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https://www.readbyqxmd.com/read/29775788/complete-genome-sequence-of-achromobacter-spanius-type-strain-dsm-23806t-a-pathogen-isolated-from-human-blood
#1
Gengmi Li, Li Yang, Tao Zhang, Xiaojiao Guo, Jian Qin, Yingjiang Cao, Qianhua Yang, Shumei You, Guoliang Yuan, Xianqi Wan, Jing Luo, Zhaoxiang Li, Lei Gao, Ying Liu, Kaifeng Jiang, Jiakui Zheng
OBJECTIVES: Achromobacter spanius is a new described, non-fermenting Gram-negative and coccoid pathogen that isolated from patient blood. In order to investigate the pathogenesis of this strain in genomic level, whole genome sequencing was carried out on this strain. METHODS: In this study, complete genome of the type strain of this species DSM 23806T was sequenced using single-molecule real-time (SMRT) DNA sequencing. RESULTS: Complete genome of DSM 23806T consists of one circular DNA chromosome of 6,425,783bp with a GC content of 64...
May 15, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29774212/alkaline-peptone-water-based-enrichment-method-for-mcr-3-from-acute-diarrheic-outpatient-gut-samples
#2
Qiaoling Sun, Yanyan Hu, Hongwei Zhou, Lingbin Shu, Hanyu Wang, Zixian Huang, Rong Zhang
A third plasmid-mediated colistin resistance gene, mcr-3 , is increasingly being reported in Enterobacteriaceae and Aeromonas spp. from animals and humans. To investigate the molecular epidemiology of mcr in the gut flora of Chinese outpatients, 152 stool specimens were randomly collected from outpatients in our hospital from May to June, 2017. Stool specimens enriched in alkaline peptone water or Luria-Bertani (LB) broth were screened for mcr-1, mcr-2 , and mcr-3 using polymerase chain reaction (PCR)-based assays...
2018: Frontiers in Medicine
https://www.readbyqxmd.com/read/29774047/genome-sequencing-and-analysis-of-the-peanut-b-genome-progenitor-arachis-ipaensis
#3
Qing Lu, Haifen Li, Yanbin Hong, Guoqiang Zhang, Shijie Wen, Xingyu Li, Guiyuan Zhou, Shaoxiong Li, Hao Liu, Haiyan Liu, Zhongjian Liu, Rajeev K Varshney, Xiaoping Chen, Xuanqiang Liang
Peanut ( Arachis hypogaea L.), an important leguminous crop, is widely cultivated in tropical and subtropical regions. Peanut is an allotetraploid, having A and B subgenomes that maybe have originated in its diploid progenitors Arachis duranensis (A-genome) and Arachis ipaensis (B-genome), respectively. We previously sequenced the former and here present the draft genome of the latter, expanding our knowledge of the unique biology of Arachis . The assembled genome of A. ipaensis is ~1.39 Gb with 39,704 predicted protein-encoding genes...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29773743/genomic-insights-into-the-emergence-and-spread-of-antimicrobial-resistant-bacterial-pathogens
#4
REVIEW
Stephen Baker, Nicholas Thomson, François-Xavier Weill, Kathryn E Holt
Whole-genome sequencing (WGS) has been vital for revealing the rapid temporal and spatial evolution of antimicrobial resistance (AMR) in bacterial pathogens. Some antimicrobial-resistant pathogens have outpaced us, with untreatable infections appearing in hospitals and the community. However, WGS has additionally provided us with enough knowledge to initiate countermeasures. Although we cannot stop bacterial adaptation, the predictability of many evolutionary processes in AMR bacteria offers us an opportunity to channel them using new control strategies...
May 18, 2018: Science
https://www.readbyqxmd.com/read/29773638/draft-genome-sequence-of-new-vancomycin-resistant-enterococcus-faecium-sequence-type-1421
#5
Kelvin W C Leong, Louise A Cooley, Ronan F O'Toole
The spread of vancomycin-resistant Enterococcus faecium (VREfm) has become a challenge to health care infection control worldwide. In 2015, a marked increase in VREfm isolation was detected in acute public hospitals in Tasmania. We report here the draft whole-genome sequence of a newly designated VREfm sequence type, sequence type 1421 (ST1421).
