scholarly journals SYN-007, an Orally Administered Beta-Lactamase Enzyme, Protects the Gut Microbiome from Oral Amoxicillin/Clavulanate without Adversely Affecting Antibiotic Systemic Absorption in Dogs

2020 ◽  
Vol 8 (2) ◽  
pp. 152 ◽  
Author(s):  
Sheila Connelly ◽  
Brian Fanelli ◽  
Nur A. Hasan ◽  
Rita R. Colwell ◽  
Michael Kaleko
Keyword(s):  
Antibiotic Resistance ◽  
Gastrointestinal Tract ◽  
Gut Microbiome ◽  
Antibiotic Resistance Genes ◽  
Systemic Absorption ◽  
Beta Lactamase ◽  
Beta Lactam ◽  
Oral Amoxicillin ◽  
Amoxicillin Clavulanate ◽  
Lactamase Inhibitor

Beta-lactamases, enzymes produced by bacteria to degrade beta-lactam antibiotics, have been harnessed as therapeutics to protect the gut microbiome from damage caused by antibiotics. Proof-of-concept of this approach using SYN-004 (ribaxamase), a beta-lactamase formulated for oral delivery with intravenous (IV) penicillins and cephalosporins, was demonstrated with animal models and in humans. Ribaxamase degraded ceftriaxone in the gastrointestinal tract, protected the gut microbiome, significantly reduced the incidence of Clostridioides difficile disease and attenuated emergence of antibiotic resistant organisms. SYN-007 is a delayed release formulation of ribaxamase intended for use with oral beta-lactams. In dogs treated with oral amoxicillin, SYN-007 diminished antibiotic-mediated microbiome disruption and reduced the emergence of antibiotic resistance without altering amoxicillin systemic absorption. Here, SYN-007 function in the presence of clavulanate, a beta-lactamase inhibitor, was investigated. Dogs received amoxicillin (40 mg/kg, orally (PO), three times a day (TID)) or the combined antibiotic/beta-lactamase inhibitor, amoxicillin/clavulanate (40 mg/kg amoxicillin, 5.7 mg/kg clavulanate, PO, TID) +/™ SYN-007 (10 mg, PO, TID) for five days. Serum amoxicillin levels were not significantly different +/™ SYN-007 compared to amoxicillin alone or amoxicillin/clavulanate alone as controls for both first and last doses, indicating SYN-007 did not interfere with systemic absorption of the antibiotic. Whole genome shotgun metagenomics analyses of the fecal microbiomes demonstrated both amoxicillin and amoxicillin/clavulanate significantly reduced diversity and increased the frequency of antibiotic resistance genes. Microbiome damage appeared more severe with amoxicillin/clavulanate. In contrast, with SYN-007, microbiome diversity was not significantly altered, and frequency of antibiotic resistance genes did not increase. Importantly, SYN-007 functioned in the presence of clavulanate to protect the gut microbiome indicating that SYN-007 activity was not inhibited by clavulanate in the dog gastrointestinal tract. SYN-007 has the potential to expand microbiome protection to beta-lactam/beta-lactamase inhibitor combinations delivered orally or systemically.

scholarly journals Oral Beta-Lactamase Protects the Canine Gut Microbiome from Oral Amoxicillin-Mediated Damage

2019 ◽  
Vol 7 (5) ◽  
pp. 150 ◽  
Author(s):  
Sheila Connelly ◽  
Brian Fanelli ◽  
Nur A. Hasan ◽  
Rita R. Colwell ◽  
Michael Kaleko
Keyword(s):  
Antibiotic Resistance ◽  
Small Intestine ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Antibiotic Resistance Genes ◽  
Oral Antibiotic ◽  
Beta Lactamase ◽  
Gi Tract ◽  
Beta Lactam ◽  
Beta Lactam Antibiotics

