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Johan Gimonet, Anne-Catherine Portmann, Coralie Fournier, Leen Baert
This work shows that an incubation time reduced to 4-5 h to prepare a culture for DNA extraction followed by an automated DNA extraction can shorten the hands-on time, the turnaround time by 30% and increase the throughput while maintaining the WGS quality assessed by high quality Single Nucleotide Polymorphism analysis.
June 16, 2018: Journal of Microbiological Methods
Charlotte J Houldcroft, Sunando Roy, Sofia Morfopoulou, Ben K Margetts, Daniel P Depledge, Juliana Cudini, Divya Shah, Julianne R Brown, Erika Yara Romero, Rachel Williams, Elaine Cloutman-Green, Kanchan Rao, Joseph F Standing, John Hartley, Judith Breuer
Background: Adenoviruses are significant pathogens for the immunocompromised, arising from primary infection or reinfection. Serotyping is insufficient to support nosocomial transmission investigations. We investigate whether whole-genome sequencing (WGS) provides clinically relevant information on transmission among patients in a paediatric tertiary hospital. Methods: We developed a target-enriched adenovirus WGS technique for clinical samples and retrospectively sequenced 107 adenovirus-positive residual diagnostic samples, including viraemias (>5x104 copies/ml), from 37 patients collected January 2011 - March 2016...
June 4, 2018: Journal of Infectious Diseases
Yong-Qiang Yang, Yun-Xia Li, Chang-Wei Lei, An-Yun Zhang, Hong-Ning Wang
Objectives: To identify a novel plasmid-mediated colistin resistance gene in Klebsiella pneumoniae isolated from chickens in China. Methods: WGS was used to identify a novel colistin resistance gene. The transferability of plasmids carrying mcr-7.1 was investigated by conjugation experiments. The expression of the mcr-7.1 gene was examined using an expression vector. Results: A novel plasmid-mediated colistin resistance gene mcr-7.1, sharing 70% amino acid identity with the mcr-3 gene, was identified in three K...
April 17, 2018: Journal of Antimicrobial Chemotherapy
Lu Liu, Yu Feng, Alan McNally, Zhiyong Zong
Objectives: New Delhi MBL (NDM) is a type of carbapenemase; 20 variants of NDM have been identified to date. We have found a new variant of NDM, NDM-21, and describe it here. Methods: A carbapenem-resistant Escherichia coli was subjected to WGS using an Illumina X10 sequencer to identify the antimicrobial resistance genes and its ST. The gene encoding the new variant of NDM was cloned into E. coli DH5α, with blaNDM-5 being cloned as the control. Transformants were tested for susceptibility to carbapenems...
June 14, 2018: Journal of Antimicrobial Chemotherapy
Srinivas R Viswanathan, Gavin Ha, Andreas M Hoff, Jeremiah A Wala, Jian Carrot-Zhang, Christopher W Whelan, Nicholas J Haradhvala, Samuel S Freeman, Sarah C Reed, Justin Rhoades, Paz Polak, Michelle Cipicchio, Stephanie A Wankowicz, Alicia Wong, Tushar Kamath, Zhenwei Zhang, Gregory J Gydush, Denisse Rotem, J Christopher Love, Gad Getz, Stacey Gabriel, Cheng-Zhong Zhang, Scott M Dehm, Peter S Nelson, Eliezer M Van Allen, Atish D Choudhury, Viktor A Adalsteinsson, Rameen Beroukhim, Mary-Ellen Taplin, Matthew Meyerson
Nearly all prostate cancer deaths are from metastatic castration-resistant prostate cancer (mCRPC), but there have been few whole-genome sequencing (WGS) studies of this disease state. We performed linked-read WGS on 23 mCRPC biopsy specimens and analyzed cell-free DNA sequencing data from 86 patients with mCRPC. In addition to frequent rearrangements affecting known prostate cancer genes, we observed complex rearrangements of the AR locus in most cases. Unexpectedly, these rearrangements include highly recurrent tandem duplications involving an upstream enhancer of AR in 70%-87% of cases compared with <2% of primary prostate cancers...
