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https://www.readbyqxmd.com/read/28103259/characterization-and-genetic-variation-of-vibrio-cholerae-isolated-from-clinical-and-environmental-sources-in-thailand
#1
Achiraya Siriphap, Pimlapas Leekitcharoenphon, Rolf S Kaas, Chonchanok Theethakaew, Frank M Aarestrup, Orasa Sutheinkul, Rene S Hendriksen
Cholera is still an important public health problem in several countries, including Thailand. In this study, a collection of clinical and environmental V. cholerae serogroup O1, O139, and non-O1/non-O139 strains originating from Thailand (1983 to 2013) was characterized to determine phenotypic and genotypic traits and to investigate the genetic relatedness. Using a combination of conventional methods and whole genome sequencing (WGS), 78 V. cholerae strains were identified. WGS was used to determine the serogroup, biotype, virulence, mobile genetic elements, and antimicrobial resistance genes using online bioinformatics tools...
2017: PloS One
https://www.readbyqxmd.com/read/28100602/find-tuberculosis-strain-bank-a-resource-for-researchers-and-developers-working-on-tests-to-detect-mycobacterium-tuberculosis-and-related-drug-resistance
#2
Belay Tessema, Pamela Nabeta, Eloise Valli, Audrey Albertini, Jimena Collantes, Nguyen Huu Lan, Elena Romancenco, Nestani Tukavdze, Claudia M Denkinger, David L Dolinger
BACKGROUND: The spread of multidrug-resistant tuberculosis and extensively drug-resistant TB hampers the global efforts in the fight against tuberculosis. To enhance the development and evaluation of diagnostic tests quickly and efficiently, well characterized strains and samples from drug resistant tuberculosis patients are necessary. In this project, FIND has focused on the collection, characterization and storage of such well-characterized reference materials and to make them available to researchers and developers...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100307/the-kl24-gene-cluster-and-a-genomic-island-encoding-a-wzy-polymerase-contribute-genes-needed-for-synthesis-of-the-k24-capsular-polysaccharide-by-the-multiply-antibiotic-resistant-acinetobacter-baumannii-isolate-rch51
#3
Johanna J Kenyon, Anastasiya A Kasimova, Mikhail Shneider, Alexander S Shashkov, Nikolay P Arbatsky, Anastasiya V Popova, Konstantin A Miroshnikov, Ruth M Hall, Yuriy A Knirel
The whole genome sequence of the multiply antibiotic resistant Acinetobacter baumannii isolate RCH51 belonging to sequence type ST103 (Institut Pasteur scheme) revealed that the set of genes at the capsule locus, KL24, includes four genes predicted to direct the synthesis of 3-acetamido-3,6-dideoxy-D-galactose (D-Fuc3NAc) and this sugar was found in the capsular polysaccharide (CPS). One of these genes, fdtE, encodes a novel bifunctional protein with an N-terminal FdtA 3,4-ketoisomerase domain and a C-terminal acetyltransferase domain...
January 17, 2017: Microbiology
https://www.readbyqxmd.com/read/28099825/transmission-of-extensively-drug-resistant-tuberculosis-in-south-africa
#4
N Sarita Shah, Sara C Auld, James C M Brust, Barun Mathema, Nazir Ismail, Pravi Moodley, Koleka Mlisana, Salim Allana, Angela Campbell, Thuli Mthiyane, Natashia Morris, Primrose Mpangase, Hermina van der Meulen, Shaheed V Omar, Tyler S Brown, Apurva Narechania, Elena Shaskina, Thandi Kapwata, Barry Kreiswirth, Neel R Gandhi
Background Drug-resistant tuberculosis threatens recent gains in the treatment of tuberculosis and human immunodeficiency virus (HIV) infection worldwide. A widespread epidemic of extensively drug-resistant (XDR) tuberculosis is occurring in South Africa, where cases have increased substantially since 2002. The factors driving this rapid increase have not been fully elucidated, but such knowledge is needed to guide public health interventions. Methods We conducted a prospective study involving 404 participants in KwaZulu-Natal Province, South Africa, with a diagnosis of XDR tuberculosis between 2011 and 2014...
19, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28098550/determination-of-elizabethkingia-diversity-by-maldi-tof-mass-spectrometry-and-whole-genome-sequencing
#5
Helle Brander Eriksen, Heidi Gumpert, Cecilie Haase Faurholt, Henrik Westh
In a hospital-acquired infection with multidrug-resistant Elizabethkingia, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene analysis identified the pathogen as Elizabethkingia miricola. Whole-genome sequencing, genus-level core genome analysis, and in silico DNA-DNA hybridization of 35 Elizabethkingia strains indicated that the species taxonomy should be further explored.
