimicrobial therapy could be useful in stratified patients, such as AIEC carriers. We examined the antimicrobial resistance profiles of AIEC strains to identify which therapies could be effective or confer a risk for such patients. Phenotypic resistance to 30 antimicrobials was tested according to CLSI standards. AIEC (n = 22) and non-pathogenic E. coli (non-AIEC) strains (n = 37) isolated from the gut mucosa of 31 CD patients and 18 controls were studied. De novo genome sequencing was carried out for 39 of the 59 strains, and AMR genes were searched using the DeepARG database in these genomes and 33 additional AIEC publicly available genomes. The strains isolated from CD and controls showed similar phenotypic AMR profiles. The genomic analysis did not reveal an increased prevalence of AMR genes. However, AIEC strains were more frequently resistant to β-lactams than non-AIEC strains (11 AIEC (50%) and 5 non-AIEC (22%) strains were resistant to at least one β-lactam; p < 0.042). Two AIEC strains were resistant to expanded-spectrum cephalosporins. One strain carried a plasmid-mediated AmpC β-lactamase (CMY-69), and the other presented mutations in the promotor of the intrinsic chromosomal AmpC related to the hyperproduction of this enzyme. The rest of the strains were resistant to β-lactams not including expanded-spectrum cephalosporins. The majority carried TEM-related β-lactamases. Genomic analysis including external AIEC revealed that the gene sul1 encoding for sulphonamide resistance was more frequent in AIEC strains than non-AIEC strains (34.6% vs. 9.5%, p = 0.030). AMR in AIEC is a matter of concern regarding the putative implication of the pathotype in CD. The high proportion of AIEC resistant to β-lactams warrants caution about the risk there may be in the use of these antimicrobials in AIEC-colonized CD patients.

scholarly journals Genomic Surveillance for Antimicrobial Resistance inMannheimia haemolyticaUsing Nanopore Single Molecule Sequencing Technology

2018 ◽  
Author(s):  
Alexander Lim ◽  
Bryan Naidenov ◽  
Haley Bates ◽  
Karyn Willyerd ◽  
Timothy Snider ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Single Molecule ◽  
Resistant Strain ◽  
De Novo ◽  
Gene Annotation ◽  
Cost Effective ◽  
Multidrug Resistant ◽  
Oxford Nanopore ◽  
Long Read

AbstractDisruptive innovations in long-range, cost-effective direct template nucleic acid sequencing are transforming clinical and diagnostic medicine. A multidrug resistant strain and a pan-susceptible strain ofMannheimia haemolytica, isolated from pneumonic bovine lung samples, were respectively sequenced at 146x and 111x coverage with Oxford Nanopore Technologies MinION.De novoassembly produced a complete genome for the non-resistant strain and a nearly complete assembly for the drug resistant strain. Functional annotation using RAST (Rapid Annotations using Subsystems Technology), CARD (Comprehensive Antibiotic Resistance Database) and ResFinder databases identified genes conferring resistance to different classes of antibiotics including beta lactams, tetracyclines, lincosamides, phenicols, aminoglycosides, sulfonamides and macrolides. Antibiotic resistance phenotypes of theM. haemolyticastrains were confirmed with minimum inhibitory concentration (MIC) assays. The sequencing capacity of highly portable MinION devices was verified by sub-sampling sequencing reads; potential for antimicrobial resistance determined by identification of resistance genes in the draft assemblies with as little as 5,437 MinION reads corresponded to all classes of MIC assays. The resulting quality assemblies and AMR gene annotation highlight efficiency of ultra long-read, whole-genome sequencing (WGS) as a valuable tool in diagnostic veterinary medicine.

scholarly journals Nanopore long reads enable the first complete genome assembly of a Malaysian Vibrio parahaemolyticus isolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease

