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https://www.readbyqxmd.com/read/28198411/the-secondary-resistome-of-multidrug-resistant-klebsiella-pneumoniae
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/27959344/co-occurrence-of-antibiotic-and-metal-resistance-genes-revealed-in-complete-genome-collection
#15
Li-Guan Li, Yu Xia, Tong Zhang
The high frequency of antibiotic resistance is a global public health concern. More seriously, widespread metal pressure in the environment may facilitate the proliferation of antibiotic resistance via coselection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). Given the lack of comprehensive understanding of the ARG and MRG coselection, in this study both abundance relationship and genetic linkage between ARGs and MRGs were rigorously investigated by performing a genomic analysis of a large complete genome collection...
March 2017: ISME Journal
https://www.readbyqxmd.com/read/27934260/long-term-impact-of-field-applications-of-sewage-sludge-on-soil-antibiotic-resistome
#16
Wan-Ying Xie, Steve P McGrath, Jian-Qiang Su, Penny R Hirsch, Ian M Clark, Qirong Shen, Yong-Guan Zhu, Fang-Jie Zhao
Land applications of municipal sewage sludge may pose a risk of introducing antibiotic resistance genes (ARGs) from urban environments into agricultural systems. However, how the sewage sludge recycling and application method influence soil resistome and mobile genetic elements (MGEs) remains unclear. In the present study, high through-put quantitative PCR was conducted on the resistome of soils from a field experiment with past (between 1994 and 1997) and annual (since 1994) applications of five different sewage sludges...
December 6, 2016: Environmental Science & Technology
https://www.readbyqxmd.com/read/27929110/a-diverse-intrinsic-antibiotic-resistome-from-a-cave-bacterium
#17
Andrew C Pawlowski, Wenliang Wang, Kalinka Koteva, Hazel A Barton, Andrew G McArthur, Gerard D Wright
Antibiotic resistance is ancient and widespread in environmental bacteria. These are therefore reservoirs of resistance elements and reflective of the natural history of antibiotics and resistance. In a previous study, we discovered that multi-drug resistance is common in bacteria isolated from Lechuguilla Cave, an underground ecosystem that has been isolated from the surface for over 4 Myr. Here we use whole-genome sequencing, functional genomics and biochemical assays to reveal the intrinsic resistome of Paenibacillus sp...
December 8, 2016: Nature Communications
https://www.readbyqxmd.com/read/27913093/genome-of-the-carbapenemase-producing-clinical-isolate-elizabethkingia-miricola-em_chuv-and-comparative-genomics-with-elizabethkingia-meningoseptica-and-elizabethkingia-anophelis-evidence-for-intrinsic-multidrug-resistance-trait-of-emerging-pathogens
#18
Onya Opota, Seydina M Diene, Claire Bertelli, Guy Prod'hom, Philippe Eckert, Gilbert Greub
Elizabethkingia miricola is a Gram-negative non-fermenting rod emerging as a life-threatening human pathogen. The multidrug-resistant (MDR) carbapenemase-producing clinical isolate E. miricola EM_CHUV was recovered in the setting of severe nosocomial pneumonia. In this study, the genome of E. miricola EM_CHUV was sequenced and a functional analysis was performed, including a comparative genomic study with Elizabethkingia meningoseptica and Elizabethkingia anophelis. The resistome of EM_CHUV revealed the presence of a high number of resistance genes, including the presence of the blaGOB-13 and blaB-9 carbapenemase-encoding genes...
January 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/27864179/prevalence-of-antibiotic-resistance-genes-among-human-gut-derived-bifidobacteria
#19
Sabrina Duranti, Gabriele Andrea Lugli, Leonardo Mancabelli, Francesca Turroni, Christian Milani, Marta Mangifesta, Chiara Ferrario, Rosaria Anzalone, Alice Viappiani, Douwe van Sinderen, Marco Ventura
: The microbiota of the human gastrointestinal tract (GIT) may regularly be exposed to antibiotics, which are used to prevent and treat infectious diseases caused by bacteria and fungi. Bacterial communities of the gut retain a reservoir of antibiotic resistance (AR) genes, and antibiotic therapy thus positively selects for those microorganisms that harbor such genetic features, causing microbiota modulation. During the first months following birth, bifidobacteria represent some of the most dominant components of the human gut microbiota, although little is known about their AR gene complement (or resistome)...
February 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27825482/unraveling-genomic-and-phenotypic-nature-of-multidrug-resistant-mdr-pseudomonas-aeruginosa-vrfpa04-isolated-from-keratitis-patient
#20
Murugan N, Malathi J, Umashankar V, Madhavan H N
Multidrug-resistant (MDR) Pseudomonas aeruginosa VRFPA04, obtained from a keratitis patient was found to exhibit resistance to betalactam (Penicillins, cephalosporins, including carbapenems, except aztreonam), aminoglycosides, quinolone group of drugs and susceptible to colistin. The complete genome sequencing of the ocular isolate to measure and ascertain the degree of multidrug resistance in VRFPA04 strain resulted in 6,818,030bp (6.8Mb) genome sizes, which happen to be the third largest genome available in the Genbank to date...
December 2016: Microbiological Research
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