February 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28096484/evolutionary-dynamics-of-pandemic-methicillin-sensitive-staphylococcus-aureus-st398-and-its-international-spread-via-routes-of-human-migration
#6
Anne-Catrin Uhlemann, Paul R McAdam, Sean B Sullivan, Justin R Knox, Hossein Khiabanian, Raul Rabadan, Peter R Davies, J Ross Fitzgerald, Franklin D Lowy
: Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for the majority of S. aureus infections globally, and yet surprisingly little is known about its clonal evolution. We applied comparative whole-genome sequencing (WGS) analyses to epidemiologically and geographically diverse ST398-MSSA, a pandemic lineage affecting both humans and livestock. Bayesian phylogenetic analysis predicted divergence of human-associated ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and veterinarians differed substantially from those in New York City (NYC)...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28095770/the-unique-genomic-landscape-surrounding-the-epsps-gene-in-glyphosate-resistant-amaranthus-palmeri-a-repetitive-path-to-resistance
#7
William T Molin, Alice A Wright, Amy Lawton-Rauh, Christopher A Saski
BACKGROUND: The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment...
January 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28093659/clinical-and-molecular-relevance-of-mutant-allele-tumor-heterogeneity-in-breast-cancer
#8
Ding Ma, Yi-Zhou Jiang, Xi-Yu Liu, Yi-Rong Liu, Zhi-Ming Shao
PURPOSE: Intra-tumor heterogeneity (ITH) plays a pivotal role in driving breast cancer progression and therapeutic resistance. We used a mutant-allele tumor heterogeneity (MATH) algorithm to measure ITH and explored its correlation with clinical parameters and multi-omics data. METHODS: We assessed 916 female breast cancer patients from The Cancer Genome Atlas. We calculated the MATH values from whole-exome sequencing data and further investigated their correlation with clinical characteristics, somatic mutations, somatic copy number alterations (SCNAs), and gene enrichment...
January 16, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28092681/genomic-analysis-of-globally-diverse-mycobacterium-tuberculosis-strains-provides-insights-into-the-emergence-and-spread-of-multidrug-resistance
#9
Abigail L Manson, Keira A Cohen, Thomas Abeel, Christopher A Desjardins, Derek T Armstrong, Clifton E Barry, Jeannette Brand, Sinéad B Chapman, Sang-Nae Cho, Andrei Gabrielian, James Gomez, Andreea M Jodals, Moses Joloba, Pontus Jureen, Jong Seok Lee, Lesibana Malinga, Mamoudou Maiga, Dale Nordenberg, Ecaterina Noroc, Elena Romancenco, Alex Salazar, Willy Ssengooba, A A Velayati, Kathryn Winglee, Aksana Zalutskaya, Laura E Via, Gail H Cassell, Susan E Dorman, Jerrold Ellner, Parissa Farnia, James E Galagan, Alex Rosenthal, Valeriu Crudu, Daniela Homorodean, Po-Ren Hsueh, Sujatha Narayanan, Alexander S Pym, Alena Skrahina, Soumya Swaminathan, Martie Van der Walt, David Alland, William R Bishai, Ted Cohen, Sven Hoffner, Bruce W Birren, Ashlee M Earl
Multidrug-resistant tuberculosis (MDR-TB), caused by drug-resistant strains of Mycobacterium tuberculosis, is an increasingly serious problem worldwide. Here we examined a data set of whole-genome sequences from 5,310 M. tuberculosis isolates from five continents. Despite the great diversity of these isolates with respect to geographical point of isolation, genetic background and drug resistance, the patterns for the emergence of drug resistance were conserved globally. We have identified harbinger mutations that often precede multidrug resistance...
January 16, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28087944/laboratory-diagnosis-and-susceptibility-testing-for-mycobacterium-tuberculosis
#10
Gary W Procop
The laboratory, which utilizes some of the most sophisticated and rapidly changing technologies, plays a critical role in the diagnosis of tuberculosis. Some of these tools are being employed in resource-challenged countries for the rapid detection and characterization of Mycobacterium tuberculosis. Foremost, the laboratory defines appropriate specimen criteria for optimal test performance. The direct detection of mycobacteria in the clinical specimen, predominantly done by acid-fast staining, may eventually be replaced by rapid-cycle PCR...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28087649/identification-of-unique-essential-proteins-from-a-m-tuberculosis-f15-lam4-kzn-phage-secretome-library
#11
Thamsanqa Emmanuel Chiliza, Manormoney Pillay, Balakrishna Pillay
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis disease (TB), the leading cause of death from bacterial infection worldwide. Although treatable, the resurgence of multi- and extensively-drug resistance TB is a major setback for the fight against TB globally. Consequently, there is an urgent need for new Mtb derived biomarkers for use in the design of new drugs and rapid point-of-care diagnostic or prognostic tools for management of TB transmission. Therefore, the present study aimed to identify unique Mtb secreted proteins from the extensively drug resistant Mtb F15/LAM4/KZN phage secretome library...