2019 ◽  
Author(s):  
Han Ming Gan ◽  
Christopher M. Austin
Keyword(s):  
Genome Assembly ◽  
Vibrio Parahaemolyticus ◽  
De Novo ◽  
Genomic Analysis ◽  
Binary Toxin ◽  
Comparative Genomic ◽  
Chromosome 2 ◽  
Toxin Genes ◽  
Long Reads ◽  
Long Read

AbstractBackgroundVibrio parahaemolyticus MVP1 was isolated from a Malaysian aquaculture farm affected with shrimp acute hepatopancreatic necrosis disease (AHPND). Its genome was previously sequenced on the Illumina MiSeq platform and assembled de novo producing a relatively fragmented assembly. Despite identifying the binary toxin genes in the MVP1 draft genome that were linked to AHPND, the toxin genes were localized on a very small contig precluding proper analysis of gene neighbourhood.MethodsThe genome of Vibrio parahaemolyticus MVP1 was sequenced on the Nanopore MinION device to obtain long reads that can span longer repeats and improve genome contiguity. De novo genome assembly was subsequently performed using long-read only assembler (Flye) followed by genome polishing as well as hybrid assembler (Unicycler).ResultsLong-read only assembly produced three complete circular MVP1 contigs consisting of chromosome 1, chromosome 2 and the pVa plasmid that pirABvp binary toxin genes. Polishing of the long read assembly with Illumina short reads was necessary to remove indel errors. The complete assembly of the pVa plasmid could not be achieved using Illumina reads due to the presence of identical repetitive elements flanking the binary toxin genes leading to multiple contigs. Whereas these regions were fully spanned by the Nanopore long reads resulting in a single contig. In addition, alignment of Illumina reads to the complete genome assembly indicated there is sequencing bias as read depth was lowest in low-GC genomic regions. Comparative genomic analysis revealed the presence of a gene cluster coding for additional insecticidal toxins in chromosome 2 of MVP1 that may further contribute to host pathogenesis pending functional validation. Scanning of all publicly available V. parahaemolyticus genomes revealed the presence of a single AinS-family quorum-sensing system in this species that can be targeted for future microbial management.ConclusionsWe generated the first chromosome-scale genome assembly of a Malaysian pirABVp-bearing V. parahaemolyticus isolate. Structural variations identified from comparative genomic analysis provide new insights into the genomic features of V. parahaemolyticus MVP1 that may be associated with host colonization and pathogenicity.

scholarly journals De Novo Sequencing Provides Insights Into the Pathogenicity of Foodborne Vibrio parahaemolyticus

2021 ◽  
Vol 11 ◽  
Author(s):  
Jianfei Liu ◽  
Kewei Qin ◽  
Chenglin Wu ◽  
Kaifei Fu ◽  
Xiaojie Yu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Vibrio Parahaemolyticus ◽  
De Novo ◽  
Genomic Analysis ◽  
Pathogenicity Test ◽  
Evolutionary Potential ◽  
Gastrointestinal Infections ◽  
Functional Region ◽  
Genomic Change ◽  
The Difference

Vibrio parahaemolyticus is a common pathogenic marine bacterium that causes gastrointestinal infections and other health complications, which could be life-threatening to immunocompromised patients. For the past two decades, the pathogenicity of environmental V. parahaemolyticus has increased greatly, and the genomic change behind this phenomenon still needs an in-depth exploration. To investigate the difference in pathogenicity at the genomic level, three strains with different hemolysin expression and biofilm formation capacity were screened out of 69 environmental V. parahaemolyticus strains. Subsequently, 16S rDNA analysis, de novo sequencing, pathogenicity test, and antibiotic resistance assays were performed. Comparative genome-scale interpretation showed that various functional region differences in pathogenicity of the selected V. parahaemolyticus strains were due to dissimilarities in the distribution of key genetic elements and in the secretory system compositions. Furthermore, the genomic analysis-based hypothesis of distinct pathogenic effects was verified by the survival rate of mouse models infected with different V. parahaemolyticus strains. Antibiotic resistance results also presented the multi-directional evolutionary potential in environmental V. parahaemolyticus, in agreement with the phylogenetic analysis results. Our study provides a theoretical basis for better understanding of the increasing pathogenicity of environmental V. parahaemolyticus at the genome level. Further, it has a key referential value for the exploration of pathogenicity and prevention of environmental V. parahaemolyticus in the future.

