A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC blaNDM-1- and armA-carrying Plasmid

Background. Patients colonized with multiple species of carbapenemase-producing Enterobacterales (CPE) are increasingly observed. This phenomenon can be due to the high local prevalence of these pathogens, the presence of important host risk factors, and the great genetic promiscuity of some carbapenemase genes. Methods. We analyzed 4 CPE (Escherichia coli, Klebsiella pneumoniae, Providencia stuartii, Citrobacter sedlakii), 1 extended-spectrum cephalosporin-resistant K. pneumoniae (ESC-R-Kp), and 1 carbapenemase-producing Acinetobacter baumannii simultaneously isolated from a patient transferred from Macedonia. Susceptibility tests were performed using a microdilution MIC system. The complete genome sequences were obtained by using both short-read and long-read whole-genome sequencing technologies. Results. All CPE presented high-level resistance to all aminoglycosides due to the expression of the armA 16S rRNA methylase. In C. sedlakii and E. coli (ST69), both the carbapenemase blaNDM-1 and armA genes were located on an identical IncC plasmid of type 1a. The K. pneumoniae (ST268) and P. stuartii carried chromosomal blaNDM-1 and blaOXA-48, respectively, while the ESC-R-Kp (ST395) harbored a plasmid-located blaCTX-M-15. In the latter 3 isolates, armA-harboring IncC plasmids similar to plasmids found in C. sedlakii and E. coli were also detected. The A. baumannii strain possessed the blaOXA-40 carbapenemase gene. Conclusions. The characterization of the genetic organization of IncC-type plasmids harbored by 3 different species from the same patient offered insights into the evolution of these broad- host-range plasmids. Moreover, we characterized here the first complete genome sequence of a carbapenemase-producing C. sedlakii strain, providing a reference for future studies on this rarely reported species.

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Complete Genome Resequencing of Thermus thermophilus Strain TMY by Hybrid Assembly of Long- and Short-Read Sequencing Technologies

Microbiology Resource Announcements ◽

10.1128/mra.00979-21 ◽

2021 ◽

Vol 10 (46) ◽

Author(s):

Kentaro Miyazaki ◽

Natsuko Tokito

Keyword(s):

Complete Genome ◽

Thermus Thermophilus ◽

Genomic Analysis ◽

Comparative Genomic ◽

Hybrid Assembly ◽

Genome Resequencing ◽

Short Read ◽

Content Type ◽

Sequencing Technologies ◽

Long Read

Complete genome resequencing was conducted for Thermus thermophilus strain TMY by hybrid assembly of Oxford Nanopore Technologies long-read and MGI short-read data. Errors in the previously reported genome sequence determined by PacBio technology alone were corrected, allowing for high-quality comparative genomic analysis of closely related T. thermophilus genomes.

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Complete Genome Sequence of Mycobacterium marinum ATCC 927T, Obtained Using Nanopore and Illumina Sequencing Technologies

Genome Announcements ◽

10.1128/genomea.00397-18 ◽

2018 ◽

Vol 6 (20) ◽

Cited By ~ 2

Author(s):

Mitsunori Yoshida ◽

Hanako Fukano ◽

Yuji Miyamoto ◽

Keigo Shibayama ◽

Masato Suzuki ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Mycobacterium Marinum ◽

Broad Host Range ◽

Mycobacterial Species ◽

Essential Information ◽

Content Type ◽

Sequencing Technologies ◽

Diseased Fish

ABSTRACT Mycobacterium marinum is a slowly growing, broad-host-range mycobacterial species. Here, we report the complete genome sequence of a Mycobacterium marinum type strain that was isolated from tubercles of diseased fish. This sequence will provide essential information for future taxonomic and comparative genome studies of its relatives.

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First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep

Gut Pathogens ◽

10.1186/s13099-019-0330-9 ◽

2019 ◽

Vol 11 (1) ◽

Cited By ~ 3

Author(s):

Laura Uelze ◽

Maria Borowiak ◽

Carlus Deneke ◽

Cécile Jacobs ◽

István Szabó ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Salmonella Enterica ◽

Complete Genome ◽

De Novo ◽

Host Adaptation ◽

Genomic Islands ◽

Genetic Mechanism ◽

Sequencing Technologies ◽

High Level

Abstract Background The Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) (SASd) has been found to be host-adapted to sheep, with a high prevalence in sheep herds worldwide. Infections are usually sub-clinical, however the serovar has the potential to cause diarrhea, abortions and chronic proliferative rhinitis. Although occurrence and significance of SASd infections in sheep have been extensively studied, the genetic mechanism underlying this unusual host-adaptation have remained unknown, due to a lack of (a) available high-quality genome sequence(s). Results We utilized Nanopore and Illumina sequencing technologies to generate a de novo assembly of the 4.88-Mbp complete genome sequence of the SASd strain 16-SA00356, isolated from the organs of a deceased sheep in 2016. We annotated and analyzed the genome sequence with the aim to gain a deeper understanding of the genome characteristics associated with its pathogenicity and host adaptation to sheep. Overall, we found a number of interesting genomic features such as several prophage regions, a VirB4/D4 plasmid and novel genomic islands. By comparing the genome of 16-SA00356 to other S. enterica serovars we found that SASd features an increased number of pseudogenes as well as a high level of genomic rearrangements, both known indicators of host-adaptation. Conclusions With this sequence, we provide the first complete and closed genome sequence of a SASd strain. With this study, we provide an important basis for an understanding of the genetic mechanism that underlie pathogenicity and host adaptation of SASd to sheep.