May 17, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29771278/a-pelota-like-gene-regulates-root-development-and-defence-responses-in-rice
#6
Wona Ding, Jing Wu, Jin Ye, Wenjuan Zheng, Shanshan Wang, Xinni Zhu, Jiaqin Zhou, Zhichong Pan, Botao Zhang, Shihua Zhu
Background and Aims: Pelota (Pelo) are evolutionarily conserved genes reported to be involved in ribosome rescue, cell cycle control and meiotic cell division. However, there is little known about their function in plants. The aim of this study was to elucidate the function of an ethylmethane sulphonate (EMS)-derived mutation of a Pelo-like gene in rice (named Ospelo). Methods: A dysfunctional mutant was used to characterize the function of OsPelo. Analyses of its expression and sub-cellular localization were performed...
May 16, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29771232/methicillin-resistant-staphylococcus-argenteus-misidentified-as-methicillin-resistant-staphylococcus-aureus-emerging-in-western-sweden
#7
Erika Tång Hallbäck, Nahid Karami, Ingegerd Adlerberth, Sofia Cardew, Maria Ohlén, Hedvig Engström Jakobsson, Liselott Svensson Stadler
Two strains included in a whole-genome sequencing project for methicillin-resistant Staphylococcus aureus (MRSA) were identified as non-Staphylococcus aureus when the sequences were analysed using the bioinformatics software ALEX (www.1928diagnostics.com, Gothenburg, Sweden). Sequencing of the sodA gene of these strains identified them as Staphylococcus argenteus. The collection of MRSA in western Sweden was checked for additional strains of this species. A total of 18 strains of S. argenteus isolated between 2011 and December 2017 were identified...
May 17, 2018: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29769160/cross-border-outbreak-of-extensively-drug-resistant-tuberculosis-linked-to-a-university-in-romania
#8
O Popovici, Ph Monk, D Chemtob, D Chiotan, P J Freidlin, R Groenheit, M Haanperä, D Homorodean, M Mansjö, E Robinson, E Rorman, G Smith, H Soini, M J Van Der Werf
Extensively drug-resistant (XDR) tuberculosis (TB) poses a threat to public health due to its complicated, expensive and often unsuccessful treatment. A cluster of three XDR TB cases was detected among foreign medical students of a Romanian university. The contact investigations included tuberculin skin testing or interferon gamma release assay, chest X-ray, sputum smear microscopy, culture, drug susceptibility testing, genotyping and whole-genome sequencing (WGS), and were addressed to students, personnel of the university, family members or other close contacts of the cases...
May 2018: Epidemiology and Infection
https://www.readbyqxmd.com/read/29769016/whole-genome-sequencing-data-of-1110-mycobacterium-tuberculosis-isolates-identifies-insertions-and-deletions-associated-with-drug-resistance
#9
Xi Zeng, Jamie Sui-Lam Kwok, Kevin Yi Yang, Kenneth Siu-Sing Leung, Mai Shi, Zhiyuan Yang, Wing-Cheong Yam, Stephen Kwok-Wing Tsui
BACKGROUND: Drug resistance in Mycobacterium tuberculosis (MTB) is one of the major challenges in tuberculosis (TB) treatment. However, known mutations cannot explain all of the cases of resistance and little research has focused on the relationship between insertions / deletions (indels) and drug resistance. RESULTS: Here, we retrieved whole genome sequencing data of 743 drug-resistant MTB strains and 367 pan-susceptible strains from TB patients from the public domain to identify novel genomic markers of drug resistance...
May 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29766351/comparative-whole-genome-re-sequencing-analysis-in-upland-new-rice-for-africa-insights-into-the-breeding-history-and-respective-genome-compositions
#10
Naoki Yamamoto, Richard Garcia, Tomohiro Suzuki, Celymar Angela Solis, Yuichi Tada, Ramaiah Venuprasad, Ajay Kohli
BACKGROUND: Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing biodiversity across the two different rice crop species. Upland NERICA varieties (NU) exhibit agronomic traits of value for the harsh eco-geography, including shorter duration, higher yield and stress tolerance, compared to local African varieties...
