scholarly journals Whole genome characterization of Neisseria meningitidis serogroup W isolates, circulating in Moscow

2017 ◽  
Vol 16 (4) ◽  
pp. 33-38 ◽  
Author(s):  
K. O. Mironov ◽  
V. A. Zhivotova ◽  
S. V. Matosova
Keyword(s):  
Antibiotic Resistance ◽  
Next Generation Sequencing ◽  
Neisseria Meningitidis ◽  
Ribosomal Protein ◽  
Meningococcal Disease ◽  
Core Genome ◽  
Ribosomal Protein Genes ◽  
The Core ◽  
Generation Sequencing ◽  
Discriminating Ability

Introduction. The invasive meningococcal disease (meningitis and/or septicemia) is actual problem of public health in Russia. Neisseria meningitidis isolates are classified into serogroups, PorA/FetA VRs, sequence types and clonal complexes. The growth of the invasive forms of meningococcal infection caused by isolates with «W: P1.5,2: F1-1: ST-11 (cc11)» profile requires attention for extended genotyping because the discriminating ability of classical MLST and antigens typing does not allow to answer the question about genetic and antigenic features of the pathogens and their epidemic potential. Materials and Methods. Four N. meningitidis serogroup W isolates associated with invasive meningococcal disease in Moscow (Russia) were characterized by next-generation sequencing. Three isolates were sequenced directly from cerebrospinal fluid samples and one -as a bacterial culture. All isolates were characterized earlier and the data were published in the PubMLST data base (id38565, id38573, id50225 and id50241). Genomic DNA was sequenced on Illumina MiSeq instrument. Results and Discussion. Obtained sequences allowed us to characterize four meningococci isolates for more than 1400 loci from the core genome MLST scheme. We have analyzed the core genome MLST scheme information about surface-antigen coding sequences. Housekeeping genes sequences were used to determine eMLST profile, ribosomal protein genes and some antibiotic resistance associated genes. We have characterized some ribosomal protein genes and antibiotic resistance associated genes. Based on eMLST profiles we noticed that there are at list two clones of N. meningitidis serogroup W inside complex ST-11/ET-37 clonal complex circulating in Moscow during 2016. An eMLST profile of isolates id50225 and id50241 differs in 3 loci out of 20. Application of the approach based on next-generation sequencing in routine epidemiological surveillance dramatically increases the amount of data and genotyping discriminating ability.

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.

scholarly journals Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies

2016 ◽  
Vol 94 ◽  
pp. 605-617 ◽  
Author(s):  
Andrew G. Gardner ◽  
Emily B. Sessa ◽  
Pryce Michener ◽  
Eden Johnson ◽  
Kelly A. Shepherd ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
The Core ◽  
Floral Form ◽  
Generation Sequencing

scholarly journals Next generation sequencing and the classical HLA loci in full heritage Pima Indians of Arizona: Defining the core HLA variation for North American Paleo-Indians

2019 ◽  
Vol 80 (12) ◽  
pp. 955-965
Author(s):  
Robert C. Williams ◽  
William C. Knowler ◽  
Alan R. Shuldiner ◽  
Nehal Gosalia ◽  
Cristopher Van Hout ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
North American ◽  
Next Generation ◽  
Pima Indians ◽  
The Core ◽  
Generation Sequencing ◽  
Paleo Indians

scholarly journals Genetic characterization of a Neisseria meningitidis cluster in Queensland, Australia

2017 ◽  
Vol 63 (7) ◽  
pp. 644-647
Author(s):  
N.R. Abady ◽  
C.J.D. Guglielmino ◽  
R.M. Graham ◽  
J. Adelskov ◽  
H.V. Smith ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Meningococcal Disease ◽  
Core Genome ◽  
Molecular Detection ◽  
Genetic Characterization ◽  
Genomic Analysis ◽  
Rural Region ◽  
Disease Cluster ◽  
Sporadic Disease

