Limited assessment and lack of focus on low abundance organisms
The above results indicate that reporting strategies, rather than methodology, may contribute to the underreporting of less abundant pathogens in metagenomic vaginal microbiome studies during pregnancy. As the majority of studies in our review explored the compositional variation of vaginal microbiome during pregnancy, underreporting can be a serious issue because known pathogens may not be analyzed as potential contributors to pregnancy complications, which can lead to limited clinical treatment.
We observed differences in threshold determinants for analysis or reporting. Among the 32 studies that did not report GBS, 24 analyzed the microbiome at the species level, but only reported the most prevalent genus (i.e., Lactobacillus species). This may lead to a misclassification error, in which only the most abundant bacteria or species is associated with the outcome of interest. Additionally, 20 studies reported Streptococcus at the genus level, but did not conduct further species-level analysis. It is possible that studies that did not specify Streptococcus had GBS present within their population, a result which could be re-evaluated if raw sequencing data is made available.
Moreover, four studies that did not report GBS in their results or microbiome data identified GBS-positive women in their study based on culture-based clinical testing.8–11 This suggests that there may be a benefit to using both sequence-based and culture-based methods to verify presence or absence of low abundance microbes within vaginal microbiome communities. Previous studies have shown discordance in culture-based GBS colonization results between antenatal screening and culture on admission for delivery.5,18 In a study by McCoy and colleagues, that rate was about 40%.5 Alternatively, Hussain et al. reported a discordance rate of 11%.18 While the transient nature of GBS colonization is known, factors that contribute to loss or gain of maternal GBS colonization remain uncertain.6
Evaluation of culture-based GBS screening determined that GBS transmission to neonates is more likely when maternal colonization is heavy, as determined by the number of colonies grown at the time of screening.19,20 However, it is unclear how well clinical culture-based microbial assessments correlate with the detection of clinically relevant pathogens in sequencing-based vaginal microbiome studies. Furthermore, much of the research investigating risk of neonatal GBS infection related to maternal bacterial load was completed in the 1980s and has not been evaluated relative to sequencing-based methods.20 Future studies that concurrently evaluate the accuracy of GBS reporting within microbial communities via metagenomic sequencing approaches and culture-based methods are needed.