January 12, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28081260/comparative-genome-sequencing-reveals-within-host-genetic-changes-in-neisseria-meningitidis-during-invasive-disease
#12
Johanna Klughammer, Marcus Dittrich, Jochen Blom, Vera Mitesser, Ulrich Vogel, Matthias Frosch, Alexander Goesmann, Tobias Müller, Christoph Schoen
Some members of the physiological human microbiome occasionally cause life-threatening disease even in immunocompetent individuals. A prime example of such a commensal pathogen is Neisseria meningitidis, which normally resides in the human nasopharynx but is also a leading cause of sepsis and epidemic meningitis. Using N. meningitidis as model organism, we tested the hypothesis that virulence of commensal pathogens is a consequence of within host evolution and selection of invasive variants due to mutations at contingency genes, a mechanism called phase variation...
2017: PloS One
https://www.readbyqxmd.com/read/28081123/yersinia-enterocolitica-a-neglected-cause-of-human-enteric-infections-in-c%C3%A3-te-d-ivoire
#13
Daniel Saraka, Cyril Savin, Stephane Kouassi, Bakary Cissé, Eugène Koffi, Nicolas Cabanel, Sylvie Brémont, Hortense Faye-Kette, Mireille Dosso, Elisabeth Carniel
BACKGROUND: Enteropathogenic Yersinia circulate in the pig reservoir and are the third bacterial cause of human gastrointestinal infections in Europe. In West Africa, reports of human yersiniosis are rare. This study was conducted to determine whether pathogenic Yersinia are circulating in pig farms and are responsible for human infections in the Abidjan District. METHODOLOGY/PRINCIPAL FINDINGS: From June 2012 to December 2013, pig feces were collected monthly in 41 swine farms of the Abidjan district...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28074120/complete-genome-sequence-of-the-heavy-metal-resistant-bacterium-agromyces-aureus-ar33-t-and-comparison-with-related-actinobacteria
#14
Erika Corretto, Livio Antonielli, Angela Sessitsch, Stéphane Compant, Christoph Höfer, Markus Puschenreiter, Günter Brader
Agromyces aureus AR33(T) is a Gram-positive, rod-shaped and motile bacterium belonging to the Microbacteriaceae family in the phylum Actinobacteria that was isolated from a former zinc/lead mining and processing site in Austria. In this study, the whole genome was sequenced and assembled combining sequences obtained from Illumina MiSeq and Sanger sequencing. The assembly resulted in the complete genome sequence which is 4,373,124 bp long and has a GC content of 70.1%. Furthermore, we performed a comparative genomic analysis with other related organisms: 6 Agromyces spp...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28074024/whole-genome-sequencing-of-invasion-resistant-cells-identifies-laminin-%C3%AE-2-as-a-host-factor-for-bacterial-invasion
#15
Xander M van Wijk, Simon Döhrmann, Björn M Hallström, Shangzhong Li, Bjørn G Voldborg, Brandon X Meng, Karen K McKee, Toin H van Kuppevelt, Peter D Yurchenco, Bernhard O Palsson, Nathan E Lewis, Victor Nizet, Jeffrey D Esko
: To understand the role of glycosaminoglycans in bacterial cellular invasion, xylosyltransferase-deficient mutants of Chinese hamster ovary (CHO) cells were created using clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated gene 9 (CRISPR-cas9) gene targeting. When these mutants were compared to the pgsA745 cell line, a CHO xylosyltransferase mutant generated previously using chemical mutagenesis, an unexpected result was obtained. Bacterial invasion of pgsA745 cells by group B Streptococcus (GBS), group A Streptococcus, and Staphylococcus aureus was markedly reduced compared to the invasion of wild-type cells, but newly generated CRISPR-cas9 mutants were only resistant to GBS...
