Clinical Trial Details
— Status: Completed
Administrative data
| NCT number |
NCT03199287 |
| Other study ID # |
2017-00114 |
| Secondary ID |
|
| Status |
Completed |
| Phase |
|
| First received |
|
| Last updated |
|
| Start date |
June 8, 2017 |
| Est. completion date |
March 30, 2021 |
Study information
| Verified date |
April 2021 |
| Source |
University Hospital, Geneva |
| Contact |
n/a |
| Is FDA regulated |
No |
| Health authority |
|
| Study type |
Observational
|
Clinical Trial Summary
Infective endocarditis (IE) is an infection of cardiac valves. IE mainly involves bacteria,
more rarely fungi. IE is an uncommon diseases with an estimated incidence of 1-12 cases per
100,000 inhabitants per year. The diagnostic of IE relies on the culture of biological
samples (blood cultures and per-operative samples) in the bacteriology laboratory in order to
identify the pathogen and its susceptibility to antimicrobials. Nonetheless in about 10% of
the cases, the blood cultures remain negative, due to antibiotics taken before harvesting, to
non-culturable bacteria or to aseptic phenomena.
Clinical metagenomics is defined as the application of high-throughput sequencing (NGS)
followed by a specific bioinformatics analysis to obtain clinical information, i.e. pathogen
identification and the prediction of their susceptibility to antimicrobials. The metagenome
of a sample (i.e. all the genomes of the organisms present) virtually contains all the
information necessary for bacteriological diagnosis: what is the pathogenic bacteria , and to
which antibiotics it is susceptible.
Hence, using clinical metagenomics in the context of IE appears seducing in order to overcome
the limitations of conventional methods based on culture. Here, we propose to assess the
performance of clinical metagenomics in the diagnostic of IE.
Description:
Background and Rationale Infective endocarditis (IE) is an infection of cardiac valves. IE
mainly involves bacteria, more rarely fungi. IE is an uncommon diseases with an estimated
incidence of 1-12 cases per 100,000 inhabitants per year. The diagnostic of IE relies on the
collection of biological samples (blood cultures and per-operative samples) and their culture
in the bacteriology laboratory, referred to as conventional methods.
This process, practically unchanged since the time of Pasteur at the end of the 19th century,
has the disadvantage of allowing the only detection of the bacteria that can be grown under
the usual conditions of a laboratory. If most pathogenic bacteria can do so, some bacteria
that may be involved in IE (eg Coxiella sp., Bartonella sp., Tropheryma whipplei) require
very specific conditions to multiply. In addition, the prior intake of antibiotics by the
patient before the sample collection may negatively influence the culture of the samples. The
diagnosis of IE is evoked by considering a range of clinical arguments (fever,
microbiological risk behavior (positive blood culture(s), serology (for Coxiella burnettii),
echography (presence of an intra-cardiac mass, abscess, leakage and / or disinsertion of a
valve), all of which are minor and major criteria for determining the certainty of IE. The
treatment of IE is based on prolonged antibiotics (4 to 6 weeks for the majority of cases)
and valvular surgery (according to precise indications).
In about 10% of the cases, however, the blood cultures remain negative. These are known as
negative culture IE, which may be due to antibiotics taken before sampling, to non-culturable
bacteria or to aseptic phenomena. The broad-range PCR which consists of amplifying by PCR
then sequencing a fraction of the 16S RNA encoding gene can then be used. It allows the
identification of the pathogenic bacterium, but does not give information on any resistance
acquired to antibiotics.
Concept of clinical metagenomics Clinical metagenomics is defined as the application of
high-throughput sequencing (NGS) followed by a specific bioinformatics analysis to obtain
clinical information, i.e. pathogen identification and the prediction of their susceptibility
to antimicrobials. The metagenome of a sample (i.e. all the genomes of the organisms present)
virtually contains all the information necessary for bacteriological diagnosis: what is / are
the pathogenic bacteria (s), and to which antibiotics it/they is/are susceptible. The concept
of clinical metagenomics has developed in parallel with the new DNA sequencing technologies
introduced in the mid-2000s and much more efficient in terms of throughput than the
sequencing method described by Sanger. While this concept is attractive, there are still many
obstacles to its implementation. First, clinical specimens from bacterial infections usually
contain a high concentration of leukocytes, the genome of which is about 1000 times larger
than that of bacteria. Thus, the first limiting step for clinical metagenomics is the need to
obtain sufficient bacterial DNA to allow the preparation of quality libraries for sequencing,
but also to reduce the concentration of human DNA whose sequencing is unnecessary in this
context . Methods are available but their evaluation for clinical metagenomics purposes is
necessary. Secondly, the complexity of the bioinformatics data to be managed by a
microbiologist requires that data be exploited as automated as possible together with a
user-friendly interface, which is not the case today even if online platforms are being
developed. The taxonomic assignment of sequences, their assembly, the identification of genes
and chromosomal mutations associated with antibiotic resistance, and the establishment of a
link between the resistance determinant and the host bacterium are additional obstacles to
the implementation of clinical metagenomics. Finally, if the time taken to obtain results
that can be exploited by the microbiologist tends to decrease, it is now comparable to that
of culture, at a much higher cost. However, sustained competition between sequencer
manufacturers should maintain their decline as has been the case over the last decade.
Relevance of the use of clinical metagenomics in IE
The use of clinical metagenomics in the context of IE therefore seems relevant for several
reasons:
- Most IE are monomicrobial, which support the good performance of clinical metagenomics
according to our preliminary results.
- The culture of intraoperative samples performed in an IE context is sometimes negative,
due to antibiotic pre-treatment and / or non-cultivation under the routine conditions of
the pathogen (eg Bartonella spp or Coxiella spp.), leaving room for improvement.
- The treatment of IE is a long-term treatment that requires accurate diagnosis in
accordance with pathogens' susceptibility to antibiotics. If the pathogen is not found
in culture, broad spectrum antibiotics should be administered to the patient with a
double risk of treatment failure and toxicity. However, clinical metagenomics could
provide information on antibiotic sensitivity even in the case of a negative culture.
- In most cases, the microbiological diagnosis of IE is not an emergency diagnosis, which
is compatible with the use of clinical metagenomics for which the time of implementation
is at best 48-72h.
Hence, we propose to assess the performance of clinical metagenomics in the diagnostic of IE.
