University of Birmingham
Stunted microbiota and opportunistic pathogen
colonization in caesarean-section birth
Shao, Yan; Forster, Samuel C; Tsaliki, Evdokia; Vervier, Kevin; Strang, Angela; Simpson,
Nandi; Kumar, Nitin; Stares, Mark D; Rodger, Alison; Brocklehurst, Peter; Field, Nigel;
Lawley, Trevor D
DOI:
10.1038/s41586-019-1560-1
License:
None: All rights reserved
Document Version
Peer reviewed version
Citation for published version (Harvard):
Shao, Y, Forster, SC, Tsaliki, E, Vervier, K, Strang, A, Simpson, N, Kumar, N, Stares, MD, Rodger, A,
Brocklehurst, P, Field, N & Lawley, TD 2019, 'Stunted microbiota and opportunistic pathogen colonization in
caesarean-section birth', Nature, vol. 574, no. 7776, pp. 117-121. https://doi.org/10.1038/s41586-019-1560-1
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Download date: 10. Aug. 2022
1
Stunted microbiota and opportunistic pathogen colonisation associated with
1
C-section birth
2
Yan Shao
1
, Samuel C. Forster
1,2,3
, Evdokia Tsaliki
4
, Kevin Vervier
1
, Angela Strang
4
, Nandi Simpson
4
,
3
Nitin Kumar
1
, Mark D. Stares
1
, Alison Rodger
4
, Peter Brocklehurst
5
, Nigel Field
4, §
,
4
Trevor D. Lawley
1,§
5
1
Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, United Kingdom
6
2
Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
7
3
Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
8
4
Institute for Global Health, University College London, London, United Kingdom
9
5
Birmingham Clinical Trials Unit, University of Birmingham, Birmingham, United Kingdom
10
11
§
corresponding authors
12
Trevor D. Lawley: Wellcome Sanger Institute, Hinxton, United Kingdom, CB10 1SA, Phone 01223 495 391, Fax
13
01223 495 239, Email: tl2@sanger.ac.uk
14
Nigel Field: Institute for Global Health, University College London, London, United Kingdom, WC1N 1EH,
15
Email: nigel.field@ucl.ac.uk
16
17
Running title: Caesarean section predisposes neonates to healthcare-associated opportunistic pathogen colonisation
18
Keywords: gastrointestinal microbiome, early-life microbiota colonisation, clinical metagenomics, neonatal, c-
19
section, intrapartum antibiotic prophylaxis, paediatric, opportunistic pathogens, antimicrobial resistance (AMR),
20
Enterococcus, Klebsiella
21
2
Abstract
22
Immediately after birth, newborn babies experience rapid colonisation by microorganisms from their
23
mothers and the surrounding environment
1
. Diseases in childhood and later in life are potentially mediated
24
through perturbation of the infant gut microbiota colonisations
2
. However, the impact of modern clinical
25
practices, such as caesarean section delivery and antibiotic usage, on the earliest stages of gut microbiota
26
acquisition and development during the neonatal period (≤1 month) remains controversial
3,4
. Here we report
27
disrupted maternal transmission of Bacteroides strains and high-level colonisation by healthcare-associated
28
opportunistic pathogens, including Enterococcus, Enterobacter and Klebsiella species, in babies delivered
29
by caesarean section (C-section), and to a lesser extent, in those delivered vaginally with maternal antibiotic
30
prophylaxis or not breastfed during the neonatal period. Applying longitudinal sampling and whole-genome
31
shotgun metagenomic analysis on 1,679 gut microbiotas of 772 full term, UK-hospital born babies and
32
mothers, we demonstrate that the mode of delivery is a significant factor impacting gut microbiota
33
composition during the neonatal period that persists into infancy (1 month - 1 year). Matched large-scale
34
culturing and whole-genome sequencing (WGS) of over 800 bacterial strains cultured from these babies
35
identified virulence factors and clinically relevant antimicrobial resistance (AMR) in opportunistic
36
pathogens that may predispose to opportunistic infections. Our findings highlight the critical early roles of
37
the local environment (i.e. mother and hospital) in establishing the gut microbiota in very early life, and
38
identifies colonisation with AMR carrying, healthcare-associated opportunistic pathogens as a previously
39
unappreciated risk factor.
40
3
Main
41
The acquisition and development of the early-life gut microbiota follow successive waves of
42
microbial exposures and colonisation that shapes the longer-term microbiota composition and function
5
.
43
Early life events, including Caesarean section delivery
1,6
, formula feeding
7,8
and antibiotic exposure
8,9
that
44
could perturb the gut microbiota composition are associated with the development of childhood asthma and
45
atopy
10-12
. While recent studies
8,9,13-15
have provided substantial insights into the gut microbiota
46
development during the first 3 years of life, many were limited by the taxonomic resolution provided by
47
16S rRNA gene profiling, small sample size or limited sampling during the first month of life (neonatal
48
period). High-resolution metagenomic studies of large, longitudinal cohorts are required to establish the
49
impact and risks of early life events on the gut microbiota assembly, particularly during the neonatal period
50
where pioneering microbes could influence subsequent microbiota and immune system development
16,17
.
