Mashtree: a rapid comparison of whole genome sequence files

Katz, Lee S.; Griswold, Taylor; Morrison, Shatavia S.; Caravas, Jason; Zhang, Shaokang; Bakker, Henk C. den; Deng, Xiangyu; Carleton, Heather

doi:10.21105/joss.01762

Cited by 154 publications

(154 citation statements)

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“…Mash v2.0 42 was used to determine distances between genomes using the raw sequence reads, and a phylogeny was constructed with mashtree v0.33 43 . For the analysis of the core genome (the set of homologous nucleotides present in all the isolates when mapped against the same reference) and the core sequence of the pOXA-48 plasmid, an alignment of the single nucleotide polymorphisms (SNPs) obtained with Snippy v2.5 (https://github.com/tseemann/snippy) was used to infer a phylogeny.…”

Section: Methodsmentioning

confidence: 99%

Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting

León‐Sampedro

DelaFuente

Díaz-Agero

et al. 2020

Preprint

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Introductory paragraph 28 Infections caused by carbapenemase-producing enterobacteria (CPE) are a major 29 concern in clinical settings worldwide. Two fundamentally different processes shape 30 the epidemiology of CPE in hospitals: the dissemination of CPE clones from patient to 31 patient (between-patient transfer), and the transfer of carbapenemase-encoding 32 plasmids between enterobacteria in the gut microbiota of individual patients (within-33 patient transfer). The relative contribution of each process to the overall dissemination 34 of carbapenem resistance in hospitals remains poorly understood. Here, we used 35 mechanistic models combining epidemiological data from more than 9,000 patients 36 with whole genome sequence information from 250 enterobacteria clones to 37 characterise the dissemination routes of the carbapenemase-encoding plasmid pOXA-38 48 in a hospital setting over a two-year period. Our results revealed frequent between-39 patient transmission of high-risk pOXA-48-carrying clones, mostly of Klebsiella 40 pneumoniae and sporadically Escherichia coli. The results also identified pOXA-48 41 dissemination hotspots within the hospital, such as specific wards and individual rooms 42 within wards. Using high-resolution plasmid sequence analysis, we uncovered the 43 pervasive within-patient transfer of pOXA-48, suggesting that horizontal plasmid 44 transfer occurs in the gut of virtually every colonised patient. The complex and 45 multifaceted epidemiological scenario exposed by this study provides new insights for 46 the development of intervention strategies to control the in-hospital spread of CPE. 47 48 frequency with which this occurs in the clinical settings and its importance for the 56 dissemination of resistance at a local level remain poorly defined. 57 One of the most clinically relevant groups of nosocomial pathogens are enterobacteria 58 that produce carbapenemases (ß-lactamase enzymes able to degrade carbapenem 59 antibiotics). Among carbapenemase-producing enterobacteria (CPE), clones of 60 Klebsiella pneumoniae and Escherichia coli carrying plasmid-encoded 61 carbapenemases pose the highest clinical threat 5 . Despite their clinical relevance, 62 major gaps remain in our understanding of the epidemiology of CPE and of 63 carbapenemase-encoding plasmids. Previous work has highlighted the importance of 64 in-hospital CPE transmission from patient to patient 6,7 (between-patient transfer). 65 However, the dissemination and evolution of CPE in hospitals present an additional 66 layer of complexity: the transfer of carbapenemase-encoding plasmids between 67 enterobacteria clones in the gut microbiota of individual patients (within-patient 68 transfer) 8,9 . Understanding the relative importance of between-patient and within-69 patient transfer is of central importance for understanding the epidemiology of CPE 70 and informing intervention strategies to control the spread of carbapenem resistance 71 in clinical settings. 72One of the most frequent carbapenemases in enterobacteria is O...

