MRSA Transmission in Intensive Care Units: Genomic Analysis of Patients, Their Environments, and Healthcare Workers

Abstract Background Methicillin-resistant Staphylococcus aureus (MRSA)—and now USA300 MRSA—is a significant intensive care unit (ICU) pathogen; healthcare worker (HCW) contamination may lead to patient cross-transmission. Methods From September 2015 to February 2016, to study the spread of MRSA, we enrolled HCWs in 4 adult ICUs caring for patients on MRSA contact precautions. Samples were collected from patient body sites and high-touch surfaces in patient rooms. HCW hands, gloves, and personal protective equipment were sampled pre/post-patient encounter. Whole genome sequencing (WGS) was used to compare isolates from patients, HCWs, and environment. Results There were 413 MRSA isolates sequenced (38% USA300, 52% USA100) from 66 patient encounters. Six of 66 HCWs were contaminated with MRSA prior to room entry. Isolates from a single patient encounter were typically either USA100 or USA300; in 8 (12%) encounters both USA300 and USA100 were isolated. WGS demonstrated that isolates from patients, HCWs, and environment often were genetically similar, although there was substantial between-encounter diversity. Strikingly, there were 5 USA100 and 1 USA300 clusters that contained similar strains (<22 single-nucleotide variants [SNVs], with most <10 SNVs) within the cluster despite coming from different encounters, suggesting intra- and inter-ICU spread of strains, that is, 4 of these genomic clusters were from encounters in the same ICU; 5 of 6 clusters occurred within 1 week. Conclusions We demonstrated frequent spread of MRSA USA300 and USA100 strains among patients, environment, and HCWs. WGS identified possible spread within and even between ICUs. Future analysis with detailed contact tracing in conjunction with genomic data may further elucidate pathways of MRSA spread and points for intervention.

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SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity

Virus Evolution ◽

10.1093/ve/veab013 ◽

2021 ◽

Author(s):

Juliana D Siqueira ◽

Livia R Goes ◽

Brunna M Alves ◽

Pedro S de Carvalho ◽

Claudia Cicala ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Cancer Patients ◽

Disease Severity ◽

Healthcare Workers ◽

Viral Population ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Consensus Sequences ◽

Vulnerable Patients

Abstract Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (non-cancer controls) by deep sequencing and investigated the within-host viral population of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers from the Brazilian National Cancer Institute were collected in April–May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%) among the consensus sequences. Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to healthcare workers. This difference was independent of SARS-CoV-2 Ct values obtained at the diagnostic tests, which did not differ between the two groups. The most common nucleotide changes of intrahost SNVs in both groups were consistent with APOBEC and ADAR activities. Intrahost genetic diversity in cancer patients was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Moreover, the presence of metastasis, either in general or specifically in the lung, was not associated with intrahost diversity among cancer patients. Cancer patients carried significantly higher numbers of minor variants compared to non-cancer counterparts. Further studies on SARS-CoV-2 diversity in especially vulnerable patients will shed light onto the understanding of the basis of COVID-19 different outcomes in humans.

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Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers

10.1101/2021.12.14.472689 ◽

2021 ◽

Author(s):

Zachary L Skidmore ◽

Jason Kunisaki ◽

Yiing Lin ◽

Kelsy C Cotto ◽

Erica K Barnell ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Copy Number Variants ◽

Genomic Analysis ◽

Structural Variants ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Tert Promoter Mutations ◽

