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Infection, Genetics and Evolution

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https://www.readbyqxmd.com/read/28214557/quadruple-first-line-drug-resistance-in-mycobacterium-tuberculosis-in-vietnam-what-can-we-learn-from-genes
#1
Huy Quang Nguyen, Nhung Viet Nguyen, Lucie Contamin, Thanh Hoa Thi Tran, Thuong Thi Vu, Hung Van Nguyen, Ngoc Lan Thi Nguyen, Son Thai Nguyen, Anh Duc Dang, Anne-Laure Bañuls, Van Anh Thi Nguyen
In Vietnam, a country with high tuberculosis (137/100.000 population) and multidrug-resistant (MDR)-TB burdens (7.8/100.000 population), little is known about the molecular signatures of drug resistance in general and more particularly of second line drug (SLD) resistance. This study is specifically focused on Mycobacterium tuberculosis isolates resistant to four first-line drugs (FLDs) that make TB much more difficult to treat. The aim is to determine the proportion of SLD resistance in these quadruple drug resistant isolates and the genetic determinants linked to drug resistance to better understand the genetic processes leading to quadruple and extremely drug resistance (XDR)...
February 15, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28192210/phylogenomics-of-trypanosoma-cruzi-few-evidence-of-tci-tcii-mosaicism-in-tciii-challenges-the-hypothesis-of-an-ancient-tci-tcii-hybridization
#2
Nicolás Tomasini, Patricio Diosque
Phylogenetic relationships among major lineages of Trypanosoma cruzi are still debatable. Particularly, it is controversial the origin of two main lineages: TcIII and TcIV. Some authors proposed that these lineages have been the result of an ancient hybridization between TcI and TcII, and this was one of the most accepted evolutionary models in the scientific community for several years. In the present paper we analyse several genomes of T. cruzi in order to examine if there is evidence supporting that TcIII is an ancient TcI/TcII hybrid...
February 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28189889/genome-wide-analysis-reveals-class-and-gene-specific-codon-usage-adaptation-in-avian-paramyxoviruses-1
#3
Tonya L Taylor, Kiril M Dimitrov, Claudio L Afonso
In order to characterize the evolutionary adaptations of avian paramyxovirus 1 (APMV-1) genomes, we have compared codon usage and codon adaptation indexes among groups of Newcastle disease viruses that differ in biological, ecological, and genetic characteristics. We have used available GenBank complete genome sequences, and compared codon usage of class I (CI-29 sequences containing 132,675 codons) and class II (CII-259 sequences containing 1,184,925 codons) APMV-1 genomes. We also compared available complete fusion protein gene sequences (CI-175 sequences containing 96,775 codons; CII-1166 sequences containing 644,798 codons)...
February 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28189888/genomic-sequencing-of-a-strain-of-acinetobacter-baumannii-and-potential-mechanisms-to-antibiotics-resistance
#4
Lei Zhao, Hongru Li, Ziwen Zhu, Mark R Wakefield, Yujiang Fang, Ying Ye
Acinetobacter baumannii has been becoming a great challenge to clinicians due to their resistance to almost all available antibiotics. In this study, we sequenced the genome from a multiple antibiotics resistant Acinetobacter baumannii stain which was named A. baumannii-1isolated from China by SMRT sequencing technology to explore its potential mechanisms to antibiotic resistance. We found that several mechanisms might contribute to the antibiotic resistance of Acinetobacter baumannii. Specifically, we found that SNP in genes associated with nucleotide excision repair and ABC transporter might contribute to its resistance to multiple antibiotics; we also found that specific genes associated with bacterial DNA integration and recombination, DNA-mediated transposition and response to antibiotics might contribute to its resistance to multiple antibiotics; Furthermore, specific genes associated with penicillin and cephalosporin biosynthetic pathway and specific genes associated with CHDL and MBL β-lactamase genes might contribute to its resistance to multiple antibiotics...
