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https://www.readbyqxmd.com/read/28395597/genome-sequencing-and-comparative-analysis-of-an-ndm-1-producing-klebsiella-pneumoniae-st15-isolated-from-a-refugee-patient
#1
Tamara Salloum, Harout Arabaghian, Sahar Alousi, Edmond Abboud, Sima Tokajian
The escalating problem of antibiotic resistance, specifically cabarpenemase and extended-spectrum β-lacatamase (ESBL) producing K. pneumoniae strains, is directly correlated with increased patient morbidity and mortality and prolonged hospitalization and costs. In this study, a comprehensive genomic analysis encompassing the resistomics, virulence repertoire and mobile genetic elements of an NDM-1 positive ESBL-producing K. pneumoniae EA-MEH ST15 isolated from a urine sample collected from a Syrian refugee was conducted...
April 11, 2017: Pathogens and Global Health
https://www.readbyqxmd.com/read/28392565/next-generation-approaches-to-understand-and-combat-the-antibiotic-resistome
#2
REVIEW
Terence S Crofts, Andrew J Gasparrini, Gautam Dantas
Antibiotic resistance is a natural feature of diverse microbial ecosystems. Although recent studies of the antibiotic resistome have highlighted barriers to the horizontal transfer of antibiotic resistance genes between habitats, the rapid global spread of genes that confer resistance to carbapenem, colistin and quinolone antibiotics illustrates the dire clinical and societal consequences of such events. Over time, the study of antibiotic resistance has grown from focusing on single pathogenic organisms in axenic culture to studying antibiotic resistance in pathogenic, commensal and environmental bacteria at the level of microbial communities...
April 10, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28389536/whole-genome-sequencing-of-drug-resistant-salmonella-enterica-isolated-from-dairy-cattle-and-humans-in-new-york-and-washington-states-reveals-source-and-geographic-associations
#3
Laura M Carroll, Martin Wiedmann, Henk den Bakker, Julie Siler, Steven Warchocki, David Kent, Svetlana Lyalina, Margaret Davis, William Sischo, Thomas Besser, Lorin D Warnick, Richard V Pereira
Multidrug-resistant (MDR) Salmonella enterica can be spread from cattle to humans through direct contact with animals shedding Salmonella, as well as through the food chain, making MDR Salmonella a serious threat to human health. The objective of this study was to use whole-genome sequencing to compare antimicrobial-resistant (AMR) S. Typhimurium, Newport, and Dublin isolated from dairy cattle and humans in Washington state and New York state at a genotypic and phenotypic level. A total of 90 isolates were selected for the study (37 Typhimurium, 32 Newport, 21 Dublin)...
April 7, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28383665/a-pan-genomic-approach-to-understand-the-basis-of-host-adaptation-in-achromobacter
#4
J Jeukens, L Freschi, A T Vincent, J G Emond-Rheault, I Kukavica-Ibrulj, S J Charette, R C Levesque
Over the past decade, there has been a rising interest in Achromobacter sp., an emerging opportunistic pathogen responsible for nosocomial and cystic fibrosis (CF) lung infections. Species of this genus are ubiquitous in the environment, can outcompete resident microbiota, and are resistant to commonly used disinfectants as well as antibiotics. Nevertheless, the Achromobacter genus suffers from difficulties in diagnosis, unresolved taxonomy and limited understanding of how it adapts to the CF lung, not to mention other host environments...
April 5, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28334267/resistomap-online-visualization-of-human-gut-microbiota-antibiotic-resistome
#5
Konstantin S Yarygin, Boris A Kovarsky, Tatyana S Bibikova, Damir S Melnikov, Alexander V Tyakht, Dmitry G Alexeev
Summary: We created ResistoMap - a Web-based interactive visualization of the presence of genetic determinants conferring resistance to antibiotics, biocides and heavy metals in human gut microbiota. ResistoMap displays the data on more than 1500 published gut metagenomes of world populations including both healthy subjects and patients. Multiparameter display filters allow visual assessment of the associations between the meta-data and proportions of resistome. The geographic map navigation layer allows to state hypotheses regarding the global trends of antibiotic resistance and correlate the gut resistome variations with the national clinical guidelines on antibiotics application...