Antibiotics damage the gut microbiome, which can result in overgrowth of pathogenic microorganisms and emergence of antibiotic resistance. Inactivation of antibiotics in the small intestine represents a novel strategy to protect the colonic microbiota. SYN-004 (ribaxamase) is a beta-lactamase formulated for oral delivery intended to degrade intravenously administered beta-lactam antibiotics in the gastrointestinal (GI) tract. The enteric coating of ribaxamase protects the enzyme from stomach acid and mediates pH-dependent release in the upper small intestine, the site of antibiotic biliary excretion. Clinical benefit was established in animal and human studies in which ribaxamase was shown to degrade ceftriaxone in the GI tract, thereby preserving the gut microbiome, significantly reducing Clostridioides difficile disease, and attenuating antibiotic resistance. To expand ribaxamase utility to oral beta-lactams, delayed release formulations of ribaxamase, SYN-007, were engineered to allow enzyme release in the lower small intestine, distal to the site of oral antibiotic absorption. Based on in vitro dissolution profiles, three SYN-007 formulations were selected for evaluation in a canine model of antibiotic-mediated gut dysbiosis. Dogs received amoxicillin (40 mg/kg, PO, TID) +/- SYN-007 (10 mg, PO, TID) for five days. Serum amoxicillin levels were measured after the first and last antibiotic doses and gut microbiomes were evaluated using whole genome shotgun sequence metagenomics analyses of fecal DNA prior to and after antibiotic treatment. Serum amoxicillin levels did not significantly differ +/- SYN-007 after the first dose for all SYN-007 formulations, while only one SYN-007 formulation did not significantly reduce systemic antibiotic concentrations after the last dose. Gut microbiomes of animals receiving amoxicillin alone displayed significant loss of diversity and emergence of antibiotic resistance genes. In contrast, for animals receiving amoxicillin + SYN-007, microbiome diversities were not altered significantly and the presence of antibiotic resistance genes was reduced. These data demonstrate that SYN-007 diminishes amoxicillin-mediated microbiome disruption and mitigates emergence and propagation of antibiotic resistance genes without interfering with antibiotic systemic absorption. Thus, SYN-007 has the potential to protect the gut microbiome by inactivation of beta-lactam antibiotics when administered by both oral and parenteral routes and to reduce emergence of antibiotic-resistant pathogens.

scholarly journals 1140 – Syn-007, an Oral Beta-Lactamase Prevents Gut Microbime Dysbiosis Caused by Oral Amoxicillin and Oral Amoxicillin/Clavulanate Without Affecting Amoxicillin Systemic Absorption in Dogs

2019 ◽  
Vol 156 (6) ◽  
pp. S-241-S-242
Author(s):  
Sheila Connelly ◽  
Christian Furlan Freguia ◽  
Brian C. Fanelli ◽  
Nur A. Hasan ◽  
Rita Colwell ◽  
...  
Keyword(s):  
Systemic Absorption ◽  
Beta Lactamase ◽  
Oral Amoxicillin ◽  
Amoxicillin Clavulanate

scholarly journals ACI-1 class A beta-lactamase is widespread across human gut microbiomes due to transposons harboured by tailed prophages

2017 ◽  
Author(s):  
Chris M Rands ◽  
Elizaveta V Starikova ◽  
Harald Brüssow ◽  
Evgenia V Kriventseva ◽  
Vadim M Govorun ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antibiotic Resistance Genes ◽  
Mobile Element ◽  
Antibiotics Resistance ◽  
Beta Lactamase ◽  
Mobile Dna ◽  
Beta Lactam ◽  
Human Gut ◽  
Class A ◽  
The Usa

