Clinical Trial Details
— Status: Completed
Administrative data
| NCT number |
NCT04786938 |
| Other study ID # |
16943 |
| Secondary ID |
|
| Status |
Completed |
| Phase |
Phase 4
|
| First received |
|
| Last updated |
|
| Start date |
April 7, 2016 |
| Est. completion date |
June 9, 2017 |
Study information
| Verified date |
September 2021 |
| Source |
Universidad San Francisco de Quito |
| Contact |
n/a |
| Is FDA regulated |
No |
| Health authority |
|
| Study type |
Interventional
|
Clinical Trial Summary
Eradication therapy against Helicobacter pylori (Hp) carries adverse effects, such as
altering the intestinal microbiota's structure and function and selecting commensals and
pathogens resistant to antibiotics. This last undesirable effect turns the microbiota into a
reservoir of resistance genes. Saccharomyces boulardii CNCM I-745 (Sb) can improve dysbiosis
and reduce the abundance of multi-resistant bacteria. The objective of the current project is
to characterize the resistome of individuals treated with anti-H. pylori therapy in the
presence or absence of Sb in fecal samples. Applying metagenomics and using next-generation
sequencing tools, the investigators seek to demonstrate the beneficial effect of Sb on the
gut microbiota by reducing the abundance of resistance genes and characterizing bacteria
modulated by this probiotic-yeast. The investigators expect to find an increase in the
diversity and relative abundance of antibiotic resistance genes (ARGs) in the intestine of
participants who did not receive Sb during Hp eradication therapy and one month after
completing treatment. The increase in ARGs is probably correlated with the presence of
Clostridia and Bacteroides.
Description:
Antibiotic use is one of the most common therapeutic strategies of modern medicine. Together
with the significant beneficial effects of antibiotic use, side effects accompany the use of
these drugs, including the increasing appearance of antibiotic-resistant microbes, a global
public health problem. Other significant side effects include gastrointestinal-related
symptoms such as diarrhea, pain, intestinal discomfort, and flatulence, which can be the
consequence of dysbiosis. A common strategy to limit antibiotic-associated side effects is
the addition of probiotics, as S. boulardii CNCM I-745 (Sb). The use of bacterial probiotics
to reduce antibiotic-associated side effects has several potential limitations, including the
destruction of probiotics, development of probiotics strains resistant to antibiotics, and
passage of antibiotic-resistant genes to pathogenic bacteria through horizontal gene
transfer. Sb is a probiotic yeast whose benefits on intestinal dysbiosis have been associated
with establishing a favorable growth environment for the normal intestinal microbiota. Due to
the yeast nature of this probiotic, the limitations of bacterial-probiotics cannot be
accounted for during Sb use. Consequently, it is crucial to study the molecular mechanism
elicited by Sb on intestinal microbiota, including changes in resistome.
In our previous study regarding the supplementation with Sb on the treatment against H.
pylori (Hp) infection, patients that received the probiotic had a significantly lower
frequency of gastrointestinal symptoms. Additionally, those patients have a higher number of
bacterial diversity evenness (P=0.0156), higher abundance of Enterobactereacea, and lower
abundance of Bacteroides and Clostridia upon treatment completion and one month later.
Bacteroides and Clostridia have been previously implicated as antibiotic multi-resistant
pro-inflammatory strains. The objective of the current project is to characterize the
resistome of individuals treated with anti-H. pylori therapy in the presence or absence of Sb
in fecal samples.
Specific aims To determine the resistome changes before and after Hp eradication treatment in
patients that have received or not Sb.
To compare the resistome patterns between patients treated for Hp infection that have
received or not SB, at the time of completion of treatment and one month after finishing
them.
Based on the shotgun metagenomics, the researchers seek to characterize the microbiome and
resistome in fecal samples and understand the microbiome's functional characteristics,
including virulence genes, metabolic pathways, and mobile genetic elements.
Methodology DNA obtained from the previous microbiome characterization will be used in this
project. In case DNA is not enough, the researchers will extract DNA from the frozen stored
samples using the Power Soil kit.
DNA will be shipped to UNC Chapel Hill or the University of Minnesota, where genomic
libraries will be constructed. Hi-Seq Illumina runs will be used to produce a sequencing
deepness of 10 million per sample.
FASTQC will be used for reads quality control and multiQC as reports generator from the raw
reads. Trimmomatic will be used to trim Illumina adapters and to cut reads on the average
quality. As human DNA is present on the fecal samples, the investigators have to remove the
host DNA using the mapping software BWA and SAMtools. Using the Resfinder database, the
investigators must align the filtered reads and generate a count table using
ResistomeAnalyzer. Finally, the researchers can create rarefaction curves based on the table
made using AMRPlusPlus.
Expected results The researchers expect to find a higher diversity and abundance of
antibiotic resistance genes (genome intrinsic and carried by mobile genetic elements) on the
group that did not receive Sb at the end of treatment and one month after its completion.
This would be correlated with the lower abundance of Clostridia and Bacteroides encountered
in the 16S rRNA gene microbiome characterization.
The investigators will also be able to sub-characterize the resistome diversity and abundance
of antibiotic resistance genes encountered typically on Enterobacteriaceae. A previous
analysis found a higher abundance of Enterobacteriaceae in the group that received Sb
(previously reported in a mouse model by Sovran et al. 2018). Additionally, since the
researchers will obtain the raw reads on the shotgun sequencing, they could further
characterize the bacteria modulated by the use of Sb at strain level (Bacteroides,
Clostridia, and Enterobacteriaceae). Together, the researchers expect to obtain valuable data
on the use of Sb regarding antibiotic resistance and further microbiome characteristics,
including genes of bacterial pathogenicity. These results will contribute to clarify the
beneficial effects of Sb addition in patients treated for Hp infection.
