scholarly journals Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
William J Watterson ◽  
Melikhan Tanyeri ◽  
Andrea R Watson ◽  
Candace M Cham ◽  
Yue Shan ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Fecal Microbiota ◽  
Biased Sampling ◽  
Growth Media ◽  
Taxonomic Richness ◽  
Fecal Microbiota Transplant ◽  
Antibiotic Resistant ◽  
Slow Growing ◽  
New Strategies ◽  
Environmental Microbes

Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivation experiments. Here we describe a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts them based on colony density to enhance slow-growing organisms. We applied our strategy to a fecal microbiota transplant (FMT) donor stool using multiple growth media, and found significant increase in taxonomic richness and larger representation of rare and clinically relevant taxa among droplet-grown cells compared to conventional plates. Furthermore, screening the FMT donor stool for antibiotic resistance revealed 21 populations that evaded detection in plate-based assessment of antibiotic resistance. Our method improves cultivation-based surveys of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.

scholarly journals Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics

2020 ◽  
Author(s):  
Lucas A. Meirelles ◽  
Elena K. Perry ◽  
Megan Bergkessel ◽  
Dianne K. Newman
Keyword(s):  
Antibiotic Resistance ◽  
Opportunistic Pathogen ◽  
Antimicrobial Treatment ◽  
Bacterial Survival ◽  
Human Pathogens ◽  
Opportunistic Pathogens ◽  
Chronic Infections ◽  
Antibiotic Resistant ◽  
Lung Infections ◽  
Environmental Microbes

SummaryAs antibiotic-resistant infections become increasingly prevalent worldwide, understanding the factors that lead to antimicrobial treatment failure is essential to optimizing the use of existing drugs. Opportunistic human pathogens in particular typically exhibit high levels of intrinsic antibiotic resistance and tolerance1, leading to chronic infections that can be nearly impossible to eradicate2. We asked whether the recalcitrance of these organisms to antibiotic treatment could be driven in part by their evolutionary history as environmental microbes, which frequently produce or encounter natural antibiotics3,4. Using the opportunistic pathogen Pseudomonas aeruginosa as a model, we demonstrate that the self-produced natural antibiotic pyocyanin (PYO) activates bacterial defenses that confer collateral tolerance to certain synthetic antibiotics, including in a clinically-relevant growth medium. Non-PYO-producing opportunistic pathogens isolated from lung infections similarly display increased antibiotic tolerance when they are co-cultured with PYO-producing P. aeruginosa. Furthermore, we show that beyond promoting bacterial survival in the presence of antibiotics, PYO can increase the apparent rate of mutation to antibiotic resistance by up to two orders of magnitude. Our work thus suggests that bacterial production of natural antibiotics in infections could play an important role in modulating not only the immediate efficacy of clinical antibiotics, but also the rate at which antibiotic resistance arises in multispecies bacterial communities.

scholarly journals High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies

2019 ◽  
Author(s):  
William J. Watterson ◽  
Melikhan Tanyeri ◽  
Andrea R. Watson ◽  
Candace M. Cham ◽  
Yue Shan ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Fold Increase ◽  
Taxonomic Composition ◽  
Biased Sampling ◽  
Human Gut ◽  
Rare Taxa ◽  
Conventional Culture ◽  
16S Ribosomal Rna Gene ◽  
Slow Growing ◽  
New Strategies

AbstractTraditional cultivation approaches in microbiology are labor-intensive, low-throughput, and often yield biased sampling of taxa due to ecological and evolutionary factors. New strategies are needed to enable ample representation of rare taxa and slow-growers that are outcompeted by fast-growing organisms. We developed a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts droplets based on colony density. We applied our strategy to mouse and human gut microbiomes and used 16S ribosomal RNA gene amplicons to characterize taxonomic composition of cells grown using different media. We found up to 4-fold increase in richness and larger representation of rare taxa among cells grown in droplets compared to conventional culture plates. Automated sorting of droplets for slow-growing colonies further enhanced the relative abundance of rare populations. Our method improves the cultivation and analysis of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.

