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1Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
Antibiotic- induced changes in the human gut microbiota for the most commonly prescribed antibiotics in primary care in the UK: a systematic review
Karen T Elvers ,1 Victoria J Wilson,2 Ashley Hammond ,2 Lorna Duncan,2 Alyson L Huntley ,2 Alastair D Hay,2 Esther T van der Werf 2,3
To cite: Elvers KT, Wilson VJ, Hammond A, et al. Antibiotic- induced changes in the human gut microbiota for the most commonly prescribed antibiotics in primary care in the UK: a systematic review. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
► Prepublication history and additional material for this paper are available online. To view these files, please visit the journal online (http:// dx. doi. org/ 10. 1136/ bmjopen- 2019- 035677).
Received 21 November 2019Revised 12 June 2020Accepted 02 July 2020
1Centre for Academic Primare Care & NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Bristol Medical School, University of Bristol, Bristol, UK2Centre of Academic Primary Care, Bristol Medical School, University of Bristol, Bristol, UK3Department of Integrative Medicine, Louis Bolk Institute, Bunnik, The Netherlands
Correspondence toDr Esther T van der Werf; e. vanderwerf@ louisbolk. nl
Original research
© Author(s) (or their employer(s)) 2020. Re- use permitted under CC BY. Published by BMJ.
ABSTRACTObjective The gut microbiota influences many aspects of human health. We investigated the magnitude and duration of changes in gut microbiota in response to antibiotics commonly prescribed in UK primary care.Methods We searched MEDLINE, EMBASE and AMED, all years up to May 2020 including all study designs, collecting and analysing data on the effect of antibiotics prescribed for respiratory and urinary tract infections. We followed the Preferred Reporting Items for Systematic Reviews and Meta- Analyses and Cochrane standard methods. Risk of bias was evaluated using the Critical Appraisal Skills Programme. Narrative synthesis was used to report the themes emerging from the data.Main outcome measures Primary outcomes were antibiotic- induced changes in the composition and/or diversity of the gut microbiota. Secondary outcome was the time for the microbiota to return to baseline.Results Thirty- one articles with low or unclear risk of bias showed that antibiotics impact the gut microbiota by causing rapid and diminished levels of bacterial diversity and changes in relative abundances. After cessation of treatment, gut bacteria recover, in most individuals, to their baseline state within a few weeks. Some studies suggested longer term effects from 2 to 6 months. Considerable heterogeneity in methodology makes the studies prone to biases and other confounding factors. Doxycycline was associated with a marked short- term decrease in Bifidobacterium diversity. Clarithromycin decreased the populations of Enterobacteria, and the anaerobic bacteria Bifidobacterium sp and Lactobacillus sp in numbers and diversity for up to 5 weeks. Phenoxymethylpenicillin, nitrofurantoin and amoxicillin had very little effect on the gut microbiome.Conclusions Despite substantial heterogeneity of the studies and small sample sizes, there is evidence that antibiotics commonly used in primary care influence the composition of the gastrointestinal microbiota. Larger population- based studies are needed to fully understand how antibiotics modulate the microbiota, and to determine if these are associated with (longer term) health consequences.PROSPERO registration number CRD42017073750.
INTRODUCTIONIn the UK, between 2000 and 2014, antibi-otic prescriptions increased from 14.3 to 19.7 defined daily doses (DDDs) per 1000 inhabitants per day. The volume of antibiotic prescribing has since decreased, reaching 18.7 DDDs per 1000 inhabitants per day in 2016 (http://www. oecd. org/). Misuse and overuse of antimicrobials, not only in medical sectors, but also in veterinary and agricultural sectors, result in increasing resistance, which globally limits our ability to control infec-tions. Decreasing antibiotic consumption is a key target to dealing with the problem, and the UK has implemented antimicrobial
Strengths and limitations of this study
► This review addresses the antibiotic- induced changes in gut microbiota for the most commonly prescribed antibiotics in UK primary care for the infections most frequently seen in general practice: respiratory tract and urinary tract infections.
► The study used a complete and inclusive search strategy complemented by manually scanning ref-erence lists of identified articles for further relevant publications.
► We searched three databases, all years up to May 2020, for any study type, with clearly defined criteria for study inclusion.
► It was not feasible to combine results in a meta- analysis as the majority of the studies were small, poorly randomised and with limited follow- up. There was considerable heterogeneity in methodology, which makes them prone to biases and other con-founding factors.
► This limits our understanding of the long- term changes induced by commonly prescribed antibi-otics, the ability to modify antibiotic treatment to each situation and to make recommendations to clinicians.
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stewardship interventions in primary care1 and detailed a 5- year action plan for tackling antimicrobial resistance.2
Data analysed from The Health Improvement Network (THIN) database stated that a median prescribing rate among participating practices was 626 antibiotic prescrip-tions/1000 patients (IQR 543–699), 69% of which could be linked to a body system and/or clinical condition.3 Of these prescriptions, 46% were linked to respiratory tract infections (RTIs) and 22.7% to infections of the urogen-ital tract. About half of all antibiotics prescribed were penicillin, of which approximately 55% was amoxicillin; this is followed by 13% macrolide use and 12% tetracy-cline.3 General practicioner (GP) consultation rates in England and Wales show that a quarter of the population will visit their GP because of an RTI each year.4 Antibiotic use to treat such infection varies between individual clini-cians and countries,4–6 but accounts for 60% of all antibi-otic prescribing in general practice.7–9 Similarly, urinary tract infections (UTIs) are commonly seen in primary care.10 Patients are frequently treated with antibiotics, even though the infection often is not microbiologically confirmed.11 The overuse of antibiotics for conditions that are not serious or where antibiotic treatment is not appropriate for the illness has led to their reduced effec-tiveness and emergence of resistant bacteria.
The normal gut microbiota consists of approximately 800–1000 different bacterial species and more than 7000 different strains.12 ‘Normal’ is defined as the commensal species predominantly and consistently found in the gut of healthy human. The composition of the oesopha-geal and gastric microbiomes is distinct from that of the colon. There is a greater diversity of species and number per gram of contents in the colon, reflecting its higher pH.13 14 The core microbiome in healthy individuals is dominated by phyla Firmicutes and Bacteroidetes (over 90%), followed by Verrucomicrobia and Actinobacteria.13 Some essential functions of a healthy gut microbiota include vitamin production, nutrient metabolism, immu-nomodulation and protection against infection by inhib-iting colonisation of the gut by pathogens. Studies into gut microbiomes from different countries have identified differences in diversity, which reflect the differences in diet, geography, early- life exposures and genetics.15 Age, diet, antibiotics, probiotics and prebiotics all contribute to the shaping of the healthy gut microbiota and this continues dynamically throughout life.13 14 16
These differences lead to microbiome dysbiosis, with increasing evidence that alterations to the human micro-biome can affect how well the immune system functions and its ability to resist infection17 18; increase the risk of developing Parkinson’s disease, multiple sclerosis and Alzheimer’s disease,19 the risk of depression, anxiety or psychosis20; and indirectly affect the health long term and risk of obesity and diabetes.21 There is increasing evidence that the microbiome is crucial in a cancer patient’s risk of infectious complications.22 Recent studies have shown that antibiotic exposure in childhood is associated with increased risk for several diseases including obesity, types
1 and 2 diabetes, inflammatory bowel diseases, Crohn’s disease, coeliac disease, autoimmune diseases such as allergies, juvenile idiopathic arthritis and asthma.23–26 It appears that these effects are most pronounced if the antibiotics are consumed within the first 2 years of life and the effects may well be cumulative.17 27 28 This is particu-larly important in young children, when the adult micro-biome has not been fully established.29 30 Once antibiotic treatment has stopped, the microbiome may present a certain degree of resilience, being capable of returning to a composition similar to the original one, but this is poorly understood and can take months or even years.17 31
Differences in perceptions about how risk- free antibi-otic treatment is may in part account for the enormous variation in rates of their use from practitioner to prac-titioner, between localities and across countries, but also within a specific group of practitioners such as GPs. The real cost of the most commonly prescribed antibiotics in primary care must be clearly understood, including the differences between particular antimicrobial agents in their effects on the microbiome. This information will be specifically useful for antimicrobial stewardship in primary care.
AIMThis study aimed to investigate the antibiotic- induced changes in gut microbiota for the most commonly prescribed antibiotics in primary care in the UK: those prescribed for RTIs and UTIs. Our primary outcome was defining any antibiotic- induced changes in the composi-tion of the gut microbiome, measured by (1) abundance and/or (2) diversity of the microbes, while our secondary outcome measured the time that is needed to restore the microbiome to a pre- antibiotic state.
METHODSA systematic literature review of studies that evaluated the association between antibiotics commonly prescribed for RTI and UTIs in primary care and their effect on the gut microbiome was conducted. Preferred Reporting Items for Systematic Reviews and Meta- analyses (PRISMA) guidelines and checklist were used as a framework for this review (see online supplemental table S1 PRISMA check-list).32 The study protocol was registered with PROSPERO number CRD42017073750 (http://www. crd. york. ac. uk/ PROSPERO).
Search strategyElectronic databases MEDLINE, EMBASE and AMED were used to identify relevant articles up to May 2020, in English and available as full text. A combination of search terms included the following keywords: (antibac-terial agents OR bacterial infections) AND (microbiota OR microbiome). The strategy was designed to identify studies conducted in any country, investigating antibiotic- induced changes in the human gut microbiota; analysed
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3Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
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at either the individual or the population level, published in any language (box 1). Reference lists of included studies and relevant reviews were hand- searched to iden-tify additional eligible studies. All selected abstracts and citations were exported from the scientific databases to the reference management software EndNote X9 (Thompson Reuters, New York, New York, USA) and duplicates excluded.
Study selection and eligibility criteriaA study was eligible for review if it reported quantitative changes to the gut microbiota due to treatment with antibiotics most commonly prescribed for RTI and UTI prescribed in primary care (table 1). RTIs included both upper respiratory tract infections (URTIs), including the common cold, laryngitis, pharyngitis/tonsillitis, acute rhinitis, acute rhinosinusitis and acute otitis media, and lower respiratory tract infections (LRTIs), including acute bronchitis, bronchiolitis, pneumonia and tracheitis. We included uncomplicated and recurrent urinary tract infections (UTI and rUTIs). We excluded any animal studies or hospital- based studies.
The main exposure of interest in this review was the effect commonly prescribed antibiotics have on the gut microbiome based on prescriptions advice included in the National Institute for Health and Care Excellence (NICE) guidelines1 8 33–35 and on current use as described in nation reports on antibiotic use.1 34 Of particular interest are those antibiotics that are commonly used in primary care for the treatment of both upper and lower RTIs (amoxicillin, phenoxymethylpenicillin, doxycy-cline, co- amoxiclav, erythromycin, clarithromycin) and UTIs (trimethoprim, nitrofurantoin, amoxicillin, cephalexin).
Screening, data extraction and managementFive reviewers (VW, KTE, EvdW, LD and AH) inde-pendently screened search results and assessed each potential study according to the inclusion and exclusion criteria. All decisions were recorded on a spreadsheet. Full- text papers for all eligible studies were obtained and three reviewers (VW, KTE, AH) independently screened the selected papers a second time.
The following data were extracted from the included studies into an Excel spreadsheet by one reviewer (KTE) and a percentage verified for accuracy by another (VW): author, journal, year of publication, study design, study country, number of participants, number of participants of interest to this review, age range, percentage of female participants, other inclusion criteria, exclusion criteria, recruitment methods, recruitment time period, sample type, primary outcome, secondary outcome, antibiotic (of interest to this review) used, any other antibiotics used, dose of antibiotics (of antibiotic of interest to this review), time course (of antibiotic of interest to this review), number of timepoints for collecting samples, time points for each sample collection, testing method, infection or condition, overall conclusion. A tabular summary was developed for this review, which included study ID, country, design, population, setting, infec-tion, antibiotic of interest, sample and analysis, primary outcome and main results (table 2).
Assessment of methodological qualitySelection bias was assessed with the Critical Appraisal Skills Programme (CASP) checklist ( www. casp- uk. net). Each component of the studies (ie, the appropriateness of the study design for the research question, the risk of selection bias, exposure measurement and outcome assessment) was graded and an overall grading used to produce quality assessment charts based on a traffic light system of ‘low’, ‘high’ and ‘unclear’ or ‘not applicable’, as recommended by Cochrane.36 Three reviewers (VW, KTE, EvdW) independently assessed the risk of bias in the studies with two reviewers (KTE, VW) assessing all studies, and discrepancies were resolved by consensus between the reviewers.
Data synthesis and analysisDue to the insufficient number of studies available, we were unable to undertake any sensitivity analysis to deter-mine robustness of the findings and the quality of the studies.36 The results are discussed descriptively.