March 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28294141/gear-a-database-of-genomic-elements-associated-with-drug-resistance
#6
Yin-Ying Wang, Wei-Hua Chen, Pei-Pei Xiao, Wen-Bin Xie, Qibin Luo, Peer Bork, Xing-Ming Zhao
Drug resistance is becoming a serious problem that leads to the failure of standard treatments, which is generally developed because of genetic mutations of certain molecules. Here, we present GEAR (A database of Genomic Elements Associated with drug Resistance) that aims to provide comprehensive information about genomic elements (including genes, single-nucleotide polymorphisms and microRNAs) that are responsible for drug resistance. Right now, GEAR contains 1631 associations between 201 human drugs and 758 genes, 106 associations between 29 human drugs and 66 miRNAs, and 44 associations between 17 human drugs and 22 SNPs...
March 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198411/the-secondary-resistome-of-multidrug-resistant-klebsiella-pneumoniae
#7
Bimal Jana, Amy K Cain, William T Doerrler, Christine J Boinett, Maria C Fookes, Julian Parkhill, Luca Guardabassi
Klebsiella pneumoniae causes severe lung and bloodstream infections that are difficult to treat due to multidrug resistance. We hypothesized that antimicrobial resistance can be reversed by targeting chromosomal non-essential genes that are not responsible for acquired resistance but essential for resistant bacteria under therapeutic concentrations of antimicrobials. Conditional essentiality of individual genes to antimicrobial resistance was evaluated in an epidemic multidrug-resistant clone of K. pneumoniae (ST258)...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198087/meta-analysis-of-the-human-gut-microbiome-from-urbanized-and-pre-agricultural-populations
#8
REVIEW
Leonardo Mancabelli, Christian Milani, Gabriele Andrea Lugli, Francesca Turroni, Chiara Ferrario, Douwe van Sinderen, Marco Ventura
Metagenomic studies of the human gut microbiome have only recently begun to explore the differences in taxonomic composition between subjects from diverse geographical origins. Here, we compared taxonomy, resistome and functional metabolic properties of publicly available shotgun datasets of human fecal samples collected from different geographical regions (Europe, North America, Asia and Oceania). Such datasets encompassed gut microbiota information corresponding to 13 developed/industrialized societies, as well as two traditional hunter-gatherer, pre-agricultural communities (Tanzanian and Peruvian individuals)...
February 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28165472/comprehensive-resistome-analysis-reveals-the-prevalence-of-ndm-and-mcr-1-in-chinese-poultry-production
#9
Yang Wang, Rongmin Zhang, Jiyun Li, Zuowei Wu, Wenjuan Yin, Stefan Schwarz, Jonathan M Tyrrell, Yongjun Zheng, Shaolin Wang, Zhangqi Shen, Zhihai Liu, Jianye Liu, Lei Lei, Mei Li, Qidi Zhang, Congming Wu, Qijing Zhang, Yongning Wu, Timothy R Walsh, Jianzhong Shen
By 2030, the global population will be 8.5 billion, placing pressure on international poultry production, of which China is a key producer(1). From April 2017, China will implement the withdrawal of colistin as a growth promoter, removing over 8,000 tonnes per year from the Chinese farming sector(2). To understand the impact of banning colistin and the epidemiology of multi-drug-resistant (MDR) Escherichia coli (using blaNDM and mcr-1 as marker genes), we sampled poultry, dogs, sewage, wild birds and flies...
