Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia

ABSTRACTMethicillin-resistantStaphylococcus aureus(MRSA) infection has increased in recent years among cystic fibrosis (CF) patients. Linezolid (LZD) is one of the antistaphylococcal antibiotics widely used in this context. Although LZD resistance is rare, it has been described as often associated with long-term treatments. Thirteen MRSA strains isolated over 5 years from one CF patient were studied for LZD resistance emergence and subjected to whole-genome sequencing (WGS). Resistance emerged after three 15-day LZD therapeutic regimens over 4 months. It was associated with the mutation of G to T at position 2576 (G2576T) in all 5rrlcopies, along with a very high MIC (>256 mg/liter) and a strong increase in the generation time. Resistant strains isolated during the ensuing LZD therapeutic regimens and until 13 months after LZD stopped harbored only 3 or 4 mutatedrrlcopies, associated with lower MICs (8 to 32 mg/liter) and low to moderate generation time increases. Despite these differences, whole-genome sequencing allowed us to determine that all isolates, including the susceptible one isolated before LZD treatment, belonged to the same lineage. In conclusion, LZD resistance can emerge rapidly in CF patients and persist without linezolid selective pressure in colonizing MRSA strains belonging to the same lineage.

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Clostridioides difficile Whole-Genome Sequencing Reveals Limited Within-Host Genetic Diversity in a Pediatric Cohort

Journal of Clinical Microbiology ◽

10.1128/jcm.00559-19 ◽

2019 ◽

Vol 57 (9) ◽

Author(s):

Aakash Balaji ◽

Egon A. Ozer ◽

Larry K. Kociolek

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Core Genome ◽

Genetic Relatedness ◽

The Other ◽

Whole Genome ◽

Content Type ◽

Clostridioides Difficile ◽

Host Genetic

ABSTRACT Whole-genome sequencing (WGS) is a highly sensitive method for identifying genetic relatedness and transmission of Clostridioides difficile strains. Previous studies suggest that as few as 3 core genome single-nucleotide variants (SNVs) discriminate between genetically distinct isolates. Because a single C. difficile colony is selected from culture for WGS, significant within-host genetic diversity could preclude identification of transmission events. To evaluate the likelihood of missed transmission events using WGS of single colonies from culture, we examined within-host genetic diversity among C. difficile isolates collected from children. We performed WGS using an Illumina MiSeq instrument on 8 C. difficile colonies randomly selected from each culture performed on stool collected from 10 children (8 children diagnosed with C. difficile infection and 2 children with asymptomatic carriage); 77/80 (96%) isolate sequences were successfully assembled. Among 8/10 (80%) children, all isolates were the same sequence type (ST). The other 2 children each had mixed infection with two STs, although one ST predominated. Among 9/10 (90%) children, isotypic isolates differed by ≤2 SNVs; an isotypic isolate in the remaining child differed by 3 to SNVs relative to the other isolates from that child. Overall, among the 77 isolates collected from 10 stool cultures, 74/77 (96%) were clonal (i.e., same ST and ≤2 core genome SNVs) to other isolates in stool culture. In summary, we identified rare C. difficile within-host genetic diversity in children, suggesting that WGS of a single colony from stool is likely to appropriately characterize isolate clonality and putative transmission events in the majority of cases.

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Genetic Heterogeneity of Australian Candida auris Isolates: Insights From a Nonoutbreak Setting Using Whole-Genome Sequencing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa158 ◽

2020 ◽

Vol 7 (5) ◽

Author(s):

Chayanika Biswas ◽

Qinning Wang ◽

Sebastiaan J van Hal ◽

David W Eyre ◽

Bernard Hudson ◽

...

Keyword(s):

Multidrug Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Heterogeneity ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Candida Auris ◽

Single Nucleotide ◽

Sporadic Cases ◽

Host Genetic

Abstract Whole-genome sequencing clustered Australian Candida auris isolates from sporadic cases within clade III. Case isolates were genomically distinct; however, unexpectedly, those from 1 case comprised 2 groups separated by >60 single nucleotide polymorphisms (SNPs) with no isolate being identical, in contrast to outbreaks where isolates from any 1 individual have differed by <3 SNPs. Multidrug resistance was absent. High within-host genetic heterogeneity should be considered when investigating C. auris infections.