Box 1 Search strategy
1. Anti- Bacterial Agents/ae, pd, tu2. Bacterial Infections/dt, mi3. Microbiota/4. (Microbiome or Microbiomes or Gut microbiome or Gut microbiomes
or Microbiota Gut or microbiota).mp5. Humans/6. 1 or 27. 3 or 48. 6 and 79. 5 and 8
Table 1 PICOS criteria for inclusion and exclusion of studies
Parameter Inclusion Exclusion
Participants Human adults and children Animals, in vitro
Intervention Specific antibiotics of interest prescribed in primary care
Other antibiotics
Comparator Negative controls or other antibiotics
None
Outcomes Changes in gut microbiota, total numbers, diversity and composition; time taken to recover
Antimicrobial resistance
Study design All study types None
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Tab
le 2
S
umm
ary
of s
tud
ies
incl
uded
in t
he r
evie
w
Stu
dy
IDC
oun
try
Des
ign
Po
pul
atio
nS
etti
ngIn
fect
ion
Ant
ibio
tic
of
inte
rest
(and
d
osa
ge)
Sam
ple
and
ana
lysi
sP
rim
ary
out
com
eR
esul
ts
Am
oxi
cilli
n
De
La C
oche
tière
et
al (
2005
)37Fr
ance
Coh
ort
N=
6 ad
ults
Volu
ntee
rsH
ealth
yA
mox
icill
in (5
00 m
g th
ree
times
a
day
for
5 d
ays)
Faec
al s
amp
les;
16S
rR
NA
P
CR
and
TTG
E g
el a
naly
sis
and
seq
uenc
e an
alys
is
To a
sses
s th
e ab
ility
of t
he
hum
an fa
ecal
mic
rob
iota
to
ret
urn
to it
s or
igin
al
dom
inan
t sp
ecie
s p
rofil
e af
ter
a 5-
day
cou
rse
of
amox
icill
in
Sim
ilarit
y in
dic
es o
f the
TTG
E
pr o
files
on
D1
rang
ed fr
om 9
3%
to 9
9%; o
n D
3 62
%–8
2% a
nd
D4
46%
–94%
. On
D30
and
D60
, th
ese
had
rai
sed
bac
k to
65%
–95
% a
nd 6
6%–9
8%, r
esp
ectiv
ely.
B
and
s ex
cise
d fr
om t
he g
el
rela
ted
to
Clo
strid
ium
nex
ile a
nd
Rum
inoc
occu
s to
rque
s (a
nd
β-P
rote
obac
teria
). N
o no
rmal
isat
ion
of b
acte
rial a
bun
dan
ce D
55 a
fter
an
tibio
tic t
reat
men
t.
Mon
real
et
al
(200
5)38
Bra
zil
Pro
spec
tive
N=
42 a
dul
ts; 2
0 co
ntro
lsE
mer
genc
y d
epar
tmen
t;
blo
od d
onor
ce
ntre
s
Bac
teria
l res
pira
tory
in
fect
ions
(sin
usiti
s,
pne
umon
ia)
Am
oxic
illin
Faec
al s
amp
les
anal
ysed
by
cultu
re a
nd C
FU o
n b
lood
ag
ar
Inve
stig
ated
the
influ
ence
of
resp
irato
ry t
ract
infe
ctio
ns
and
of a
mox
icill
in t
hera
py
on t
he n
orm
al in
test
inal
m
icro
bio
ta o
f pat
ient
s
Con
cent
ratio
ns o
f Bac
tero
ides
, B
ifid
obac
teriu
m s
pp
Lac
tob
acill
us
spp
wer
e si
gnifi
cant
ly d
ecre
ased
in
the
antib
iotic
gro
up. A
fter
30
day
s,
abun
dan
ce o
f Bifi
dob
acte
rium
and
La
ctob
acill
us h
ad n
orm
alis
ed.
Pal
lav
et a
l (20
14)39
US
AR
CT
N=
24; 8
with
am
oxic
illin
, 8
cont
rols
, 8 o
ther
Clin
ical
and
tr
ansl
atio
nal
scie
nce
cent
re
Hea
lthy
Am
oxic
illin
250
mg
thre
e tim
es
a d
ay fo
r 7
day
s16
S r
RN
A g
ene
seq
uenc
ing
regi
on n
s R
oche
454
GS
FLX
Ti
tani
um G
reen
Gen
es/R
DP
/N
CB
I Dat
abas
e
Effe
ct o
f am
oxic
illin
vs
cont
rols
The
gene
ra t
hat
are
mos
t ab
und
ant
are
Faec
alib
acte
rium
, B
acte
roid
es, R
osb
uria
, Clo
strid
ium
an
d R
umin
ococ
cus.
No
chan
ge in
b
acte
rial a
bun
dan
ce in
the
con
trol
gr
oup
. The
mos
t no
tab
le c
hang
e w
as a
n in
crea
se in
Esc
heric
hia/
Shi
gella
dur
ing
antib
iotic
tre
atm
ent.
A
lso
incr
ease
in B
acte
roid
es b
ut
dec
reas
e in
Fae
calib
acte
rium
sp
p.
Ant
ibio
tic- a
ssoc
iate
d c
hang
es
per
sist
ed t
o th
e en
d o
f the
stu
dy,
42
day
s af
ter
antib
iotic
the
rap
y en
ded
.
Ab
eles
et
al
(201
6)40
US
AC
ohor
t of
un
rela
ted
co
hab
iting
in
div
idua
ls
rand
omly
as
sign
ed
N=
56 a
dul
tsU
nive
rsity
ca
mp
usS
elf-
rep
orte
d h
ealth
st
atus
Am
oxic
illin
500
mg
twic
e d
aily
fo
r 3
and
7 d
ays
16S
rR
NA
am
plifi
ed fr
om D
NA
us
ing
QIA
GE
N s
tool
Min
i Kit;
se
que
ncin
g
Effe
cts
of c
omm
only
p
resc
ribed
ant
ibio
tics
on
mic
rob
iota
Mic
rob
iota
gre
w m
ore
dis
sim
ilar
over
tim
e b
ut n
ot s
igni
fican
t.
Mos
t ab
und
ant
taxa
in g
ut w
ere
Bac
tero
idac
eae,
Lac
hnos
pira
ceae
an
d R
umin
ococ
cace
ae.
Lach
nosp
irace
ae,
Veill
onel
lace
ae, B
acte
roid
ales
an
d P
orp
hyro
mon
adac
eae
wer
e si
gnifi
cant
ly d
ecre
ased
. Fu
sob
acte
riace
ae in
crea
sed
. B
ifid
obac
teria
les
and
E
rysi
pel
otric
haec
ae in
itial
ly
dec
reas
ed. T
here
wer
e su
stai
ned
re
duc
tions
in m
icro
bio
me
div
ersi
ty
in r
esp
onse
to
amox
icill
in o
ver
6 m
onth
s.
Man
gin
et a
l (2
010)
41C
hile
Stu
dy
tria
lN
=42
infa
nts;
31
with
tr
eatm
ent
Hea
lth c
entr
eA
cute
bro
nchi
tisA
mox
icill
in 5
0 m
g/kg
/day
in
thre
e d
aily
dos
es fo
r 7
day
sFa
ecal
; rea
l- tim
e P
CR
for
Bifi
dob
acte
rium
, TTG
E a
nd
seq
uenc
e an
alys
is
To in
vest
igat
e th
e q
uant
itativ
e an
d q
ualit
ativ
e ch
ange
s oc
curr
ing
in
the
faec
al b
ifid
obac
teria
l p
opul
atio
ns in
18-
mon
th
child
ren
afte
r a
1- w
eek
amox
icill
in t
reat
men
t
Tota
l bac
teria
and
num
ber
s of
B
ifid
obac
teria
wer
e no
t si
gnifi
cant
ly
alte
red
by
amox
icill
in t
reat
men
t.
How
ever
, tre
atm
ent
chan
ged
sp
ecie
s d
iver
sity
, a c
omp
lete
d
isap
pea
ranc
e of
B. a
dol
esce
ntis
, in
crea
se in
B. b
ifid
um. N
o ef
fect
on
B. l
ongu
m, B
. pse
udoc
aten
ulat
um/B
. ca
tenu
latu
m.
Con
tinue
d
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rotected by copyright.http://bm
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MJ O
pen: first published as 10.1136/bmjopen-2019-035677 on 21 S
eptember 2020. D
ownloaded from
5Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
Stu
dy
IDC
oun
try
Des
ign
Po
pul
atio
nS
etti
ngIn
fect
ion
Ant
ibio
tic
of
inte
rest
(and
d
osa
ge)
Sam
ple
and
ana
lysi
sP
rim
ary
out
com
eR
esul
ts
Chr
iste
nsso
n et
al
(199
1)42
Sw
eden
Ran
dom
ised
d
oub
le- b
lind
p
aral
lel
mul
ticen
tre
tria
l
N=
84 a
dul
ts; 4
4 w
ith
trea
tmen
t (3
8/44
co
mp
lete
d)
Out
pat
ient
sLo
wer
res
pira
tory
tra
ct
infe
ctio
nA
mox
icill
in 2
50 m
g tw
ice
dai
ly
for
7 d
ays
Faec
al; c
ultu
red
aer
obic
ally
an
d a
naer
obic
ally
in b
roth
to
ID p
atho
geni
c m
icro
orga
nism
an
d o
n se
lect
ive
pla
tes
for
anal
ysis
of m
icro
flora
cha
nges
To c
omp
are
cefa
clor
and
am
oxic
illin
as
trea
tmen
t fo
r lo
wer
res
pira
tory
tra
ct
infe
ctio
ns a
nd in
the
ir ab
ility
to
influ
ence
col
onis
atio
n re
sist
ance
No
chan
ge in
ab
und
ance
of
Ent
eroc
occu
s sp
p, S
tap
hylo
cocc
us
spp
or
Str
epto
cocc
us s
pp
, whi
le
ente
rob
acte
ria s
igni
fican
tly
incr
ease
d. P
seud
omon
as s
p a
nd
Can
did
a al
bic
ans
wer
e is
olat
ed
from
som
e sa
mp
les.
Ana
erob
ic
cocc
i num
ber
s w
ere
red
uced
in
som
e p
atie
nts
and
incr
ease
d in
ot
hers
. Lac
tob
acill
i, b
ifid
obac
teria
, b
acte
roid
es a
nd e
ubac
teria
in
crea
sed
. A c
oup
le o
f pat
ient
s w
ere
colo
nise
d w
ith C
. diffi
cile
.
Bris
mar
et
al
(199
3)43
Sw
eden
Sin
gle
blin
d
rand
omis
ed
tria
l
N=
20 a
dul
ts; 1
0 w
ith
trea
tmen
tN
ot s
pec
ified
Hea
lthy
volu
ntee
rsA
mox
icill
in 5
00 m
g ev
ery
8 ho
urs
for
7 d
ays
Faec
al; s
elec
tive
med
ia, M
ICs,
b
eta
lact
amas
e ac
tivity
To s
tud
y th
e or
al a
nd
inte
stin
al m
icro
flora
b
efor
e, d
urin
g an
d
afte
r ad
min
istr
atio
n of
ce
fpod
oxim
e p
roxe
til a
nd
amox
icill
in
Num
ber
s of
aer
obic
inte
stin
al
mic
roflo
ra w
ere
slig
htly
affe
cted
by
amox
icill
in a
dm
inis
trat
ion.
A m
inor
d
ecre
ase
in n
umb
ers
of s
trep
toco
cci
and
sta
phy
loco
cci,
an o
ver
grow
th
of K
leb
siel
la a
nd E
nter
obac
ter
in a
co
uple
of s
amp
les.
No
over
grow
th
of e
nter
ococ
ci o
r ye
asts
occ
urre
d.
Eub
acte
ria w
as r
educ
ed b
y am
oxic
illin
. Inc
reas
e in
am
oxic
illin
- re
sist
ant
Ent
erob
acte
ricae
ae
(E. c
oli,
Kle
bsi
ella
sp
and
E
nter
obac
ter
sp) N
o ch
ange
in
abun
dan
ce o
f Bac
tero
ides
sp
p,
Bifi
dob
acte
rium
sp
p, E
nter
ococ
cus
spp
, Lac
tob
acill
us s
pp
or
yeas
t.
No
new
col
onis
atio
n w
ith C
. d
iffici
le. N
orm
alis
atio
n of
bac
teria
l ab
und
ance
14
day
s af
ter
antib
iotic
tr
eatm
ent.
Ed
lund
et
al
(199
4)44
Sw
eden
Coh
ort
N=
44 a
dul
ts, 1
0 w
ith
trea
tmen
tN
ot s
pec
ified
Not
sp
ecifi
edA
mox
icill
in 5
00 m
g t.
i.d fo
r 7
day
sFa
ecal
; ser
ial d
ilutio
ns a
nd
sele
ctiv
e p
latin
g ae
rob
ic a
nd
anae
rob
ic
The
inve
stig
atio
n w
as fo
cuse
d o
n d
rug
conc
entr
atio
ns in
faec
es,
bet
a la
ctam
ase
pro
duc
tion
by
the
inte
stin
al m
icro
flora
, al
tera
tions
in t
he m
icro
flora
an
d s
usce
ptib
ility
pat
tern
s
Ad
min
istr
atio
n of
am
oxic
illin
af
fect
ed t
he a
erob
ic in
test
inal
m
icro
flora
to
a m
inor
ext
ent.
The
re
was
an
over
grow
th o
f Kle
bsi
ella
sp
p a
nd E
nter
obac
ter
spp
in
som
e sa
mp
les.
No
chan
ge in
ab
und
ance
of a
naer
obic
bac
teria
, B
acte
roid
es s
pp
, Bifi
dob
acte
rium
sp
p, E
nter
ococ
cus
spp
, E. c
oli,
Clo
strid
ium
sp
p, L
acto
bac
illus
sp
p
or y
east
. No
colo
nisa
tion
with
C.
diffi
cile
. Int
estin
al m
icro
flora
ret
urne
d
to n
orm
al 2
wee
ks a
fter
tre
atm
ent
stop
ped
.
