Human Microbiome Journal 16 (2020) 100071

Contents lists available at ScienceDirect

Human Microbiome Journal

journal homepage: www.elsevier.com/locate/humic

Fecal microbiota transplantation for antibiotic resistant bacteria T

decolonization
Sophie Amrane, Jean-Christophe Lagier
⁎

Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France

ARTICLE INFO ABSTRACT

Keywords: Patients colonized with antibiotic resistant bacteria are at risk of infections and spontaneous decolonization
Fecal microbiota transplantation delays are highly variable between patients. The management of these patients is therefore time-consuming;
Decolonization requires patient isolation, and cohort policies. Fecal microbiota transplantation (FMT) has been used with the
Antibiotic resistance aim of shortening this gut colonization. Here, we proposed a comprehensive literature review on FMT utilization
Vancomycin resistant Enterococcus faecium
for gut antibiotics resistant bacteria decolonization. After literature research through Pubmed indexed for
And carbapenem resistant Enterobacteriaceae
MEDLINE, we analyzed 23 studies with description of FMT utilization and analyze of gut decolonization. In total,
the data involved 197 patients, 153 of whom underwent FMT. Overall, 66.7% (102/153) of the patients were
decolonized after FMT. However, we noticed a lot of interpretation bias, such as variation in colonization de-
finition and high disparities in FMT administration modalities. Two disparities were of special interest: repeated
FMT seems to increase the effectiveness of decolonization, and gut decolonization with antibiotics before FMT
was proposed by some authors, but with too few studies to draw a conclusion. Overall, the use of FMT is a
promising perspective for intestinal decolonization, but it requires greater standardization.

1. Introduction:
Intestinal colonization with highly drug-resistant enteric bacteria i.e
Vancomycin resistant Enterococcus faecium (VRE) and carbapenem re-
sistant Enterobacteriaceae can be high, reaching up to 109 micro-
organism/g of feces in an animal model [1], which facilitated spread
between patients in hospital. Patients colonized with antibiotics re-
sistant bacteria are at risk of infection. In a study conducted on im-
munocompromised patients, VRE colonization was associated with an
increased risk of VRE infection (adjusted odd ratio 3.61(2.01–6.47))
[2]. Malignant hematologic population has a high risk of both coloni-
zation with antibiotics resistant bacteria and translocation and then
infection with those bacteria during neutropenia and damage to the
gastro-intestinal tract [3]. Amit et al. [4] retrospectively studied the
occurrence of blood stream infection in the 45 days following carba-
penem resistant -K. pneumoniae colonization portage detection. They
did not found specific exposition risk for carbapenem resistant -K.
pneumoniae bloodstream infection, but mentioned C. difficile infection
or use of broad-spectrum antibiotics as exposition risk for gram-nega-
tive roads blood stream infections. Antibiotic resistance consequences
were evaluated in 2015 at 33,110 death a year in Europa [5]. However,
this number is probably overestimated compared to reality [5] and
antibiotic resistance consequences are first experienced in day care
organization.
The management of patients colonized with antibiotics resistant
bacteria is time-consuming, requires patient isolation, screening of
contact patients and cohort policies. In a literature review in 2010,
Abad et al. recorded negative impact of isolation on patients well being
and safety [6]. They mentioned among others, higher scores of anxiety
or depression with HADS score elevation in proportion to the duration
of isolation, health care workers half as likely to enter patients' rooms in
contact isolation, more errors in processes of care (incomplete re-
cording vital signs, more days with no physician or nursing notes in the
charts), patients were eight times more likely to experience supportive
care failure, such as fall, ulcers or electrolytes abnormalities. For co-
lonized patients, the duration of hospitalization increased and their
access to reeducation centers are limited [7]. The economic cost of
antibiotics resistant bacteria is estimated at $20 billion in excess med-
ical spending each year in the United States [8]. In a German analysis of
antibiotic resistant bacteria colonization, additional costs were eval-
uated at €1480 for each hospitalization [9].
Spontaneous decolonization delays are highly variable between
studies. After ICU admission in 8 European countries, decolonization
occurred in a median of 4.8 month [10]. In a multicentric French study,
spontaneous decolonization of VRE and carbapenem resistant En-
terobacteriaceae occurred for 48.2% of the patient in a median duration