Somatic Alterations ◽

Differential Gene ◽

Promoter Mutations

Background: Liver cancer is the second leading cause of cancer-related deaths worldwide. Hepatocellular carcinoma (HCC) risk factors include chronic hepatitis, cirrhosis, and alcohol abuse, whereby tumorigenesis is induced through inflammation and subsequent fibrotic response. However, a subset of HCC arises in non-cirrhotic livers. We characterized the genomic and transcriptomic landscape of non-cirrhotic HCC to identify features underlying the disease's development and progression. Methods: Whole genome and transcriptome sequencing was performed on 30 surgically resectable tumors comprised of primarily of non-cirrhotic HCC and adjacent normal tissue. Using somatic variants, capture reagents were created and employed on an additional 87 cases of mixed cirrhotic/non-cirrhotic HCC. Cases were analyzed to identify viral integrations, single nucleotide variants (SNVs), insertions and deletions (INDELS), copy number variants, loss of heterozygosity, gene fusions, structural variants, and differential gene expression. Results: We detected 3,750 SNVs/INDELS and extensive CNVs and expression changes. Recurrent TERT promoter mutations occurred in >52% of non-cirrhotic discovery samples. Frequently mutated genes included TP53, CTNNB1, and APOB. Cytochrome P450 mediated metabolism was significantly downregulated. Structural variants were observed at MACROD2, WDPCP, and NCKAP5 in >20% of samples. Furthermore, NR1H4 fusions involving gene partners EWSR1, GNPTAB, and FNIP1 were detected and validated in 2 non-cirrhotic samples. Conclusion: Genomic analysis can elucidate mechanisms that may contribute to non-cirrhotic HCC tumorigenesis. The comparable mutational landscape between cirrhotic and non-cirrhotic HCC supports previous work suggesting a convergence at the genomic level during disease progression. It is therefore possible genomic-based treatments can be applied to both HCC subtypes with progressed disease.

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Comparative genomic analysis of the principal Cryptosporidium species that infect humans

PeerJ ◽

10.7717/peerj.10478 ◽

2020 ◽

Vol 8 ◽

pp. e10478

Author(s):

Laura M. Arias-Agudelo ◽

Gisela Garcia-Montoya ◽

Felipe Cabarcas ◽

Ana L. Galvan-Diaz ◽

Juan F. Alzate

Keyword(s):

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Single Nucleotide Variants ◽

Nucleotide Substitutions ◽

Genomic Comparison ◽

Single Nucleotide ◽

Associated Proteins ◽

Species Specific ◽

Ngs Data

Cryptosporidium parasites are ubiquitous and can infect a broad range of vertebrates and are considered the most frequent protozoa associated with waterborne parasitic outbreaks. The intestine is the target of three of the species most frequently found in humans: C. hominis, C. parvum, and. C. meleagridis. Despite the recent advance in genome sequencing projects for this apicomplexan, a broad genomic comparison including the three species most prevalent in humans have not been published so far. In this work, we downloaded raw NGS data, assembled it under normalized conditions, and compared 23 publicly available genomes of C. hominis, C. parvum, and C. meleagridis. Although few genomes showed highly fragmented assemblies, most of them had less than 500 scaffolds and mean coverage that ranged between 35X and 511X. Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed. Furthermore, deleterious nucleotide substitutions common to all three species were more common in genes associated with DNA repair, recombination, and chromosome-associated proteins. Indel events were observed in the 23 studied isolates that spanned up to 500 bases. The highest number of deletions was observed in C. meleagridis, followed by C. hominis, with more than 60 species-specific deletions found in some isolates of these two species. Although several genes with indel events have been partially annotated, most of them remain to encode uncharacterized proteins.

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Analysis of cell-free circulating tumor DNA in 419 patients with glioblastoma and other primary brain tumors

CNS Oncology ◽

10.2217/cns-2018-0015 ◽

2019 ◽

Vol 8 (2) ◽

pp. CNS34 ◽

Cited By ~ 26

Author(s):

David E Piccioni ◽

Achal Singh Achrol ◽

Lesli A Kiedrowski ◽

Kimberly C Banks ◽

Najee Boucher ◽

...

Keyword(s):

Brain Tumors ◽

Genomic Analysis ◽

Circulating Tumor Dna ◽

Single Nucleotide Variants ◽

Viable Option ◽

Single Nucleotide ◽

Primary Brain Tumors ◽

Somatic Alteration ◽

Tumor Sequencing ◽

Tumor Dna

Aim: Genomically matched trials in primary brain tumors (PBTs) require recent tumor sequencing. We evaluated whether circulating tumor DNA (ctDNA) could facilitate genomic interrogation in these patients. Methods: Data from 419 PBT patients tested clinically with a ctDNA NGS panel at a CLIA-certified laboratory were analyzed. Results: A total of 211 patients (50%) had ≥1 somatic alteration detected. Detection was highest in meningioma (59%) and gliobastoma (55%). Single nucleotide variants were detected in 61 genes, with amplifications detected in ERBB2, MET, EGFR and others. Conclusion: Contrary to previous studies with very low yields, we found half of PBT patients had detectable ctDNA with genomically targetable off-label or clinical trial options for almost 50%. For those PBT patients with detectable ctDNA, plasma cfDNA genomic analysis is a clinically viable option for identifying genomically driven therapy options.