Tab
le 2
C
ontin
ued
Con
tinue
d
on February 25, 2021 by guest. P
rotected by copyright.http://bm
jopen.bmj.com
/B
MJ O
pen: first published as 10.1136/bmjopen-2019-035677 on 21 S
eptember 2020. D
ownloaded from
6 Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
Stu
dy
IDC
oun
try
Des
ign
Po
pul
atio
nS
etti
ngIn
fect
ion
Ant
ibio
tic
of
inte
rest
(and
d
osa
ge)
Sam
ple
and
ana
lysi
sP
rim
ary
out
com
eR
esul
ts
Lad
irat
et a
l (2
014)
45Th
e N
ethe
rland
sD
oub
le-
blin
ded
ra
ndom
ised
p
aral
lel
inte
rven
tion
stud
y
N=
12 a
dul
ts (t
wo
not
anal
ysed
due
to
non-
co
mp
lianc
e)
Not
sp
ecifi
edH
ealth
y vo
lunt
eers
Am
oxic
illin
375
mg
thre
e tim
es
dai
ly fo
r 5
day
sFa
ecal
; Int
estin
al (I
)- C
hip
m
icro
arra
y, t
otal
bac
teria
and
B
ifid
obac
teriu
m s
pp
usi
ng
qP
CR
Det
erm
ined
the
effe
cts
of p
reb
iotic
inta
ke o
n th
e m
icro
bio
ta o
f hea
lthy
adul
t su
bje
cts
dur
ing
and
aft
er
trea
tmen
t w
ith a
mox
icill
in
Tota
l bac
teria
and
Bifi
dob
acte
rium
w
ere
sim
ilar
in b
oth
grou
ps
bef
ore
trea
tmen
t. N
umb
ers
of
Bifi
dob
acte
rium
dec
reas
ed o
ver
time
due
to
amox
icill
in t
reat
men
t in
bot
h gr
oup
s, b
ut m
ore
so in
the
an
tibio
tic o
nly
grou
p (n
o p
reb
iotic
). A
fter
ant
ibio
tic t
reat
men
t, n
umb
ers
in t
he a
ntib
iotic
onl
y gr
oup
wer
e st
ill lo
wer
tha
n w
ith p
reb
iotic
s.
Ab
und
ance
of B
ifid
obac
teriu
m s
pp
, B
. lon
gum
and
B. t
herm
ophi
lum
w
as s
igni
fican
tly h
ighe
r in
the
p
reb
iotic
gro
up. T
he c
omp
ositi
on
of t
he m
icro
bio
ta in
mos
t su
bje
cts
retu
rned
to
norm
al a
fter
3 w
eeks
. D
ue t
o am
oxic
illin
tre
atm
ent,
a
dec
reas
e in
the
ab
und
ance
of
Bifi
dob
acte
rium
sp
p, a
n ov
ergr
owth
of
Ent
erob
acte
riace
ae.
Floo
r et
al (
1994
)46Th
e N
ethe
rland
sR
and
omis
ed
dou
ble
- blin
d
stud
y
N=
80 a
dul
tsR
ecru
ited
fr
om 9
gen
eral
p
ract
ices
Chr
onic
bro
nchi
tis w
ith
pur
ulen
t sp
utum
Am
oxic
illin
, 500
mg
thre
e tim
es
a d
ay fo
r 7
day
sFa
ecal
; cul
ture
d a
erob
ical
ly
and
ana
erob
ical
ly o
n se
lect
ive
med
ia, t
estin
g fo
r C
. diffi
cile
, en
tero
cocc
i, st
aphy
loco
cci,
yeas
ts a
nd b
ioch
emic
al
iden
tifica
tion
Effe
ct o
f bot
h am
oxic
illin
and
lo
raca
rbef
on
orop
hary
ngea
l an
d in
test
inal
mic
roflo
ra
No
chan
ge in
ab
und
ance
of
anae
rob
ic b
acte
ria o
r E
. fae
calis
. To
tal n
umb
ers
of a
erob
ic G
ram
- ne
gativ
e b
acte
ria s
igni
fican
tly h
ighe
r on
day
s 8–
10 t
han
at b
asel
ine.
E
nter
ococ
ci c
ultu
red
in o
ne p
atie
nt
in a
mox
icill
in g
roup
. Yea
st n
umb
ers
incr
ease
d s
igni
fican
tly b
ut r
etur
ned
to
bas
elin
e on
day
s 21
–28.
Pre
senc
e of
oth
er a
erob
ic b
acte
ria o
ccur
red
in
a s
light
ly h
ighe
r p
erce
ntag
e of
p
atie
nts
in t
he a
mox
icill
in g
roup
. 13
/15
new
acq
uire
d b
acte
ria in
the
am
oxic
illin
gro
up w
ere
Kle
bsi
ella
. N
o ne
w c
olon
isat
ion
with
C. d
iffici
le.
Nor
mal
isat
ion
of b
acte
rial a
nd fu
ngal
ab
und
ance
21
day
s af
ter
trea
tmen
t.
Am
oxi
cilli
n an
d c
lavu
lani
c ac
id
Kor
pel
a et
al
(201
6)31
Finl
and
Par
t of
a
coho
rt fr
om
larg
er p
rob
iotic
tr
ial
N=
236
child
ren;
142
d
onat
ed fa
ecal
sam
ple
sD
ay- c
are
cent
res
Ant
ibio
tic u
se fo
r re
spira
tory
(88%
) oth
er
mai
nly
urin
ary
(5%
)
Pen
icill
ins
(am
oxic
illin
w
ith o
r w
ithou
t cl
avul
anic
ac
id a
nd p
enic
illin
V),
mac
rolid
es (a
zith
rom
ycin
an
d c
larit
hrom
ycin
) and
su
lpho
nam
ide–
trim
etho
prim
Faec
al b
y 16
S r
RN
A
and
seq
uenc
e an
alys
is;
oper
atio
nal t
axon
omic
un
it (O
TU);
cultu
re- b
ased
an
tibio
tic s
ensi
tivity
tes
ting
Use
of p
hylo
gene
tics,
m
etag
enom
ics
and
an
tibio
tic u
se o
n m
icro
bio
ta
com
pos
ition
and
met
abol
ism
Mac
rolid
e us
e re
duc
ed a
bun
dan
ce
of A
ctin
obac
teria
and
incr
ease
d
Bac
tero
idet
es a
nd P
rote
obac
teria
. P
enic
illin
gro
ups
did
not
hav
e d
istin
ctly
diff
eren
t p
hyla
. Firm
icut
es
was
red
uced
. The
effe
ct o
f m
acro
lide
use
was
long
last
ing
and
w
as a
ssoc
iate
d w
ith in
crea
sed
ris
k of
ast
hma
and
ant
ibio
tic- a
ssoc
iate
d
wei
ght
gain
.
Tab
le 2
C
ontin
ued
Con
tinue
d
on February 25, 2021 by guest. P
rotected by copyright.http://bm
jopen.bmj.com
/B
MJ O
pen: first published as 10.1136/bmjopen-2019-035677 on 21 S
eptember 2020. D
ownloaded from
7Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
Stu
dy
IDC
oun
try
Des
ign
Po
pul
atio
nS
etti
ngIn
fect
ion
Ant
ibio
tic
of
inte
rest
(and
d
osa
ge)
Sam
ple
and
ana
lysi
sP
rim
ary
out
com
eR
esul
ts
Man
gin
et a
l (2
012)
47Fr
ance
Tria
lN
=18
tre
ated
, no
cont
rols
Stu
dy
cent
reH
ealth
y vo
lunt
eers
875/
125
mg
oral
dos
e of
am
oxic
illin
/cla
vula
nic
acid
tw
ice
a d
ay fo
r 5
day
s
Faec
al s
amp
les,
rea
l- tim
e P
CR
TTG
EA
mox
icill
in- c
lavu
lani
c ac
id
trea
tmen
t on
tot
al b
acte
ria
and
on
Bifi
dob
acte
rium
sp
ecie
s b
alan
ce in
hum
an
colo
nic
mic
rob
iota
Tota
l bac
teria
l con
cent
ratio
ns
as w
ell a
s b
ifid
obac
teria
co
ncen
trat
ions
wer
e si
gnifi
cant
ly
red
uced
aft
er a
ntib
iotic
tre
atm
ent.
Th
e m
ean
sim
ilarit
y p
erce
ntag
es
of T
TGE
bac
teria
and
TTG
E
bifi
dob
acte
ria p
rofil
es w
ere
sign
ifica
ntly
red
uced
. Occ
urre
nce
of B
. ad
oles
cent
is, B
. bifi
dum
an
d B
. pse
udoc
aten
ulat
um/B
. ca
tenu
latu
m s
pec
ies
sign
ifica
ntly
d
ecre
ased
. Occ
urre
nce
of B
. lon
gum
re
mai
ned
sta
ble
. Mor
eove
r, th
e nu
mb
er o
f dis
tinct
Bifi
dob
acte
rium
sp
ecie
s p
er s
amp
le s
igni
fican
tly
dec
reas
ed. B
acte
rial a
bun
dan
ce
was
not
nor
mal
ised
2 m
onth
s af
ter
antib
iotic
s st
opp
ed.
Fors
sten
et
al
(201
4)48
Finl
and
Ran
dom
ised
d
oub
le- b
lind
p
lace
bo
cont
rolle
d
par
alle
l stu
dy
N=
80 a
dul
ts; 4
0:40
p
rob
iotic
:pla
ceb
oVo
lunt
eers
Hea
lthy
Aug
men
tin (8
75 m
g am
oxic
illin
an
d 1
25 m
g cl
avul
anat
e) fo
r 7
day
s
Faec
al s
amp
les;
qP
CR
for
spec
ific
mic
rob
ial g
roup
sTo
inve
stig
ate
the
effe
ct
of a
sp
ecifi
c co
mb
inat
ion
of p
rob
iotic
str
ains
on
the
inci
den
ce o
f ant
ibio
tic-
ind
uced
mic
rob
iota
d
istu
rban
ces
Gen
eral
ly, L
acto
bac
illus
and
B
ifid
obac
teriu
m w
ere
incr
ease
d/
rest
ored
in t
he p
rob
iotic
gro
up
and
red
uced
in t
he p
lace
bo
grou
p.
Ant
ibio
tics
red
uced
leve
ls o
f C
lost
ridiu
m in
bot
h gr
oup
s, b
ut
incr
ease
d E
nter
obac
teria
ceae
.
Youn
g et
al (
2004
)49U
SA
Cas
e re
por
tN
=1
adul
t m
ale
Not
det
aile
dA
cute
sin
usiti
sA
mox
icill
in- c
lavu
lani
c ac
id (8
75
and
125
mg,
res
pec
tivel
y, t
wic
e d
aily
for
10 d
ays)
Faec
al s
amp
le 1
6S r
RN
A P
CR
an
d s
eque
ncin
g an
d a
naly
sis
Mol
ecul
ar p
hylo
gene
tic
surv
ey o
f the
faec
al
mic
rob
iota
from
a p
atie
nt
who
dev
elop
ed a
ntib
iotic
- as
soci
ated
dia
rrho
ea d
urin
g th
e ad
min
istr
atio
n of
a
bro
ad- s
pec
trum
ant
ibio
tic
D0,
seq
uenc
es c
lust
ered
with
in fo
ur
bac
teria
l gro
ups:
Bac
tero
ides
sp
p,
Clo
strid
ium
sp
IV, C
lost
ridiu
m s
p
XIV
a an
d B
ifid
obac
teriu
m. A
t D
4,
Bac
tero
ides
stil
l a m
ajor
com
pon
ent,
b
ut B
. dis
taso
nis
grou
p n
ot B
. fr
agili
s cl
uste
r. N
o C
lost
ridiu
m s
p
XIV
a or
Bifi
dob
acte
rium
sp
p. 3
4%
wer
e no
w E
nter
obac
teria
ceae
. D
24, p
artia
l rev
ersa
l, B
. fra
gilis
p
red
omin
ated
and
clu
ster
XIV
a re
turn
ed, n
o E
nter
obac
teria
ceae
, no
Bifi
dob
acte
rium
sp
p n
orm
alis
atio
n of
ab
und
ance
14
day
s af
ter
trea
tmen
t.
Eng
elb
reks
ton
et a
l (2
009)
50U
SA
Pro
bio
tic-
antib
iotic
stu
dy
arm
N=
40 a
dul
tsN
ot s
pec
ified
Hea
lthy
volu
ntee
rsA
gum
entin
(am
oxic
illin
and
cl
avul
anic
aci
d),
875
mg
twic
e d
aily
for
7 d
ays
Faec
al; T
RF
anal
ysis
, PC
R
and
enz
yme
dig
est,
bac
teria
l cu
lturin
g on
sel
ectiv
e m
edia
fo
r en
umer
atio
n of
diff
eren
t sp
ecie
s
Ana
lysi
s of
faec
al t
erm
inal
re
stric
tion
frag
men
t le
ngth
p
olym
orp
hism
dat
a fo
r tr
eatm
ent
effe
cts
of p
rob
iotic
tr
eatm
ent
conc
urre
nt w
ith
antib
iotic
the
rap
y
Ther
e w
as la
rge
sub
ject
- to-
sub
ject
va
riab
ility
. Sub
ject
s fe
ll in
to t
wo
cate
gorie
s: t
hose
with
sta
ble
b
asel
ine
mic
rob
iota
and
tho
se w
here
it
varie
d s
igni
fican
tly. A
ntib
iotic
s ha
d a
sig
nific
ant
effe
ct o
n fa
ecal
m
icro
bio
ta a
cros
s al
l sub
ject
s.
Cul
ture
dat
a al
so h
ad la
rge
varia
tion
in c
ount
s. In
crea
sing
tre
nds
wer
e vi
sib
le in
Bac
tero
ides
and
ent
eric
s at
day
21.
The
re w
as n
o tr
end
see
n fo
r C
lost
ridiu
m, B
ifid
obac
teriu
m
and
Lac
tob
acill
us. T
he p
lace
bo
grou
p h
ad a
sig
nific
ant
chan
ge fr
om
bas
elin
e at
day
21
in n
umb
ers
of
bac
teria
.