⁎
Corresponding author at: Aix Marseille Univ, IRD, APHM, MEPHI, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France..
E-mail address: jclagier@yahoo.fr (J.-C. Lagier).

https://doi.org/10.1016/j.humic.2020.100071

Available online 06 May 2020

2452-2317/ © 2020 Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/BY/4.0/).
 Table 1
(Part 1): Literature review: Case or study with utilization of FMT for antibiotic-resistant bacteria decolonization.
Study Design Nr Age Sex IS Stool or Rectal swab FMT for Bowel PPI Admini Stool Fresh Stool Antibiotics Eradication
positive with lavage stration route donor Frozen volume

Singh, 2014 [36] Case report 1 60 M Yes ESBL E. coli D Yes nd ND U Fresh nd No D14
Nederland D-1 in 500 mL
S. Amrane and J.-C. Lagier

Freedman, 2014 [23] Case report 1 14 F Yes CR K.pneumoniae D Yes Yes ND R Fresh 30 g No Yes
USA D-2, D-1 (nd) in 70 mL
Jang, 2015 [26] Korea Case report 1 33 M No VRE CDI No nd 1st E R Fresh 300 g Vancomycin No
C. difficile 2nd ND in 400 mL Metronidazole until
FMT
Lagier, 2015 [42] Case report 1 82 F nd CR K. pneumoniae D Yes nd NG U Frozen 50 g in Colimycin D7
France D-1 400 mL 2,5 MUI qid,
Gentamycin
100 mg qid D-1
Lombardo, 2015 [33] Retrospective analyze of 8 Nd Nd Nd VRE CDI Yes nd Capsules U Frozen 150 g Until FMT 8/8 D28
USA prospective data C. difficile D-1 treated
with
ethanol
Bilinski, 2016 [38] Case report 1 51 M Yes CR K. pneumoniae D Yes Yes ND U Fresh 100 g No D10
Poland ESBL E. coli D-1 D-1 bid in 100 mL
Dubberke, 2016 [27] Retrospective analyze of 11 75 4M No VRE CDI nd nd E U Frozen 50 g Vancomycin 8/11 at M6, 4/5 at D30
USA prospective data 7F C. difficile in 150 mL until FMT
Eysenbach, 2016 [32] Retrospective case control 16 Nd nd nd VRE CDI nd nd nd nd nd nd nd 9/9 in FMT group
USA study C. difficile 3/7 in control group
(autologous FMT)

(Part 2): Literature review: Case or study with utilization of FMT for antibiotic-resistant bacteria decolonization.

2
Study Design Nr Age Sex IS Stool or Rectal FMT for Bowel PPI Administration Stool Fresh Stool Antibiotics Eradication
swab positive with lavage route donor Frozen volume

Garcia-Fernande, 2016 Case report 1 84 F No CR K. oxytoca CDI nd nd C R nd 100g No D6

[28] Spain C. difficile in 500mL
Sohn, 2016 [29] Korea Case report 3 72, 73 and F No VRE D nd nd E R nd 100g in No No
79 C. difficile (2/3) 200mL
Bilinski, 2017 [40] Prospective 20 51 14M Yes CRE, D Yes Yes ND U nd 100g in No 15/20 D30
Poland monocentric (22–77) 6F CR P. aeruginosa, D-1 D-1 qd, 100mL
uncontrolled study VRE, ESBL D0 bid
Davido, 2017 [37] Prospective 8 69 6M No CRE D Yes Yes ND U Frozen 50g in No 2/8 D30, 3/8 M2
France monocentric (43–87) 2F VRE D-1 D-2 qd, 250mL
uncontrolled study D-1 qd
Innes, 2017 [41] UK Case report 1 36 M Yes CRE D Yes Yes NG U Frozen nd in Vancomycin 500 mg D7
D-1 H-1 100mL qid,
Neomycin 500 mg
qid, D-5 - > D-1
Lahtien, 2017 [51] Case report 1 31 F No ESBL D nd nd C nd nd nd nd Yes D42
Finland
(continued on next page)
Human Microbiome Journal 16 (2020) 100071
 Table 1 (continued)

(Part 2): Literature review: Case or study with utilization of FMT for antibiotic-resistant bacteria decolonization.