February 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28189887/whole-genome-analysis-of-porcine-astroviruses-detected-in-japanese-pigs-reveals-genetic-diversity-and-possible-intra-genotypic-recombination
#5
Mika Ito, Moegi Kuroda, Tsuneyuki Masuda, Masataka Akagami, Kei Haga, Shinobu Tsuchiaka, Mai Kishimoto, Yuki Naoi, Kaori Sano, Tsutomu Omatsu, Yukie Katayama, Mami Oba, Hiroshi Aoki, Toru Ichimaru, Itsuro Mukono, Yoshinao Ouchi, Hiroshi Yamasato, Junsuke Shirai, Kazuhiko Katayama, Tetsuya Mizutani, Makoto Nagai
Porcine astroviruses (PoAstVs) are ubiquitous enteric virus of pigs that are distributed in several countries throughout the world. Since PoAstVs are detected in apparent healthy pigs, the clinical significance of infection is unknown. However, AstVs have recently been associated with a severe neurological disorder in animals, including humans, and zoonotic potential has been suggested. To date, little is known about the epidemiology of PoAstVs among the pig population in Japan. In this report, we present an analysis of nearly complete genomes of 36 PoAstVs detected by a metagenomics approach in the feces of Japanese pigs...
February 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28189886/circulation-of-multiple-subtypes-of-bovine-viral-diarrhoea-virus-type-1-with-no-evidence-for-hobi-like-pestivirus-in-cattle-herds-of-southern-italy
#6
G Lanave, N Decaro, M S Lucente, A Guercio, N Cavaliere, G Purpari, I Padalino, V Larocca, F Antoci, P A Marino, C Buonavoglia, G Elia
Pestiviruses of cattle include bovine viral diarrhoea 1 (BVDV-1) and 2 (BVDV-2) plus an emerging group, named HoBi-like pestivirus. In the present paper, the results of an epidemiological survey for pestiviruses circulating in cattle in southern Italy are presented. Molecular assays carried out on a total of 924 bovine samples detected 74 BVDV strains, including 73 BVDV-1 and 1 BVDV-2 viruses. Phylogenetic analysis carried out on partial 5'UTR and N(pro) sequences revealed the presence of 6 different subtypes of BVDV-1 and a single BVDV-2c strain...
February 9, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28185986/a-novel-design-of-a-multi-antigenic-multistage-and-multi-epitope-vaccine-against-helicobacter-pylori-an-in-silico-approach
#7
Beatriz Meza, Felipe Ascencio, Arturo Pedro Sierra-Beltrán, Javier Torres, Carlos Angulo
Helicobacter pylori have colonized the gastric mucosa of half of the population worldwide. This bacterium is classified as a definitive type I carcinogen by the World Health Organization and no effective vaccine has been found against it yet. Thus, a logical and rational vaccine design against H. pylori is necessary. Because of its tremendous complexity and elicited immune responses, the vaccine design should considered multiple antigens to enhance immune-protection, involved in the different stages of pathogenesis besides inducing a specific immune response by B- and T-cell multi-epitopes...
February 7, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28185987/real-time-pcr-strategy-for-the-identification-of-trypanosoma-cruzi-discrete-typing-units-directly-in-chronically-infected-human-blood
#8
Catalina Muñoz-San Martín, Werner Apt, Inés Zulantay
The protozoan Trypanosoma cruzi is the causative agent of Chagas disease, a major public health problem in Latin America. This parasite has a complex population structure comprised by six or seven major evolutionary lineages (discrete typing units or DTUs) TcI-TcVI and TcBat, some of which have apparently resulted from ancient hybridization events. Because of the existence of significant biological differences between these lineages, strain characterization methods have been essential to study T. cruzi in its different vectors and hosts...
February 6, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28179143/how-s-the-flu-getting-through-landscape-genetics-suggests-both-humans-and-birds-spread-h5n1-in-egypt
#9
Sean G Young, Margaret Carrel, Andrew Kitchen, George P Malanson, James Tamerius, Mohamad Ali, Ghazi Kayali
First introduced to Egypt in 2006, H5N1 highly pathogenic avian influenza has resulted in the death of millions of birds and caused over 350 infections and at least 117 deaths in humans. After a decade of viral circulation, outbreaks continue to occur and diffusion mechanisms between poultry farms remain unclear. Using landscape genetics techniques, we identify the distance models most strongly correlated with the genetic relatedness of the viruses, suggesting the most likely methods of viral diffusion within Egyptian poultry...