Tab
le 2
C
ontin
ued
Con
tinue
d
on February 25, 2021 by guest. P
rotected by copyright.http://bm
jopen.bmj.com
/B
MJ O
pen: first published as 10.1136/bmjopen-2019-035677 on 21 S
eptember 2020. D
ownloaded from
8 Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
Stu
dy
IDC
oun
try
Des
ign
Po
pul
atio
nS
etti
ngIn
fect
ion
Ant
ibio
tic
of
inte
rest
(and
d
osa
ge)
Sam
ple
and
ana
lysi
sP
rim
ary
out
com
eR
esul
ts
Lod
e et
al (
2001
)51G
erm
any
Volu
ntee
rsN
=12
ad
ults
Not
sp
ecifi
edH
ealth
yA
mox
icill
in/c
lavu
lani
c ac
id
1000
mg
(750
:125
mg,
re
spec
tivel
y) d
aily
Faec
al; c
ultu
re o
n se
lect
ive
agar
, col
onie
s co
unte
d,
isol
ated
and
iden
tified
to
genu
s le
vel
Inve
stig
ate
the
ecol
ogic
al
effe
cts
of li
nezo
lid,
com
par
ed w
ith t
hose
of
amox
icill
in/c
lavu
lani
c ac
id,
on t
he in
test
inal
hum
an
mic
roflo
ra
Am
oxic
illin
/Cla
vula
nic
acid
was
as
soci
ated
with
sig
nific
ant
incr
ease
in
num
ber
s of
ent
eroc
occi
and
E.
coli.
Oth
er a
erob
ic b
acte
ria w
ere
larg
ely
unaf
fect
ed. A
naer
obic
B
ifid
obac
teriu
m s
pp
, Clo
strid
ium
sp
p, L
acto
bac
illus
sp
p d
ecre
ased
si
gnifi
cant
ly. N
o ch
ange
in
abun
dan
ce o
f Bac
tero
ides
sp
p,
Gra
m- p
ositi
ve b
acill
i or
Kle
bsi
ella
sp
p. C
. diffi
cile
wer
e is
olat
ed fr
om
3 of
the
vol
unte
ers.
Som
e re
sist
ant
ente
rob
acte
ria s
uch
as E
. col
i, K
leb
siel
la s
p a
nd E
nter
obac
ter
sp
wer
e is
olat
ed. T
he m
icro
flora
was
no
rmal
ised
35
day
s af
ter
the
end
of
adm
inis
trat
ion.
Kab
ban
i et
al
(201
7)52
US
AS
ingl
e- ce
ntre
, op
en- l
abel
, ra
ndom
ised
co
ntro
lled
N=
49, 1
2 an
tiob
iotic
tr
eate
d, 1
2 co
ntro
lsC
linic
al a
nd
tran
slat
iona
l sc
ienc
e ce
ntre
Hea
lthy
volu
ntee
rsA
mox
icill
in/c
lavu
lana
te
875/
125
mg
twic
e d
aily
for
7 d
ays
16S
rR
NA
gen
e se
que
ncin
gTo
com
par
e an
d c
ontr
ast
the
effe
cts
of a
pro
bio
tic a
nd
antib
iotic
, the
mai
n en
dp
oint
w
as c
hang
e fr
om b
asel
ine
in
the
com
pos
ition
of t
he g
ut
mic
rob
iota
Low
er d
iver
sity
(OTU
s, C
hao
ind
ex)
d10
and
d21
. Inc
reas
ed a
bun
dan
ce
of P
arab
acte
roid
es s
pp
per
sist
ed
14 d
ays
afte
r an
tibio
tic t
reat
men
t w
as s
top
ped
. Con
trol
sub
ject
s ha
d
a st
able
mic
rob
iota
thr
ough
out
the
stud
y p
erio
d. S
igni
fican
t m
icro
bio
ta c
hang
es in
ant
ibio
tic
trea
tmen
t gr
oup
incl
uded
red
uced
p
reva
lenc
e of
the
gen
us R
oseb
uria
an
d in
crea
ses
in E
sche
richi
a,
Par
abac
tero
ides
and
Ent
erob
acte
r.
Mic
rob
iota
alte
ratio
ns r
ever
ted
to
war
d b
asel
ine,
but
wer
e no
t ye
t co
mp
lete
ly r
esto
red
2 w
eeks
aft
er
trea
tmen
t st
opp
ed.
Nit
rofu
rant
oin
Ste
war
dso
n et
al
(201
5)53
Sw
itzer
land
Pro
spec
tive
coho
rtN
=40
ad
ults
; 10
nitr
ofur
aton
inA
mb
ulat
ory
care
Low
er U
TIN
itrof
urat
onin
(100
mg
twic
e d
aily
for
5 d
ays)
Faec
al b
y 16
S r
RN
A a
nd
seq
uenc
e an
alys
is; O
TUC
omp
are
the
effe
cts
of c
ipro
floxa
cin
and
ni
trof
uran
toin
on
the
gut
mic
rob
iota
com
pos
ition
of
non-
hosp
italis
ed p
atie
nts
with
UTI
s co
mp
ared
with
p
atie
nts
with
out
antib
iotic
ex
pos
ure
and
hou
seho
ld
cont
acts
of p
atie
nts
rece
ivin
g ci
pro
floxa
cin
Cip
roflo
xaci
n ca
used
cha
nges
in a
nu
mb
er o
f gen
us o
f gut
bac
teria
. S
ubst
antia
l rec
over
y af
ter
4 w
eeks
. N
itrof
urat
onin
tre
atm
ent
corr
elat
ed
with
a n
on- s
igni
fican
t in
crea
se in
C
lost
ridiu
m s
pp
and
dec
reas
e in
Fa
ecal
ibac
teriu
m s
pp
. No
chan
ge
in a
bun
dan
ce o
f Alis
tipes
sp
p,
Bac
tero
ides
sp
p, B
ifid
obac
teriu
m
spp
, Bla
utia
sp
p, D
ialis
ter
spp
, E
ubac
teriu
m s
pp
. Osc
illos
pira
sp
p,
Ros
ebur
ia s
pp
or
Rum
inoc
occu
s sp
p.
Verv
oort
et
al
(201
5)54
Bel
gium
and
P
olan
dP
rosp
ectiv
e co
hort
N=
13; 5
con
trol
sA
mb
ulat
ory
pat
ient
s vi
sitin
g G
Ps
Unc
omp
licat
ed U
TIN
itrof
uran
toin
(100
mg
thre
e tim
es d
aily
for
3–15
day
s)Fa
ecal
; 16S
rD
NA
PC
R,
seq
uenc
ing
and
ana
lysi
sTh
e im
pac
t of
nitr
ofur
anto
in
trea
tmen
t on
the
ga
stro
inte
stin
al fl
ora
of
pat
ient
s w
ith u
ncom
plic
ated
U
TIs
Nitr
ofur
anto
in t
reat
men
t d
id n
ot
sign
ifica
ntly
imp
act
on t
he fa
ecal
m
icro
bio
ta o
ther
tha
n a
tem
por
ary
incr
ease
in t
he A
ctin
obac
teria
p
hylu
m (B
ifid
obac
teriu
m s
pp
). N
o ch
ange
in a
bun
dan
ce o
f B
acte
roid
etes
, Firm
icut
es,
Pro
teob
acte
ria, T
ener
icut
es o
r Ve
rruc
omic
rob
ia. N
orm
alis
atio
n in
ab
und
ance
of A
ctin
obac
teria
d31
-43
afte
r tr
eatm
ent.
Tab
le 2
C
ontin
ued
Con
tinue
d
on February 25, 2021 by guest. P
rotected by copyright.http://bm
jopen.bmj.com
/B
MJ O
pen: first published as 10.1136/bmjopen-2019-035677 on 21 S
eptember 2020. D
ownloaded from
9Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
Stu
dy
IDC
oun
try
Des
ign
Po
pul
atio
nS
etti
ngIn
fect
ion
Ant
ibio
tic
of
inte
rest
(and
d
osa
ge)
Sam
ple
and
ana
lysi
sP
rim
ary
out
com
eR
esul
ts
Mav
rom
anol
akis
et
al (1
997)
55G
reec
eR
and
omis
edN
=21
wom
en; 7
with
tr
eatm
ent
Not
sp
ecifi
edU
TI (a
t le
ast
thre
e ep
isod
es c
ause
d b
y E
nter
obac
teria
ceae
in
the
pre
ced
ing
12
mon
ths)
Nitr
ofur
anto
in (1
00 m
g d
aily
for
30 d
ays)
Faec
al s
amp
les
(and
urin
e)
cultu
red
and
pla
ted
on
sele
ctiv
e ag
ar, A
PI t
est
kits
for
iden
tifica
tion
Imp
act
of d
oses
of
norfl
oxac
in, t
rimet
hop
rim-
sulfa
met
hoxa
zole
and
ni
trof
uran
toin
on
aero
bic
b
owel
flor
a
Bef
ore
antib
iotic
tre
atm
ent,
all
stoo
ls
cont
aine
d E
nter
obac
teria
ceae
and
E
nter
ococ
cus
spp
. Nitr
ofur
anto
in
did
not
alte
r ab
und
ance
of
Ent
erob
acte
riace
ae o
r E
nter
ococ
cus
spp
in t
he c
olon
ic fl
ora
dur
ing
trea
tmen
t. N
o in
crea
sed
res
ista
nce
to n
itrof
uran
toin
in G
ram
- neg
ativ
e ae
rob
ic b
acte
ria. N
o p
atie
nt
rece
ivin
g th
e d
rug
was
foun
d t
o b
e co
loni
sed
by
yeas
ts.
Do
xycy
clin
e
Hei
md
ahl &
Nor
d
(198
3)56
Sw
eden
Tria
lN
=10
Not
sp
ecifi
edH
ealth
y vo
lunt
eers
Dox
ycyc
line
100
mg
dai
ly fo
r 7
day
sFa
ecal
cul
ture
on
sele
ctiv
e m
edia
Effe
ct o
f dox
ycyc
line
on
the
norm
al h
uman
flor
a an
d
on c
olon
isat
ion
of t
he o
ral
cavi
ty a
nd c
olon
No
chan
ge in
ab
und
ance
of
Bac
tero
ides
sp
p, B
ifid
obac
teriu
m
spp
, Clo
strid
ium
sp
p, E
ubac
teriu
m
spp
, Lac
tob
acill
us s
pp
or
Veill
onel
la
spp
. Fus
obac
teria
wer
e el
imin
ated
. A
2–3
log
dec
reas
e in
ent
eroc
occi
, st
rep
toco
cci a
nd e
nter
obac
teria
. E
mer
genc
e of
new
str
ains
K
leb
siel
la p
neum
onia
e, P
rote
us
mira
bili
s an
d E
nter
obac
ter
cloa
cae
in s
ome
sub
ject
s. A
ll co
loni
sing
m
icro
orga
nism
s w
ere
resi
stan
t to
dox
ycyc
line.
Nor
mal
isat
ion
of
aero
bic
bac
teria
l ab
und
ance
9 d
ays
afte
r an
tibio
tic t
reat
men
t.
Wal
ker
et a
l (2
005)
57U
SA
RC
TN
=69
ad
ult;
55
anal
ysed
Clin
icP
erio
don
titis
20 m
g d
oxyc
yclin
eFa
ecal
sam
ple
s p
late
d o
n a
num
ber
of s
elec
tive
agar
and
in
cub
ated
for
CFU
cou
nts
To d
eter
min
e if
a 9-
mon
th
regi
men
of s
ubop
timal
d
oxyc
yclin
e ha
d a
n ef
fect
on
eith
er t
he in
test
inal
or
the
vagi
nal m
icro
flora
The
only
sta
tistic
ally
sig
nific
ant
diff
eren
ces
bet
wee
n th
e tw
o tr
eatm
ent
grou
ps
occu
rred
in t
he
dox
ycyc
line-
resi
stan
t co
unts
at
the
bas
elin
e sa
mp
le. N
o b
etw
een-
tr
eatm
ent
diff
eren
ces
wer
e d
etec
ted
at
3- m
onth
or
9- m
onth
per
iod
eith
er
in t
he p
red
omin
ant
bac
teria
l tax
a or
in
ant
ibio
tic s
usce
ptib
ilitie
s
Mat
to e
t al
(200
8)58
Finl
and
Not
sp
ecifi
edN
=19
; 10
cont
rols
Not
sp
ecifi
edN
ot s
pec
ified
Dox
ycyc
line
150
mg
dai
ly fo
r 10
day
s w
ith p
rob
iotic
Faec
al 1
6S r
RN
A P
CR
for
Bifi
dob
acte
rium
sp
and
DG
GE
an
d c
ultu
ring
and
seq
uenc
ing
To e
valu
ate
the
influ
ence
of
dox
ycyc
line
ther
apy
on t
he
com
pos
ition
and
ant
ibio
tic
susc
eptib
ility
of i
ntes
tinal
b
ifid
obac
teria
Bifi
dob
acte
rium
div
ersi
ty w
as
mar
ked
ly h
ighe
r in
the
con
trol
gr
oup
tha
n an
tibio
tic g
roup
; ea
ch s
ubje
ct h
ad 2
–3 g
enot
ypes
in
the
con
trol
gro
up; 0
–3 in
the
an
tibio
tic g
roup
. The
isol
ated
b
ifid
obac
teria
rep
rese
nted
B.
adol
esce
ntis
⁄ B. r
umin
antiu
m,
B. l
ongu
m, B
. cat
enul
atum
⁄ B.
pse
udoc
aten
ulat
um, B
. bifi
dum
and
B
. den
tium
. Tet
racy
clin
e- re
sist
ant
Bifi
dob
acte
rium
isol
ates
wer
e m
ore
com
mon
ly d
etec
ted
in t
he a
ntib
iotic
gr
oup
tha
n in
the
con
trol
gro
up,
thus
incr
easi
ng t
he p
ool o
f res
ista
nt
com
men
sal b
acte
ria in
the
inte
stin
e.
