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https://www.readbyqxmd.com/read/29924450/challenges-in-the-identification-of-methicillin-resistant-staphylococcus-argenteus-by-routine-diagnostics
#1
Hege Smith Tunsjø, Sumana Kalyanasundaram, Colin Charnock, Truls Michael Leegaard, Aina E F Moen
Current clinical diagnostic procedures have shortcomings in the differentiation of Staphylococcus argenteus from Staphylococcus aureus. This article presents three cases of Staphylococcus argenteus obtained from clinical samples. The initial results from biochemical and molecular methods led to an incorrect identification of the isolates as methicillin-resistant Staphylococcus aureus. Whole genome sequencing and real-time PCR targeting the nonribosomal peptide synthetase gene led to their correct identification as methicillin-resistant Staphylococcus argenteus...
June 2018: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://www.readbyqxmd.com/read/29924328/homeobox-gene-duplication-and-divergence-in-arachnids
#2
Daniel J Leite, Luís Baudouin-Gonzalez, Sawa Iwasaki-Yokozawa, Jesus Lozano-Fernandez, Natascha Turetzek, Yasuko Akiyama-Oda, Nikola-Michael Prpic, Davide Pisani, Hiroki Oda, Prashant P Sharma, Alistair P McGregor
Homeobox genes are key toolkit genes that regulate the development of metazoans and changes in their regulation and copy number have contributed to the evolution of phenotypic diversity. We recently identified a whole genome duplication (WGD) event that occurred in an ancestor of spiders and scorpions (Arachnopulmonata), and that many homeobox genes, including two Hox clusters, appear to have been retained in arachnopulmonates. To better understand the consequences of this ancient WGD and the evolution of arachnid homeobox genes, we have characterised and compared the homeobox repertoires in a range of arachnids...
June 19, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29923825/classification-of-genera-of-pasteurellaceae-using-conserved-predicted-protein-sequences
#3
Henrik Christensen, Magne Bisgaard
The aim of the investigation was to investigate the phylogeny of the 49 type strains of species of Pasteurellaceae and three genomospecies, which are available with whole genomic sequences. The genomes were downloaded from National Center for Biotechnological Information and for three species of Avibacterium sequenced in the present investigation. From the predicted protein sequences of proteins, which were conserved in all genomes, 31 proteins were randomly selected for the study. The protein sequences were concatenated for each taxon, and a multiple alignment reconstructed for the 52 taxa...
June 20, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29923248/kleine-levin-syndrome-is-associated-with-lmod3-variants
#4
Saad M Al Shareef, Sulman Basit, Sha Li, Corinne Pfister, Sylvain Pradervand, Michel Lecendreux, Geert Mayer, Yves Dauvilliers, Vincenzo Salpietro, Henry Houlden, Ahmed S BaHammam, Mehdi Tafti
Kleine-Levin syndrome (KLS) is a rare periodic hypersomnia with associated behavioural abnormalities but with often favourable prognosis. There is excess risk of KLS in first-degree relatives, suggesting a strong genetic contribution. So far, no mutation is identified in KLS and comprehensive genetic analysis of affected individuals is lacking. Here we performed whole genome single-nucleotide polymorphism (SNP) genotyping and exome sequencing in a large family with seven affected members. The identified gene with a mutation was resequenced in 38 sporadic KLS patients and the expression of the gene product was mapped in the mouse brain...
June 19, 2018: Journal of Sleep Research
https://www.readbyqxmd.com/read/29922519/mlstar-automatic-multilocus-sequence-typing-of-bacterial-genomes-in-r
#5
Ignacio Ferrés, Gregorio Iraola
Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci which allows us to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has allowed us to apply and extend MLST schemes by automatic extraction of allele information from the genomes...