June 11, 2018: Cell
James Whitworth, Philip S Smith, Jose-Ezequiel Martin, Hannah West, Andrea Luchetti, Faye Rodger, Graeme Clark, Keren Carss, Jonathan Stephens, Kathleen Stirrups, Chris Penkett, Rutendo Mapeta, Sofie Ashford, Karyn Megy, Hassan Shakeel, Munaza Ahmed, Julian Adlard, Julian Barwell, Carole Brewer, Ruth T Casey, Ruth Armstrong, Trevor Cole, Dafydd Gareth Evans, Florentia Fostira, Lynn Greenhalgh, Helen Hanson, Alex Henderson, Jonathan Hoffman, Louise Izatt, Ajith Kumar, Ava Kwong, Fiona Lalloo, Kai Ren Ong, Joan Paterson, Soo-Mi Park, Rakefet Chen-Shtoyerman, Claire Searle, Lucy Side, Anne-Bine Skytte, Katie Snape, Emma R Woodward, Marc D Tischkowitz, Eamonn R Maher
Multiple primary tumors (MPTs) affect a substantial proportion of cancer survivors and can result from various causes, including inherited predisposition. Currently, germline genetic testing of MPT-affected individuals for variants in cancer-predisposition genes (CPGs) is mostly targeted by tumor type. We ascertained pre-assessed MPT individuals (with at least two primary tumors by age 60 years or at least three by 70 years) from genetics centers and performed whole-genome sequencing (WGS) on 460 individuals from 440 families...
June 12, 2018: American Journal of Human Genetics
Martina Sansone, Åsa Wiman, Maria Lind Karlberg, Maria Brytting, Lars Bohlin, Lars-Magnus Andersson, Johan Westin, Rickard Nordén
BACKGROUND/AIM: To describe a hospital outbreak of influenza B (InfB) virus infection during season 2015/2016 by combining clinical and epidemiological data with molecular methods. METHODS: Twenty patients diagnosed with InfB from a hospital outbreak during a four-week-period were included. Nasopharyngeal swabs (NPS) positive for InfB by multiplex real-time PCR were sent for lineage typing and whole genome sequencing (WGS). Medical records were retrospectively reviewed for data regarding patient characteristics, localisation, exposure and outcome and assembled into a timeline...
June 14, 2018: Journal of Hospital Infection
Xiaoming Jia, Lohith Madireddy, Stacy Caillier, Adam Santaniello, Federica Esposito, Giancarlo Comi, Olaf Stuve, Yuan Zhou, Bruce Taylor, Trevor Kilpatrick, Filippo Martinelli-Boneschi, Bruce A C Cree, Jorge R Oksenberg, Stephen L Hauser, Sergio E Baranzini
OBJECTIVE: Primary progressive multiple sclerosis (PPMS) causes accumulation of neurologic disability from disease onset without clinical attacks typical of relapsing multiple sclerosis (RMS). However, whether genetic variation influences the disease course remains unclear. We aimed to determine whether mutations causative of neurologic disorders that share features with MS contribute to risk for developing PPMS. METHODS: We examined whole-genome sequencing (WGS) data from 38 PPMS and 81 healthy subjects of European ancestry...
June 16, 2018: Annals of Neurology
Ruth E Timme, Hugh Rand, Maria Sanchez Leon, Maria Hoffmann, Errol Strain, Marc Allard, Dwayne Roberson, Joseph D Baugher
Pathogen monitoring is becoming more precise as sequencing technologies become more affordable and accessible worldwide. This transition is especially apparent in the field of food safety, which has demonstrated how whole-genome sequencing (WGS) can be used on a global scale to protect public health. GenomeTrakr coordinates the WGS performed by public-health agencies and other partners by providing a public database with real-time cluster analysis for foodborne pathogen surveillance. Because WGS is being used to support enforcement decisions, it is essential to have confidence in the quality of the data being used and the downstream data analyses that guide these decisions...