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Complete Genome Sequence of Broad-Host-Range Shiga Toxin-Converting Bacteriophage SH2026Stx1, Isolated from Escherichia coli O157:H7

Genome Announcements ◽

10.1128/genomea.00490-18 ◽

2018 ◽

Vol 6 (25) ◽

Author(s):

Mingrui Duan ◽

Samuel S. Hunter ◽

Scott A. Minnich ◽

Matthew W. Fagnan ◽

Daniel D. New ◽

...

Keyword(s):

Escherichia Coli ◽

Host Range ◽

Genome Sequence ◽

Shiga Toxin ◽

Complete Genome Sequence ◽

Complete Genome ◽

Broad Host Range ◽

Escherichia Coli O157 ◽

Content Type ◽

E Coli

ABSTRACT The Shiga toxin-encoding phage SH2026Stx1 was isolated from Escherichia coli O157:H7 strain 2026. SH2026Stx1 and its detoxified derivative can infect a broad range of E. coli strains, including commensal, enteropathogenic, and enteroaggregative strains. We report here the complete genome sequence of phage SH2026Stx1 and its important features.

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Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome

10.1101/530725 ◽

2019 ◽

Cited By ~ 4

Author(s):

S Arredondo-Alonso ◽

J Top ◽

AC Schürch ◽

A McNally ◽

S Puranen ◽

...

Keyword(s):

Enterococcus Faecium ◽

Large Scale ◽

Population Genomics ◽

Genomic Analysis ◽

Adaptive Landscape ◽

Priority List ◽

Sequencing Technologies ◽

Long Read ◽

Pathogen Populations ◽

High Level

AbstractEnterococcus faecium is a gut commensal of many mammals but is also recognized as a major nosocomial human pathogen, as it is listed on the WHO global priority list of multi-drug resistant organisms. Previous research has suggested that nosocomial strains have multiple zoonotic origins and are only distantly related to those involved in human commensal colonization. Here we present the first comprehensive population-wide joint genomic analysis of hospital, commensal and animal isolates using both short- and long-read sequencing techniques. This enabled us to investigate the population plasmidome, core genome variation and genome architecture in detail, using a combination of machine learning, population genomics and genome-wide co-evolution analysis. We observed a high level of genome plasticity with large-scale inversions and heterogeneous chromosome sizes, collectively painting a high-resolution picture of the adaptive landscape of E. faecium, and identified plasmids as the main indicator for host-specificity. Given the increasing availability of long-read sequencing technologies, our approach could be widely applied to other human and animal pathogen populations to unravel fine-scale mechanisms of their evolution.

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SVants – A long-read based method for structural variation detection in bacterial genomes

10.1101/822312 ◽

2019 ◽

Cited By ~ 1

Author(s):

BM Hanson ◽

JS Johnson ◽

SR Leopold ◽

E Sodergren ◽

GM Weinstock

Keyword(s):

Structural Variation ◽

Tandem Repeats ◽

Bacterial Genome ◽

Genetic Material ◽

Bacterial Cells ◽

Sequencing Data ◽

E Coli ◽

Sequencing Technologies ◽

Long Read ◽

New Locations

AbstractMotivationMobile genetic elements (MGEs) are genetic material that can transfer between bacterial cells and move to new locations within a single bacterial genome. These elements range from several hundred to tens of thousands of bases, and are often bordered by repeat regions, which makes resolving these elements difficult with short-read sequencing data. The development and availability of long-read sequencing technologies has opened up new opportunities in the study of structural variation but there is a lack of bioinformatics tools designed to take advantage of these longer reads.ResultsWe present an assembly-free method for identifying the location of these MGEs when compared to any reference genome (including draft genomes). Using an artificially constructed Escherichia coli genome containing single and tandem-repeats of a Tn9 transposon, we demonstrate the ability of SVants to accurately identify multiple insertion sites as well as count the number of repeats of this MGE. Additionally, we show that SVants accurately identifies the transposon of interest, Tn9, but does not erroneously identify existing IS1 regions present within the chromosome of the E. coli artificial reference.Availability and ImplementationSVants is available as open-source software at https://github.com/EpiBlake/SVants

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MBG: Minimizer-based Sparse de Bruijn Graph Construction

10.1101/2020.09.18.303156 ◽

2020 ◽

Author(s):

