High-Quality Complete Genome Sequences of Three Pseudomonas aeruginosa Isolates Retrieved from Patients Hospitalized in Intensive Care Units

Magalhães, Bárbara; Senn, Laurence; Blanc, Dominique

doi:10.1128/mra.01624-18

Cited by 7 publications

(8 citation statements)

References 7 publications

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“…The first hybrid assemblies for other-class P. aeruginosa strains were published recently 23,73,74 . In order to evaluate our pipeline in these publicly available sequencing data, we implemented our hybrid approach to the two cases with Illumina and ONT sequencing technologies.…”

Section: Discussionmentioning

confidence: 99%

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

Molina-Mora

Campos-Sánchez

Rodríguez

et al. 2020

Sci Rep

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Genotyping methods and genome sequencing are indispensable to reveal genomic structure of bacterial species displaying high level of genome plasticity. However, reconstruction of genome or assembly is not straightforward due to data complexity, including repeats, mobile and accessory genetic elements of bacterial genomes. Moreover, since the solution to this problem is strongly influenced by sequencing technology, bioinformatics pipelines, and selection criteria to assess assemblers, there is no systematic way to select a priori the optimal assembler and parameter settings. to assembly the genome of Pseudomonas aeruginosa strain AG1 (PaeAG1), short reads (Illumina) and long reads (Oxford Nanopore) sequencing data were used in 13 different non-hybrid and hybrid approaches. PaeAG1 is a multiresistant high-risk sequence type 111 (ST-111) clone that was isolated from a Costa Rican hospital and it was the first report of an isolate of P. aeruginosa carrying both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes. To assess the assemblies, multiple metrics regard to contiguity, correctness and completeness (3C criterion, as we define here) were used for benchmarking the 13 approaches and select a definitive assembly. In addition, annotation was done to identify genes (coding and RNA regions) and to describe the genomic content of PaeAG1. Whereas long reads and hybrid approaches showed better performances in terms of contiguity, higher correctness and completeness metrics were obtained for short read only and hybrid approaches. A manually curated and polished hybrid assembly gave rise to a single circular sequence with 100% of core genes and known regions identified, >98% of reads mapped back, no gaps, and uniform coverage. The strategy followed to obtain this high-quality 3C assembly is detailed in the manuscript and we provide readers with an all-in-one script to replicate our results or to apply it to other troublesome cases. The final 3C assembly revealed that the PaeAG1 genome has 7,190,208 bp, a 65.7% GC content and 6,709 genes (6,620 coding sequences), many of which are included in multiple mobile genomic elements, such as 57 genomic islands, six prophages, and two complete integrons with blaVIM-2 and blaIMP-18 MBL genes. Up to 250 and 60 of the predicted genes are anticipated to play a role in virulence (adherence, quorum sensing and secretion) or antibiotic resistance (β-lactamases, efflux pumps, etc). Altogether, the assembly and annotation of the PaeAG1 genome provide new perspectives to continue studying the genomic diversity and gene content of this important human pathogen. Genotyping methods and genome sequencing are indispensable to reveal genomic structure and evolution of bacterial clones with high resolution 1. In this sense, production of large amounts of short sequencing data from genomes (reads) has been facilitated by continuous advances in Next Generation Sequencing (NGS) technologies.

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Section: Discussionmentioning

confidence: 99%

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

Molina-Mora

Campos-Sánchez

Rodríguez

et al. 2020

Sci Rep

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“…ICEclc has evolved to a remarkably efficient transfer machine, operating within "the window of opportunity" that it creates in a few individual cells to not disturb its host population (too much) and still transfer highly efficiently 24 . Understanding this process and its adaptation is crucial, given the broad occurrence of ICE in prokaryotic genomes 46 , and the particular wide distribution of the ICEclc family of elements 25,30 , also among important opportunistic pathogens 47,48 with ICE-carried antibiotic resistance genes [27][28][29] . A further central question to solve is the influence of environmental or physiological cues (such as 3CBA metabolism in case of ICEclc) on the proportion of appearing tc cells.…”

Section: Discussionmentioning

confidence: 99%

“…The clc integrative and conjugative element in Pseudomonas (ICEclc) that we use here, stands model for a widespread family occurring in opportunistic bacteria including pathogenic Pseudomonas aeruginosa 25,26 . ICEclc-type elements have been implicated in transmission of antibiotic resistances [27][28][29] and xenobiotic metabolism 25,30 , lending broad significance for understanding the molecular and regulatory basis of their evolutionary success.…”

Section: Introductionmentioning

confidence: 99%

A bistable orthogonal prokaryotic differentiation system underlying development of conjugative transfer competence

Sulser

Vucicevic

Bellini

et al. 2021

Preprint

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The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that stands model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. The ICE only transfers from a small fraction of cells in a population, which we uncover here, results from a dedicated transfer competence program imposed by the ICE. Transfer competence is orthogonally maintained in individual cells in which it is activated, making them the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements.

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“…The depth threshold was set to 70× since this was the minimum read depth observed in our dataset. Complete reference genomes were created by sequencing the first collected clinical isolate of each ST with both PacBio and Illumina HiSeq technologies (27). The subsampled reads were then mapped against their respective complete reference genome with BWA-MEM (https://arxiv.org/abs/1303.…”

Section: Snps and Phylogenetic Analysismentioning

confidence: 99%

Combining Standard Molecular Typing and Whole Genome Sequencing to Investigate Pseudomonas aeruginosa Epidemiology in Intensive Care Units

Magalhães

Valot

Abdelbary

et al. 2020

Front. Public Health

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Pseudomonas aeruginosa is one of the main pathogens responsible for nosocomial infections, particularly in Intensive Care Units (ICUs). Due to the complexity of P. aeruginosa ecology, only powerful typing methods can efficiently allow its surveillance and the detection during expanding outbreaks. An increase in P. aeruginosa incidence was observed in the ICUs of the Lausanne University Hospital between 2010 and 2014. All clinical and environmental isolates retrieved during this period were typed with Double locus sequence typing (DLST), which detected the presence of three major genotypes: DLST 1-18, DLST 1-21, and DLST 6-7. DLST 1-18 (ST1076) isolates were previously associated with an epidemiologically well-described outbreak in the burn unit. Nevertheless, DLST 1-21 (ST253) and DLST 6-7 (ST17) showed sporadic occurrence with only few cases of possible transmission between patients. Whole genome sequencing (WGS) was used to further investigate the epidemiology of these three major P. aeruginosa genotypes in the ICUs. WGS was able to differentiate between outbreak and non-outbreak isolates and confirm suspected epidemiological links. Additionally, whole-genome single nucleotide polymorphisms (SNPs) results considered isolates as closely related for which no epidemiological links were suspected, expanding the epidemiological investigation to unsuspected links. The combination of a first-line molecular typing tool (DLST) with a more discriminatory method (WGS) proved to be an accurate and cost-efficient typing strategy for the investigation of P. aeruginosa epidemiology in the ICUs.

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High-Quality Complete Genome Sequences of Three Pseudomonas aeruginosa Isolates Retrieved from Patients Hospitalized in Intensive Care Units

Abstract: Pseudomonas aeruginosa is one of the major Gram-negative pathogens responsible for hospital-acquired infections. Here, we present high-quality genome sequences of isolates from three P. aeruginosa genotypes retrieved from patients hospitalized in intensive care units.

Cited by 7 publications

References 7 publications

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

A bistable orthogonal prokaryotic differentiation system underlying development of conjugative transfer competence

Combining Standard Molecular Typing and Whole Genome Sequencing to Investigate Pseudomonas aeruginosa Epidemiology in Intensive Care Units

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