AbstractAntibiotic resistance is increasing among pathogens at unprecedented rates and the human body contains a large pool of antibiotic resistance genes that can be spread among bacteria by mobile genetic elements. Acidaminococcus intestini, a bacterium found in the human gut that belongs to the class of Negativicutes, is the first gram-negative coccus shown to be resistant to beta-lactam antibiotics. Resistance is conferred by aci1, a gene encoding the ACI-1 class A beta-lactamase, but the evolutionary history of aci1 and its distribution across other Negativicutes and in the human gut microbiota remains obscure. We discovered that ACI-1 proteins are phylogenetically distinct from class A beta-lactamases of gram-positive Firmicutes and that the aci1 gene occurs in bacteria scattered across the Negativicutes clade, suggesting possible mobilization. In the reference A. intestini RyC-MR95 strain, we found that aci1 is surrounded by mobile DNA, transposon derived sequences directly flank aci1 and are likely the vehicle for its mobility. These transposon sequences reside within a prophage context consisting of two likely degraded tailed prophages, the first prophages to be characterised in A. intestini. We found aci1 in at least 56 (4.4%) out of 1,267 human gut metagenome samples, mostly hosted within A. intestini, and, where could be determined, mostly within a similar constellation of mobile elements to that found in the reference A. intestini genome. These human samples are from individuals in Europe, China and the USA, showing that aci1 is widely distributed globally. Additionally, we examined the nine different Negativicute genome assemblies that contain aci1, and found that only two of these strains show a similar mobile element context around aci1 to the reference A. intestini with transposons adjacent to a tailed prophage. However, in all nine cases aci1 is flanked by transposon derived sequences, and these sequences are diverse, suggesting the activity and degradation of multiple transposons. Overall, we show that ACI-1 proteins form a distinct class A beta lactamase family, and that the aci1 gene is present in human guts worldwide within Negativicute bacterial hosts, due to transposons, sometimes inserted into tailed prophages.

scholarly journals 673. Novel Delayed-Release Formulation of an Oral β-Lactamase Prevents Gut Microbiome Damage and Attenuates Antibiotic Resistance Caused by Oral Amoxicillin/Clavulanate without Interfering with Amoxicillin Systemic Absorption in Dogs

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S307-S307
Author(s):  
Sheila Connelly ◽  
Christian Furlan-Freguia ◽  
Brian Fanelli ◽  
Nur A Hasan ◽  
Rita R Colwell ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Small Intestine ◽  
Gut Microbiome ◽  
Clinical Stage ◽  
Serum Levels ◽  
Systemic Absorption ◽  
Release Formulation ◽  
Microbiome Composition ◽  
Delayed Release ◽  
Oral Amoxicillin

Abstract Background Exposure of the gut microbiota to antibiotics can alter the composition of the microbiome and lead to the emergence and spread of antibiotic resistance. SYN-004 (ribaxamase) is a clinical-stage β-lactamase intended to degrade certain IV β-lactam antibiotics in the GI tract to preserve the gut microbiome. In a phase 2b clinical study, ribaxamase significantly reduced C. difficile infection in patients treated with IV ceftriaxone. A new delayed-release ribaxamase formulation, SYN-007, intended for use with oral β-lactams, was evaluated in dogs that received oral amoxicillin plus the β-lactamase inhibitor, clavulanate (amox/clav). Methods SYN-007 was engineered for release in the lower small intestine, distal to the site of antibiotic absorption. Dogs received amox/clav (40 mg/kg amox/5.7 mg/kg clav, PO, TID) +/- SYN-007 (10 mg, PO, TID) for 16 doses. Amoxicillin serum levels were measured by LC/MS/MS after the first and last doses. DNA, isolated from feces collected before and after antibiotic treatment, was analyzed by whole-genome shotgun sequencing using CosmosID, Inc. metagenomics software. Results Serum amoxicillin levels were not significantly different +/- SYN-007 after the first and last doses of amox/clav. Microbiome analyses revealed that amox/clav disrupted the gut microbiome resulting in loss of some species and overgrowth of other taxa. SYN-007 attenuated changes to gut microbiome composition. Amox/clav exposure resulted in the emergence of many, mainly TEM β-lactamase genes that was reduced with SYN-007. Conclusion Oral amox/clav disrupted the gut microbiome in dogs and resulted in the emergence of β-lactamase genes. SYN-007 diminished amox/clav-mediated microbiome disruption and attenuated emergence of β-lactamase genes. SYN-007 did not interfere with amox systemic absorption indicating that the β-lactamase was not released in the upper small intestine, the site of oral amoxicillin absorption. Antibiotic inactivation represents a potential new treatment paradigm for preservation of the gut microbiome and reduction of antibiotic resistance. SYN-007 has the potential to expand β-lactamase-mediated microbiome protection to oral as well as IV β-lactam antibiotics. Disclosures All authors: No reported disclosures.