Study Design Nr Age Sex IS Stool or Rectal FMT for Bowel PPI Administration Stool Fresh Stool Antibiotics Eradication
swab positive with lavage route donor Frozen volume

Ponte, 2017 [52] Case report 1 66 F nd CR K. pneumoniae CDI nd nd ND nd nd nd in nd D15

S. Amrane and J.-C. Lagier

Portugal C. difficile 50mL

Stalenhoef, 2017 [25] Case report 1 34 M No CR P. aeruginosa, D Yes nd ND U Fresh 75g in No Yes D7, No
Nederland ESBL D-1 300mL eradication of ESBL

(Part 3): Literature review: Case or study with utilization of FMT for antibiotic-resistant bacteria decolonization

Study Design Nr Age Sex IS Stool or Rectal FMT for Bowel PPI Administration Stool Fresh Stool Antibiotics Eradication
swab positive lavage route donor Frozen Volume
with

Dias, 2018 [31] Cases report 2 66 and 70 F No CRE CDI nd nd nd nd nd nd nd D30

Portugal C. difficile
Dinh, 2018 [35] Prospective 17 73 11 M 6F No CRE D Yes Yes NG U Frozen 70-100g No 3/8 CRE, 3/9 VRE D7; 4/8
France multicentric (43–87) VRE D-1 D-2 qd, in 250mL CRE, 7/8 VRE M3 (no
controlled study D-1 qd statistical difference)
Saidani, 2018 [7] Retrospective 30 59,9 24 M No CRE D Yes Yes NG U Frozen 50-100g Colimycin 8/10 D14,
France matched case (21–88) 6F A. baumanii D-5, D-1 D-1 qd, in 400mL 6MUI qid, 2/20 in control group
control study H-1, Aminoglycoside
D1-D2 200mg qid
qd D-6 - > D-1
Singh, Prospective 15 56 5M Yes ESBL D Yes nd ND U Fresh 50g No 3/15 D14 (20%),
2018 [34] monocentric (21–76) 10F (5/ D-1 in nd 2 FMT for 7 patients

3
Nederland uncontrolled study 15) with 3/7 success
- > 6/15 (40%) D14
Battipaglia, Retrospective 10 48 4M Yes CRE, D nd nd E (9), U (2) Frozen 8, 84g No 4/4 before allo HSCT, 3/6
2019 [24] monocentric study (16–64) 6F CR P. NG (1) R (8) Fresh 2 in 200mL after allo HSCT,
France aeruginosa, VRE 2 FMT for 3 patients
(time to decolonization
not precised)
Davido, 2019 [53] Prospective 8 65,5 5M nd VRE D Yes Yes NG U (2 Frozen 50g No 5/8 M1, 7/8 M3
France monocentric (50–80) 3F D-1 D-2 qd, donors) in 250mL
uncontrolled study D-1 qd
Huttner, 2019 [22] Randomized open 39 65 18 M No CRE, D No Yes NG U Frozen, 40g Colimycin 9/22 M1,
Switzerland label superiority (57–72) 21F ESBL D-1 qd, or in 80mL 2MUI qid, 5/17 in control group,
trial D0 qd Capsules Neomycin OR 1,7 (0,4–6,4)
350 mg qid,
D-6- > D-1