51
To characterise the trajectory of gut microbiota acquisition and development during the neonatal
52
period, we enrolled 596 healthy, term babies (39.5 ± 1.37 gestation weeks, 314 vaginal and 282 C-section
53
births, Fig. 1a, Extended Data Table 1) through the Baby Biome Study (BBS). Faecal samples were
54
collected from all babies at least once during their neonatal period (<1 month) with 302 babies re-sampled
55
later in infancy (8.75 ± 1.98 months). Maternal faecal samples were also obtained from 175 mothers paired
56
with 178 babies. Metagenomic analysis of 1,679 faecal samples from 772 babies and mothers revealed
57
temporal dynamics of the gut microbiota development (Fig. 1b) and increased diversity with age (Extended
58
Data Fig. 1a). Strikingly, the gut microbiotas exhibited substantial heterogeneity (inter-individual) and
59
instability (intra-individual) during the first weeks of life (Extended Data Fig. 1b). Inter-individual
60
differences explained 57% of the microbial taxonomic variation (Permutational multivariate analysis of
61
variance (PERMANOVA), P < 0.001, 1,000 permutations), followed by sampling age at 5.7% of the
62
variance (P < 0.001). These results indicate that the gut microbiotas were highly dynamic and
63
individualised during the neonatal period, even more than observed in infancy (Extended Data Fig. 1c).
64
To determine the impact of clinical covariates on the composition of the gut microbial community,
65
we performed cross-sectional PERMANOVA, stratified by age. Mode of delivery was the most significant
66
factor driving gut microbiota variation during the neonatal period (Fig. 2a, Supplementary Table 2), while
67
other clinical covariates associated with hospital birth (e.g. perinatal antibiotics, duration of hospital stay)
68
4
and breastfeeding exhibited smaller effects (Supplementary Note 1). The largest effect of delivery mode
69
was observed on day 4 (Fig. 2b, R
2
=7.64%, P<0.001), which dissipated with age but remained significant
70
at the point of infancy sampling (R
2
=1.00%, P<0.01). No difference was observed in maternal gut
71
microbiotas by delivery modes or neonatal gut microbiotas between elective and emergency C-section
72
births (Supplementary Table 3).
73
Given the significant effect of the mode of delivery during the neonatal period, we next sought to
74
understand how the microbiota composition and developmental trajectory were altered. Samples from
75
babies delivered vaginally were enriched with Bifidobacterium (e.g. B. longum, B. breve), Escherichia (E.
76
coli) and Bacteroides/Parabacteroides species (e.g. B. vulgatus, P. distasonis) with these commensal
77
genera comprising 68.3% (95% CI 65.7-71.0%) of the neonatal gut microbial communities (Fig. 2c,
78
Supplementary Table 5), which validated the recent observations in other cohorts
4,13
. In contrast, the gut
79
microbiota of C-section delivered babies were depleted of these commensal genera and instead were
80
dominated by Enterococcus (E. faecalis, E. faecium), Staphylococcus epidermis, Streptococcus
81
parasanguinis, Klebsiella (K. oxytoca, K. pneumoniae), Enterobacter cloacae and Clostridium perfringens,
82
which are commonly associated with hospital environments
18
and hospitalised preterm babies
19-21
. On day
83
4, species belonging to these genera accounted for 68.25% (95% CI 62.74-73.75%) of the total microbiota
84
composition in C-section delivered babies (Fig. 2c).
85
Previous studies reported that, compared to C-section delivered babies, the gut microbiotas of
86
vaginally delivered babies were enriched in lactobacilli associated with the mother’s vaginal microbiota
1,22
.
87
However, here we observed no statistical difference in the prevalence (vaginal 11.9% vs C-section 15.7%
88
present at over 1% abundance) or abundance of Lactobacillus between vaginally (1.217%, 95% CI 0.81-
89
1.621%) or C-section (2.21%, 95% CI 1.54-2.88%) delivered babies. Rather, commensal species from the
90
Bacteroides genus were detected at high abundance in the gut microbiota of 49.0% (154/314) of vaginally
91
delivered babies (mean relative abundance 8.13%, 95% CI 6.88-9.39%, Extended Data Fig. 3). In contrast,
92
Bacteroides species were low or absent in 99.6% (281/282) C-section delivered babies (mean relative
93
abundance 0.43%, 95% CI 0.11-0.74). In 60.6% (86/142) of the C-section babies, this low-Bacteroides
94
profile (defined in Methods) persisted into infancy, when Bacteroides became the only differentially
95
abundant species between vaginally and C-section delivered babies (Supplementary Table 5). Although we
96