REVERSION OF ANTIBIOTIC RESISTANCE WITH BETA-LACTAMASE INHIBITOR FROM MEDICINAL PLANTS

2017 ◽  
Vol 10 (10) ◽  
pp. 204
Author(s):  
Sneha Arora ◽  
Shoma Paul Nandi
Keyword(s):  
Antibiotic Resistance ◽  
Medicinal Plants ◽  
Ethyl Acetate ◽  
Ethyl Acetate Extract ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Beta Lactamase ◽  
Beta Lactam ◽  
Lactamase Inhibitor

  Objective: Screening of medicinal plants for the presence of beta-lactamase inhibitor identified three plants; Terminalia chebula, Terminalia bellirica, and Ocimum tenuiflorum, extracts of which inhibit beta-lactamase enzyme in vitro. The objective of this study was to evaluate and compare beta-lactamase inhibiting potential of these plant extracts.Methods: Extracts of these plants were prepared with 6 solvents of different polarity. Beta-lactamase inhibition study was performed using antibiotic-resistant bacteria in bioassay and by micro-iodometric assay. Multidrug-resistant clinical strains of Escherichia coli and laboratory strain with plasmid carrying beta-lactamase gene as positive control were used.Results: Our results from bioassay, as well as micro-iodometric assay for enzyme activity, confirmed the presence of beta-lactamase inhibitor in these plant extracts. Among the extracts made by different solvents, hexane and ethyl acetate extract of T. chebula, hexane extract of T. bellirica, and all extracts of O. tenuiflorum except dichloromethane, possessed beta-lactamase inhibitor. Multidrug-resistant clinical isolate of E. coli AIIMS-1 could be reverted by applying 50 μg/μl of extract of all the medicinal plants. The micro-iodometric result showed highest beta-lactamase inhibition with O. tenuiflorum extracts. Comparative evaluation of the O. tenuiflorum extracts with increasing concentration of inhibitor suggests that ethyl acetate extract of O. tenuiflorum contains the highest inhibition potential, which is comparable with clavulanic acid.Conclusion: The results demonstrated that the ethyl acetate extract of O. tenuiflorum contain the highest level of beta-lactamase inhibitor, which in the future can be used as an alternative to synthetic beta-lactamase inhibitors that are presently being used to control beta-lactam antibiotic resistance

An Orally Delivered Beta-Lactamase Protects the Gut Microbiome from Antibiotic-Mediated Damage and Mitigates the Propagation of Antibiotic-Resistance Genes in a Porcine Dysbiosis Model

2017 ◽  
Vol 152 (5) ◽  
pp. S1305-S1306
Author(s):  
Sheila Connelly ◽  
Christian Furlan Freguia ◽  
Poorani Subramanian ◽  
Nur A. Hasan ◽  
Rita R. Colwell ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Antibiotic Resistance Genes ◽  
Beta Lactamase

scholarly journals Detection of ESBL and MBL Antibiotic Resistance Genes in 100 Clinical Isolates of Escherichia Coli by Multiplex PCR

2021 ◽  
Author(s):  
bahman Ghadami Petroudi ◽  
Rahman Shokri ◽  
Davoud Esmaeili
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Multiplex Pcr ◽  
Bacterial Infections ◽  
Antibiotic Resistance Genes ◽  
Test Method ◽  
Antibiotic Administration ◽  
Beta Lactamase ◽  
Beta Lactam ◽  
Biochemical Tests