June 15, 2018: Microbial Genomics
Zhen Liu, Zongyang Lu, Guang Yang, Shisheng Huang, Guanglei Li, Songjie Feng, Yajing Liu, Jianan Li, Wenxia Yu, Yu Zhang, Jia Chen, Qiang Sun, Xingxu Huang
A recently developed adenine base editor (ABE) efficiently converts A to G and is potentially useful for clinical applications. However, its precision and efficiency in vivo remains to be addressed. Here we achieve A-to-G conversion in vivo at frequencies up to 100% by microinjection of ABE mRNA together with sgRNAs. We then generate mouse models harboring clinically relevant mutations at Ar and Hoxd13, which recapitulates respective clinical defects. Furthermore, we achieve both C-to-T and A-to-G base editing by using a combination of ABE and SaBE3, thus creating mouse model harboring multiple mutations...
June 14, 2018: Nature Communications
Christine Martineau, Xuejing Li, Cindy Lalancette, Thérèse Perreault, Eric Fournier, Julien Tremblay, Milagros Gonzales, Étienne Yergeau, Caroline Quach
Serratia marcescens is an environmental bacterium commonly associated with outbreaks in neonatal intensive care units (NICU). Investigation of S. marcescens outbreaks requires efficient recovery and typing of clinical and environmental isolates. In this study, we described how the use of next-generation sequencing applications, such as bacterial whole-genome sequencing (WGS) and bacterial community profiling, could improve S. marcescens outbreak investigation. Phylogenomic links and potential antibiotic resistance genes and plasmids in S...
June 13, 2018: Journal of Clinical Microbiology
Lauren A Cowley, Fernanda C Petersen, Roger Junges, Med Jimson D Jimenez, Donald A Morrison, William P Hanage
Homologous recombination in the genetic transformation model organism Streptococcus pneumoniae is thought to be important in the adaptation and evolution of this pathogen. While competent pneumococci are able to scavenge DNA added to laboratory cultures, large-scale transfers of multiple kb are rare under these conditions. We used whole genome sequencing (WGS) to map transfers in recombinants arising from contact of competent cells with non-competent 'target' cells, using strains with known genomes, distinguished by a total of ~16,000 SNPs...
June 13, 2018: PLoS Genetics
Felix Lange, Niels Pfennigwerth, Rainer Hartl, Heidrun Kerschner, Dagmar Achleitner, Sören G Gatermann, Martin Kaase
Objectives: To identify and characterize a novel MBL gene conferring carbapenem resistance to an isolate of Enterobacter cloacae from Austria. Methods: The novel MBL gene was heterologously expressed in Escherichia coli TOP10 to conduct comparative MIC studies and biochemical assays. Furthermore, WGS was performed using Illumina MiSeq and Oxford Nanopore MinION instruments to analyse the genetic environment of the novel MBL gene. Results: The novel MBL showed highest sequence homology to a predicted MBL precursor from the marine bacterium Rheinheimera pacifica and hence belongs to Ambler subgroup B3...
June 11, 2018: Journal of Antimicrobial Chemotherapy
Jason R Schwartz, Michael P Walsh, Jing Ma, Tamara Lamprecht, Shuoguo Wang, Gang Wu, Susana Raimondi, Brandon Triplett, Jeffery Klco
Donor-derived hematologic malignancies are rare complications of hematopoietic cell transplantation (HCT). Although these are commonly either a myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML), in general, they are a heterogeneous group of diseases and a unified mechanism for their development has remained elusive. Here we report next generation sequencing, including whole exome sequencing (WES), whole genome sequencing (WGS), and targeted sequencing, of a case of donor-derived MDS (dMDS) following HCT for high-risk B-lymphoblastic leukemia (B-ALL) in an adolescent...
June 11, 2018: Cold Spring Harbor Molecular Case Studies
Kathryn Bernard, Tamara Burdz, Deborah Wiebe, Michelle Alfa, Anne-Marie Bernier
A description of an outbreak of necrotizing enterocolitis among neonates, linked to the putative novel species Clostridium neonatale and assignable to the genus Clostridium, was previously reported in brief but that name had never been validly published (Alfa et al. Clin Inf Dis 2002;35:S101-S105). Features of this taxon group and its phylogenetic position with respect to contemporary species in the genus Clostridium were recently reviewed and still found to be unique. Therefore, we provide here a description based on biochemical, chemotaxonomic and antimicrobial susceptibility testing (AST), matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, 16S rRNA gene sequencing as well as information obtained by whole genome sequencing (WGS) for strains 99A005T and 99A006...