2018: PeerJ
https://www.readbyqxmd.com/read/29922308/cloning-and-characterization-of-a-flavonol-synthase-gene-from-litchi-chinensis-and-its-variation-among-litchi-cultivars-with-different-fruit-maturation-periods
#6
Wei Liu, Zhidan Xiao, Chao Fan, Nonghui Jiang, Xiangchun Meng, Xu Xiang
Litchi ( Litchi chinensis ) is an important subtropical fruit tree with high commercial value. However, the short and centralized fruit maturation period of litchi cultivars represents a bottleneck for litchi production. Therefore, the development of novel cultivars with extremely early fruit maturation period is critical. Previously, we showed that the genotypes of extremely early-maturing (EEM), early-maturing (EM), and middle-to-late-maturing (MLM) cultivars at a specific locus SNP51 (substitution type C/T) were consistent with their respective genetic background at the whole-genome level; a homozygous C/C genotype at SNP51 systematically differentiated EEM cultivars from others...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29922263/comparative-genomic-analysis-of-re-emergent-human-adenovirus-type-55-pathogens-associated-with-adult-severe-community-acquired-pneumonia-reveals-conserved-genomes-and-capsid-proteins
#7
Zetao Cheng, Yuqian Yan, Shuping Jing, Wen-Gang Li, Wei-Wei Chen, Jing Zhang, Min Li, Shan Zhao, Na Cao, Junxian Ou, Suhui Zhao, Xianbo Wu, Bin Cao, Qiwei Zhang
Human adenovirus type 55 (HAdV-B55) is a recently identified acute respiratory disease (ARD) pathogen in HAdV species B with a recombinant genome between renal HAdV-B11 and respiratory HAdV-B14. Since HAdV-B55 first appeared in China school in 2006, no more ARD cases associated with it had been reported until 2011, when there was an outbreak of adult severe community-acquired pneumonia (CAP) in Beijing, China. Reported here is the bioinformatics analysis of the re-emergent HAdV-B55 responsible for this outbreak...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29921692/recurrent-rarb-translocations-in-acute-promyelocytic-leukemia-lacking-rara-translocation
#8
Tomoo Osumi, Shin-Ichi Tsujimoto, Moe Tamura, Meri Uchiyama, Kazuhiko Nakabayashi, Kohji Okamura, Masanori Yoshida, Daisuke Tomizawa, Akihiro Watanabe, Hiroyuki Takahashi, Tsukasa Hori, Shohei Yamamoto, Kazuko Hamamoto, Masahiro Migita, Hiroko Ogata-Kawata, Toru Uchiyama, Hiroe Kizawa, Hitomi Ueno-Yokohata, Ryota Shirai, Masafumi Seki, Kentaro Ohki, Junko Takita, Takeshi Inukai, Seishi Ogawa, Toshio Kitamura, Kimikazu Matsumoto, Kenichiro Hata, Nobutaka KIyokawa, Susumu Goyama, Motohiro Kato
Translocations of retinoic acid receptor-α (RARA), typically PML-RARA, are a genetic hallmark of acute promyelocytic leukemia (APL). However, because a small fraction of APL lack translocations of RARA, we focused here on APL cases without RARA translocation to elucidate the molecular etiology of RARA-negative APL. We performed whole-genome sequencing, PCR, and FISH for five APL cases without RARA translocations. Four of five RARA-negative APL cases had translocations involving retinoic acid receptor-β (RARB) translocations, and TBL1XR1-RARB was identified as an in-frame fusion in three cases; one case had an RARB rearrangement detected by FISH, although the partner gene could not be identified...
June 19, 2018: Cancer Research
https://www.readbyqxmd.com/read/29921229/carriers-of-mitochondrial-dna-macrohaplogroup-l3-basal-lineages-migrated-back-to-africa-from-asia-around-70-000-years-ago
#9
Vicente M Cabrera, Patricia Marrero, Khaled K Abu-Amero, Jose M Larruga
BACKGROUND: The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya...
June 19, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29920818/positive-selection-on-sociobiological-traits-in-invasive-fire-ants
#10
Eyal Privman, Pnina Cohen, Amir B Cohanim, Oksana Riba-Grognuz, DeWayne Shoemaker, Laurent Keller
The fire ant Solenopsis invicta and its close relatives are highly invasive. Enhanced social cooperation may facilitate invasiveness in these and other invasive ant species. We investigated whether invasiveness in Solenopsis fire ants was accompanied by positive selection on sociobiological traits by applying a phylogenomics approach to infer ancient selection, and a population genomics approach to infer recent and ongoing selection in both native and introduced S. invicta populations. A combination of whole-genome sequencing of 40 haploid males and reduced-representation genomic sequencing of 112 diploid workers identified 1,758,116 and 169,682 polymorphic markers, respectively...