Tab
le 2
C
ontin
ued
Con
tinue
d
on February 25, 2021 by guest. P
rotected by copyright.http://bm
jopen.bmj.com
/B
MJ O
pen: first published as 10.1136/bmjopen-2019-035677 on 21 S
eptember 2020. D
ownloaded from
10 Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
Stu
dy
IDC
oun
try
Des
ign
Po
pul
atio
nS
etti
ngIn
fect
ion
Ant
ibio
tic
of
inte
rest
(and
d
osa
ge)
Sam
ple
and
ana
lysi
sP
rim
ary
out
com
eR
esul
ts
Ras
hid
et
al
(201
3)59
Sw
eden
Dou
ble
- blin
d,
rand
omis
ed,
pla
ceb
o-
cont
r olle
d,
par
alle
l gro
up
stud
y
N=
34, 1
7 tr
eate
d, 1
7 co
ntro
lsC
linic
al t
rial
unit
Hea
lthy
volu
ntee
rsD
oxyc
yclin
e 40
mg
cap
sule
s or
ally
onc
e d
aily
Cul
ture
on
sele
ctiv
e m
edia
ae
rob
ic a
nd a
naer
obic
Prim
ary
obje
ctiv
e of
thi
s st
udy
was
to
asse
ss t
he
imp
act
of a
ntim
icro
bia
l tr
eatm
ent
on t
he
orop
hary
ngea
l and
inte
stin
al
mic
roflo
ra d
urin
g an
d a
fter
ad
min
istr
atio
n of
40
mg
dox
ycyc
line
cap
sule
giv
en
once
dai
ly t
o he
alth
y vo
lunt
eers
Dox
ycyc
line
was
det
ecta
ble
in
stoo
l up
to
16 w
eeks
. No
chan
ges
in a
bun
dan
ce (>
2 lo
g C
FU/g
) of
Bac
tero
ides
sp
p, B
ifid
obac
teriu
m
spp
, Clo
strid
ium
sp
p, C
and
ida
spp
, Lac
tob
acill
us s
pp
or
Ent
erob
acte
riace
ae a
naer
obic
in
test
inal
mic
roflo
ra. N
o ne
w
colo
nisa
tion
with
C. d
iffici
le. A
t w
eek
20, t
he a
naer
obic
mic
roflo
ra
was
nor
mal
. In
aero
bic
inte
stin
al
mic
roflo
ra, t
here
wer
e ch
ange
s (2
log
CFU
/g) i
n th
e nu
mb
ers
of
ente
roco
cci a
nd E
. col
i dur
ing
the
16- w
eek
trea
tmen
t. O
ther
m
icro
orga
nism
s su
ch a
s ot
her
ente
rob
acte
ria, C
and
ida
spp
and
ot
her
mic
roor
gani
sms
wer
e no
t af
fect
ed. T
he a
erob
ic m
icro
flora
w
as n
orm
al a
t w
eek
20. I
ncre
ase
in d
oxyc
yclin
e re
sist
ance
in
Bifi
dob
acte
rium
sp
p, a
naer
obic
co
cci a
nd G
ram
- pos
itive
rod
s.
Cla
rith
rom
ycin
Bris
mar
et
al
(199
1)60
Sw
eden
Coh
ort
stud
yN
=10
ad
ults
Not
sp
ecifi
edH
ealth
y vo
lunt
eers
Cla
rithr
omyc
in 2
50 m
g tw
ice
dai
ly fo
r 7
day
sC
ultu
re o
n se
lect
ive
and
non
- se
lect
ive
agar
To c
omp
are
the
effe
ct
of c
larit
hrom
ycin
and
er
ythr
omyc
in o
n th
e no
rmal
flo
ra
Cla
rithr
omyc
in d
ecre
ased
the
nu
mb
ers
of B
acte
roid
es s
pp
, B
ifid
obac
teriu
m s
pp
, Lac
tob
acill
us
spp
and
Str
epto
cocc
us s
pp
. A
naer
obic
coc
ci in
crea
sed
and
C
. alb
ican
s w
as is
olat
ed fr
om
two
pat
ient
s. N
o ch
ange
s in
th
e ab
und
ance
of B
acill
us s
pp
, C
lost
ridiu
m s
pp
, Cor
yneb
acte
rium
sp
p, E
nter
ococ
cus
spp
, E
ubac
teriu
m s
pp
, Mic
roco
ccus
sp
p,
Sta
phy
loco
ccus
sp
p o
r Ve
illon
ella
sp
p. N
orm
alis
atio
n in
ab
und
ance
of
Ent
erob
acte
riace
ae, L
acto
bac
illus
sp
p a
nd S
trep
toco
ccus
sp
p
but
not
of B
acte
roid
es s
pp
and
B
ifid
obac
teriu
m s
pp
14
day
s af
ter
antib
iotic
tre
atm
ent.
Tab
le 2
C
ontin
ued
Con
tinue
d
on February 25, 2021 by guest. P
rotected by copyright.http://bm
jopen.bmj.com
/B
MJ O
pen: first published as 10.1136/bmjopen-2019-035677 on 21 S
eptember 2020. D
ownloaded from
11Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
Stu
dy
IDC
oun
try
Des
ign
Po
pul
atio
nS
etti
ngIn
fect
ion
Ant
ibio
tic
of
inte
rest
(and
d
osa
ge)
Sam
ple
and
ana
lysi
sP
rim
ary
out
com
eR
esul
ts
Ed
lund
et
al
(200
0)61
Sw
eden
Hea
lthy
volu
ntee
rsN
=12
mal
e ad
ult
Not
sp
ecifi
edH
ealth
yC
larit
hrom
ycin
500
mg
twic
e d
aily
for
7 d
ays
Faec
al; i
nhib
ition
ass
ay,
cultu
re o
n se
lect
ive
and
non
- se
lect
ive
agar
To in
vest
igat
e th
e ec
olog
ical
ef
fect
s of
mox
iflox
acin
with
th
ose
of c
larit
hrom
ycin
on
the
inte
stin
al h
uman
m
icro
flora
Cla
rithr
omyc
in s
igni
fican
tly r
educ
ed
E. c
oli i
n nu
mb
ers
dur
ing
trea
tmen
t b
ut r
etur
ned
to
pre
trea
tmen
t le
vels
at
day
35.
Six
sub
ject
s w
ere
colo
nise
d b
y re
sist
ant
aero
bic
Gra
m- n
egat
ive
r od
s,
Citr
obac
ter,
Kle
bsi
ella
, Pro
teus
and
P
seud
omon
as. N
o ov
ergr
owth
of
yeas
ts. T
otal
num
ber
of a
naer
obic
b
acte
ria d
ecre
ased
dur
ing
trea
tmen
t.
Bifi
dob
acte
ria w
ere
elim
inat
ed
or s
tron
gly
red
uced
. Bac
tero
ides
d
eclin
ed. L
acto
bac
illi a
nd c
lost
ridia
w
ere
mar
ked
ly d
eclin
ed b
ut n
ot
sign
ifica
ntly
. Onl
y m
inor
alte
ratio
ns
in n
umb
ers
of p
epto
stre
pto
cocc
i, ve
illon
ella
cocc
i. N
o ov
ergr
owth
of
C. d
iffici
le. B
acte
rial a
bun
dan
ce w
as
norm
alis
ed 2
8 d
ays
afte
r an
tibio
tic
trea
tmen
t.
Ed
lund
et
al
(200
0)62
Sw
eden
Ran
dom
ised
d
oub
le- b
lind
co
ntro
lled
st
udy
N=
20 a
dul
tsN
ot s
pec
ified
Hea
lthy
Cla
rithr
omyc
in 5
00 m
g fo
r 10
day
sFa
ecal
; cul
ture
on
sele
ctiv
e ag
ar a
erob
ic a
nd
anae
rob
ic, G
ram
sta
in a
nd
bio
chem
ical
tes
ts, g
as li
qui
d
chro
mat
ogra
phy
Ass
ess
the
imp
act
of
antib
iotic
on
inte
stin
al
mic
roflo
ra
Mod
erat
e d
istu
rban
ces
in a
erob
ic
inte
stin
al m
icro
flora
, num
ber
of E
. co
li si
gnifi
cant
ly r
educ
ed a
t d
ay 1
0.
Ove
rgro
wth
of K
leb
siel
la, C
itrob
acte
r an
d E
nter
obac
ter
spp
occ
urre
d in
six
su
bje
cts
rece
ivin
g cl
arith
rom
ycin
. No
sign
ifica
nt o
verg
row
th o
f Can
did
a sp
p. T
here
was
a m
arke
d r
educ
tion
in B
ifid
obac
teriu
m s
pp
, Clo
strid
ia
spp
, Lac
tob
acill
us s
pp
, Mic
roco
ccus
sp
p a
nd S
tap
hylo
cocc
us s
pp
. No
chan
ge in
the
tot
al n
umb
ers
of
anae
rob
ic b
acte
ria, E
nter
ococ
cus
spp
, Pep
tost
rep
toco
ccus
sp
p,
Bac
tero
ides
sp
p, C
and
ida
spp
, S
trep
toco
ccus
sp
p o
r Ve
illon
ella
sp
p. T
he lo
wer
num
ber
s of
B
ifid
obac
teriu
m s
pp
and
La
ctob
acill
us s
pp
per
sist
ed
even
aft
er 1
4 d
ays
of n
o
antib
iotic
s.
Mat
ute
et a
l (2
002)
63Th
e N
ethe
rland
sD
oub
le b
lind
- ra
ndom
ised
tr
ial
N=
18, 6
tre
atm
ent,
6
cont
rols
Med
ical
cen
tre
Hea
lthy
volu
ntee
rsC
larit
hrom
ycin
500
mg
twic
e a
day
ora
lly fo
r 7
day
sFa
ecal
cul
ture
on
sele
ctiv
e ag
ar a
erob
ic a
nd a
naer
obic
To c
omp
are
the
effe
ct
of 3
- day
, tw
ice
dai
ly
clar
ithro
myc
in a
nd w
ith
pla
ceb
o on
the
faec
al
mic
roflo
ra
No
chan
ge in
ab
und
ance
of
Can
did
a sp
p o
r E
nter
ococ
cus
spp
. No
new
col
onis
atio
n w
ith
C. d
iffici
le o
r no
n- fe
rmen
ters
. No
incr
ease
in c
larit
hrom
ycin
- res
ista
nt
bac
teria
. The
num
ber
of o
rgan
ism
s of
the
fam
ily E
nter
obac
teria
ceae
d
ecre
ased
slig
htly
aft
er a
ntib
iotic
, b
ut le
vels
nor
mal
ised
by
day
21
afte
r th
erap
y. T
he t
otal
num
ber
of
anae
rob
ic b
acte
ria w
as n
ot a
ffect
ed
in t
he s
tud
y gr
oup
.
Phe
noxy
met
hylp
enic
illin
Tab
le 2
C
ontin
ued
Con
tinue
d
on February 25, 2021 by guest. P
rotected by copyright.http://bm
jopen.bmj.com
/B
MJ O
pen: first published as 10.1136/bmjopen-2019-035677 on 21 S
eptember 2020. D
ownloaded from
12 Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
Stu
dy
IDC
oun
try
Des
ign
Po
pul
atio
nS
etti
ngIn
fect
ion
Ant
ibio
tic
of
inte
rest
(and
d
osa
ge)
Sam
ple
and
ana
lysi
sP
rim
ary
out
com
eR
esul
ts
Hei
md
ahl &
Nor
d
(197
9)64
Sw
eden
Tria
lN
=20
, 10
with
p
heno
xym
ethy
lpen
icill
inR
esea
rch
Inst
itute
Hea
lthy
volu
ntee
rsP
heno
xym
ethy
lpen
icill
in
800
mg
as a
load
ing
dos
e,
800
mg
twic
e d
aily
for
7 d
ays
Faec
al c
ultu
r e o
n se
lect
ive
med
ia u
nder
aer
obic
and
an
aero
bic
con
diti
ons.
B
acte
rial i
den
tifica
tion
by
AP
I str
ips
Effe
ct o
f p
heno
xym
ethy
lpen
icill
in (a
nd
clin
dam
ycin
) on
the
aero
bic
an
d a
naer
obic
mic
roflo
ra
in t
he h
uman
mou
th, t
hroa
t an
d c
olon
No
chan
ge in
ab
und
ance
of
Aci
dam
inoc
occu
s sp
p, B
acte
roid
es
spp
, Bifi
dob
acte
rium
sp
p,
Clo
strid
ium
sp
p, E
nter
obac
teric
aeae
, E
nter
ococ
cus
spp
, Eub
acte
rium
sp
p, F
usob
acte
rium
sp
p,
Lact
obac
illus
sp
p, M
egas
haer
a sp
p,
Str
epto
cocc
us s
pp
or
Veill
onel
la s
pp
Ad
amss
on e
t al
(1
997)
65S
wed
enH
ealth
y vo
lunt
eers
N=
20 a
dul
ts; 1
0 w
ith
trea
tmen
tN
ot s
pec
ified
Hea
lthy
Phe
noxy
met
hylp
enic
illin
10
00 m
g tw
ice
a d
ay fo
r 10
d
ays
Faec
al a
ntim
icro
bia
l ass
ay
and
cul
ture
To in
vest
igat
e th
e ec
olog
ical
effe
cts
of
phe
noxy
met
hylp
enic
illin
, on
the
oro
pha
ryng
eal a
nd
inte
stin
al h
uman
mic
roflo
ra
No
chan
ge in
ab
und
ance
of
Bac
illus
sp
p, B
acte
roid
es s
pp
, E
nter
ococ
cus
spp
or
Str
epto
cocc
us
spp
. The
re w
ere
min
or a
ltera
tions
in
num
ber
s of
E. c
oli.