June 11, 2018: International Journal of Systematic and Evolutionary Microbiology
Magdalena Nüesch-Inderbinen, Nicole Cernela, Daniel Wüthrich, Adrian Egli, Roger Stephan
Shiga toxin-producing E. coli (STEC) O80:H2 is an uncommon hybrid pathotype that has recently emerged in France. We analysed 18 STEC O80:H2 isolated from humans in Switzerland during 2010-2017. All isolates carried stx2a or stx2d, the rare eae variant eae-ξ and at least seven virulence genes associated with pS88, a plasmid that is found in extraintestinal pathogenic E. coli (ExPEC). Whole genome sequencing (WGS) identified additional chromosomal extraintestinal virulence genes encoding for type 1 fimbria (fimA, fimC and fimH), aerobactin (iuc/iutA) and afimbrial adhesins (afaA/C/D/E-VIII)...
June 1, 2018: International Journal of Medical Microbiology: IJMM
Maren Mylius, Johannes Dreesman, Matthias Pulz, Gerhard Pallasch, Konrad Beyrer, Katja Claußen, Franz Allerberger, Angelika Fruth, Christina Lang, Rita Prager, Antje Flieger, Sabine Schlager, Daniela Kalhöfer, Elke Mertens
Following a school ski-trip to Austria from 10 to 18/02/2017, nine of 25 participants of the group from Lower Saxony (Germany) developed gastroenteritis. The students and teachers (17-41 years) shared meals in a hotel. Active case finding revealed further cases among German school groups from North Rhine-Westphalia and Schleswig-Holstein, staying at the same hotel in February 2017. We conducted two retrospective cohort studies using self-administered questionnaires on clinical symptoms and food consumption...
May 29, 2018: International Journal of Medical Microbiology: IJMM
Sara Lomonaco, Matthew A Crawford, Christine Lascols, Ruth E Timme, Kevin Anderson, David R Hodge, Debra J Fisher, Segaran P Pillai, Stephen A Morse, Erum Khan, Molly A Hughes, Marc W Allard, Shashi K Sharma
The emergence and dissemination of carbapenemases, bacterial enzymes able to inactivate most β-lactam antibiotics, in Enterobacteriaceae is of increasing concern. The concurrent spread of resistance against colistin, an antibiotic of last resort, further compounds this challenge further. Whole-genome sequencing (WGS) can play a significant role in the rapid and accurate detection/characterization of existing and emergent resistance determinants, an essential aspect of public health surveillance and response activities to combat the spread of antimicrobial resistant bacteria...
2018: PloS One
Luca Persani, Tiziana de Filippis, Carla Colombo, Davide Gentilini
The technological advancements in genetics produced a profound impact on the research and diagnostics of non-communicable diseases. The availability of Next Generation Sequencing (NGS) allowed the identification of novel candidate genes but also an in depth modification of the understanding of the architecture of several endocrine diseases. Several different NGS approaches are available allowing the sequencing of several regions of interest or the whole exome or genome (WGS, WES, or targeted NGS), with highly variable costs, potentials and limitations that should be clearly known before designing the experiment...
June 7, 2018: European Journal of Endocrinology
Laila Parvaresh, Taryn Crighton, Elena Martinez, Andrea Bustamante, Sharon Chen, Vitali Sintchenko
BACKGROUND: The recurrence of tuberculosis (TB) disease in treated patients can serve as a marker of the efficacy of TB control programs. Recurrent disease represents either endogenous reactivation with the same strain of Mycobacterium tuberculosis due to non-compliance or inadequate therapy or exogenous reinfection with a new strain. Genotyping or whole genome sequencing (WGS) of M. tuberculosis isolates from initial and recurrent cases can differentiate between reinfection and reactivation...
June 7, 2018: BMC Infectious Diseases
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