Neisseria meningitidis serogroups B and C have been responsible for the majority of invasive meningococcal disease in Australia, with serogroup B strains causing an increasing proportion of cases in recent years. Serogroup Y has typically caused sporadic disease in Australia. In 2002, a cluster of 4 cases was reported from a rural region in Queensland. Three of these cases were serogroup C, with 1 case diagnosed by molecular detection only, and the fourth case was identified as a serogroup Y infection. Genomic analysis, including antigen finetyping, multilocus sequence typing (MLST), and core genome MLST, demonstrated that the serogroup Y case, though spatially and temporally linked to a serogroup C disease cluster, was not the product of a capsule switch and that one of the serogroup C isolates had a deletion of the entire porA sequence.

scholarly journals Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Yu Tanouchi ◽  
Markus W. Covert
Keyword(s):  
Genetic Diversity ◽  
Antibiotic Resistance ◽  
Next Generation Sequencing ◽  
Phage Genome ◽  
Bacterial Motility ◽  
Lambda Phage ◽  
Host Chromosome ◽  
Integration Sites ◽  
Experimental Technology ◽  
Generation Sequencing

ABSTRACT During its lysogenic life cycle, the phage genome is integrated into the host chromosome by site-specific recombination. In this report, we analyze lambda phage integration into noncanonical sites using next-generation sequencing and show that it generates significant genetic diversity by targeting over 300 unique sites in the host Escherichia coli genome. Moreover, these integration events can have important phenotypic consequences for the host, including changes in cell motility and increased antibiotic resistance. Importantly, the new technologies that we developed to enable this study—sequencing secondary sites using next-generation sequencing and then selecting relevant lysogens using clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based selection—are broadly applicable to other phage-bacterium systems. IMPORTANCE Bacteriophages play an important role in bacterial evolution through lysogeny, where the phage genome is integrated into the host chromosome. While phage integration generally occurs at a specific site in the host chromosome, it is also known to occur at other, so-called secondary sites. In this study, we developed a new experimental technology to comprehensively study secondary integration sites and discovered that phage can integrate into over 300 unique sites in the host genome, resulting in significant genetic diversity in bacteria. We further developed an assay to examine the phenotypic consequence of such diverse integration events and found that phage integration can cause changes in evolutionarily relevant traits such as bacterial motility and increases in antibiotic resistance. Importantly, our method is readily applicable to other phage-bacterium systems. IMPORTANCE Bacteriophages play an important role in bacterial evolution through lysogeny, where the phage genome is integrated into the host chromosome. While phage integration generally occurs at a specific site in the host chromosome, it is also known to occur at other, so-called secondary sites. In this study, we developed a new experimental technology to comprehensively study secondary integration sites and discovered that phage can integrate into over 300 unique sites in the host genome, resulting in significant genetic diversity in bacteria. We further developed an assay to examine the phenotypic consequence of such diverse integration events and found that phage integration can cause changes in evolutionarily relevant traits such as bacterial motility and increases in antibiotic resistance. Importantly, our method is readily applicable to other phage-bacterium systems.

scholarly journals Virulence and antibiotic resistance plasticity of Arcobacter butzleri: insights on the genomic diversity of an emerging human pathogen

2019 ◽  
Author(s):  
Joana Isidro ◽  
Susana Ferreira ◽  
Miguel Pinto ◽  
Fernanda Domingues ◽  
Mónica Oleastro ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Comparative Genomics ◽  
Core Genome ◽  
Human Pathogen ◽  
Genome Diversity ◽  
Pathogenic Potential ◽  
The Core ◽  
Pan Genome ◽  
Arcobacter Butzleri ◽  
Genome Scale