June 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29920304/optimization-of-subculture-and-dna-extraction-steps-within-the-whole-genome-sequencing-workflow-for-source-tracking-of-salmonella-enterica-and-listeria-monocytogenes
#11
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
https://www.readbyqxmd.com/read/29917114/use-of-whole-genome-sequencing-of-adenovirus-in-immunocompromised-paediatric-patients-to-identify-nosocomial-transmission-and-mixed-genotype-infection
#12
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
https://www.readbyqxmd.com/read/29916803/genome-analysis-of-methicillin-resistance-in-macrococcus-caseolyticus-from-dairy-cattle-in-england-and-wales
#13
Alison C MacFadyen, Elizabeth A Fisher, Ben Costa, Cassie Cullen, Gavin K Paterson
Species of the genus Macrococcus are widespread commensals of animals but are becoming increasingly recognised as veterinary pathogens. They can encode methicillin resistance and are implicated in its spread to the closely-related, but more pathogenic, staphylococci. In this study we have identified 33 isolates of methicillin-resistant Macrococcus caseolyticus from bovine bulk tank milk from England and Wales. These isolates were characterised to provide insight into the molecular epidemiology of M. caseolyticus and to discern the genetic basis for their methicillin resistance...
June 19, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29916797/clermontyping-an-easy-to-use-and-accurate-in-silico-method-for-escherichia-genus-strain-phylotyping
#14
Johann Beghain, Antoine Bridier-Nahmias, Hervé Le Nagard, Erick Denamur, Olivier Clermont
The genus Escherichia is composed of Escherichia albertii, E. fergusonii, five cryptic Escherichia clades and E. coli sensu stricto. Furthermore, the E. coli species can be divided into seven main phylogroups termed A, B1, B2, C, D, E and F. As specific lifestyles and/or hosts can be attributed to these species/phylogroups, their identification is meaningful for epidemiological studies. Classical phenotypic tests fail to identify non-sensu stricto E. coli as well as phylogroups. Clermont and colleagues have developed PCR assays that allow the identification of most of these species/phylogroups, the triplex/quadruplex PCR for E...
June 19, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29915331/oak-genome-reveals-facets-of-long-lifespan
#15
Christophe Plomion, Jean-Marc Aury, Joëlle Amselem, Thibault Leroy, Florent Murat, Sébastien Duplessis, Sébastien Faye, Nicolas Francillonne, Karine Labadie, Grégoire Le Provost, Isabelle Lesur, Jérôme Bartholomé, Patricia Faivre-Rampant, Annegret Kohler, Jean-Charles Leplé, Nathalie Chantret, Jun Chen, Anne Diévart, Tina Alaeitabar, Valérie Barbe, Caroline Belser, Hélène Bergès, Catherine Bodénès, Marie-Béatrice Bogeat-Triboulot, Marie-Lara Bouffaud, Benjamin Brachi, Emilie Chancerel, David Cohen, Arnaud Couloux, Corinne Da Silva, Carole Dossat, François Ehrenmann, Christine Gaspin, Jacqueline Grima-Pettenati, Erwan Guichoux, Arnaud Hecker, Sylvie Herrmann, Philippe Hugueney, Irène Hummel, Christophe Klopp, Céline Lalanne, Martin Lascoux, Eric Lasserre, Arnaud Lemainque, Marie-Laure Desprez-Loustau, Isabelle Luyten, Mohammed-Amin Madoui, Sophie Mangenot, Clémence Marchal, Florian Maumus, Jonathan Mercier, Célia Michotey, Olivier Panaud, Nathalie Picault, Nicolas Rouhier, Olivier Rué, Camille Rustenholz, Franck Salin, Marçal Soler, Mika Tarkka, Amandine Velt, Amy E Zanne, Francis Martin, Patrick Wincker, Hadi Quesneville, Antoine Kremer, Jérôme Salse
Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes 1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times 2 . With 450 species spread throughout Asia, Europe and America 3 , oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans...