January 10, 2017: MBio
https://www.readbyqxmd.com/read/28073968/variants-of-abgri3-carrying-the-arma-gene-in-extensively-antibiotic-resistant-acinetobacter-baumannii-from-singapore
#16
Grace A Blackwell, Kathryn E Holt, Stephen D Bentley, Li Yang Hsu, Ruth M Hall
OBJECTIVES: To investigate the context of the ribosomal RNA methyltransferase gene armA in carbapenem-resistant global clone 2 (GC2) Acinetobacter baumannii isolates from Singapore. METHODS: Antibiotic resistance was determined using disc diffusion; PCR was used to identify resistance genes. Whole genome sequences were determined and contigs were assembled and ordered using PCR. Resistance regions in unsequenced isolates were mapped. RESULTS: Fifteen GC2 A...
January 10, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28072891/molecular-epidemiology-and-resistome-analysis-of-multidrug-resistant-st11-klebsiella-pneumoniae-strain-containing-multiple-copies-of-extended-spectrum-%C3%AE-lactamase-genes-using-whole-genome-sequencing
#17
Roshan DSouza, Naina Adren Pinto, Insik Hwang, Hwang Younjee, YoungLag Cho, Hyunsoo Kim, Dongeun Yong, Jongrak Choi, Kyungwon Lee, Yunsop Chong
The aim of this work was to investigate the mechanism responsible for multidrug resistance in ST11 Klebsiella pneumoniae YMC 2013/7/B3993 containing multiple copies of ESBL genes using multiple parallel sequencing technology. In-depth analysis of the strain revealed multiple copies of ESBL genes, 2 copies of blaSHV-12 and 1 copy of blaCTX-M-15. Furthermore, 1 copy of blaOXA-9 and 3 copies of blaTEM-1 were found. The insertion of Tn1331 was detected, which consisted of blaOXA-9, blaTEM-1, aac(6')-lb-cr, and aadA1 genes...
January 10, 2017: New Microbiologica
https://www.readbyqxmd.com/read/28069647/ribosomal-mutations-conferring-macrolide-resistance-in-legionella-pneumophila
#18
Ghislaine Descours, Christophe Ginevra, Nathalie Jacotin, Françoise Forey, Joëlle Chastang, Elisabeth Kay, Jerome Etienne, Gérard Lina, Patricia Doublet, Sophie Jarraud
OBJECTIVES: Monitoring the emergence of antibiotic resistance is a recent issue in the treatment of Legionnaires' disease. Macrolides are recommended as first-line therapy but resistance mechanisms have not been studied in Legionella species. Our aim was to determine the molecular basis of macrolide resistance in L. pneumophila METHODS: Twelve independent lineages were propagated under erythromycin or azithromycin pressure towards a high-level macrolide resistance from a common susceptible L...
January 9, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28067407/analysis-of-whole-exome-sequencing-with-cardiometabolic-traits-using-family-based-linkage-and-association-in-the-iras-family-study
#19
Keri L Tabb, Jacklyn N Hellwege, Nicholette D Palmer, Latchezar Dimitrov, Satria Sajuthi, Kent D Taylor, Maggie C Y Ng, Gregory A Hawkins, Yii-der Ida Chen, W Mark Brown, David McWilliams, Adrienne Williams, Carlos Lorenzo, Jill M Norris, Jirong Long, Jerome I Rotter, Joanne E Curran, John Blangero, Lynne E Wagenknecht, Carl D Langefeld, Donald W Bowden
Family-based methods are a potentially powerful tool to identify trait-defining genetic variants in extended families, particularly when used to complement conventional association analysis. We utilized two-point linkage analysis and single variant association analysis to evaluate whole exome sequencing (WES) data from 1205 Hispanic Americans (78 families) from the Insulin Resistance Atherosclerosis Family Study. WES identified 211,612 variants above the minor allele frequency threshold of ≥0.005. These variants were tested for linkage and/or association with 50 cardiometabolic traits after quality control checks...
January 9, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/28067073/translating-genomic-profiling-to-gastrointestinal-cancer-treatment
#20
Kazuto Harada, Dilsa Mizrak Kaya, Yusuke Shimodaira, Shumei Song, Hideo Baba, Jaffer A Ajani
Next-generation sequencing enables faster, cheaper and more accurate whole-genome sequencing, allowing genome profiling and discovery of molecular features. As molecular targeted drugs are developed, treatment can be tailored according to molecular subtype. Gastric and colorectal cancers have each been divided into four subtypes according to molecular features. Profiling of the esophageal cancer genome is underway and its classification is anticipated. To date, identification of HER2 expression in gastric adenocarcinoma and KRAS, NRAS and BRAF mutations in colon cancer have proved essential for treatment decisions...
9, 2017: Future Oncology
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