Thre
e su
bje
cts
bec
ame
colo
nise
d w
ith K
leb
siel
la
and
one
with
hig
h nu
mb
ers
of
non-
ferm
enta
tive
gram
- neg
ativ
e ro
d. N
umb
ers
of C
lost
ridiu
m
incr
ease
d. N
o ch
ange
in t
otal
nu
mb
ers
of a
erob
ic o
r an
aero
bic
b
acte
ria. N
orm
alis
atio
n of
bac
teria
l ab
und
ance
day
14
afte
r an
tibio
tic
trea
tmen
t.
Ery
thro
myc
in
Hei
md
ahl &
Nor
d
(198
2)66
Sw
eden
Tria
lN
=10
Res
earc
h in
stitu
teH
ealth
y vo
lunt
eers
Ery
thro
myc
in s
tear
ate
was
gi
ven
oral
ly in
dos
es o
f 500
mg
twic
e d
aily
for
7 d
ays
Faec
al s
pec
imen
s w
ere
take
n up
to
16 d
ays
for
culti
vatio
n of
aer
obic
and
ana
erob
ic
bac
teria
The
imp
act
of e
ryth
rom
ycin
ad
min
istr
atio
n on
the
no
rmal
hum
an fl
ora
and
on
col
onis
atio
n of
the
ora
l ca
vity
, thr
oat
and
col
on
Sup
pre
ssio
n of
bot
h ae
rob
ic a
nd
anae
rob
ic fa
ecal
flor
a oc
curr
ed.
All
sub
ject
s w
ere
colo
nise
d
by
eryt
hrom
ycin
- res
ista
nt
ente
rob
acte
ria, c
lost
ridia
or
yeas
ts
in t
he c
olon
. In
aero
bes
, the
num
ber
of
ent
erob
acte
ria, e
nter
ococ
ci
and
str
epto
cocc
i wer
e re
duc
ed. I
n an
aero
bes
, no
chan
ge in
ab
und
ance
of
Bifi
dob
acte
rium
sp
p, E
ubac
teriu
m
spp
or
Lact
obac
illus
sp
p. H
owev
er,
Bac
tero
ides
, fus
obac
teria
and
Ve
illon
ella
wer
e el
imin
ated
in s
ome
sub
ject
s.
Bris
mar
et
al
(199
1)60
Sw
eden
Coh
ort
stud
yN
=10
ad
ults
Not
sp
ecifi
edH
ealth
yE
ryth
rom
ycin
100
0 m
g tw
ice
dai
ly fo
r 7
day
sFa
ecal
cul
ture
on
sele
ctiv
e m
edia
Com
par
e th
e ef
fect
of
cla
rithr
omyc
in a
nd
eryt
hrom
ycin
on
inte
stin
al
mic
roflo
ra
Cha
nges
in t
he in
test
inal
aer
obic
an
d a
naer
obic
mic
roflo
ra.
Str
epto
cocc
i elim
inat
ed,
ente
rob
acte
ria s
tron
gly
sup
pre
ssed
. M
inor
red
uctio
n in
ent
eroc
occi
and
co
ryne
bac
teria
l. S
tap
hylo
cocc
i and
C
. alb
ican
s in
crea
sed
. Nor
mal
isat
ion
in a
bun
dan
ce o
f Bifi
dob
acte
rium
sp
p a
nd L
acto
bac
illus
sp
p 1
4 d
ays
afte
r tr
eatm
ent.
Ana
erob
ic,
lact
obac
illi,
bifi
dob
acte
ri, c
lost
ridia
an
d b
acte
roid
es r
educ
ed. N
o no
rmal
isat
ion
in a
bun
dan
ce o
f B
acte
roid
es s
pp
and
Clo
strid
ium
sp
p 1
4 d
ays
afte
r an
tibio
tic
trea
tmen
t.
CFU
, col
ony-
form
ing
unit
; GP
s, g
ener
al p
ract
ition
ers;
RC
T, r
and
omis
ed c
ontr
olle
d t
rial;
TTG
E, t
emp
oral
tem
per
atur
e gr
adie
nt g
el e
lect
rop
hore
sis;
UTI
, urin
ary
trac
t in
fect
ion.
Tab
le 2
C
ontin
ued
on February 25, 2021 by guest. P
rotected by copyright.http://bm
jopen.bmj.com
/B
MJ O
pen: first published as 10.1136/bmjopen-2019-035677 on 21 S
eptember 2020. D
ownloaded from
13Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
Patient and public involvementThis research was done without patient involvement.
RESULTSOverallThe database searches returned 2475 articles (May 2020). Following removal of duplicates and screening of records by title or abstract, 2164 were excluded, based on our selection criteria (figure 1). One hundred and fifty- nine full- text articles were evaluated and a further 128 were excluded with reasons detailed in figure 1. Thirty- one studies were eligible and included in the present review. The included studies are summarised in table 2 and are briefly described below.31 37–66 Twelve of the studies were published by different authors from the same Swedish study group, although one of the studies was carried out in Germany.42–44 51 56 59–62 64–66
Publication dates ranged from 1979 to 2017. The studies measured the effects on gut microbiota following clinical treatment of the patient or experimental expo-sure of volunteers to different antimicrobial agents.
The 31 publications involved 1068 patients, although not all of these received the antibiotics of interest and some were comparative control groups. Most studies orig-inated from European countries, Sweden (11), Finland (3), The Netherlands (3), France (2) and one each for,
Germany, Switzerland, Belgium/Poland and Greece. The remaining studies were conducted in the USA (6), Chile (1) and Brazil (1).
STUDY CHARACTERISTICSSamplingFaecal samples have generally been accepted as repre-sentative of the intestinal microbiota. Studies conducted before 2000 used cultured homogenised faecal samples on non- selective and selective media to enumerate different colony types. Some isolated pure cultures for identification to genus level. The effect of the antibiotic was measured by comparing the numbers of bacteria present from each genus before treatment with the decrease, increase overgrowth or proliferation of other bacteria. However, it is known that many types of gut bacteria, about 80%, have not been cultured.67 Predomi-nantly, later studies used more rapid molecular methods.
Analytical techniquesAll studies analysed faecal samples, either by culture (17 studies) or molecular techniques (13 studies), one study used both methods. Eighteen of the studies used healthy volunteers, four of the studies looked at patients with a respiratory infection, three studies patients had a UTI, one study reported patients with urinary and respiratory
Figure 1 Preferred Reporting Items for Systematic Reviews and Meta- Analyses flowchart for study selection.
on February 25, 2021 by guest. P
rotected by copyright.http://bm
jopen.bmj.com
/B
MJ O
pen: first published as 10.1136/bmjopen-2019-035677 on 21 S
eptember 2020. D
ownloaded from
14 Elvers KT, et al. BMJ Open 2020;10:e035677. doi:10.1136/bmjopen-2019-035677
Open access
infections, one study patients had sinusitis, one study they had periodontitis, another study relied on self- reported infections and two studies did not specify the health status of the subjects.
Risk of biasThe risk of bias among the studies was assessed using the CASP checklists for case controls, randomised controlled trials (RCTs), other trials and cohort studies (figure 2). There was 1 case control appraisal, 15 cohort studies and 15 trials. All the studies adequately stated their study aims and hypothesis and this part of the assessment was rated as ‘low’ risk.
Case controlThere was one case control study included in our review of a patient presenting with onset of diarrhoea not associ-ated with Clostridium infection, within 24 hours of antibi-otic administration.49 It was shown that this was associated with changes in the diversity of the gut microbiota. In terms of bias, the study trends toward overall unclear risk as there is lack of controls and the report details just one patient in a clinical setting with a symptom of interest (figure 2A). However, they did use very robust molecular methods to study these temporal changes in the diversity of the microbiota.
CohortsThere were 15 cohort studies included in our review. Assessment relating to the validity of the study is covered within questions 1–6 (figure 2B). Generally, these studies were of low risk. The reliability of the studies determined by the size of the effect and how precisely this was esti-mated are covered with questions 7–9 and are of low or unclear risk. There is greater unclear risk when it comes to the applicability of the results (questions 10–12), the usefulness for clinical decision- making, often the popu-lation size was too small to extrapolate results to a larger population as a whole.
TrialsFifteen studies included in this review were trials/RCTs and overall the risk was more unclear. The validity of the studies (Q1-6), randomisation and masking of treatment allocation was generally of low risk. The baseline charac-teristics of the study were of low or unclear risk as most studies stated age, gender and health status, a few excep-tions stated body mass index and ethnicity. Follow- up of study participants was of low risk, with most studies taking samples up to 4 weeks after antibiotic administration (although there are some indications that this needs to be longer). Controlling for confounding factors (Q6) was unclear in most of the studies. The size of treatment effect (Q7) was well reported, but precision (Q8) was unclear, mostly due to small population size and lack of statistical analysis. The transferability of the results to other popula-tions (Q9 and 11) was of unclear risk.
Antibiotic effects on the gutThe studies analysed employed different methodologies to explore the effect of antibiotics on the gut microbiota. They have been consistent in demonstrating that dysbiosis develops on antibiotic administration, which is rapid and results in losses of diversity and shifts in abundance of gut microbes either up or down. After antibiotic treatment, the composition generally returns to a similar pretreat-ment state within several weeks, but not in all cases. Here, we describe the results in more detail per antibiotic of interest.
AmoxicillinTen studies examined the impact of orally administered amoxicillin on the normal intestinal microflora and are summarised in table 3.37–46 In brief, administration of amoxicillin leads to an increase or overgrowth of Entero-bacteria (six studies). The changes in the anaerobic population (includes Lactobacillus, Bifidobacterium and Bacteroides) varied enormously between studies: from no change, to increases and/or decreases, as well as changes in diversity. There were two reports that isolated Clostridium and Candida and two where no change in numbers were observed. Eight of the studies had some longer term follow- up and most of these reported that the populations returned to normal within 2–4 weeks. Three of the studies reported that significant alterations in the microbiome diversity or abundance were still evident from 42 days to 6 months after the final antibiotic dose. Other longer term effects were a persistence of Candida at 6 weeks, appearance of other aerobic or resistant Gram- negative bacteria (species not specified) at 28 days, and a persistent decrease in Lachnospiraceae at 6 months, with no similarities in the populations treated.
Christensson et al42 conducted a culture- dependent randomised study of 84 subjects with lower respiratory tract infections, 38 of whom completed treatment with amoxicillin (the remaining received cefaclor and will not be discussed further here). They showed that the numbers of enterobacteria, anaerobic Gram- positive Lactobacilli, Bifidobacteria and Eubacteria, and anaer-obic Bacteroides increased significantly in the amoxicillin group. The number of anaerobic cocci was reduced in 18 patients and increased in 11 patients. There was no change in the abundance of Enterococcus spp, Staphylococcus spp or Streptococcus spp. Four patients became colonised with Pseudomonas sp and five with C. albicans. Although C. albicans was also isolated from two patients pretreatment and three patients 6 weeks after treatment C. difficile was isolated from two patients during treatment.
The effect of amoxicillin on the intestinal microflora of patients with bronchitis was evaluated in a randomised study by Floor et al.46 The anaerobic flora remained unchanged, both during and after therapy with amoxi-cillin. The total number of aerobic Gram- negative rods increased significantly, and in 37.5% of the patients with newly acquired bacteria, the main species identified were Klebsiella. Enterococci were cultured in only one patient.
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Figure 2 Overall risk of bias assessment, for case studies (A), cohort studies (B) and trials (C).
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Tab
le 3
Im
pac
t of
am
oxic
illin
on
the
gast
roin
test
inal
mic
roflo
ra
Stu
dy
Do
se
(mg
/d
ay)
Day
s o
f ad
min
istr
atio
n
Num
ber
o
f p
atie
nts
Imp
act
on
Ove
rgr o
wth
Aer
ob
ic
GP
co
cci
Pse
ud
omon
asE
nter
ob
acte
ria
Ana
ero
bic
Lact
obac
illu
sB
ifid
obac
teri
um
Bac
tero
ides
Clo
stri
diu
mC
and
ida
Chr
iste
nsso
net
al (
1991
)4225
0×3
738
No
chan
geis
olat
ed 4
p
atie
nts
Incr
ease
Incr
ease
Incr
ease
Incr
ease
Isol
ated
tw
o p
atie
nts
Isol
ated
10
p
atie
nts
Floo
r et
al
(199
4)46
500×
37
40S
light
ch
ange
–In
crea
seN
o ch
ange
––
––
Incr
ease
Man
gin
et a
l (2
010)
4150
/kg/
day
731
––
––
–C
hang
es in
div
ersi
ty–
––
Mon
real
et
al
(200
5)38
––
22–
––
–D
ecre
ase
Dec
reas
eD
ecre
ase
––
Lad
irat
et a
l (2
014)
4537
5×3
512
––
Ove
rgro
wth
––
Dec
reas
e–
––
Pal
lav
et a
l (2
014)
3925
0×3
78
––
Incr
ease
Dec
reas
e–
–In
crea
se–
–
Bris
mar
et
al
(199
3)43
500×
37
10M
inor
d
ecre
ase
–In
crea
seN
o ch
ange
No
chan
geN
o ch
ange
No
chan
geN
one
No
chan
ge
Ed
lund
et
al
(199
4)44
500×
37
10–
–O
verg
row
th–
No
chan
geN
o ch
ange
No
chan
geN
o ch
ange
No
chan
ge
De
La C
oche
tiere
et
al (
2005
)*37
500×
36
5–
––
––
––
––
Fuso
bac
teri
acea
eLa
chno
spir
acea
eB
ifid
ob
acte
ria/
Ery
sip
elo
tric
hace
aeB
acte
roid
ales
/Ve
illo
nella
ceae
/P
orp
hyro
mo
nad
acea
e
Ab
eles
et
al
(201
6)†40
500×
23/
66/
6
In
crea
seD
imin
ishe
d e
ven
afte
r 6
mon
ths
Dec
reas
e th
en
incr
ease
Dec
reas
e
*Thi
s p
aper
mea
sure
d s
imila
rity
ind
ices
of T
GG
E p
rofil
es a
nd s
how
ed s
hift
s in
dom
inan
t sp
ecie
s on
ant
ibio
tic t
reat
men
t.†A
lso
a re
duc
tion
in d
iver
sity
.–,
not
rep
orte
d; G
P, g
ram
pos
itive
; TTG
E, t
emp
oral
tem
per
atur
e gr
adie
nt g
el e
lect
rop
hore
sis.