February 6, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28149696/antibiotic-resistance-potential-of-the-healthy-preterm-infant-gut-microbiome
#10
Graham Rose, Alexander G Shaw, Kathleen Sim, David J Wooldridge, Ming-Shi Li, Saheer Gharbia, Raju Misra, John Simon Kroll
BACKGROUND: Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. RESULTS: Dominant clinically important species identified within the microbiomes included C...
2017: PeerJ
https://www.readbyqxmd.com/read/28134918/continental-scale-pollution-of-estuaries-with-antibiotic-resistance-genes
#11
Yong-Guan Zhu, Yi Zhao, Bing Li, Chu-Long Huang, Si-Yu Zhang, Shen Yu, Yong-Shan Chen, Tong Zhang, Michael R Gillings, Jian-Qiang Su
Antibiotic resistance genes (ARGs) have moved from the environmental resistome into human commensals and pathogens, driven by human selection with antimicrobial agents. These genes have increased in abundance in humans and domestic animals, to become common components of waste streams. Estuarine habitats lie between terrestrial/freshwater and marine ecosystems, acting as natural filtering points for pollutants. Here, we have profiled ARGs in sediments from 18 estuaries over 4,000 km of coastal China using high-throughput quantitative polymerase chain reaction, and investigated their relationship with bacterial communities, antibiotic residues and socio-economic factors...
January 30, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28129018/challenges-in-fecal-donor-selection-and-screening-for-fecal-microbiota-transplantation-a-review
#12
Michael H Woodworth, Cynthia Carpentieri, Kaitlin L Sitchenko, Colleen S Kraft
Fecal microbiota transplantation is best understood as an effective and inexpensive therapy for recurrent Clostridium difficile infection but fecal donor selection and screening should be periodically revised. Here, we review current recommendations for selection and screening of fecal donors for fecal microbiota transplantation. We recommend considering diabetes mellitus, prior cardiovascular events, and clinical healthcare exposure as fecal donor exclusion criteria until more is known about the association of these conditions with the human gut microbiome...
January 27, 2017: Gut Microbes
https://www.readbyqxmd.com/read/28124734/importance-of-whole-genome-sequencing-for-the-assessment-of-outbreaks-in-diagnostic-laboratories-analysis-of-a-case-series-of-invasive-streptococcus-pyogenes-infections
#13
F Tagini, B Aubert, N Troillet, T Pillonel, G Praz, P A Crisinel, G Prod'hom, S Asner, G Greub
Outbreaks of Streptococcus pyogenes hypervirulent clones are constant public health threats. In western Switzerland, an increase of severe cases of S. pyogenes invasive infections was observed between December 2015 and March 2016. Our aim was (i) to investigate these cases by the use of Whole Genome Sequencing (WGS) and (ii) to determine the specific virulome and resistome of each isolate in order to undertake adequate public health measures. Eleven Streptococcus pyogenes strains isolated from 11 patients with severe invasive infections between December 13, 2015 and March 12, 2016 were included in our study...
January 26, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28120869/change-in-microbial-community-in-landfill-refuse-contaminated-with-antibiotics-facilitates-denitrification-more-than-the-increase-in-arg-over-long-term
#14
Dong Wu, Guanzhou Chen, Xiaojun Zhang, Kai Yang, Bing Xie
In this study, the addition of sulfamethazine (SMT) to landfill refuse decreased nitrogen intermediates (e.g. N2O and NO) and dinitrogen (N2) gas fluxes to <0.5 μg-N/kg-refuse·h(-1), while the N2O and N2 flux were at ~1.5 and 5.0 μg-N/kg-refuse·h(-1) respectively in samples to which oxytetracycline (OTC) had been added. The ARG (antibiotic resistance gene) levels in the refuse increased tenfold after long-term exposure to antibiotics, followed by a fourfold increase in the N2 flux, but SMT-amended samples with the largest resistome facilitated the denitrification (the nitrogen accumulated as NO gas at ~6 μg-N/kg-refuse·h(-1)) to a lesser extent than OTC-amended samples...
