SAUTE: sequence assembly using target enrichment

Souvorov, Alexandre; Agarwala, Richa

doi:10.1186/s12859-021-04174-9

Cited by 13 publications

(10 citation statements)

References 48 publications

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“…All fluoroquinolones requiring SNP confirmation were verified by identifying the SNPs conferring resistance in Tablet [44] using the AMR++ output. For annotation by AMR FinderPlus, fastq files were aligned against the AMRFinder Plus database using SAUTE [45] on the CFSAN HPC. https://github.com/ncbi/amr/wiki/Methods.…”

Section: Bioinformatic Analysesmentioning

confidence: 99%

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

et al. 2022

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The National Antimicrobial Resistance Monitoring System (NARMS) has monitored antimicrobial resistance (AMR) associated with pathogens of humans and animals since 1996. In alignment with One Health strategic planning, NARMS is currently exploring the inclusion of surface waters as an environmental modality for monitoring AMR. From a One Health perspective, surface waters function as key environmental integrators between humans, animals, agriculture, and the environment. Surface waters however, due to their dilute nature present a unique challenge for monitoring critically important antimicrobial resistance. Selective enrichments from water paired with genomic sequencing effectively describe AMR for single genomes but do not provide data to describe a broader environmental resistome. Metagenomic data effectively describe a broad range of AMR from certain matrices however, depth of coverage is usually insufficient to describe clinically significant AMR from aquatic matrices. Thus, the coupling of biological enrichments of surface water with shotgun NGS sequencing has been shown to greatly enhance the capacity to report an expansive profile of clinically significant antimicrobial resistance genes. Here we demonstrate, using water samples from distinct sites (a creek in close proximity to a hospital and a reservoir used for recreation and municipal water), that the AMR portfolio provided by enriched (quasimetagenomic) data is capable of describing almost 30% of NARMS surveillance targets contrasted to only 1% by metagenomic data. Additionally, the quasimetagenomic data supported reporting of statistically significant (P< 0.05) differential abundance of specific AMR genes between sites. A single time-point for two sites is a small pilot, but the robust results describing critically important AMR determinants from each water source, provide proof of concept that quasimetagenomics can be applied to aquatic AMR surveillance efforts for local, national, and global monitoring.

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Section: Bioinformatic Analysesmentioning

confidence: 99%

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

et al. 2022

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“…Traditional phylogenetic marker loci were often selected because they are amenable to reliable Sanger sequencing due in part to their multi-copy nature (rDNA) or presence on the highly abundant mitochondrial genome (COI and cytB). In contrast, these attributes are detrimental to de novo assembly as within-genome copy variation often confounds assembly methods ( Souvorov and Agarwala, 2021 ) resulting in fragmented or missing loci. Despite this limitation we were able to construct an HSP90 phylogeny from our sequence data using targeted assembly of the single-copy nuclear gene thereby allowing comparison to previously published work.…”

Section: Discussionmentioning

confidence: 99%

“…A single-gene phylogeny was constructed for Heat Shock Protein 90 (HSP90) to facilitate comparison to other Globodera sequences available in Genbank. A single 1402 bp HSP90 sequence from G. ellingtonae (MK105568.1) was used as a reference to anchor the assembly of the locus from each sample using the software package SAUTE ( Souvorov and Agarwala, 2021 ). Sequences from identified Globodera and Cactodera (outgroup) from PopSet 1780190675 ( Skantar et al, 2021 ) were used for comparison, as were the partial HSP90 sequences obtained by Lax et al (2014) from a G. ellingtonae population collected in Argentina.…”

Section: Methodsmentioning

confidence: 99%

Characterization of Globodera ellingtonae Populations from Chile Utilizing Whole Genome Sequencing