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A third of patients had other aerobic bacteria different from baseline on days 21–28. Bacterial and fungal abun-dance returned to baseline levels 21 days after treatment.
Mangin et al41 studied 18- month old children with acute bronchitis. Both total bacteria and numbers of Bifidobacteria were similar during the course of antibi-otic treatment. However, changes in Bifidobacterium at the species level showed decreased diversity. Amoxicillin treatment induced a complete disappearance of Bifido-bacterium adolescentis species, a significant decrease in the occurrence rate of Bifidobacterium bifidum, but did not affect Bifidobacterium longum and Bifidobacterium pseudoca-tenulatum/Bifidobacterium catenulatum. They did not study longer term effects.
Monreal et al38 used culture- based methods to examine the populations of faecal bacteria in 22 patients with RTIs treated with amoxicillin. Bacteroides spp, Bifidobacterium spp and Lactobacillus spp were decreased with antibiotic treatment. However, this was only transient, and 30 days after the end of treatment, the levels of Bifidobacterium and Lactobacillus had recovered to their normal values. Bacteroides were slower to recover.
Ladirat et al45 studied a small number of healthy volun-teers with amoxicillin and a prebiotic specifically looking at total bacteria and Bifidobacterium. Numbers of Bifidobac-terium decreased over time due to amoxicillin treatment, especially in the group with no prebiotic. Amoxicillin affected the abundance and diversity of Bifidiobacterium spp and there was an overgrowth of Enterobacteriaceae. The observations were highly individual dependent. In the follow- up period (3 weeks after the discontinuation of amoxicillin treatment), the levels of bifidobacterial in faeces returned to the initial levels.
Amoxicillin was administered randomly to a small number of healthy volunteers and the impact on intestinal microflora (and oropharyngeal) was studied by Brismar et al.43 In the aerobic intestinal flora, a minor decrease in the numbers of streptococci and staphylococci was observed. Overgrowth of Klebsiella species was seen in six subjects and of Enterobacter species in two subjects. No overgrowth of enterococci or yeasts occurred. In the anaerobic micro-flora, only the number of eubacteria was reduced. There was no colonisation by C. difficile. Two weeks after admin-istration of amoxicillin, the microbiota had returned to baseline levels.
Another study on the effect of amoxicillin on intestinal microflora of healthy volunteers showed only small alter-ations in the aerobic faecal microflora.44 All major anaer-obic bacterial groups were unaffected by amoxicillin and there was no colonisation by C. difficile. There was an over-growth of Klebsiella spp in six subjects and Enterobacter in two subjects. Intestinal microflora returned to normal 2 weeks after treatment had been discontinued.
Six healthy volunteers received oral amoxicillin for 5 days and their faecal microbiota examined by 16S rRNA gene amplification and gradient gel electrophoresis until 60 days.37 Dominant species diversity profiles were compared on the basis of similarity with percentages on
first sampling ranging from 93% to 99%. During the 5- day course of amoxicillin treatment, these percentages decreased to an average of 73%, but there was huge varia-tion between individuals. By day 60, five of the six subject gel profiles had returned to their near initial composi-tion. Gel banding patterns were examined in more detail for three individuals and were shown to correspond to Clostridium nexile, Ruminococcus torques and β- Proteobacteria.
Abeles et al40 studied cohabiting individuals over 6 months where one was given an antibiotic and the other a placebo. The microbiota of subjects taking amoxicillin grew more dissimilar over time, although not statisti-cally significant, as similar trends were also seen in those subjects taking placebo. Taxonomic compositions of the gut differed after amoxicillin therapy. Lachnospiraceae were significantly diminished and remained diminished at 6 months. Veillonellaceae, Bacteroidales and Porphy-romonadaceae were significantly decreased in response to amoxicillin, while Fusobacteriaceae were increased. Bifidobacteriales and Erysipelotrichaceae were initially decreased and subsequently increased in comparison to their housemates taking placebo.
Pallav et al39 studied the effect of amoxicillin treatment with and without a prebiotic. Eight subjects that received just the antibiotic had substantial microbiome changes, most notably an increase in Escherichia/Shigella. There was no change in abundance in the control group. Antibiotic- associated changes persisted to the end of the study, 42 days after antibiotic therapy ended.
Amoxicillin with clavulanic acidSeven studies have looked at the impact of amoxicillin in combination with clavulanic acid on the gut micro-biota.31 47–52 These are summarised in table 4. Briefly, the combination of amoxicillin with clavulanic acid caused mild to moderate changes in microbiome composition, mainly increases in Enterobacteria with varying effects on anaerobic bacteria Bifidobacterium sp, Lactobacillus sp and Bacteroides sp and a general decrease in diversity. One study reported that bacterial abundance was not normalised 2 months after antibiotic treatment was stopped, and four reported levels similar to baseline within 35 days.
Administration of amoxicillin/clavulanic acid to healthy people caused increased numbers of enterococci and Escherichia coli strains in the aerobic microflora, while Bifidobacteria, Lactobacilli and Clostridia decreased significantly.51 Numbers of anaerobic cocci and Bacteroides were not markedly altered. C. difficile strains were recov-ered from three of the volunteers. The microflora was normalised in all volunteers after 35 days.
Young and Schmidt49 investigated the short- term impact of amoxicillin/clavulanic acid prescribed for a male patient with acute sinusitis, who developed antibiotic- associated diarrhoea. It was shown that the major bacte-rial groups were partially restored 14 days after antibiotic treatment, except for Bifidobacterium. During antibiotic administration, no sequences corresponding to butyrate- producing Clostridium cluster XIVa were detected, but
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Tab
le 4
Im
pac
t of
am
oxic
illin
with
cla
vula
nic
acid
on
the
gast
roin
test
inal
mic
roflo
ra.
Stu
dy
Do
se(m
g/d
ay)
D
ays
of
adm
inis
trat
ion
Num
ber
o
f p
atie
nts
Imp
act
on
Ove
rgro
wth
Aer
ob
ic
GP
co
cci
Pse
ud
omon
asE
nter
ob
acte
ria
incl
. E. c
oli
Ana
ero
bic
co
cci
Lact
obac
illu
sB
ifid
ob
acte
ria
Bac
tero
ides
Clo
stri
diu
mC
and
ida
Lod
e et
al (
2001
)5187
5/12
57
12In
crea
se–
Incr
ease
Litt
le c
hang
eD
ecre
ase
Dec
reas
eLi
ttle
cha
nge
Dec
reas
e
Youn
g &
Sch
mid
t (2
004)
*4987
5/12
5×2
101
––
Clu
ster
s p
rese
nt–
–C
lust
ers
pre
sent
Clu
ster
s p
rese
ntTw
o cl
uste
rs
Eng
elb
rekt
son
et a
l (20
09)†
5087
5/?x
27
32–
–In
crea
se–
No
tren
dN
o tr
end
Incr
ease
No
tren
d
Fors
sten
et
al
(201
4)†48
875/
125
780
Incr
ease
d
N
ot a
ffect
ed in
p
rob
iotic
gro
upD
ecre
ased
in
the
pla
ceb
o gr
oup
Dec
reas
ed
Kor
pel
a et
al
(201
6)‡31
––
142
Slig
ht d
ecre
ase
Two
fold
ele
vate
d
Par
abac
tero
ides
Kab
ban
i et
al
2017
5287
5/12
5×2
712
Incr
ease
Incr
ease
d
D
ecre
ased
Dec
reas
edIn
crea
sed
Dec
reas
ed
Man
gin
et a
l (2
012)
4787
5/12
5×2
518
Incr
ease
d
D
ecre
ased
*Thi
s p
aper
rep
orte
d s
hift
s in
the
rep
rese
ntat
ion
of t
he m
ajor
bac
teria
l gro
ups.
†Pro
bio
tic a
lso
give
n.‡A
nd p
enic
illin
V.
GP,
gra
m p
ositi
ve.
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2 weeks after cessation of antibiotics, there was a reap-pearance of this cluster. In this case study, the decrease in this cluster may be linked to the antibiotic- associated diarrhoea.
One arm of a study by Engelbrektson et al50 observed the effects of probiotic treatment concurrent with antibi-otic therapy on faecal communities. They analysed their data by measuring individual divergences from baseline levels after treatment to address the problem of subject- to- subject variability. Subjects fell into two categories: those with a stable baseline microbiota and those where it varied significantly. Culture data showed increasing numbers of Bacteroides and Enterobacteriaceae, but no trend for Clostridium, Bifidobacterium and Lactobacillus. The antibiotic group (without probiotic) had a significant change in numbers of bacteria from baseline at day 21.
Forssten et al48 also studied antibiotic administration in combination with probiotic. Consumption of the probi-otic combination mainly led to an increase in the faecal levels of the species included in the preparation. The antibiotic had only minor effects on Lactobacillus, Bifido-bacterium, Bacteroides, Enterobacteriaceae and Clostridium.
Korpela et al31 looked at the macrolides amoxicillin with and without clavulanic acid and penicillin V. Macro-lide use reduced the abundance of Actinobacteria and increased Bacteroidetes and Proteobacteria. Penicillin groups did not have distinctly different phyla composi-tion. Firmicutes was reduced. The effect of macrolide use was long lasting and was associated with increased risk of asthma and antibiotic- associated weight gain.
Twelve healthy subjects received amoxicillin/clavulanate for 7 days and their stool specimens were analysed using 16s rRNA gene pyrosequencing.52 Antibiotic- associated changes included reduced prevalence of the genus Rose-buria and increases in Escherichia, Parabacteroides and Entero-bacter. Microbiota alterations reverted toward baseline, but were not completely restored 2 weeks after treatment.
Real- time PCR with temporal temperature gradient gel electrophoresis (TTGE) showed that at the end of a 5- day course of amoxicillin- clavulanic acid, total bacterial and Bifidobacteria concentrations were significantly reduced in 18 healthy volunteers.47 At the same time, the mean similarity percentage profiles were significantly reduced and the number of distinct Bifidobacterium species per sample significantly decreased. Two months after anti-biotic exposure, the mean similarity percentage had not normalised.
NitrofurantoinThree studies investigated the effect of nitrofurantoin macrocrystals on faecal microbiota compositions.53–55 Two studies used 16S rRNA gene sequencing and one study bacterial culture and these are summarised in table 2. Nitrofurantoin inhibits bacterial DNA, RNA and cell wall protein synthesis. It is used prophylactically as a urinary anti- infective agent against most gram- positive and gram- negative organisms and for long- term suppres-sion of infections. On oral administration, most of the
nitrofurantoin is rapidly absorbed in the small intestine and eliminated primarily by kidney glomerular filtration into urine, where it reaches higher and more effective therapeutic concentrations. Only a small amount reaches the colon, which may account for the minor impact on intestinal microflora.
One of the studies investigated a small population of women (n=7) with recurrent UTI and it showed that nitrofurantoin did not alter either the Enterobacteria, Enterococci or yeasts of the colonic flora during treat-ment.55 No resistant strains of Gram- negative aerobic bacteria were detected.
Stewardson et al53 treated patients with UTI (n=10) with nitrofurantoin macrocrystals and showed that it was not associated with a statistically significant global impact on the gut microbiota (weak effect). Nitrofurantoin treat-ment was associated with an increase in the proportion of the genus Faecalibacterium and a decrease in the proportion Clostridium (Clostridiaceae) at the end of the antibiotic treatment. Another small study (n=8) treated uncompli-cated UTIs and did not show any significant impact of nitrofurantoin treatment on the faecal microbiota other than a temporary increase in the Actinobacteria phylum, more specifically in the beneficial Bifidobacterium genus.54 Bacterial abundance had returned to pre- antibiotic levels 31 to 43 days after stopping antibiotic treatment, while the other study did not do follow- up testing.53 54
DoxycyclineFour studies reported on the effect of doxycycline on faecal microbiota, one at suboptimal dosage (20 mg for 9 months) in patients with periodontitis57 and two at usual dose 100–150 mg for 7–10 days, although one also with a probiotic,56 58 and another at low dose (40 mg for 16 weeks),59 as described in table 2. Doxycycline treat-ment did not significantly affect counts of total anaer-obic bacteria, candida, total enterics, Staphylococcus or doxycycline- resistant bacteria recovered at any of the sample periods and did not result in the development of multi- antibiotic resistance.57 Matto et al58 specifically evaluated the influence of doxycycline therapy on the composition and antibiotic susceptibility of intestinal Bifidobacteria in nine subjects while they were also taking a probiotic and compared these to adults consuming only probiotics. A marked decrease in diversity of Bifido-bacterium populations was observed during doxycycline therapy. Tetracycline- resistant Bifidobacterium isolates were more commonly detected in the antibiotic group than in the control group, thus increasing the pool of resistant commensal bacteria in the intestine.