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Section: Methodsmentioning

confidence: 99%

Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting

León‐Sampedro

DelaFuente

Díaz-Agero

et al. 2020

Preprint

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“…De novo assembly of all our isolate genomes and genomes from reference (Matsumura et al, 2017) was performed using SPAdes (v. 3.13.0) (Bankevich et al, 2012) using custom k-mer lengths (31, 55, 79, 103, and 127 bp), and in silico ST-131 clade typing for our ST-131 isolates was performed using ThermonucleotideBLAST (v. 2.04) (Gans and Wolinsky, 2008) using clade-specific primers obtained from Matsumura et al (2017). Phylogenies for sequenced isolates supplemented with publicly available genomes were generated using Mashtree (v. 0.57) (Katz et al, 2019) for each ST.…”

Section: Bioinformatic Analysesmentioning

confidence: 99%

Epidemiology of E. coli in Cystic Fibrosis Airways Demonstrates the Capacity for Persistent Infection but Not Patient-Patient Transmission

et al. 2020

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Escherichia coli is frequently isolated from the respiratory secretions of cystic fibrosis (CF) patients yet is not considered a classical CF pathogen. Accordingly, little is known about the natural history of this organism in the CF airways, as well as the potential for patientto-patient transmission. Patients attending the Calgary Adult CF Clinic (CACFC) between January 1983 and December 2016 with at least one E. coli-positive sputum culture were identified by retrospective review. Annual E. coli isolates from the CACFC biobank from each patient were typed by pulsed-field gel electrophoresis (PFGE) and isolates belonging to shared pulsotypes were sequenced. Single nucleotide polymorphism (SNP) and phylogenetic analysis were used to investigate the natural history of E. coli infection and identify potential transmission events. Forty-five patients with E. coli-positive sputum cultures were identified. Most patients had a single infection episode with a single pulsotype, while replacement of an initial pulsotype with a second was observed in three patients. Twenty-four had E. coli recovered from their sputum more than once and 18 patients had persistent infections (E. coli carriage >6 months with ≥3 positive cultures). Shared pulsotypes corresponded to known extraintestinal pathogenic E. coli strains: ST-131, ST-73, and ST-1193. Phylogenetic relationships and SNP distances among isolates within shared pulsotypes were consistent with independent acquisition of E. coli by individual patients. Most recent common ancestor date estimates of isolates between patients were inconsistent with patient-to-patient transmission. E. coli infection in CF is a dynamic process that appears to be characterized by independent acquisition within our patient population and carriage of unique sets of strains over time by individual patients.

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“…Detailed command lines used for each analysis step are implemented on our Snakemake script (54) available on https://github.com/MaevaTecher/varroa-host-jump. Briefly, we assessed demultiplexed fastq read quality using FastQC (55) and outliers were quickly visualized using Mashtree (56). We mapped reads to the V. destructor reference genome on NCBI [GCF_002443255.1] (16) separately from the complete mitogenome [NC_004454.2] (57) using Bowtie2 v2.6 (58) and NextGenMap v0.5.0 in parallel (59).…”

Section: Alignment and Variant Callingmentioning

confidence: 99%

The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range

Techer

Roberts

Cartwright

et al. 2020

Preprint

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Host switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study them in real time and their demographic parameters remain poorly understood. As a result, fundamental factors that control subsequent parasite evolution, such as the size of the switching population or the extent of immigration from the original host, remain largely unknown. To shed light on the host switching process, we explored how host switches occur in independent host shifts by two ectoparasitic honey bee mites (Varroa destructor and V. jacobsoni). Both switched to the western honey bee (Apis mellifera) after it was brought into contact with their ancestral host (Apis cerana), ~70 and ~12 years ago, respectively. Varroa destructor subsequently caused worldwide collapses of honey bee populations. Using whole-genome sequencing on 44 mites collected in their native ranges from both the ancestral and novel hosts, we were able to reconstruct the known temporal dynamics of the switch. We further found that hundreds of haploid genomes were involved in the initial host switch, and, despite being greatly reduced, some gene flow remains between mites adapted to different hosts remains. Our findings suggest that while reproductive isolation may facilitate fixation of traits beneficial for exploitation of the new host, ongoing genetic exchange may allow genetic amelioration of inbreeding effects.

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Mashtree: a rapid comparison of whole genome sequence files

Cited by 154 publications

References 11 publications

Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting

Dissemination routes of the carbapenem resistance plasmid pOXA-48 in a hospital setting

Epidemiology of E. coli in Cystic Fibrosis Airways Demonstrates the Capacity for Persistent Infection but Not Patient-Patient Transmission

The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range

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