June 18, 2018: Nature Plants
https://www.readbyqxmd.com/read/29915208/ruminant-and-chicken-important-sources-of-campylobacteriosis-in-france-despite-a-variation-of-source-attribution-in-2009-and-2015
#16
Amandine Thépault, Valérie Rose, Ségolène Quesne, Typhaine Poezevara, Véronique Béven, Edouard Hirchaud, Fabrice Touzain, Pierrick Lucas, Guillaume Méric, Leonardos Mageiros, Samuel K Sheppard, Marianne Chemaly, Katell Rivoal
Pathogen source attribution studies are a useful tool for identifying reservoirs of human infection. Based on Multilocus Sequence Typing (MLST) data, such studies have identified chicken as a major source of C. jejuni human infection. The use of whole genome sequence-based typing methods offers potential to improve the precision of attribution beyond that which is possible from 7 MLST loci. Using published data and 156 novel C. jejuni genomes sequenced in this study, we performed probabilistic host source attribution of clinical C...
June 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29914851/integrative-methylome-and-transcriptome-analysis-to-dissect-key-biological-pathways-for-psoriasis-in-chinese-han-population
#17
Lili Tang, Yuyan Cheng, Caihong Zhu, Chao Yang, Lu Liu, Yuanjing Zhang, Leilei Wen, Xuejun Zhang, Fusheng Zhou, Sen Yang
BACKGROUND: Recent studies have revealed that DNA methylation (DNAm) could modulate gene expression in psoriasis (Ps). However, the relationship between whole-genome DNAm and gene expression in Ps has not been studied yet. OBJECTIVES: To better characterize the relationship between DNAm and gene expression, and to identify biological pathways triggered by changes in methylation involved in the pathogenesis of Ps. METHODS: Differentially methylated sites (DMSs) and differentially expressed genes (DEGs) were analysed by comparing 20 involved psoriatic (PP) skin, 20 uninvolved psoriatic (PN) skin and 20 normal (NN) skin biopsies...
June 9, 2018: Journal of Dermatological Science
https://www.readbyqxmd.com/read/29914659/microbial-source-tracking-of-cronobacter-spp
#18
Steve Forsythe
Being able to track bacterial pathogens is essential for epidemiological purposes as well as monitoring in-house production facilities. Common bacterial pathogens, such as Salmonella serovars, are already been well defined, and their detection methods are very advanced. However, this will not be the case for emergent bacterial pathogens, as was the case for Cronobacter. The clinical significance of the organism is due to its association with rare sporadic infections in adults, and severe life-threatening outbreaks of necrotizing enterocolitis and meningitis in newborn babies...
2018: Advances in Applied Microbiology
https://www.readbyqxmd.com/read/29914504/evolutionary-analysis-of-rabies-virus-isolates-from-guangxi-province-of-southern-china
#19
Xian-Kai Wei, Xiao-Xia He, Yan Pan, Cheng Liu, Hai-Bo Tang, Yi-Zhi Zhong, Xiao-Ning Li, Jing-Jing Liang, Ting Rong Luo
BACKGROUND: Rabies is a severe epidemic in Guangxi province, China, with hundreds of deaths occurring each year. In the past six decades, rabies has emerged three times in Guangxi, and the province has reported the largest number of rabies cases in China. The domestic dog is the principal vector for rabies, and 95% of human cases are associated with transmission from dogs. RESULTS: To understand the genetic relationship between street rabies virus (RABV) from Guangxi, genetic diversity analysis was performed using RABV isolates collected between 1999 and 2012...
June 18, 2018: BMC Veterinary Research
https://www.readbyqxmd.com/read/29914373/characterization-of-the-populus-rab-family-genes-and-the-function-of-ptrabe1b-in-salt-tolerance
#20
Jin Zhang, Yu Li, Bobin Liu, Lijuan Wang, Li Zhang, Jianjun Hu, Jun Chen, Huanquan Zheng, Mengzhu Lu
BACKGROUND: Rab proteins form the largest family of the Ras superfamily of small GTP-binding proteins and regulate intracellular trafficking pathways. However, the function of the Rab proteins in woody species is still an open question. RESULTS: Here, a total of 67 PtRabs were identified in Populus trichocarpa and categorized into eight subfamilies (RabA-RabH). Based on their chromosomal distribution and duplication blocks in the Populus genome, a total of 27 PtRab paralogous pairs were identified and all of them were generated by whole-genome duplication events...
June 18, 2018: BMC Plant Biology
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