In another study on 10 healthy volunteers, doxycy-cline decreased the abundance of Enterobacteriaceae, Enterococcus spp, E. coli and Streptococcus spp.56 With the exception of Fusobacterium spp, which was eliminated, the number of anaerobic bacteria in faeces was not influenced by doxycycline.56 After doxycycline admin-istration, bacterial abundance was reported to have returned to pre- antibiotic levels 9 days after stopping
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treatment.56 The fourth study also looked at a low dose over a period of 16 weeks.59 There were 2 log decreases in the numbers of enterococci and E. coli. Other aerobic microorganisms including enterobacteria, Candida spp, were not affected. There were no significant changes in the numbers of anaerobic lactobacilli, bifidobacteria, clostridia and Bacteroides during doxycycline administra-tion.59 No C. difficile strains were isolated. The aerobic and anaerobic microflora was normal at 28 days after stopping treatment.59 In summary, doxycycline inter-feres with a microorganism’s ability to manufacture proteins. At suboptimal dosage, it has little effect on the gut microbiota with the exception of enterococci and E. coli. At normal dosage it markedly affects the diversity of Bifidobacteria populations in one study and eliminated Fusobacterium sp in another. The effect on populations of other gut bacteria seems transient and normalisation was reported by 28 days. Longer term effects are not known.
ClarithromycinThere were four articles on influence of clarithromycin included. Three were from the same research institute, and these examined the intestinal microflora of healthy volunteers before, during and after administration of clarithromycin. The study design was similar in all three studies and involved small numbers, 10 (a mix of male and female subjects) in two studies60 62 and 12 men only61 as described in table 2. Dosing and faecal sampling strategy and analysis were also similar, 250 mg twice daily for 7days,59 500 mg twice daily for 7 days,60 and 250 mg twice daily for 10 days,62 sampling three times during and three to four times after administration up to 35 days. The male- only subjects were administered another antibi-otic with a 6- week washout period; it is not clear whether this was before or after clarithromycin administration.
The main impact in the earlier study was a reduction in the numbers of Enterobacteria and Streptococci. Lacto-bacilli, Bifidobacteria and Bacteroides were suppressed in the anaerobic microflora.60
Clarithromycin caused a significant reduction of E. coli during 7 days of treatment but levels returned to normal 28 days after the end of the course.61 Six subjects were colonised by resistant aerobic Gram- negative rods, Citrobacter, Klebsiella, Proteus and Pseudomonas. The total numbers of anaerobic bacteria decreased. Bifidobacteria and Bacteroides were significantly reduced, and Lactoba-cilli and Clostridia were suppressed but this was not signif-icant. There was no overgrowth of C. difficile or yeasts. The microflora returned to normal in all subjects after 35 days.
In the final study, the numbers of E. coli were signifi-cantly reduced, and in six individuals, overgrowth of Kleb-siella, Citrobacter and Enterobacter spp occurred.62 The total number of anaerobic intestinal bacteria was not affected, but the numbers of Lactobacilli and Bifidobacteria were significantly reduced which persisted for the duration of the study. There was no significant overgrowth of Candida spp and no subjects were colonised by C. difficile.
A fourth study from a different group on six healthy volunteers showed no change in the abundance of Candida spp, Enterococcus spp or anaerobic bacteria. There was no new colonisation by C. difficile. Numbers of Entero-bacteriaceae decreased slightly. Levels were reported to have returned to baseline by day 21 after the course of clarithromycin.
To summarise, all four studies reported reduction in Enterobacteria and three reported suppression of anaer-obic bacteria after administration of clarithromycin. This reduction was transient for most species, except Lacto-bacilli and Bifidobacteria. Only one studied reported isolation of C. albicans.60 None reported new colonisation or overgrowth of C. difficile. All reported normalisation to baseline levels within 28 days of finishing antibiotic treatment.
PhenoxymethylpenicillinPhenoxymethylpenicillin did not have much effect on gut microbiome, as shown by two studies that investigated the effect on the oropharyngeal and intestinal microflora of healthy volunteers (table 2).64 65 A very early study reported no effect of phenoxymethylpenicillin on abundance of various species comprising the aerobic and anaerobic flora of faecal samples.64 A later study showed no signifi-cant alterations in the total aerobic and anaerobic of the intestinal microflora were observed, although three volun-teers became newly colonised with Klebsiella sp and one harboured high numbers of a non- fermentative Gram- negative rod. The numbers of viridans streptococci, entero-cocci and Bacillus were unaffected by the administration of phenoxymethylpenicillin, while minor alterations were noticed in the numbers of E. coli. The median values of Clos-tridium species increased during administration, while the numbers of Bacteroides species were unaffected during the study period. The microflora became normalised 2 weeks after withdrawal of the drugs.
ErythromycinIn an early study,66 it was shown that the administration of 500 mg of erythromycin twice daily for 7 days to 10 volun-teers resulted in decreased abundance of both aerobic and anaerobic faecal flora. In addition, potentially patho-genic erythromycin- resistant enterobacteria, clostridia or yeasts colonised all subjects.66 Brismar and colleagues60 administered erythromycin orally for 7 days to 10 volun-teers and evaluated its effect on the colonic bacteria. They found decreases in the numbers of streptococci, enterococci and enterobacteria during administration, increases in staphylococci and alteration of the anaerobic bacteria.
DISCUSSIONMain findingsThis systematic review examined the use of the most commonly prescribed antibiotics in primary care to treat RTI and UTI and their impact on gut microbiota.
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First, the studies showed that antibiotics have an impact on the abundances of the bacteria in the gut commu-nity, causing rapid and diminished levels of bacte-rial diversity and taxonomic richness, increases and decreases in the relative abundances of certain taxa, leading to dysbiosis, as well as antibiotic and individual host- specific effects.
Second, once treatment has stopped, there was some, but poor, evidence that the gut bacteria show resilience and are capable of some degree of recovery, in most indi-viduals, to their initial state. However, the microbiota is often not totally recovered, suggesting some antibiotics have a persistent effect on certain species. These observa-tions underline the importance of restrictive and proper use of antibiotics in order to prevent long- term ecological disturbances of the indigenous microbiota.
Comparative observationsOther reviews have also reported and summarised how antibiotics change the abundance and diversity of the intestinal microbiota.68–70 Here, we focus on those antibi-otics routinely prescribed by general practitioners (GPs) in primary care. Often GPs inappropriately prescribe antibiotics for infections caused by viruses, or prescribe a broad- spectrum antibiotic, when an antibiotic for a specific bacteria should be used. They may also prescribe the incorrect dose or for the wrong length of time. Health professionals are concerned that antibiotics are used too often and incorrectly, which contributes to antimicrobial resistance and with the additional disruption to the micro-biome also can have other negative (long term) health effects, such as metabolic and immune disorders.71 72 These additional effects will further impact on the patient and potentially on the primary care burden. Inappropriate prescribing is due to many factors including patients who insist on antibiotics, GPs who do not have enough time to explain why antibiotics are not necessary those who do not know how to recognise a serious bacterial infection or those who are overly cautious.
Quantifying antibiotic therapy effect on gut flora is challenging. Although the literature describes ‘normal’, it really means those commensal species which are consistently and predominantly found in the healthy human gut. Studies quantifying changes in flora would be easier to interpret if a baseline populations were established in each case. We found a lack of large- scale trials (including RCTs) and observational studies and heterogeneity regarding methodology and outcomes. The heterogeneity is apparent by the inconsistency in the dosage, duration of treatment and follow- up, selec-tion and spectrum of antibiotics used, all contributing to varying faecal concentrations. The health status and age of the participant also have an effect, most studies did not clearly define baseline characteristics, which causes problems with comparing outcomes. The majority of studies did not report adverse events or any other factors which might affect the efficacy of the antibiotic which
in turn might influence the outcome on the micro-biome. The studies included used different methods, for example, random allocation of antibiotics to healthy volunteers, or non- randomised treatment where all healthy subjects in the study received antibiotics, also some studies participants were masked to which treat-ment they received and others were not. There were differences between studies in the way outcomes are defined and measured, for example, culturing versus molecular techniques. These differing analytical tech-niques may lead to differences in the observed interven-tion effects. A number of the included studies originate from one research group which could add additional bias to the outcomes. The different classes of antibiotics also have different effects on the microbiome, making it difficult to compare across studies.
The composition of the gut microbiota among humans varies considerably from subject to subject. Grouping of data from several individuals can result in loss of statistical significance. The studies do not consider any confounding factors such as diet, age of subjects, child-hood exposure to antibiotics, geographical location, stress or taking probiotic supplements, all of which can complicate the specific antibiotic treatment effects on the gut microbiome profile. These factors can change over a lifetime.
Strengths and limitationsThe primary strength of this study is our focus on the most commonly prescribed antibiotics in primary care and their effect on gut microbiota. Information on how these commonly prescribed antibiotics affect our gut microbiome could influence GP decision- making when prescribing antibiotics. Also, the adverse impact of antibiotics on the gut microbiome is of great importance because when disrupted, it can be associated with a variety of diseases, including susceptibility to infections, autoimmune diseases (such as inflammatory bowel disease), diabetes, depression and obesity. The main limitations of this review are that the majority of the studies included were small, not prop-erly randomised nor they were large observational studies. The considerable heterogeneity is prone to biases and confounding factors.
Inherent in many studies that address the impact of antibiotics on the intestinal microbiota are the limita-tions of techniques available for analysis. Many have been performed using laborious culture- based methodology which do not lend themselves to analysis of large numbers of samples. The older studies included in our analysis all used culture- based techniques to examine gut microbiota composition, which increases the risk of detection bias. The disadvantage of using culturing is that despite the use of specific selective media and anaerobic incubation conditions, there remains a substantial part of the micro-biota, approximately 80 %,67 that has not yet been cultured. Culture media choice and sample handling can also skew the data.
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The limitations of culture- based techniques can be largely overcome by using molecular approaches.73 These methods are based on 16S rRNA gene amplifica-tion and give us a broader less biassed view of gut bacte-rial composition. The amplified genes are characterised by methods, such as terminal- restriction fragment length polymorphism, denaturing or temperature gradient gel electrophoresis, deep shotgun metagenome and full- length sequencing, some of which are used in the more recent papers in our review. These bioinformatic techniques also have limitations in that they are often more difficult to understand and interpret. The use of different techniques makes it more difficult to compare results, and generalisation of conclusions is a result of this diversity in determination and quantification.
CONCLUSIONSThe widespread and often overuse of antibiotics has led to the establishment of antibiotic- resistant bacteria and the transfer of resistance genes, which has become a global challenge for infection control and the untreatable nature of bacterial infections. Almost 80% of the antibiotics prescribed within the National Health Service are within primary care.1 The effects of excessive antibiotic exposure can also be seen in the symbiotic microbiotas of the human body.74 As a result, the microbiota imbalances caused by antibiotics can negatively affect health by increasing suscep-tibility to infections, compromising immune homeostasis (indicative in increased allergies), asthma, seen by obesity, metabolic syndrome and diabetes.75
Antibiotics have an impact on the gut microbiota, causing rapid and diminished levels of bacterial diver-sity and increases and decreases in the relative abun-dances, leading to dysbiosis. Once treatment has stopped, there was some evidence that the gut bacteria are capable of some degree of recovery, in most individ-uals, to their baseline state. The studies do not consider that recovery of the microbiome after antibiotic therapy in the elderly may be affected by age- associated physi-ological alterations and other drug–drug interactions.
This systematic review highlights the lack of research and understanding of the effects of commonly prescribed antibiotics on the gut microbiome and shows it is an area that requires studies on larger populations with extended sampling to understand the long- term impacts. Embed-ding of this knowledge in antimicrobial stewardship programmes in primary care will be essential.
Contributors KTE and VW performed the searches. VW, ETvdW, AH, LD and KTE identified eligible studies. KTE, VW and ETvdW appraised study quality and extracted data. KTE and VW drafted the first sections of the text and KTE completed data analysis, text and tables to circulate to all authors for their contribution to the final draft. ALH advised on search strategy and RoB and read and contributed to the draft. ADH was involved in the main concept, advised on the antibiotics included and read and contributed to the draft. ETvdW is the guarantor and attests that all listed authors meet authorship criteria and that no others meeting the criteria have been omitted. All authors had full access to the data in the study and can take responsibility for the integrity of the data and the accuracy of the data analysis.
Funding This research was supported by the NIHR Health Protection Research Unit in Evaluation of Interventions at the University of Bristol. The views expressed in this article are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care.
Competing interests All authors had financial support from the University of Bristol for the submitted work; no financial relationships with any organisations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work.
Patient consent for publication Not required.
Provenance and peer review Not commissioned; externally peer reviewed.
Data availability statement Data are available upon reasonable request. All data relevant to the study are included in the article or uploaded as supplementary information. Data sharing. If necessary data not included in the paper can be shared.
Supplemental material This content has been supplied by the author(s). It has not been vetted by BMJ Publishing Group Limited (BMJ) and may not have been peer- reviewed. Any opinions or recommendations discussed are solely those of the author(s) and are not endorsed by BMJ. BMJ disclaims all liability and responsibility arising from any reliance placed on the content. Where the content includes any translated material, BMJ does not warrant the accuracy and reliability of the translations (including but not limited to local regulations, clinical guidelines, terminology, drug names and drug dosages), and is not responsible for any error and/or omissions arising from translation and adaptation or otherwise.
Open access This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license, which permits others to copy, redistribute, remix, transform and build upon this work for any purpose, provided the original work is properly cited, a link to the licence is given, and indication of whether changes were made. See: https:// creativecommons. org/ licenses/ by/ 4. 0/.
ORCID iDsKaren T Elvers http:// orcid. org/ 0000- 0001- 5345- 8662Ashley Hammond http:// orcid. org/ 0000- 0002- 6657- 1514Alyson L Huntley http:// orcid. org/ 0000- 0001- 9409- 7891Esther T van der Werf http:// orcid. org/ 0000- 0002- 5330- 5735
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