Abstract Bckground: Increasing use of beta-lactam antimicrobials in the treatment of bacterial infections has increased resistance against them. Objectives: This study aimed to investigate the patterns of antibiotic susceptibility to beta-lactam antibiotics and to investigate the presence of beta-lactamase and Metallo-beta-lactamase genes blaKPC, blaTEM, blaAmpc, blaIND, blaSIM, and blaGIM in clinical specimens of Escherichia coli.Methods: In this study, 100 urine samples were collected from different wards of hospitals and treatment centers in the west of Tehran province, and 100 strains of Escherichia coli were confirmed by biochemical tests. In the next step, a susceptibility test was performed on 3 selected antibiotics. Then, using the Combine Disk Test method, ESBL and MBL strains were identified. Finally, using the multiplex PCR method, the strains producing KPC, TEM, Ampc, IND, GIM, and SIM enzymes were identified.Results: In this study, the highest resistance of strains to cefotaxime was observed. n = 52 (52%) and their highest sensitivity to imipenem was seen n = 95 (95%). Also, n = 53 (53%) of the samples had ESBL genes. Also, 41 isolates (77%) of the studied strains contained the blaTEM gene, 12 isolates (23%) of the strains contained the blaAmpc gene and 20 isolates (38%) of the strains contained blakpc gene. Also, n= 19 (19%) of the samples had MBL genes. Also, 4 isolates (21%) of the strains contained the IND gene, 4 isolates (21%) of the strains contained the GIM gene, 7 isolates (37%) contained the SIM gene.Conclusion: Due to the high percentage of resistance to third-generation cephalosporins, careful antibiogram testing before antibiotic administration in infections caused by ESBL and MBL-producing organisms is an unavoidable necessity. Therefore, by quickly and correctly identifying the pattern of antibiotic resistance, the physician will be able to select the appropriate antibiotic therapy and prevent the spread of antibiotic resistance.

scholarly journals Detection of ESBL and MBL Antibiotic Resistance Genes in 100 Clinical Isolates of Escherichia Coli by Multiplex PCR

2021 ◽  
Author(s):  
Bahman Ghadami Petroudi ◽  
Rahman Shokri ◽  
Davoud Esmaeili
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Multiplex Pcr ◽  
Bacterial Infections ◽  
Antibiotic Resistance Genes ◽  
Test Method ◽  
Antibiotic Administration ◽  
Beta Lactamase ◽  
Beta Lactam ◽  
Biochemical Tests

Abstract Background: Increasing use of beta-lactam antimicrobials in the treatment of bacterial infections has increased resistance against them. Objectives: This study aimed to investigate the patterns of antibiotic susceptibility to beta-lactam antibiotics and to investigate the presence of beta-lactamase and Metallo-beta-lactamase genes blaKPC, blaTEM, blaAmpc, blaIND, blaSIM, and blaGIM in clinical specimens of Escherichia coli.Methods: In this study, 100 urine samples were collected from different wards of hospitals and treatment centers in the west of Tehran province, and 100 strains of Escherichia coli were confirmed by biochemical tests. In the next step, a susceptibility test was performed on 3 selected antibiotics. Then, using the Combine Disk Test method, ESBL and MBL strains were identified. Finally, using the multiplex PCR method, the strains producing KPC, TEM, Ampc, IND, GIM, and SIM enzymes were identified.Results: In this study, the highest resistance of strains to cefotaxime was observed. n = 52 (52%) and their highest sensitivity to imipenem was seen n = 95 (95%). Also, n = 53 (53%) of the samples had ESBL genes. Also, 41 isolates (77%) of the studied strains contained the blaTEM gene, 12 isolates (23%) of the strains contained the blaAmpc gene and 20 isolates (38%) of the strains contained blakpc gene. Also, n= 19 (19%) of the samples had MBL genes. Also, 4 isolates (21%) of the strains contained the IND gene, 4 isolates (21%) of the strains contained the GIM gene, 7 isolates (37%) contained the SIM gene.Conclusion: Due to the high percentage of resistance to third-generation cephalosporins, careful antibiogram testing before antibiotic administration in infections caused by ESBL and MBL-producing organisms is an unavoidable necessity. Therefore, by quickly and correctly identifying the pattern of antibiotic resistance, the physician will be able to select the appropriate antibiotic therapy and prevent the spread of antibiotic resistance.

scholarly journals Machine learning leveraging genomes from metagenomes identifies influential antibiotic resistance genes in the infant gut microbiome