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The Prevotella copri complex comprises four distinct clades that are underrepresented in Westernised populations

10.1101/600593 ◽

2019 ◽

Cited By ~ 7

Author(s):

Adrian Tett ◽

Kun D. Huang ◽

Francesco Asnicar ◽

Hannah Fehlner-Peach ◽

Edoardo Pasolli ◽

...

Keyword(s):

Meta Analysis ◽

Genomic Analysis ◽

Fold Increase ◽

Single Nucleotide Variants ◽

Human Gut ◽

High Quality ◽

Single Nucleotide ◽

Out Of Africa ◽

Global Population ◽

Dietary Modifications

AbstractPrevotella copri is a common inhabitant of the human gut. Interest in P. copri has gathered pace due to conflicting reports on whether it is beneficial or detrimental to health. In a cross-continent meta-analysis exploiting >6,500 available metagenomes supported by new isolate sequencing and recovery of high-quality genomes from metagenomes, we obtained >1,000 P. copri genomes. This 100-fold increase over existing isolate genomes allowed the genetic and global population structure of P. copri to be explored at an unprecedented depth. We demonstrate P. copri is not a monotypic species, but encompasses four distinct clades (>10% inter-clade vs. <4% intra-clade average single nucleotide variants) for which we propose the name P. copri complex, comprising clades A, B, C and D. We show the complex is near ubiquitous in non-Westernised populations (95.4% versus 29.6% in Westernised populations), where all four clades are typically co-present within an individual (61.6% of the cases), in contrast to Westernised populations (4.6%). Genomic analysis of the complex reveals substantial and complementary functional diversity, including the potential for utilisation of complex carbohydrates, suggestive that multi-generational dietary modifications may be a driver for the reduced P. copri prevalence in Westernised populations. Analysis of ancient stool microbiomes highlights a similar pattern of P. copri presence consistent with modern non-Westernised populations, allowing us to estimate the time of clade delineation to pre-date human migratory waves out of Africa. Our analysis reveals P. copri to be far more diverse than previously appreciated and this diversity appears to be underrepresented in Western-lifestyle populations.

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Single Nucleotide Variants in A Family of Monozygotic Twins Discordant for the Phenotype Congenital Megaureter: A Genomic Analysis

The Open Urology & Nephrology Journal ◽

10.2174/1874303x01710010011 ◽

2017 ◽

Vol 10 (1) ◽

pp. 11-19

Author(s):

Augusto C. Soares dos Santos Junior ◽

Luciana B. Rodrigues ◽

Raony G. Corrêa Do Carmo Lisboa Cardenas ◽

Patricia G.P. Couto ◽

Luiz A. Cunha de Marco ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Monozygotic Twins ◽

Genomic Analysis ◽

Genetic Variations ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Whole Exome ◽

Sequencing Technique ◽

Related Individuals

Introduction: Congenital megaureter constitutes the second most frequent cause of hydronephrosis in children. There is still much debate on what extent environmental or genetic factors are involved in the pathogenesis of congenital megaureter. Objectives: This study aimed at investigating a pair of monozygotic twins discordant for the expression of bilateral congenital megaureter using the whole exome sequencing technique. Methods: Peripheral blood DNA was extracted and then sequenced using the whole exome technique from a pair of twins discordant for the presence of bilateral congenital refluxing unobstructed megaureter, his parents and a set of 11 non-related individuals with confirmed diagnosis of congenital megaureter. The DNA of the set of 11 non-related individuals was pooled in three groups. The monozygotic twins and their parents had DNA samples sequenced separately. Sanger validation was performed after data was filtered. Results: In the proband were identified 256 candidate genes, including TBX3, GATA6, DHH, LDB3, and HNF1, which are expressed in the urinary tract during the embryonic period. After Sanger validation, the SNVs found in the genes TBX3, GATA6, DHH and LDB3 were not confirmed in the proband. The SNV chr17:36104650 in the HNF1b gene was confirmed in the proband, his twin brother and the mother, however was not found in the pool of 11 non-related individuals with congenital megaureter. Conclusion: Due to the possible complex causative network of genetic variations and the challenges regarding the use of the whole exome sequencing technique we could not unequivocally associate the genetic variations identified in this study with the development of the congenital megaureter.