Nr: Number of patients, ID: Immunosuppressed patients, FMT: fecal microbiota transplantation, PPI: Proton pomp inhibitors, M: Male, F: Female, CRE: Carbapenem Resistant Enterobacteria, VRE: Vancomycine resistant
E. faecium, ESBL: extended spectrum β-lactamase Enterobacteriaceae, D: Decolonization, CDI: C. difficile infection, NG: Nasogastric, ND: Nasoduodenal, E: Enema, C: Colonoscopy, U: unrelated, R: related, nd: no data
available.
Human Microbiome Journal 16 (2020) 100071
S. Amrane and J.-C. Lagier
Table 2
Number of patients treated by FMT for gut colonization with antibiotic resistant bacteria and success rate classified by bacteria.
Colonization with N° of patients N° of eradication
Acinetobacter 2 2 (100%)
CR Enterobacteriaceae 66 44 (66.7%)
ESBL 52 28 (53.8%)
CR P. aeruginosa 7 6 (85.7%)
S. maltophila 1 1 (100%)
VRE 54 44 (81.5%)
of 49 days (1–1091) [11]. In a German study, decolonization occurred
for majority (65%) of the patients after 6 months of follow up [12], the
duration of colonization was correlated with the length of hospital stay.
In an other study, without intervention colonization rates of carba-
penem resistant Enterobacteriaceae and extended spectrum beta-lacta-
mase (ESBL) Enterobacteriaceae dropped from 76.7% at one month to
35.2% at twelve months of follow up [13].
To shorten this decolonization period, fecal microbiota transplan-
tation (FMT) is currently experienced. Gut microbiota composition
analysis [14] led to a new approach in understanding of some diseases.
Disruption of the gut microbiota composition has been fund during
Clostridium difficile infection (CDI) and identified as the triggering factor
of the diseases [15]. In the aim to restore gut homeostasis, FMT method
has been developed for CDI treatment, mainly for recurrent infections,
but as a primary indication for serious infections [16]. Millan et al. [17]
demonstrated by shotgun metagenomics and DNA microarray targeting
354 resistant genes, a reduction of antibiotic resistant bacteria genes
after FMT (formerly done for CDI treatment). These data were con-
firmed by Jouhten et al. [18]. The authors draw attention to the risk of
antibiotic resistant bacteria genes transmission from donor to receiver,
donor screening for antibiotic resistant bacteria gene should be pro-
posed in selection criteria.
Here, we proposed a comprehensive literature review on the use of
FMT for gut antibiotics resistant bacteria decolonization.
1.1. Method
We conducted a literature review from January 2000 to March 2020
through Pubmed indexed for MEDLINE with “FMT AND colonization”;
“FMT AND decolonization”; “FMT and multi-drug resistant”; “FMT and
carbapenem resistant”; “FMT and vancomycin resistant” queries. The
search was limited to articles written in English language and involving
humans. We selected by reading the title or the abstract of case reports
or clinical studies on this subject. Several cases were added by cross-
referencing using references cited in the articles.
We obtained a selection of 26 studies with a description of the use of
FMT for intestinal decolonization. By reading the articles, we excluded
three studies: the first because no specific evaluation of antibiotics re-
sistant bacteria colonization was performed, authors just mentioned a
decreased of events (colonization or infection) after FMT performed for
CDI infection [19], the second because VRE colonization was char-
acterized by metagenomic relative abundance (which declined after
FMT) [20], and the third because FMT was proposed for MRSA enteritis
treatment without indication on gut colonization with enteric anti-
biotics resistant bacteria [21].
2. Results:
2.1. FMT indication, efficiency and side effects
Overall, we analyzed 23 studies with a description of the use of FMT
and an analysis of intestinal decolonization (Table 1). Articles reviewed
were highly heterogeneous; they ranged from 2014 to 2019. They have