May 15, 2018: Rice
https://www.readbyqxmd.com/read/29765372/is-iqg-607-a-potential-metallodrug-or-metallopro-drug-with-a-defined-molecular-target-in-mycobacterium-tuberculosis
#11
REVIEW
Bruno L Abbadi, Valnês da Silva Rodrigues-Junior, Adilio da Silva Dadda, Kenia Pissinate, Anne D Villela, Maria M Campos, Luiz G de França Lopes, Cristiano V Bizarro, Pablo Machado, Eduardo H S Sousa, Luiz A Basso
The emergence of strains of Mycobacterium tuberculosis resistant to isoniazid (INH) has underscored the need for the development of new anti-tuberculosis agents. INH is activated by the mycobacterial katG -encoded catalase-peroxidase, forming an acylpyridine fragment that is covalently attached to the C4 of NADH. This isonicotinyl-NAD adduct inhibits the activity of 2- trans -enoyl-ACP(CoA) reductase (InhA), which plays a role in mycolic acid biosynthesis. A metal-based INH analog, Na3 [FeII (CN)5 (INH)]·4H2 O, IQG-607, was designed to have an electronic redistribution on INH moiety that would lead to an intramolecular electron transfer to bypass KatG activation...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29761214/analysis-of-resistance-genes-of-clinical-pannonibacter-phragmitetus-strain-31801-by-complete-genome-sequencing
#12
De-Song Ming, Qing-Qing Chen, Xiao-Tin Chen
To clarify the resistance mechanisms of Pannonibacter phragmitetus 31801, isolated from the blood of a liver abscess patient, at the genomic level, we performed whole genomic sequencing using a PacBio RS II single-molecule real-time long-read sequencer. Bioinformatic analysis of the resulting sequence was then carried out to identify any possible resistance genes. Analyses included Basic Local Alignment Search Tool searches against the Antibiotic Resistance Genes Database, ResFinder analysis of the genome sequence, and Resistance Gene Identifier analysis within the Comprehensive Antibiotic Resistance Database...
May 14, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29760690/two-new-lytic-bacteriophages-of-the-myoviridae-family-against-carbapenem-resistant-acinetobacter-baumannii
#13
Weilong Zhou, Yu Feng, Zhiyong Zong
Two lytic bacteriophages, WCHABP1 and WCHABP12, were recovered from hospital sewage and were able to infect 9 and 12 out of 18 carbapenem-resistant Acinetobacter baumannii clinical strains, which belonged to different clones. Electron microscopy scan showed that both bacteriophages had the similar morphology as those of the Myoviridae family. Whole genomic sequencing revealed 45.4- or 45.8-kb genome with a 37.6% GC content for WCHABP1 and WCHABP12, both of which showed significant DNA sequence similarity with bacteriophages of the Ap22virus genus within the Myoviridae family...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29755957/molecular-targets-related-drug-resistance-mechanisms-in-mdr-xdr-and-tdr-mycobacterium-tuberculosis-strains
#14
REVIEW
H M Adnan Hameed, Md Mahmudul Islam, Chiranjibi Chhotaray, Changwei Wang, Yang Liu, Yaoju Tan, Xinjie Li, Shouyong Tan, Vincent Delorme, Wing W Yew, Jianxiong Liu, Tianyu Zhang
Tuberculosis (TB) is a formidable infectious disease that remains a major cause of death worldwide today. Escalating application of genomic techniques has expedited the identification of increasing number of mutations associated with drug resistance in Mycobacterium tuberculosis . Unfortunately the prevalence of bacillary resistance becomes alarming in many parts of the world, with the daunting scenarios of multidrug-resistant tuberculosis (MDR-TB), extensively drug-resistant tuberculosis (XDR-TB) and total drug-resistant tuberculosis (TDR-TB), due to number of resistance pathways, alongside some apparently obscure ones...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29755435/analysis-of-phylogenetic-variation-of-stenotrophomonas-maltophilia-reveals-human-specific-branches
#15
Joerg Steinmann, Uwe Mamat, Ebrahim M Abda, Lisa Kirchhoff, Wolfgang R Streit, Ulrich E Schaible, Stefan Niemann, Thomas A Kohl
Stenotrophomonas maltophilia is a non-fermenting Gram-negative bacterium that is ubiquitous in the environment. In humans, this opportunistic multi-drug-resistant pathogen is responsible for a plethora of healthcare-associated infections. Here, we utilized a whole genome sequencing (WGS)-based phylogenomic core single nucleotide polymorphism (SNP) approach to characterize S. maltophilia subgroups, their potential association with human infection, and to detect any possible transmission events. In total, 89 isolates (67 clinical and 22 environmental) from Germany were sequenced...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29755420/characterization-of-two-novel-bacteriophages-infecting-multidrug-resistant-mdr-acinetobacter-baumannii-and-evaluation-of-their-therapeutic-efficacy-in-vivo