February 4, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28179142/rna-seq-in-kinetoplastids-a-powerful-tool-for-the-understanding-of-the-biology-and-host-pathogen-interactions
#10
REVIEW
Luz Helena Patino, Juan David Ramírez
The kinetoplastids include a large number of parasites responsible for serious diseases in humans and animals (Leishmania and Trypanosoma brucei) considered endemic in several regions of the world. These parasites are characterized by digenetic life cycles that undergo morphological and genetic changes that allow them to adapt to different microenvironments on their vertebrates and invertebrates hosts. Recent advances in ´omics´ technology, specifically transcriptomics have allowed to reveal aspects associated with such molecular changes...
February 4, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28167145/the-miia-motif-is-a-common-marker-present-in-polytopic-surface-proteins-of-oral-and-urinary-tract-invasive-bacteria
#11
Antonio J Martín-Galiano
Many surface virulence factors of bacterial pathogens show mosaicism and confounding phylogenetic origin. The Streptococcus gordonii platelet-binding GspB protein, the Streptococcus sanguinis SrpA adhesin and the Streptococcus pneumoniae DiiA protein, share an imperfect 27-residue motif. Given the disparate domain architectures of these proteins and its association to invasive disease, this motif was named MiiA from Multiarchitecture invasion-involved motif A. MiiA is predicted to adopt a beta-sheet folding, probably related to the Ig-like fold, with a symmetrical positioning of two conserved aspartic residues...
February 4, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28163236/evolution-of-the-merozoite-surface-protein-7-msp7-family-in-plasmodium-vivax-and-p-falciparum-a-comparative-approach
#12
Andreína I Castillo, M Andreína Pacheco, Ananias A Escalante
Malaria parasites (genus Plasmodium) are a diverse group found in many species of vertebrate hosts. These parasites invade red blood cells in a complex process comprising several proteins, many encoded by multigene families, one of which is merozoite surface protein 7 (msp7). In the case of Plasmodium vivax, the most geographically widespread human-infecting species, differences in the number of paralogs within multigene families have been previously explained, at least in part, as potential adaptations to the human host...
February 2, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28161473/first-identification-and-phylogenetic-analysis-of-equine-hepacivirus-in-korea
#13
Ho-Seong Kim, Hyun-Woo Moon, Haan Woo Sung, Hyuk Moo Kwon
Non-primate hepacivirus (NPHV) corresponds a group of isolates recently characterized in horses and dogs that present similar genomic organization and are closely related to hepatitis C virus. Since canine hapacivirus, NPHV identified in dogs, was first discovered in dogs in the United States, equine hepacivirus (EqHV, NPHV identified in horses) has been identified in horses in several countries. However, no epidemiological studies have investigated EqHV in horses in Korea. In this study, a total of 74 (n=74) serum samples collected from horses in four regions of Korea were tested for EqHV RNA using nested RT-PCR...
February 1, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28137625/evolution-of-fseg-cseg-dimorphism-in-region-iii-of-the-plasmodium-falciparum-eba-175-gene
#14
Yoshiki Yasukochi, Izumi Naka, Jintana Patarapotikul, Hathairad Hananantachai, Jun Ohashi
The 175-kDa erythrocyte binding antigen (EBA-175) of the malaria parasite Plasmodium falciparum is important for its invasion into human erythrocytes. The primary structure of eba-175 is divided into seven regions, namely I to VII. Region III contains highly divergent dimorphic segments, termed Fseg and Cseg. The allele frequencies of segmental dimorphism within a P. falciparum population have been extensively examined; however, the molecular evolution of segmental dimorphism is not well understood. A comprehensive comparison of nucleotide sequences among 32 P...
January 27, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28132927/antigenic-and-genetic-characterization-of-influenza-viruses-circulating-in-bulgaria-during-the-2015-2016-season
#15
Neli Korsun, Svetla Angelova, Viki Gregory, Rodney Daniels, Irina Georgieva, John McCauley
Influenza virological surveillance is an essential tool for early detection of novel genetic variants of epidemiologic and clinical significance. The aim of this study was to determine the antigenic and molecular characteristics of influenza viruses circulating in Bulgaria during the 2015/2016 season. The season was characterized by dominant circulation of A(H1N1)pdm09 viruses, accounting for 66% of detected influenza viruses, followed by B/Victoria-lineage viruses (24%) and A(H3N2) viruses (10%). All sequenced influenza A(H1N1)pdm09, A(H3N2) and B/Victoria-lineage viruses belonged to the 6B...