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Whole genome sequencing to identify host genetic risk factors for severe outcomes of hepatitis a virus infection

Journal of Medical Virology ◽

10.1002/jmv.24007 ◽

2014 ◽

Vol 86 (10) ◽

pp. 1661-1668 ◽

Cited By ~ 5

Author(s):

Dustin Long ◽

Oren K. Fix ◽

Xutao Deng ◽

Mark Seielstad ◽

Adam S. Lauring ◽

...

Keyword(s):

Risk Factors ◽

Virus Infection ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Risk ◽

Hepatitis A ◽

Hepatitis A Virus ◽

Genetic Risk Factors ◽

Whole Genome ◽

Host Genetic

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Whole-Genome Sequencing of Retinoblastoma Reveals the Diversity of Rearrangements Disrupting RB1 and Uncovers a Treatment-Related Mutational Signature

Cancers ◽

10.3390/cancers13040754 ◽

2021 ◽

Vol 13 (4) ◽

pp. 754

Author(s):

Helen R. Davies ◽

Kevin D. Broad ◽

Zerrin Onadim ◽

Elizabeth A. Price ◽

Xueqing Zou ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Driver Mutations ◽

Whole Genome ◽

Rb1 Gene ◽

Clinical Screening ◽

Genetic Changes ◽

Alternative Pathways ◽

Mutational Signature ◽

New Mutations

The development of retinoblastoma is thought to require pathological genetic changes in both alleles of the RB1 gene. However, cases exist where RB1 mutations are undetectable, suggesting alternative pathways to malignancy. We used whole-genome sequencing (WGS) and transcriptomics to investigate the landscape of sporadic retinoblastomas derived from twenty patients, sought RB1 and other driver mutations and investigated mutational signatures. At least one RB1 mutation was identified in all retinoblastomas, including new mutations in addition to those previously identified by clinical screening. Ten tumours carried structural rearrangements involving RB1 ranging from relatively simple to extremely complex rearrangement patterns, including a chromothripsis-like pattern in one tumour. Bilateral tumours obtained from one patient harboured conserved germline but divergent somatic RB1 mutations, indicating independent evolution. Mutational signature analysis showed predominance of signatures associated with cell division, an absence of ultraviolet-related DNA damage and a profound platinum-related mutational signature in a chemotherapy-exposed tumour. Most RB1 mutations are identifiable by clinical screening. However, the increased resolution and ability to detect otherwise elusive rearrangements by WGS have important repercussions on clinical management and advice on recurrence risks.

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Decoding human cancer with whole genome sequencing: a review of PCAWG Project studies published in February 2020

Cancer and Metastasis Reviews ◽

10.1007/s10555-021-09969-z ◽

2021 ◽

Author(s):

Simona Giunta

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Cancer Genetics ◽

Cancer Genome ◽

The Cancer Genome Atlas ◽

Driver Mutations ◽

Causative Mutation ◽

Whole Genome ◽

Genetic Changes ◽

Pan Cancer

AbstractCancer is underlined by genetic changes. In an unprecedented international effort, the Pan-Cancer Analysis of Whole Genomes (PCAWG) of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) sequenced the tumors of over two thousand five hundred patients across 38 different cancer types, as well as the corresponding healthy tissue, with the aim of identifying genome-wide mutations exclusively found in cancer and uncovering new genetic changes that drive tumor formation. What set this project apart from earlier efforts is the use of whole genome sequencing (WGS) that enabled to explore alterations beyond the coding DNA, into cancer’s non-coding genome. WGS of the entire cohort allowed to tease apart driving mutations that initiate and support carcinogenesis from passenger mutations that do not play an overt role in the disease. At least one causative mutation was found in 95% of all cancers, with many tumors showing an average of 5 driver mutations. The PCAWG Project also assessed the transcriptional output altered in cancer and rebuilt the evolutionary history of each tumor showing that initial driver mutations can occur years if not decades prior to a diagnosis. Here, I provide a concise review of the Pan-Cancer Project papers published on February 2020, along with key computational tools and the digital framework generated as part of the project. This represents an historic effort by hundreds of international collaborators, which provides a comprehensive understanding of cancer genetics, with publicly available data and resources representing a treasure trove of information to advance cancer research for years to come.