scholarly journals Deep repeat resolution—the assembly of the Drosophila Histone Complex

2018 ◽  
Vol 47 (3) ◽  
pp. e18-e18 ◽  
Author(s):  
Philipp Bongartz ◽  
Siegfried Schloissnig
Keyword(s):  
De Novo ◽  
Machine Learning Algorithms ◽  
Single Nucleotide Variants ◽  
Major Step ◽  
Base Pairs ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Wide Range ◽  
Long Read ◽  
Genome Assemblies

Abstract Though the advent of long-read sequencing technologies has led to a leap in contiguity of de novo genome assemblies, current reference genomes of higher organisms still do not provide unbroken sequences of complete chromosomes. Despite reads in excess of 30 000 base pairs, there are still repetitive structures that cannot be resolved by current state-of-the-art assemblers. The most challenging of these structures are tandemly arrayed repeats, which occur in the genomes of all eukaryotes. Untangling tandem repeat clusters is exceptionally difficult, since the rare differences between repeat copies are obscured by the high error rate of long reads. Solving this problem would constitute a major step towards computing fully assembled genomes. Here, we demonstrate by example of the Drosophila Histone Complex that via machine learning algorithms, it is possible to exploit the underlying distinguishing patterns of single nucleotide variants of repeats from very noisy data to resolve a large and highly conserved repeat cluster. The ideas explored in this paper are a first step towards the automated assembly of complex repeat structures and promise to be applicable to a wide range of eukaryotic genomes.

scholarly journals Nanopore long reads enable the first complete genome assembly of a Malaysian Vibrio parahaemolyticus isolate bearing the pVa plasmid associated with acute hepatopancreatic necrosis disease

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 2108 ◽  
Author(s):  
Han Ming Gan ◽  
Christopher M Austin
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Genomic Analysis ◽  
Binary Toxin ◽  
Comparative Genomic ◽  
Chromosome 2 ◽  
Toxin Genes ◽  
Long Reads ◽  
Long Read ◽  
Acute Hepatopancreatic Necrosis Disease

Background: The genome of Vibrio parahaemolyticus MVP1, isolated from a Malaysian aquaculture farm with shrimp acute hepatopancreatic necrosis disease (AHPND), was previously sequenced using Illumina MiSeq and assembled de novo, producing a relatively fragmented assembly. Despite identifying the binary toxin genes in the MVP1 draft genome that were linked to AHPND, the toxin genes were localized on a very small contig precluding proper analysis of gene neighbourhood. Methods: The genome of MVP1 was sequenced on Nanopore MinION to obtain long reads to improve genome contiguity. De novo genome assembly was performed using long-read only assembler followed by genome polishing and hybrid assembler. Results: Long-read assembly produced three complete circular MVP1 contigs: chromosome 1, chromosome 2 and the pVa plasmid encoding pirABvp binary toxin genes. Polishing of the long-read assembly with Illumina short reads was necessary to remove indel errors. Complete assembly of the pVa plasmid could not be achieved using Illumina reads due to identical repetitive elements flanking the binary toxin genes leading to multiple contigs. These regions were fully spanned by the Nanopore long-reads resulting in a single contig. Alignment of Illumina reads to the complete genome assembly indicated there is sequencing bias as read depth was lowest in low-GC genomic regions. Comparative genomic analysis revealed a gene cluster coding for additional insecticidal toxins in chromosome 2 of MVP1 that may further contribute to host pathogenesis pending functional validation. Scanning of publicly available V. parahaemolyticus genomes revealed the presence of a single AinS-family quorum-sensing system that can be targeted for future microbial management. Conclusions: We generated the first chromosome-scale genome assembly of a Malaysian pirABVp-bearing V. parahaemolyticus isolate. Structural variations identified from comparative genomic analysis provide new insights into the genomic features of V. parahaemolyticus MVP1 that may be associated with host colonization and pathogenicity.