January 25, 2017: Scientific Reports
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
#15
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 2017: New Microbiologica
https://www.readbyqxmd.com/read/28062856/rapid-resistome-mapping-using-nanopore-sequencing
#16
Eric van der Helm, Lejla Imamovic, Mostafa M Hashim Ellabaan, Willem van Schaik, Anna Koza, Morten O A Sommer
The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine. The outcome of antibiotic treatment can be affected by the composition of the gut. Accordingly, knowledge of the gut resistome composition could enable more effective and individualized treatment of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping...
January 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28012687/assessing-the-risk-of-antibiotic-resistance-transmission-from-the-environment-to-humans-non-direct-proportionality-between-abundance-and-risk
#17
REVIEW
Célia M Manaia
The past decade has witnessed a burst of study regarding antibiotic resistance in the environment, mainly in areas under anthropogenic influence. Therefore, impacts of the contaminant resistome, that is, those related to human activities, are now recognized. However, a key issue refers to the risk of transmission of resistance to humans, for which a quantitative model is urgently needed. This opinion paper makes an overview of some risk-determinant variables and raises questions regarding research needs. A major conclusion is that the risks of transmission of antibiotic resistance from the environment to humans must be managed under the precautionary principle, because it may be too late to act if we wait until we have concrete risk values...
December 21, 2016: Trends in Microbiology
https://www.readbyqxmd.com/read/28002024/the-cancer-cell-adhesion-resistome-mechanisms-targeting-and-translational-approaches
#18
Ellen Dickreuter, Nils Cordes
Cell adhesion-mediated resistance limits the success of cancer therapies and is a great obstacle to overcome in the clinic. Since the 90s, where it became clear that adhesion of tumor cells to the extracellular matrix is an important mediator of therapy resistance, a lot of work has been conducted to understand the fundamental underlying mechanisms and two paradigms were deduced: cell adhesion-mediated radioresistance (CAM-RR) and cell adhesion-mediated drug resistance (CAM-DR). Preclinical work has evidently demonstrated that targeting of integrins, adapter proteins and associated kinases comprising the cell adhesion resistome is a promising strategy to sensitize cancer cells to both radiotherapy and chemotherapy...
December 20, 2016: Biological Chemistry
https://www.readbyqxmd.com/read/27999667/antimicrobial-usage-and-resistance-in-beef-production
#19
REVIEW
Andrew Cameron, Tim A McAllister
Antimicrobials are critical to contemporary high-intensity beef production. Many different antimicrobials are approved for beef cattle, and are used judiciously for animal welfare, and controversially, to promote growth and feed efficiency. Antimicrobial administration provides a powerful selective pressure that acts on the microbial community, selecting for resistance gene determinants and antimicrobial-resistant bacteria resident in the bovine flora. The bovine microbiota includes many harmless bacteria, but also opportunistic pathogens that may acquire and propagate resistance genes within the microbial community via horizontal gene transfer...
2016: Journal of Animal Science and Biotechnology
https://www.readbyqxmd.com/read/27965630/evaluation-of-machine-learning-and-rules-based-approaches-for-predicting-antimicrobial-resistance-profiles-in-gram-negative-bacilli-from-whole-genome-sequence-data
#20
Mitchell W Pesesky, Tahir Hussain, Meghan Wallace, Sanket Patel, Saadia Andleeb, Carey-Ann D Burnham, Gautam Dantas
The time-to-result for culture-based microorganism recovery and phenotypic antimicrobial susceptibility testing necessitates initial use of empiric (frequently broad-spectrum) antimicrobial therapy. If the empiric therapy is not optimal, this can lead to adverse patient outcomes and contribute to increasing antibiotic resistance in pathogens. New, more rapid technologies are emerging to meet this need. Many of these are based on identifying resistance genes, rather than directly assaying resistance phenotypes, and thus require interpretation to translate the genotype into treatment recommendations...
2016: Frontiers in Microbiology
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