all been conducted in rich countries: Europa, USA, Israel or Korea. We
found only one randomized controlled trial [22] and twelve cases
4
Human Microbiome Journal 16 (2020) 100071
Delay of eradication References
D14 D30 [7,40]
D7-M2 [7,22–24,28,30,31,35,37,38,40]–[42]
D7-M2 [22,25,34,36,38,40,51]
D7- D30 [24,25,40]
D30 [40]
D10-M6 [24,26,27,29,32,33,35,37,40,53]
reports or case series. In total, the data involved 197 patients, 153 of
whom underwent FMT. Only two case reports concerned an infant (14
and 16 years-old) [23,24]. Antibiotic resistant bacteria colonization
were various between studies, concerning VRE, carbapenem resistant
Enterobacteriaceae, carbapenem resistant-P. aeruginosa, A. baumanii, or
ESBL Enterobacteriacae (Table 2). In two case reports and one study
[23–25] (or for five patients), antibiotics resistant bacteria were im-
plicated in systemic infections and not only colonization. Primary in-
dication of FMT was the treatment of CDI for 40 patients in four case
reports and three studies [26–33].
Regarding the efficiency, overall, 66.7% (102/153) of the patients
were decolonized after FMT. In the twelve case reports, 11/15 (73%)
patients were decolonized within two months following FMT. For the
eleven other studies, the decolonization rate was highly variable, from
20% [34] to 100% [32,33]. Dinh et al. [35] proposed comparison of
FMT efficiency for gut decolonization of carbapenem resistant En-
terobacteriaceae versus VRE, and reported no statistical differences.
Saidani et al. [7], in a retrospective match controlled study, reported a
decolonization rate of 80% (8/10) two weeks after FMT, compared to
10% (2/20) in the control group. Decolonization protocol included
three days of naso-pharyngeal decolonization with chlorhexidine, two
bowel lavages, five days oral antibiotic decolonization and a patient
room change after FMT. Huttner at al. [22], in a randomized trial,
obtained decolonization for 41% patients (9/22) versus 30% (5/17) in
the control group, OR 1.7 (0.4–6.4).
Only one serious adverse event was described: a woman followed
for liver cirrhosis with former recurrent encephalopathy was hospita-
lized two weeks after FMT for acute encephalopathy [22]. For the other
studies, no severe secondary effects were described after FMT.
2.2. Interpretation biases:
Several biases limit the interpretation of these results. First, we
observed a lack of standardization for colonization and decolonization
definitions. For colonization definition, most of the authors just men-
tioned a positive culture more or less PCR confirmation. Singh et al.,
Sohn et al., Davido et al. added some details: colonization was defined
by three or four consecutive positive rectal swabs one week apart
[29,36,37]. Davido et al. specified that the last positive swab should be
performed in the week prior to FMT [37]. Decolonization definition was
also often unclear: negative culture more or less negative PCR result.
Some authors added details: with two or three negative rectal swab at
one week interval [7,24,38,39]. Secondly, the modes of evaluation and
length of follow up were strongly heterogeneous in the different studies.
As an example in prospective studies, Billinski et al. and Singh et al.
proposed follow up until one month after FMT [34,40], Davido at al.
and Dinh at al. until three months [35,37,39], and Huttner et al. after
six months [22]. Thirdly, in the different studies reviewed, FMT ad-
ministration was very diverse with volume of stool from 30 to 300 g.
Stools were more often reconstituted with a sterile saline solution.
Product was often frozen and donors unrelated. Preferred route of ad-
ministration was naso-duodenal or nasogastric. Two authors used an
oral administration with capsules: in Huttner et al. [22] study, two
centers administrated FMT though lyophilized capsules. Lombardo
et al. [33] used a preparation called SER-109: stools from donors were
S. Amrane and J.-C. Lagier Human Microbiome Journal 16 (2020) 100071