scholarly journals Fecal Microbiota Transplant in Cirrhosis Reduces Gut Microbial Antibiotic Resistance Genes: Analysis of Two Trials

2020 ◽  
Author(s):  
Jasmohan S. Bajaj ◽  
Amirhossein Shamsaddini ◽  
Andrew Fagan ◽  
Richard K. Sterling ◽  
Edith Gavis ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Fecal Microbiota ◽  
Fecal Microbiota Transplant

scholarly journals Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut

Science ◽  
2019 ◽  
Vol 363 (6423) ◽  
pp. 181-187 ◽  
Author(s):  
Xiaofang Jiang ◽  
A. Brantley Hall ◽  
Timothy D. Arthur ◽  
Damian R. Plichta ◽  
Christian T. Covington ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Phase Variation ◽  
Antibiotic Resistance Genes ◽  
Fecal Microbiota ◽  
Metagenomic Data ◽  
Fecal Microbiota Transplant ◽  
Dna Inversion ◽  
Gut Colonization ◽  
Selective Forces

Phase variation, the reversible alternation between genetic states, enables infection by pathogens and colonization by commensals. However, the diversity of phase variation remains underexplored. We developed the PhaseFinder algorithm to quantify DNA inversion–mediated phase variation. A systematic search of 54,875 bacterial genomes identified 4686 intergenic invertible DNA regions (invertons), revealing an enrichment in host-associated bacteria. Invertons containing promoters often regulate extracellular products, underscoring the importance of surface diversity for gut colonization. We found invertons containing promoters regulating antibiotic resistance genes that shift to the ON orientation after antibiotic treatment in human metagenomic data and in vitro, thereby mitigating the cost of antibiotic resistance. We observed that the orientations of some invertons diverge after fecal microbiota transplant, potentially as a result of individual-specific selective forces.

Gut resistome presents a unique biome signature in chronic multi-symptom illness patients and links persistent pro-inflammatory phenotype in a mouse model reversible by fecal microbiota transfer

2021 ◽  
Author(s):  
Dipro Bose ◽  
Somdatta Chatterjee ◽  
Ethan Older ◽  
Ratanesh Seth ◽  
Patricia Janulewicz Lloyd ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Mouse Model ◽  
Resistance Genes ◽  
Intestinal Inflammation ◽  
Antibiotic Resistance Genes ◽  
Chronic Fatigue ◽  
Fecal Microbiota ◽  
Mouse Serum ◽  
War Veterans ◽  
Fecal Microbiota Transplant

Abstract Chronic multi-symptom illness (CMI) affects a subsection of elderly and war veterans and is associated with systemic inflammation, chronic fatigue, pain and neuroinflammation. We showed previously that an altered gut microbiome-inflammation axis aids to the symptom reporting and persistence. Here, a mouse model of CMI and a group of Gulf War veterans’ with CMI showed the presence of an altered host resistome, a signature of antibiotic resistance genes within the microbiome. Results showed that antibiotic resistance genes were significantly altered in the CMI group in both mice and GW veterans when compared to the control. Fecal samples from GW veterans with persistent CMI showed a significant increase of resistance to a wide class of antibiotics and exhibited an array of mobile genetic elements distinct than normal healthy controls. Strikingly, the altered resistome and gene signature were correlated with mouse serum IL6 levels. Altered resistome in mice also correlated strongly with intestinal inflammation, decreased synaptic plasticity that was reversible with fecal microbiota transplant (FMT), a tool to restore a healthy biome. The results indicate an emerging linkage of the gut resistome and CMI and might be significant in understanding the risks to treating hospital acquired infections in this population.

scholarly journals Fecal Transplant: How an Ancient Therapy Is Finding a New Use in Today’s Antibiotic-Resistant Era

2019 ◽  
Vol 8 (1) ◽  
pp. 19-29
Author(s):  
Andrea McBeth ◽  
Piper Dobner
Keyword(s):  
Cost Effective ◽  
Standard Of Care ◽  
The United States ◽  
Fecal Microbiota ◽  
Fecal Transplant ◽  
Healthy Human ◽  
Fecal Microbiota Transplant ◽  
Antibiotic Resistant ◽  
Effective Manner ◽  
Human Stool