January 27, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28132926/microrna-expression-profiling-of-primary-sheep-testicular-cells-in-response-to-bluetongue-virus-infection
#16
Junzheng Du, Shandian Gao, Zhancheng Tian, Shanshan Xing, Dexuan Huang, Guorui Zhang, Yadong Zheng, Guangyuan Liu, Jianxun Luo, Huiyun Chang, Hong Yin
Bluetongue virus (BTV) is a member of the genus Orbivirus within the family Reoviridae and causes a non-contagious, insect-transmitted disease in domestic and wild ruminants, mainly in sheep and occasionally in cattle and some species of deer. Virus infection can trigger the changes of the cellular microRNA (miRNA) expression profile, which play important post-transcriptional regulatory roles in gene expression and can greatly influence viral replication and pathogenesis. Here, we employed deep sequencing technology to determine which cellular miRNAs were differentially expressed in primary sheep testicular (ST) cells infected with BTV...
January 27, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28131866/genetic-characterization-and-molecular-survey-of-babesia-sp-xinjiang-infection-in-small-ruminants-and-ixodid-ticks-in-china
#17
Qingli Niu, Zhijie Liu, Jifei Yang, Shandian Gao, Yuping Pan, Guiquan Guan, Jianxun Luo, Hong Yin
Babesia sp. Xinjiang is a large ovine Babesia species that was recently isolated in China. Compared with other ovine Babesia species, it has different morphological features, pathogenicity and vector tick species. The known transmitting vector is Hyalomma anatolicum. In this study, the distribution and the presence of Babesia sp. Xinjiang in small ruminants and ixodid ticks in China were assessed by specific nested-PCR assay based on the rap-1a gene. A total of 978 blood samples from sheep or goats from 15 provinces and 797 tick specimens from vegetation from 10 provinces were collected and analysed for the presence of the Babesia sp...
January 25, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28130168/anaplasma-platys-like-strains-in-ruminants-from-tunisia
#18
Mourad Ben Said, Hanène Belkahia, Narjesse El Mabrouk, Mariem Saidani, Alberto Alberti, Rosanna Zobba, Amal Cherif, Tarek Mahjoub, Ali Bouattour, Lilia Messadi
Molecular diagnosis of Anaplasma platys and related strains (A. platys-like) in carnivores and ruminants is challenging due to co-infections with cross-reacting strains, and require post-amplification sequencing of the hemi-nested PCR products traditionally generated by targeting the groEL gene. In this study, a Restriction Enzyme Fragment Length Polymorphism (RFLP) assay coupled to hemi-nested groEL PCR was developed to discriminate among A. platys and genetically related strains. This novel approach was used for investigating A...
January 24, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28126562/genetic-diversity-and-evolution-of-dengue-virus-serotype-3-a-comparative-genomics-study
#19
Vaishali P Waman, Mohan M Kale, Urmila Kulkarni-Kale
Dengue virus serotype 3 (DENV-3), one of the four serotypes of Dengue viruses, is geographically diverse. There are five distinct genotypes (I-V) of DENV-3. Emerging strains and lineages of DENV-3 are increasingly being reported. Availability of genomic data for DENV-3 strains provides opportunity to study its population structure. Complete genome sequences are available for 860 strains of four genotypes (I, II, III and V) isolated worldwide and were analyzed using population genetics and evolutionary approaches to map landscape of genomic diversity...
January 23, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28122249/genetic-diversity-and-molecular-epidemiology-of-anaplasma
#20
REVIEW
Mara Battilani, Stefano De Arcangeli, Andrea Balboni, Francesco Dondi
Anaplasma are obligate intracellular bacteria of cells of haematopoietic origin and are aetiological agents of tick-borne diseases of both veterinary and medical interest common in both tropical and temperate regions. The recent disclosure of their zoonotic potential has greatly increased interest in the study of these bacteria, leading to the recent reorganisation of Rickettsia taxonomy and to the possible discovery of new species belonging to the genus Anaplasma. This review is particularly focused on the common and unique characteristics of Anaplasma marginale and Anaplasma phagocytophilum, with an emphasis on genetic diversity and evolution, and the main distinguishing features of the diseases caused by the different Anaplasma spp...
January 22, 2017: Infection, Genetics and Evolution
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