2017 ◽  
Author(s):  
Sumayah F. Rahman ◽  
Matthew R. Olm ◽  
Michael J. Morowitz ◽  
Jillian F. Banfield
Keyword(s):  
Machine Learning ◽  
Antibiotic Resistance ◽  
Relative Abundance ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Statistical Tests ◽  
Antibiotic Resistance Genes ◽  
Major Facilitator Superfamily ◽  
Antibiotic Administration ◽  
Beta Lactamase

AbstractAntibiotic resistance in pathogens is extensively studied, yet little is known about how antibiotic resistance genes of typical gut bacteria influence microbiome dynamics. Here, we leverage genomes from metagenomes to investigate how genes of the premature infant gut resistome correspond to the ability of bacteria to survive under certain environmental and clinical conditions. We find that formula feeding impacts the resistome. Random forest models corroborated by statistical tests revealed that the gut resistome of formula-fed infants is enriched in class D beta-lactamase genes. Interestingly,Clostridium difficilestrains harboring this gene are at higher abundance in formula-fed infants compared toC. difficilelacking this gene. Organisms with genes for major facilitator superfamily drug efflux pumps have faster replication rates under all conditions, even in the absence of antibiotic therapy. Using a machine learning approach, we identified genes that are predictive of an organism’s direction of change in relative abundance after administration of vancomycin and cephalosporin antibiotics. The most accurate results were obtained by reducing annotated genomic data into five principal components classified by boosted decision trees. Among the genes involved in predicting if an organism increased in relative abundance after treatment are those that encode for subclass B2 beta-lactamases and transcriptional regulators of vancomycin resistance. This demonstrates that machine learning applied to genome-resolved metagenomics data can identify key genes for survival after antibiotics and predict how organisms in the gut microbiome will respond to antibiotic administration.ImportanceThe process of reconstructing genomes from environmental sequence data (genome-resolved metagenomics) allows for unique insight into microbial systems. We apply this technique to investigate how the antibiotic resistance genes of bacteria affect their ability to flourish in the gut under various conditions. Our analysis reveals that strain-level selection in formula-fed infants drives enrichment of beta-lactamase genes in the gut resistome. Using genomes from metagenomes, we built a machine learning model to predict how organisms in the gut microbial community respond to perturbation by antibiotics. This may eventually have clinical and industrial applications.

scholarly journals Impact of Hospital Wastewater on the Occurrence and Diversity of Beta-Lactamase Genes During Wastewater Treatment with an Emphasis on Carbapenemase Genes: A Metagenomic Approach

2021 ◽  
Vol 9 ◽  
Author(s):  
Jakub Hubeny ◽  
Sławomir Ciesielski ◽  
Monika Harnisz ◽  
Ewa Korzeniewska ◽  
Tomasz Dulski ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
High Throughput Sequencing ◽  
Municipal Wastewater ◽  
Wastewater Treatment Plants ◽  
Antibiotic Resistance Genes ◽  
Taxonomic Diversity ◽  
Beta Lactamase ◽  
Hospital Wastewater ◽  
Beta Lactam

The diversity of beta-lactam antibiotic resistance genes, with particular emphasis on carbapenemase genes, during the treatment process at two wastewater treatment plants (WWTPs) with different levels of hospital wastewater inflow was investigated using high-throughput sequencing. An additional aspect of the study was to determine the taxonomic diversity of microorganisms in the studied samples. The obtained results suggest that bacteria of the Fusobacteriaceae family, not associated to date with this phenomenon, may be involved in the spread of antibiotic resistance in the environment. In samples from both wastewater treatment plants, the dominant beta-lactamase genes included blaOXA, blaGES, blaBEL, blaCfxA, and blaTEM. It is worth noting that the blaKPC and blaNDM genes were only found in untreated municipal wastewater with a higher hospital wastewater content. Moreover, an increase in the abundance of the blaIMP gene after the biological treatment stage in the studied treatment plants was found. In wastewater characterized by a higher proportion of hospital wastewater, 94 correlations were observed, while in wastewater with its lower proportion, 41 correlations were noted. Considering the above, the current research indicates that the inflow of hospital wastewater contributes to the spread of antibiotic resistance in the aquatic environment.

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