Fecal transplant refers to any method of delivery of healthy human stool to the colon of a recipient. This therapy is now gaining standard-of-care designation in the United States, Australia, and many parts of Europe for treating resistant Clostridium difficile infection). This literature review describes fecal transplant protocols. It highlights the variety of techniques used to screen stool donors; prepare and deliver treatment; and how, despite these variations, safety and efficacy remain high. It highlights the various ways to best mitigate safety while also recommending the direction in which clinical and research communities can move to continue to provide access to fecal microbiota transplant in a cost-effective manner.

Self-Administered Home Series Fecal “Minitransplants” for Recurrent Clostridium difficile Infection on a Rectal Remnant

2015 ◽  
Vol 24 (4) ◽  
pp. 531-533 ◽  
Author(s):  
Daniel Popa ◽  
Mihaela Laszlo ◽  
Lidia Ciobanu ◽  
Elena Ucenic ◽  
Manuela Mihalache ◽  
...  
Keyword(s):  
Magnetic Resonance Imaging ◽  
Clostridium Difficile ◽  
Clostridium Difficile Infection ◽  
Toxic Megacolon ◽  
Fecal Microbiota ◽  
Recurrent Infections ◽  
Resonance Imaging ◽  
Vaginal Infection ◽  
Fecal Microbiota Transplant ◽  
Recurrent Clostridium Difficile Infection

A fecal microbiota transplant has proved to be an extremely effective method for patients with recurrent infections with Clostridium difficile. We present the case of a 65-year-old female patient with multiple Clostridium difficile infection (CDI) relapses on the rectal remnant, post-colectomy for a CDI-related toxic megacolon. The patient also evidenced associated symptomatic Clostridium difficile vaginal infection. She was successfully treated with serial fecal “minitransplants” (self-administered at home) and metronidazole ovules.Abbreviations: GI: gastrointestinal; MRI: magnetic resonance imaging; CDI: Clostridium difficile infection; FMT: fecal microbiota transplant.

Relationship of antibiotic resistance to results of treatment in sepsis patients in Hue Central Hospital 2017 – 2018

2019 ◽  
pp. 48-54
Author(s):  
Duy Binh Nguyen ◽  
Trung Tien Phan ◽  
Trong Hanh Hoang ◽  
Van Tuan Mai ◽  
Xuan Chuong Tran
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Infection ◽  
Resistant Bacteria ◽  
Central Hospital ◽  
International Consensus ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Results Of Treatment ◽  
Amoxicillin Clavulanic Acid ◽  
Relationship Of

Sepsis is a serious bacterial infection. The main treatment is using antibiotics. However, the rate of antibiotic resistance is very high and this resistance is related to the outcome of treatment. Objectives: To evaluate the situation of antibiotic resistance of some isolated bacteria in sepsis patients treated at Hue Central Hospital; to evaluate the relationship of antibiotic resistance to the treatment results in patients with sepsis. Subjects and methods: prospective study of 60 sepsis patients diagnosed according to the criteria of the 3rd International Consensus-Sepsis 3 and its susceptibility patterns from April 2017 to August 2018. Results and Conclusions: The current agents of sepsis are mainly S. suis, Burkhoderiae spp. and E. coli. E. coli is resistant to cephalosporins 3rd, 4th generation and quinolone group is over 75%; resistance to imipenem 11.1%; the ESBL rate is 60%. S. suis resistant to ampicilline 11.1%; no resistance has been recorded to ceftriaxone and vancomycine. Resistance of Burkholderiae spp. to cefepime and amoxicillin/clavulanic acid was 42.9% and 55.6%, resistant to imipenem and meropenem is 20%, resistance to ceftazidime was not recorded. The deaths were mostly dued to E. coli and K. pneumoniae. The mortality for patients infected with antibiotic-resistant bacteria are higher than for sensitive groups. Key words: Sepsis, bacterial infection, antibiotics

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