scholarly journals Machine-Learning-Based Radiomics MRI Model for Survival Prediction of Recurrent Glioblastomas Treated with Bevacizumab

Diagnostics ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1263
Author(s):  
Samy Ammari ◽  
Raoul Sallé de Chou ◽  
Tarek Assi ◽  
Mehdi Touat ◽  
Emilie Chouzenoux ◽  
...  
Keyword(s):  
Machine Learning ◽  
Therapeutic Option ◽  
Binary Classification ◽  
Progression Free Survival ◽  
Recurrent Glioblastoma ◽  
Machine Learning Algorithms ◽  
Survival Prediction ◽  
Classification Models ◽  
Angiogenic Therapy ◽  
Recurrent Gbm

Anti-angiogenic therapy with bevacizumab is a widely used therapeutic option for recurrent glioblastoma (GBM). Nevertheless, the therapeutic response remains highly heterogeneous among GBM patients with discordant outcomes. Recent data have shown that radiomics, an advanced recent imaging analysis method, can help to predict both prognosis and therapy in a multitude of solid tumours. The objective of this study was to identify novel biomarkers, extracted from MRI and clinical data, which could predict overall survival (OS) and progression-free survival (PFS) in GBM patients treated with bevacizumab using machine-learning algorithms. In a cohort of 194 recurrent GBM patients (age range 18–80), radiomics data from pre-treatment T2 FLAIR and gadolinium-injected MRI images along with clinical features were analysed. Binary classification models for OS at 9, 12, and 15 months were evaluated. Our classification models successfully stratified the OS. The AUCs were equal to 0.78, 0.85, and 0.76 on the test sets (0.79, 0.82, and 0.87 on the training sets) for the 9-, 12-, and 15-month endpoints, respectively. Regressions yielded a C-index of 0.64 (0.74) for OS and 0.57 (0.69) for PFS. These results suggest that radiomics could assist in the elaboration of a predictive model for treatment selection in recurrent GBM patients.

scholarly journals Next Generation Sequencing for the Prediction of the Antibiotic Resistance in Helicobacter pylori: A Literature Review

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 437
Author(s):  
Ilaria Maria Saracino ◽  
Matteo Pavoni ◽  
Angelo Zullo ◽  
Giulia Fiorini ◽  
Tiziana Lazzarotto ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Next Generation Sequencing ◽  
Literature Review ◽  
Molecular Mechanisms ◽  
World Health ◽  
Next Generation ◽  
Culture Methods ◽  
Phenotypic Resistance ◽  
H Pylori ◽  
Generation Sequencing

Background and aims: Only a few antimicrobials are effective against H. pylori, and antibiotic resistance is an increasing problem for eradication therapies. In 2017, the World Health Organization categorized clarithromycin resistant H. pylori as a “high-priority” bacterium. Standard antimicrobial susceptibility testing can be used to prescribe appropriate therapies but is currently recommended only after the second therapeutic failure. H. pylori is, in fact, a “fastidious” microorganism; culture methods are time-consuming and technically challenging. The advent of molecular biology techniques has enabled the identification of molecular mechanisms underlying the observed phenotypic resistance to antibiotics in H. pylori. The aim of this literature review is to summarize the results of original articles published in the last ten years, regarding the use of Next Generation Sequencing, in particular of the whole genome, to predict the antibiotic resistance in H. pylori.Methods: a literature research was made on PubMed. The research was focused on II and III generation sequencing of the whole H. pylori genome. Results: Next Generation Sequencing enabled the detection of novel, rare and complex resistance mechanisms. The prediction of resistance to clarithromycin, levofloxacin and amoxicillin is accurate; for other antimicrobials, such as metronidazole, rifabutin and tetracycline, potential genetic determinants of the resistant status need further investigation.

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