Abstract
Infection and inflammation are well recognized causes of spontaneous preterm delivery (PTD) (<37 gestational weeks) and adverse infant outcomes. To date, there has been very little investigation into bacterial communities in amniotic fluid using next generation sequencing technology. In particular, it is important to characterize amniotic fluid bacterial profiles in complicated pregnancies as well as in asymptomatic women to identify predictive bacterial DNA signatures. Here, 1198 mid-trimester amniotic fluid samples from a cohort of Swedish women undergoing mid-trimester genetic amniocentesis were screened for bacterial DNA using qPCR protocols specifically designed to reduce the impacts of reagent contamination and human DNA mispriming. The majority of samples were devoid of detectable bacterial DNA; however, approximately a fifth of the cohort (19.9%) were 16S rRNA gene positive in duplicate screening. Among these, nine women had a spontaneous PTD. These nine women were matched with 18 healthy women with a delivery at term. We used PacBio SMRT technology, coupled with appropriate negative extraction and PCR controls, to sequence the full-length 16S rRNA gene in this subset of 27 women. The amniotic fluid samples contained low-abundance and low-diversity bacterial DNA profiles. Species typically associated with spontaneous PTD were absent. We were not able to identify any differences in the amniotic fluid bacterial DNA profiles of women with a subsequent spontaneous PTD compared to women who delivered at term. The findings suggest that, in a minor proportion of pregnancies, DNA from non-pathogenic bacteria may be present in the amniotic fluid far earlier than previously reported. Early detection of bacterial DNA in the amniotic fluid was, in this study, not associated with spontaneous PTD.
Highlights
The existence of a fetal or in utero microbiome in normal pregnancy remains controversial (Collado et al, 2016; Stinson et al, 2016; de Goffau et al, 2019)
Bacterial DNA Is Present in Amniotic Fluid in Mid-Pregnancy
Of the 1198 mid-trimester amniotic fluid samples screened by qPCR, 238 (19.9%) contained detectable levels of bacterial DNA
Summary
The existence of a fetal or in utero microbiome (an ecosystem of interacting microorganisms) in normal pregnancy remains controversial (Collado et al, 2016; Stinson et al, 2016; de Goffau et al, 2019). Numerous studies have investigated bacterial colonization of the amniotic fluid in both complicated and healthy pregnancies using culture-dependant and cultureindependent techniques These studies have reported a diverse range of results, with some finding that amniotic fluid was devoid of bacteria (Rowlands et al, 2017), some finding that all amniotic fluid samples contain bacteria (Collado et al, 2016; Urushiyama et al, 2017; Wang et al, 2018; Zhu et al, 2018), and yet others reporting a combination of positive and negative samples (Watts et al, 1992; Mandar et al, 2001; Bearfield et al, 2002; Mendz et al, 2013; Cobo et al, 2017; Kayem et al, 2018; Lim et al, 2018; Morimoto et al, 2018; Stinson et al, 2019a). As bacterial populations in the amniotic fluid are likely to influence fetal skin and gut colonization (via swallowing of the amniotic fluid which begins at the end of the first trimester) which could have important implications for the development and maturation of the fetal immune system
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