Bacterial genome reduction as a result of short read sequence assembly

Ch, Williamson; Sanchez, Angélica Bianchini; Vazquez, Adam J.; Gutman, Julie; Jw, Sahl

doi:10.1101/091314

Cited by 3 publications

(4 citation statements)

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“…Genome assembly methods using short reads are not well suited for genomes with high frequencies of repeated elements [ 76 ]. Because repeat sequences comprise ~40–50 % of the O. tsutsugamushi genome [ 10, 11 ], our genome assemblies were small and highly fragmented, most likely due to repeat collapse [ 17 ]. To demonstrate the effect of un-resolvable repeats on the quality of the genome assembly, we simulated Illumina reads from the completed Boryong genome and assembled them with the same pipeline that was used for real sequence data.…”

Section: Resultsmentioning

confidence: 99%

“…The reduction of the O. tsutsugamushi genome assembled with short-read sequencing demonstrates the limitations of this approach and suggests that long-read sequencing approaches would be more appropriate in characterizing the complete genome from this highly repetitive species. We have previously demonstrated that this genome reduction can result in the appearance of missing coding regions [ 17 ], which can complicate comparative pan-genomic analyses. For phylogenetics, the high level of homoplasy complicates inferring all relationships, and demonstrates the importance of quantifying the extent and location of homoplasy before making conclusions on evolutionary relationships.…”

Section: Discussionmentioning

confidence: 99%

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Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity

et al. 2018

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Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity

et al. 2018

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“…The amplicons that were used for in silico ribotyping were identified from only three complete ST1 genomes; draft genomes are not useful for the identification of predicted amplicons due to the potential collapse of repeat regions (e.g. 16S rRNA genes) [122]. As additional complete genomes are generated from diverse ribotypes, this method can be modified to associate ribotype information with whole genome sequence and MLST data, which is useful for bridging between different methodologies.…”

Section: Discussionmentioning

confidence: 99%

A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

et al. 2019

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“…The amplicons that were used for in silico ribotyping were identified from only three complete ST1 genomes; draft genomes are not useful for the identification of predicted amplicons due to the potential collapse of repeat regions (e.g. 16S rRNA genes) (112). As additional complete genomes are generated from diverse ribotypes, this method can be modified to associate ribotype information with whole genome sequence and MLST data, which is useful for bridging between different methodologies.…”

Section: Difficile Isolates Have Been Differentiated Using a Variementioning

confidence: 99%

A global to local genomics analysis ofClostridioides difficileST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

Williamson

Stone

Nunnally

et al. 2019

Preprint

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Clostridioides difficile is a ubiquitous, diarrheagenic pathogen often associated with healthcare-acquired infections that can cause a range of symptoms from mild, selflimiting disease to toxic megacolon and death. Since the early 2000s, a large proportion of C. difficile cases have been attributed to the ribotype 027 (RT027) lineage, which is associated with sequence type 1 (ST1) in the C. difficile multilocus sequence typing (MLST) scheme. The spread of ST1 has been attributed, in part, to resistance to fluoroquinolones used to treat un-related infections, which creates conditions ideal for C. difficile colonization and proliferation. In this study, we analyzed 27 isolates from a healthcare network in northern Arizona, USA, and 1,352 public ST1 genomes to place locally-sampled isolates into a global context. Core genome, single nucleotide polymorphism (SNP) analysis demonstrated that at least 6 separate introductions of ST1 were observed in healthcare facilities in northern Arizona over an 18-month sampling period. A reconstruction of transmission networks identified potential nosocomial transmission of isolates following two of these introductions, which were only identified via whole genome sequence analysis. Antibiotic resistance Page 2 of 34 heterogeneity was observed among ST1 genomes, including variability in resistance profiles among locally sampled ST1 isolates. To investigate why ST1 genomes are so common globally, we compared all high-quality C. difficile genomes and identified that ST1 genomes have gained and lost a number of genomic regions compared to all other C. difficile genomes; analyses of other toxigenic C. difficile sequence types demonstrates that this loss may be anomalous and could be related to niche specialization. These results suggest that a combination of antimicrobial resistance and gain and loss of specific genes may explain the prominent association of this sequence type with C. difficile infection cases worldwide. The degree of genetic variability in ST1 suggests that classifying all ST1 genomes into a quinolone-resistant hypervirulent clone category may not be appropriate. Whole genome sequencing of clinical C. difficile isolates provides a high-resolution surveillance strategy for monitoring persistence and transmission of C. difficile and for assessing the performance of infection prevention and control strategies.

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Bacterial genome reduction as a result of short read sequence assembly

Abstract: 7High-throughput comparative genomics has changed our view of bacterial 8 evolution and relatedness. Many genomic comparisons, especially those 9 regarding the accessory genome that is variably conserved across strains in a

Cited by 3 publications

References 47 publications

Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity

Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity

A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

A global to local genomics analysis ofClostridioides difficileST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

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