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Cross-transmission Is Not the Source of New Mycobacterium abscessus Infections in a Multicenter Cohort of Cystic Fibrosis Patients

Clinical Infectious Diseases ◽

10.1093/cid/ciz526 ◽

2019 ◽

Vol 70 (9) ◽

pp. 1855-1864 ◽

Cited By ~ 2

Author(s):

Ronan M Doyle ◽

Marc Rubio ◽

Garth Dixon ◽

John Hartley ◽

Nigel Klein ◽

...

Keyword(s):

Cystic Fibrosis ◽

Control Policy ◽

Mycobacterium Abscessus ◽

Fixed Number ◽

Full Potential ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Conflicting Evidence ◽

Whole Genomes ◽

Cross Transmission

Abstract Background Mycobacterium abscessus is an extensively drug–resistant pathogen that causes pulmonary disease, particularly in cystic fibrosis (CF) patients. Identifying direct patient-to-patient transmission of M. abscessus is critically important in directing an infection control policy for the management of risk in CF patients. A variety of clinical labs have used molecular epidemiology to investigate transmission. However, there is still conflicting evidence as to how M. abscessus is acquired and whether cross-transmission occurs. Recently, labs have applied whole-genome sequencing (WGS) to investigate this further and, in this study, we investigated whether WGS can reliably identify cross-transmission in M. abscessus. Methods We retrospectively sequenced the whole genomes of 145 M. abscessus isolates from 62 patients, seen at 4 hospitals in 2 countries over 16 years. Results We have shown that a comparison of a fixed number of core single nucleotide variants alone cannot be used to infer cross-transmission in M. abscessus but does provide enough information to replace multiple existing molecular assays. We detected 1 episode of possible direct patient-to-patient transmission in a sibling pair. We found that patients acquired unique M. abscessus strains even after spending considerable time on the same wards with other M. abscessus–positive patients. Conclusions This novel analysis has demonstrated that the majority of patients in this study have not acquired M. abscessus through direct patient-to-patient transmission or a common reservoir. Tracking transmission using WGS will only realize its full potential with proper environmental screening, as well as patient sampling.

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Genomic Analysis of Human Noroviruses Using Hybrid Illumina-Nanopore Data

10.1101/2021.03.30.437798 ◽

2021 ◽

Author(s):

Annika Flint ◽

Spencer Reaume ◽

Jennifer Harlow ◽

Emily Hoover ◽

Kelly A Weedmark ◽

...

Keyword(s):

Genomic Analysis ◽

High Viral Load ◽

Full Length ◽

Whole Genome Sequence ◽

Full Genome ◽

Single Nucleotide Variants ◽

Viral Titre ◽

Single Nucleotide ◽

Oxford Nanopore ◽

Metagenomic Approach

Whole genome sequence (WGS) analysis of noroviruses is routinely performed by employing a metagenomic approach. While this methodology has several advantages, such as allowing for examination of co-infection, it has some limitations such as the requirement of high viral load to achieve full-length or near full-length genomic sequences. In this study, we used an amplification approach to obtain full-length genomic amplicons from 39 Canadian GII isolates followed by deep sequencing on Illumina and Oxford Nanopore platforms. This approach significantly reduced the required viral titre to obtain full-genome coverage. Herein, we compared the coverage and sequences obtained by both platforms and provided an in-depth genomic analysis of the obtained sequences, including the presence of single nucleotide variants (SNVs) and recombination events.

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