TY - JOUR
T1 - Enrichment of clinically relevant organisms in spontaneous preterm-delivered placentas and reagent contamination across all clinical groups in a large pregnancy cohort in the United Kingdom
AU - Leon, Lydia J.
AU - Doyle, Ronan
AU - Diez-Benavente, Ernest
AU - Clark, Taane G.
AU - Klein, Nigel
AU - Stanier, Philip
AU - Moore, Gudrun E.
N1 - Funding Information:
We thank Wellbeing of Women and Lord Mayor's funding. This research was funded by the United Kingdom Medical Research Council (MRC), the Biological Research Council, and Great Ormond Street Hospital Children's Charity (Ph.D. fellowship to L.J.L.) and was supported by the National Institute for Health Research Biomedical Research Centre at Great Ormond Street Hospital for Children, the NHS Foundation Trust, and University College London. P.S. is supported by Great Ormond Street Hospital Children's Charity and the MRC (MR/K022741/1 and MR/M004597/1). R.D. and N.K. were supported by the UCL Great Ormond Street Institute of Child Health and the Reuben Centre for Pediatric Virology and Metagenomics and by the Food and Nutrition Technical Assistance III Project (FANTA). T.G.C. is funded by the United Kingdom MRC (grant no. MR/K000551/1, MR/M01360X/1, MR/N010469/1, and MC_PC_15103). The MRC eMed-Lab computing resource was used for bioinformatics and statistical analyses. We also thank all participating hospital staff and families. We report no conflict of interest
Publisher Copyright:
© 2018 American Society for Microbiology.
PY - 2018/7/1
Y1 - 2018/7/1
N2 - In this study, differences in the placental microbiota from term and preterm deliveries in a large pregnancy cohort in the United Kingdom were studied by using 16S-targeted amplicon sequencing. The impacts of contamination from DNA extraction, PCR reagents, and the delivery itself were also examined. A total of 400 placental samples from 256 singleton pregnancies were analyzed, and differences between spontaneous preterm-, nonspontaneous preterm-, and term-delivered placentas were investigated. DNA from recently delivered placentas was extracted, and screening for bacterial DNA was carried out by using targeted sequencing of the 16S rRNA gene on the Illumina MiSeq platform. Sequenced reads were analyzed for the presence of contaminating operational taxonomic units (OTUs) identified via sequencing of negative extraction and PCR-blank samples. Differential abundances and between-sample (beta) diversity metrics were then compared. A large proportion of the reads sequenced from the extracted placental samples mapped to OTUs that were also found for negative extractions. Striking differences in the compositions of samples were also observed, according to whether the placenta was delivered abdominally or vaginally, providing strong circumstantial evidence for delivery contamination as an important contributor to observed microbial profiles. When OTU- and genus-level abundances were compared between the groups of interest, a number of organisms were enriched in the spontaneous preterm-delivery cohort, including organisms that have been associated previously with adverse pregnancy outcomes, specifically Mycoplasma spp. and Ureaplasma spp. However, analyses of the overall community structure did not reveal convincing evidence for the existence of a reproducible "preterm placental microbiome.".
AB - In this study, differences in the placental microbiota from term and preterm deliveries in a large pregnancy cohort in the United Kingdom were studied by using 16S-targeted amplicon sequencing. The impacts of contamination from DNA extraction, PCR reagents, and the delivery itself were also examined. A total of 400 placental samples from 256 singleton pregnancies were analyzed, and differences between spontaneous preterm-, nonspontaneous preterm-, and term-delivered placentas were investigated. DNA from recently delivered placentas was extracted, and screening for bacterial DNA was carried out by using targeted sequencing of the 16S rRNA gene on the Illumina MiSeq platform. Sequenced reads were analyzed for the presence of contaminating operational taxonomic units (OTUs) identified via sequencing of negative extraction and PCR-blank samples. Differential abundances and between-sample (beta) diversity metrics were then compared. A large proportion of the reads sequenced from the extracted placental samples mapped to OTUs that were also found for negative extractions. Striking differences in the compositions of samples were also observed, according to whether the placenta was delivered abdominally or vaginally, providing strong circumstantial evidence for delivery contamination as an important contributor to observed microbial profiles. When OTU- and genus-level abundances were compared between the groups of interest, a number of organisms were enriched in the spontaneous preterm-delivery cohort, including organisms that have been associated previously with adverse pregnancy outcomes, specifically Mycoplasma spp. and Ureaplasma spp. However, analyses of the overall community structure did not reveal convincing evidence for the existence of a reproducible "preterm placental microbiome.".
KW - Contamination
KW - Infection
KW - Microbiome
KW - Pregnancy
KW - Preterm birth
UR - http://www.scopus.com/inward/record.url?scp=85049879238&partnerID=8YFLogxK
U2 - 10.1128/AEM.00483-18
DO - 10.1128/AEM.00483-18
M3 - Article
C2 - 29776928
AN - SCOPUS:85049879238
SN - 0099-2240
VL - 84
JO - Applied and Environmental Microbiology
JF - Applied and Environmental Microbiology
IS - 14
M1 - e00483-18
ER -