treated with ethanol solution with the aim of promoting sporulation

Estimated Study Completion Date
and selected Firmicutes bacteria, which were then administrated in
capsules. Other parts of the protocol varied, such as bowel preparation,
mentioned in thirteen studies, and often performed the day prior to
FMT. Only one author proposed two bowel lavages (one five days prior
to FMT and one the day before) [7]. Fasting before the FMT was spe-
cified only in two studies [33,41]. If notified, authors used proton pump
March

2019 June

2022 June
2023 Nov
inhibitor before FMT administration. Saidani et al. administered also
Dec

2019 Dec

2020 Dec

2023 Dec
Jun

2025 Jun
2024 Jan

2019 Fev
2019 Oct
2020 Oct
Jul

150 mL bicarbonate sodium before FMT [7], Innes et al. mentioned

2020
2018
2022
2021

administration of metoclopramide one hour before FMT for its proki-

netic effect [41]. Finally, antibiotics for decolonization are used by
some teams before FMT administration [7,22,41,42], other antibiotics
were for C. difficile treatment.
Estimated/Actual Study

2.3. FMT implication in treatment of other colonization sites

2019 March

2019 March

2020 March
started Date

2017 June

Among the articles reviewed, some authors analyzed other coloni-

2022 Sept
2014 Nov

2019 Nov
Aug

2017 Aug
Dec

2019 Dec
Fev

2018 Fev

2018 Fev
Jul

zation sites: Singh et al. proposed swabbing of pelvic region and throat
2015
2016
2016
2016

[36], Stalenhoef et al. and Saidani et al. proposed swabbing of the skin,
throat and a sample of urine [7,25]. In another study, Singh et al.
Switzerland

Hong Kong

sampled urine [34]. However, the results of colonization or decoloni-

Belgium
Country

Canada

Canada
France

zation of these other locations have not been reported in the articles.
Israel
Israel

Israel
USA

USA
USA

USA

USA

USA

Gut decolonization could have an impact on urinary infections fre-

quency. Stripling et al. mentioned no VRE infection relapse (urinary
Fecal Transplant, a Hope to Eradicate Colonization of Patient Harboring eXtreme Drug Resistant

A Trial of Encapsulated Fecal Microbiota for Vancomycin Resistant Enterococcus Decolonization

tract infection) after FMT (vesicle device was not mentioned in the
Fecal Microbiota Transplantation for Eradication of Carbapenem-resistant Enterobacteriaceae

Decolonization of Gram-negative Multi-resistant Organisms (MDRO) With Donor Microbiota

article) [20]. In 2014, Sing et al. proposed the use of FMT for gut de-
Eradication of Antibiotic-resistant Bacteria Through Antibiotics and Fecal Bacteriotherapy

FMT for multidrug resistant organisms Colonization After Infection in Renal Transplant

colonization of an ESBL-E. coli [36]. One patient had recurrent urinary

Autologous Fecal Microbiota Transplantation to Prevent Antibiotic Resistant Bacteria

Effectiveness of Fecal Flora Alteration for Eradication of Carbapenemase-producing

tract infection with ESBL microorganism with severe renal graft failure.
After FMT, he presented no more urinary tract infection. In a retro-
Fecal Microbiota Transplantation for Carbapenem-resistant Enterobacteriaceae
FMT for multidrug resistant organisms Colonization in Solid Organ Transplant

spective case controlled study, Tariq et al. analyzed urinary tract in-
fection frequency before and after FMT (for recurrent CDI treatment).
Phase II Trial of Fecal Microbiota Transplant for VRE and CRE Patients

They demonstrated a reduction in the incidence of these infections with

a median of four infections in the year preceding the FMT and one in
the year following the FMT [43]. In a recent publication, Hocquart et al.
presented a case of a woman with inflammatory bowel disease and
Fecal Microbiota Transplantation for Eradication of CRE

recurrent urinary tract infection, eight months after FMT she had no
recurrence of urinary infection [44].
FMT for Multidrug Resistant Organism Reversal

Fecal Microbiota Transplantation for CRE/VRE

Fecal Transplant for MDRO Decolonization

2.4. Modality of FMT protocol that could modify success rates

Among the decolonization procedures described, some author pro-

Enterobacteriaceae Colonization

posed oral antibiotics before FMT. In a literature review, Cheng et al.