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Genome Evolution Analysis of Recurrent Testicular Malignant Mesothelioma by Whole-Genome Sequencing

Cellular Physiology and Biochemistry ◽

10.1159/000486355 ◽

2018 ◽

Vol 45 (1) ◽

pp. 163-174 ◽

Cited By ~ 6

Author(s):

Shigeng Zhang ◽

Qi Zhang ◽

Qing Sun ◽

Jinlong Tang ◽

Jimin Chen ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Malignant Mesothelioma ◽

Clonal Evolution ◽

Parallel Evolution ◽

Whole Genome ◽

Tunica Vaginalis ◽

Genetic Changes ◽

Genomic Change ◽

Tunica Vaginalis Testis

Background/Aims: Malignant mesothelioma of the tunica vaginalis testis is a rare and lethal disease. The genomic characteristics and genetic changes of tumor cells during the progression of this disease are unknown. Methods: we performed whole-genome sequencing of four successive tumor samples derived from surgery and a blood sample in a single patient. Results: All tumors were found to have significant C-to-T and T-to-C mutations, and amplification of copy number in chromosomes 1 and 12 were notified in all tumor samples. Subclone analysis revealed a parallel evolution of the tumor in this patient. We also identified some mutations in mesothelioma-associated genes such as KIF25, AHNAK, and PRDM2. Conclusions: The results showed a comprehensive genomic change in malignant mesothelioma of the tunica vaginalis testis and provide a better understanding of the clonal evolution during tumor recurrence and metastasis.

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Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing

Applied and Environmental Microbiology ◽

10.1128/aem.01496-16 ◽

2016 ◽

Vol 82 (19) ◽

pp. 5910-5917 ◽

Cited By ~ 15

Author(s):

Madikay Senghore ◽

Sion C. Bayliss ◽

Brenda A. Kwambana-Adams ◽

Ebenezer Foster-Nyarko ◽

Jainaba Manneh ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Host Adaptation ◽

The Gambia ◽

Sub Saharan Africa ◽

Whole Genome ◽

Genetic Changes ◽

Content Type ◽

Green Monkeys

ABSTRACTStaphylococcus aureusis an important pathogen of humans and animals. We genome sequenced 90S. aureusisolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions ofS. aureusfrom humans to green monkeys (Chlorocebus sabaeus) in The Gambia over different time scales. We report a novel monkey-associated clade ofS. aureusthat emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission ofS. aureusfrom monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens.IMPORTANCEThe population structures ofStaphylococcus aureusin humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission ofS. aureusbetween humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host.

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Whole Genome Sequencing and Custom Liquid Biopsy Markers in Sarcomas

10.21203/rs.3.rs-1049792/v1 ◽

2021 ◽

Author(s):

Felix Haglund de Flon ◽

Cecilia Arthur ◽

Hero Nikdin Awier ◽

Yi Chen ◽

Jesper Eisfeldt ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Fusion Gene ◽

Whole Genome ◽

Single Nucleotide Variants ◽

Liquid Biopsies ◽

Prognostic Information ◽

Genetic Changes ◽

Rare Tumours

Abstract Background: Sarcomas are rare tumours with heterogeneous clinical behaviour including varying rates of metastasis. Clinical treatment and follow-up rely on crude grading systems with uncertain accuracy for individual patients. Whole genome sequencing (WGS) detects both structural variation and single nucleotide variants and may thus add important diagnostic/prognostic information. Liquid biopsies (LB) may potentially identify hematogenous spread and treatment response rate but further evaluation in sarcomas is needed. Methods: In this study we explore the performance of individualized LB in four patients with different types of sarcomas. Fresh frozen tumour tissue was sequenced using WGS and whole transcriptome sequencing. Three putative driver variants or one fusion gene were selected per case and custom digital droplet PCR (ddPCR) assays were designed, evaluated on tumour DNA and used to assess levels of cell free tumour DNA in plasma taken prior to surgery. Results: In LB, ddPCR identified three variants in one patient with metastatic disease. The remaining three patients had negative LBs and were without disease at follow-up (>18 months after surgery). Conclusions: WGS is a powerful tool to detect all types of genetic changes in sarcoma and can facilitate clinical diagnosis/classification while custom LB may add prognostic information.

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