Hesse

Pardo

Fuentes

et al. 2021

Journal of Nematology

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Globodera ellingtonae was originally described from populations collected in the United States. In the original description, ribosomal DNA loci from Globodera sp. collected in Chile and Argentina were similar to G. ellingtonae, suggesting this nematode originated in this region of South America. In an effort to find additional populations of G. elllingtonae, collection trips were conducted in 2017 and 2020 in the Antofagasta and Arica y Parinacota Regions in Northern Chile, respectively. Globodera sp. were more prevalent in Antofagasta (17 samples collected, 53% positive for Globodera sp.) than in Arica y Parincota (16 samples collected, 13% positive for Globodera sp.). The genomes of single cysts (N ≥ 3) from four fields were sequenced. Additionally, the genomes of the G. ellingtonae population from Oregon and a Globodera sp. population originally collected in Antofagasta Region but maintained in culture in France were also sequenced. Based upon a HSP90 sequenced data mined from WSG data, all of the populations from the Antofagasta Region were G. ellingtonae and grouped in a monophyletic clade. A population collected from the Arica y Parincota Region was identified as G. rostochiensis based upon HSP90 data. Genome-wide SNP patterns of the G. ellingtonae populations showed strong clustering based on geographic location indicating that G. ellingtonae has high genetic diversity within Chile. A phylogenetic tree derived from 168,354 binary SNPs in the nuclear genome showed separate but distinct clustering of the Oregon population and the population from Antofagasta maintained in France. The Oregon G. ellingtonae population subtended the Chilean clades and placed on a long branch representing approximately twice the genetic variation observed among all Chilean G. ellingtonae populations. The possibility remains that G. ellingtonae from Chile may be sufficiently diverged to constitute a new species from G. ellingtonae originally described from a population collected in Oregon.

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“…(v0.6.2; (accessed on 27 January 2022)) was used to filter the paired-end reads (Q > 30 and length > 50 bp) [ 23 ]. De novo assembly was performed using SKESA v2.3.0 ( (accessed on 27 January 2022)) and the assembled contigs were polished using Shovill (v1.1.0; (accessed on 27 January 2022)) [ 24 , 25 ]. Assembly metrics were calculated using QUAST (v5.0.2; (accessed on 27 January 2022)) [ 26 ].…”

Section: Methodsmentioning

confidence: 99%

In Vitro Activity of Ceftolozane-Tazobactam against Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa Obtained from Blood Cultures from Sentinel Public Hospitals in South Africa

2023

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Multidrug-resistant (MDR) Gram-negative bacteria are responsible for the majority of healthcare-associated infections and pose a serious threat as they complicate and prolong clinical care. A novel cephalosporin-β-lactamase-inhibitor combination, ceftolozane-tazobactam (C/T) was introduced in 2014, which improved the treatment of MDR pathogens. This study aimed to evaluate the activity of C/T against Escherichia coli (n = 100), Klebsiella pneumoniae (n = 100), and Pseudomonas aeruginosa (n = 100) blood culture isolates in South Africa (SA). Isolates were sequentially selected (2010 to 2020) from the Group for Enteric, Respiratory, and Meningeal Diseases Surveillance (GERMS) programme in SA. Organism identification was performed using the matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF MS) instrument (Microflex, Bruker Daltonics, Bremen, Germany), and antibiotic susceptibility was performed using the Sensititre instrument (Trek Diagnostic Systems, East Grinstead, UK). C/T resistance was reported in 16 E. coli, 28 K. pneumoniae and 13 P. aeruginosa isolates. Fifty percent of the C/T resistant isolates were subjected to whole-genome sequencing (WGS). According to the whole genome multilocus sequence typing (MLST) analysis, the E. coli isolates (n = 8) belonged to sequence type (ST)10, ST131, ST405, and ST410, the K. pneumoniae isolates (n = 14) belonged to ST1, ST37, ST73, ST101, ST231, ST307, ST336 and ST6065 (novel ST), and the P. aeruginosa isolates (n = 7) belonged to ST111, ST233, ST273, and ST815. The WGS data also showed that all the E. coli isolates harboured aminoglycoside (aph (3′′)-Ib, aph (6)-Id), macrolide (mdfA, mphA), and sulphonamide (sul2) antibiotic resistance genes, all the K. pneumoniae isolates harboured β-lactam (blaCTX-M-15), and sulphonamide (sul2) antibiotic resistance genes, and all the P. aeruginosa isolates harboured aminoglycoside (aph (3′)-IIb), β-lactam (PAO), fosfomycin (fosA), phenicol (catB7), quinolone (crpP), and disinfectant (qacE) antibiotic resistance genes. It is evident that E. coli, K. pneumoniae and P. aeruginosa can adapt pre-existing resistance mechanisms to resist newer β-lactam molecules and inhibitors, since these isolates were not exposed to ceftolozane-tazobactam previously.

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SAUTE: sequence assembly using target enrichment

Cited by 13 publications

References 48 publications

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

Characterization of Globodera ellingtonae Populations from Chile Utilizing Whole Genome Sequencing

In Vitro Activity of Ceftolozane-Tazobactam against Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa Obtained from Blood Cultures from Sentinel Public Hospitals in South Africa

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