[45] reported former uses of oral antibiotics for gut VRE decolonization
(more or less probiotic administration) with success rates ranging from
17.8% to 100%. In their work, the authors were the first to propose a
bowel lavage during the decontamination procedure; they obtained
VRE decolonization for 75% of their patients. Machuca et al. [46] de-
Colonization

Colonization
Recipients

monstrated a reduction of global mortality and a reduction carbapenem

Bacteria?
Current interventional study on FMT and gut decolonization.

(FMT)

resistant -K. pneumoniae infection with oral decontamination with

Title

aminoglycosides. Among the articles reviewed, two case reports

[41,42] proposed oral antibiotics for gut carbapenem resistant En-
terobacteriaceae decolonization before FMT, procedure succeeded in
Single group open label trial

Single group open label trial

Single group open label trial

Single group open label trial

Type of interventional study

Randomized open label trial

Randomized open label trial

Randomized open label trial

Randomized open label trial

Randomized open label trial

Randomized open label trial
Non randomized open label
Randomized blinded trial

Randomized blinded trial

Randomized blinded trial

Randomized blinded trial

both cases. Saidani et al. used antibiotics (Colimycin and Aminogly-

cosides) in their protocol with success for 8/10 (80%) patients [7].
Huttner et al. also included antibiotics (Colimycin and Neomycin) in
their protocol, eradication was obtained for 9/22 (41%) of the patients
[22].
Three authors mentioned more than one FMT for their patients with
trial

increased decolonization rate. Singh et al. [34] treated 15 patients, they

obtained 3/15 (20%) decolonization after one FMT, seven patients
Clinical trial number

underwent two FMT with a success rate of 3/7 (43%), bringing the
overall success rate to 6/15 (40%). Battipaglia et al. [24] treated ten
NCT02312986
NCT02472600
NCT02816437
NCT02922816

NCT03029078

NCT03061097

NCT03063437
NCT03167398
NCT03391674

NCT03479710

NCT03643887
NCT03802461

NCT04146337
NCT04181112
NCT04188743

patients, they obtained 5/10 (50%) decolonization after one FMT, 2/3
(67%) after two FMT with an overall success rate at 7/10 (70%). Sai-
Table 3

dani et al. [7], treated ten patients, they obtained 4/10 (40%) decolo-
nization after one FMT, 4/5 (80%) after two FMT with and overall

5
S. Amrane and J.-C. Lagier
success rate at 8/10 (80%) patients. Repeating FMT could increase the
chances of decolonization by a factor of almost two.
3. Conclusion:
We reviewed 23 articles on the use of FMT for gut decolonization.
To date, only one randomized controlled trial has been published.
Fifteen other trials results are expected (Table 3), their results will
contribute to expend our knowledge on this problematic. Some of these
trials propose FMT via oral capsule administration, this route of ad-
ministration has been used by Huttner et al. for 16/22 patients [22].
Oral capsules administration has former been evaluated for CDI treat-
ment [47] with non-inferiority compare to FMT administration via
colonoscopy. Repeated FMT appears to be necessary in some cases for
the eradication of antibiotic-resistant bacteria in the intestine, the use
of capsules could facilitate repeated administration.
Another area of research on the decolonization of antibiotic-re-
sistant bacteria with microbiota manipulation could be the adminis-
tration of specific bacteria. Ubeda et al. explored by 16S rRNA gene
sequencing bacteria population before and after reintroduction of a
diverse intestinal microbiota in a mice model. Barnesiella species were
associated with VRE clearance [1]. Lombardo et al. administrated a
consortium of bacteria (Firmicutes) to treat patients with recurrent C.
difficile infection and observed eradication of VRE carriage for 8/8
patients [33]. Association of selected bacteria have been tested with
success for C. difficile infection treatment [48,49] and tentative to find
the good consortium of bacteria are in progress [50]. The same tenta-
tive could be explored for the eradication of antibiotic-resistant bac-
teria.
Competing interest
None to declare.
Funding
None to declare.
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