#16
Kyoungeun Cha, Hynu K Oh, Jae Y Jang, Yunyeol Jo, Won K Kim, Geon U Ha, Kwan S Ko, Heejoon Myung
Acinetobacter baumannii is emerging as a challenging nosocomial pathogen due to its rapid evolution of antibiotic resistance. We report characterization of two novel bacteriophages, PBAB08 and PBAB25, infecting clinically isolated, multidrug-resistant (MDR) A. baumannii strains. Both phages belonged to Myoviridae of Caudovirales as their morphology observed under an electron microscope. Their genomes were double stranded linear DNAs of 42,312 base pairs and 40,260 base pairs, respectively. The two phages were distinct from known Acinetobacter phages when whole genome sequences were compared...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29755416/complete-genomic-analysis-of-a-salmonella-enterica-serovar-typhimurium-isolate-cultured-from-ready-to-eat-pork-in-china-carrying-one-large-plasmid-containing-mcr-1
#17
Wei Wang, Zulqarnain Baloch, Mingyuan Zou, Yinping Dong, Zixin Peng, Yujie Hu, Jin Xu, Nafeesa Yasmeen, Fengqin Li, Séamus Fanning
One mcr-1 -carrying ST34-type Salmonella Typhimurium WW012 was cultured from 3,200 ready-to-eat (RTE) pork samples in 2014 in China. Broth dilution method was applied to obtain the antimicrobial susceptibility of Salmonella Typhimurium WW012. Broth matting assays were carried out to detect transferability of this phenotype and whole-genome sequencing was performed to analyze its genomic characteristic. Thirty out of 3,200 RTE samples were positive for Salmonella and the three most frequent serotypes were identified as S ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29748406/draft-genome-sequencing-of-an-acinetobacter-ursingii-isolate-from-healthy-human-skin-carrying-multidrug-resistance-genes
#18
Lenka Palkova, Gabriel Minarik, Katarina Soltys
In this paper, we report the data from whole-genome shotgun sequencing of an Acinetobacter ursingii isolate from healthy human skin of the forearm. The bacterial genome includes 3,473 genes and carries beta-lactamase resistance genes as well as resistance genes for several heavy metals.
May 10, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29744043/genome-based-analysis-of-carbapenemase-producing-klebsiella-pneumoniae-isolates-from-german-hospital-patients-2008-2014
#19
Laura Becker, Martin Kaase, Yvonne Pfeifer, Stephan Fuchs, Annicka Reuss, Anja von Laer, Muna Abu Sin, Miriam Korte-Berwanger, Sören Gatermann, Guido Werner
Background: By using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing K. pneumoniae isolated from hospitalized patients in Germany between 2008 and 2014. Methods: We selected a representative subset of 107 carbapenemase-producing K. pneumoniae clinical isolates possessing the four most prevalent carbapenemase types in Germany (KPC-2, KPC-3, OXA-48, NDM-1). Isolates were processed via illumina NGS. Data were analysed using different SNP-based mapping and de-novo assembly approaches...
2018: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/29743642/genomic-epidemiology-of-shigella-in-the-united-kingdom-shows-transmission-of-pathogen-sublineages-and-determinants-of-antimicrobial-resistance
#20
Kate S Baker, Timothy J Dallman, Nigel Field, Tristan Childs, Holly Mitchell, Martin Day, François-Xavier Weill, Sophie Lefèvre, Mathieu Tourdjman, Gwenda Hughes, Claire Jenkins, Nicholas Thomson
Shigella are globally important diarrhoeal pathogens that are endemic in low-to-middle income nations and also occur in high income nations, typically in travellers or community-based risk-groups. Shigella phylogenetics reveals population structures that are more reliable than those built with traditional typing methods, and has identified sublineages associated with specific geographical regions or patient groups. Genomic analyses reveal temporal increases in Shigella antimicrobial resistance (AMR) gene content, which is frequently encoded on mobile genetic elements...
May 9, 2018: Scientific Reports
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