AbstractArcobacter butzleri is a food and waterborne bacteria and an emerging human pathogen, frequently displaying a multidrug resistant character. Still, no comprehensive genome-scale comparative analysis has been performed so far, which has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. In total, 49 A. butzleri strains (collected from human, animal, food and environmental sources) were screened.A. butzleri (genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small core-genome with 1165 genes. The core-genome is highly diverse (≥55% of the core genes presenting at least 40/49 alleles), being enriched with genes associated with housekeeping functions. In contrast, the accessory genome presented a high proportion of loci with an unknown function, also being particularly overrepresented by genes associated with defence mechanisms. A. butzleri revealed a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA, a putative type I secretion system (T1SS) harboring another agglutinin potentially related to adherence and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) (ten “core” and nine differentially present) and other antibiotic resistant determinants. We provide the first description of a genetic determinant of macrolides resistance in A. butzleri, by associating the inactivation of a TetR repressor (likely regulating an EP) with erythromycin resistance. Fluoroquinolones resistance correlated with the Thr-85-Ile substitution in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the porin- and adhesin-encoding main antigen PorA, this study strongly supports that this pathogen is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats detected potential phase-variable genes related to adaptation and host/environment interaction, such as lipopolysaccharide modification and motility/chemotaxis, suggesting that phase variation likely modulate A. butzleri key adaptive functions.In summary, this study constitutes a turning point on A. butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast virulence and antibiotic resistance arsenals, which, coupled with its remarkable core- and pan-genome diversity, opens a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.IMPACT STATEMENTDiarrhoeal diseases are the most common cause of human illness caused by foodborne hazards, but the surveillance of diarrhoeal diseases is biased towards the most commonly searched infectious agents (namely Campylobacter jejuni and C. coli). In fact, other less studied pathogens are frequently found as the etiological agent when refined non-selective culture conditions are applied. A hallmark example is the diarrhoeal-causing Arcobacter butzleri which, despite being also associated with extra-intestinal diseases, such as bacteremia in humans and mastitis in animals, and displaying high rates of antibiotic resistance, has not yet been profoundly investigated regarding its epidemiology, diversity and pathogenicity. To overcome the general lack of knowledge on A. butzleri comparative genomics, we provide the first comprehensive genome-scale analysis of A. butzleri focused on exploring the intraspecies virulome content and diversity, resistance determinants, as well as how this pathogen shapes its genome towards ecological adaptation and host invasion. The unveiled scenario of A. butzleri rampant diversity and plasticity reinforces the pathogenic potential of this food and waterborne hazard, while opening multiple research lines that will certainly contribute to the future development of more robust species-oriented diagnostics and molecular surveillance of A. butzleri.DATA SUMMARYA. butzleri raw sequence reads generated in the present study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB34441). The assembled contigs (.fasta and .gbk files), the nucleotide sequences of the predicted transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) are available at http://doi.org/10.5281/zenodo.3434222. Detailed ENA accession numbers, as well as the draft genome statistics are described in Table S1.

scholarly journals Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11842
Author(s):  
Yen-Yi Liu ◽  
Bo-Han Chen ◽  
Chih-Chieh Chen ◽  
Chien-Shun Chiou
Keyword(s):  
Next Generation Sequencing ◽  
Core Genome ◽  
Read Depth ◽  
Sequence Type ◽  
Performance Ratio ◽  
Next Generation ◽  
Food Borne ◽  
The Cost ◽  
Generation Sequencing

With the reduction in the cost of next-generation sequencing, whole-genome sequencing (WGS)–based methods such as core-genome multilocus sequence type (cgMLST) have been widely used. However, gene-based methods are required to assemble raw reads to contigs, thus possibly introducing errors into assemblies. Because the robustness of cgMLST depends on the quality of assemblies, the results of WGS should be assessed (from sequencing to assembly). In this study, we investigated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. Different combinations of read lengths and read depths were simulated from the complete genomes of three common food-borne pathogens: Escherichia coli, Listeria monocytogenes, and Salmonella enterica. We found that the quality of assemblies was mainly affected by read depth, irrespective of the assembler used. In addition, we suggest several cutoff values for future cgMLST experiments. Furthermore, we recommend the combinations of read lengths, read depths, and assemblers that can result in a higher cost/performance ratio for cgMLST.

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