Mikko Rautiainen ◽

Tobias Marschall

Keyword(s):

Source Code ◽

Error Rates ◽

Read Length ◽

De Bruijn Graph ◽

De Bruijn Graphs ◽

E Coli ◽

Link Type ◽

Sequencing Technologies ◽

Long Read ◽

De Bruijn

MotivationDe Bruijn graphs can be constructed from short reads efficiently and have been used for many purposes. Traditionally long read sequencing technologies have had too high error rates for de Bruijn graph-based methods. Recently, HiFi reads have provided a combination of long read length and low error rate, which enables de Bruijn graphs to be used with HiFi reads.ResultsWe have implemented MBG, a tool for building sparse de Bruijn graphs from HiFi reads. MBG outperforms existing tools for building dense de Bruijn graphs, and can build a graph of 50x coverage whole human genome HiFi reads in four hours on a single core. MBG also assembles the bacterial E. coli genome into a single contig in 8 seconds.AvailabilityPackage manager: https://anaconda.org/bioconda/mbg and source code: https://github.com/maickrau/MBG

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Mutations in aarE, the ubiA Homolog of Providencia stuartii, Result in High-Level Aminoglycoside Resistance and Reduced Expression of the Chromosomal Aminoglycoside 2′-N-Acetyltransferase

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.42.4.959 ◽

1998 ◽

Vol 42 (4) ◽

pp. 959-962 ◽

Cited By ~ 10

Author(s):

Michael R. Paradise ◽

Gregory Cook ◽

Robert K. Poole ◽

Philip N. Rather

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Amino Acid Identity ◽

Second Step ◽

Aminoglycoside Resistance ◽

Acid Identity ◽

E Coli ◽

Small Colony ◽

Providencia Stuartii ◽

High Level

ABSTRACT The aarE1 allele was identified on the basis of the resulting phenotype of increased aminoglycoside resistance. TheaarE1 mutation also resulted in a small-colony phenotype and decreased levels of aac(2′)-Ia mRNA. The deduced AarE gene product displayed 61% amino acid identity to theEscherichia coli UbiA protein, an octaprenyltransferase required for the second step of ubiquinone biosynthesis. Complementation experiments in both Providencia stuartiiand E. coli demonstrated that aarE andubiA are functionally equivalent.

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Complete or High-Quality Draft Genome Sequences of Six Xanthomonas hortorum Strains Sequenced with Short- and Long-Read Technologies

Microbiology Resource Announcements ◽

10.1128/mra.00828-20 ◽

2020 ◽

Vol 9 (41) ◽

Author(s):

Nay C. Dia ◽

Fabio Rezzonico ◽

Theo H. M. Smits ◽

Joël F. Pothier

Keyword(s):

Complete Genome ◽

Draft Genome ◽

Species Level ◽

Genome Sequences ◽

High Quality ◽

Content Type ◽

Sequencing Technologies ◽

Long Read

ABSTRACT We report the genome sequences of six Xanthomonas hortorum species-level clade members, X. hortorum pathovars taraxaci, pelargonii, cynarae, and gardneri (complete genome sequences) and X. hortorum pathovars carotae and vitians (high-quality draft genome sequences). Both short- and long-read sequencing technologies were used.

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Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

10.1101/2020.01.27.915470 ◽

2020 ◽

Author(s):

Harmeet Singh Chawla ◽

HueyTyng Lee ◽

Iulian Gabur ◽

Suriya Tamilselvan-Nattar-Amutha ◽

Christian Obermeier ◽

...

Keyword(s):

Agronomic Traits ◽

Crop Improvement ◽

Screening Methods ◽

Crop Species ◽

Gene Variation ◽

Plant Genomes ◽

Sequencing Technologies ◽

Long Read ◽

Genome Screening ◽

High Level

SummaryGenome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single nucleotide polymorphism (SNP). In recent years there have been a number of studies associating large, chromosomal scale SV ranging from hundreds of kilobases all the way up to a few megabases to key agronomic traits in plant genomes. However, there have been little or no efforts towards cataloging small (30 to 10,000 bp) to mid-scale (10,000 bp to 30,000 bp) SV and their impact on evolution and adaptation related traits in plants. This might be attributed to complex and highly-duplicated nature of plant genomes, which makes them difficult to assess using high-throughput genome screening methods. Here we describe how long-read sequencing technologies can overcome this problem, revealing a surprisingly high level of widespread, small to mid-scale SV in a major allopolyploid crop species, Brassica napus. We found that up to 10% of all genes were affected by small to mid-scale SV events. Nearly half of these SV events ranged between 100 bp to 1000 bp, which makes them challenging to detect using short read Illumina sequencing. Examples demonstrating the contribution of such SV towards eco-geographical adaptation and disease resistance in oilseed rape suggest that revisiting complex plant genomes using medium-coverage, long-read sequencing might reveal unexpected levels of functional gene variation, with major implications for trait regulation and crop improvement.

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