To date, primary research outcomes for studies investigating intrapartum antibiotic administration have been related to maternal illness and health outcomes [
53]. Intrapartum antibiotic administration prior to initiating the incision when cesarean deliveries are performed significantly decreases infectious morbidity outcomes in women [
54]. Ledger and Blaser pose that U.S. physicians prescribe too many antibiotics for the pregnant woman and fetus in utero [
10]. They cited practice modifications to prevent group B streptococcus (GBS) infections in newborn and postpartum maternal infection after caesarean delivery has led to the use of pre-delivery antibiotics of ≥40 % of women in labour, which cross to the fetus. However, there has been little research regarding the long-term effects of antepartum or intrapartum antibiotic use on the infant. In their review of 86 studies, Smaill and Gyte [
53] noted the effects of intrapartum antibiotic administration on the infant are largely unknown, limiting the ability to accurately evaluate the potential benefit and/or harm of intrapartum administration. A 2009 Cochrane Review reported that the recommendations for neonatal GBS antibiotic prophylaxis are based on flawed studies, and that, due to current clinical protocols, it is unlikely unbiased studies will be initiated [
55]. The incidence of neonatal GBS sepsis during the first 7 days of life has declined 80 % (though the same cannot be said for late onset GBS) since implementation of prophylactic antibiotic administration in women colonized with GBS, suggesting a straightforward recommendation for routine prophylactic treatment, at first glance [
56]. However, despite the methodological and ethical difficulties, future studies are needed to weigh the risks and harms of antibiotic exposure during birth. This is increasingly apparent as evidence accumulates around the potential risks of routine prophylactic use of antibiotics, including increased rates of asthma in early childhood associated with maternal antibiotic use, which suggests a role for bacterial ecology in the perinatal period [
57,
58]. There are also studies showing associations between maternal antibiotic use before and during pregnancy and infant allergy to cow’s milk [
59]; and that administration of antibiotics to children under the age of 6 months is linked with higher rates of obesity for children of parents at normal weight, independent of mode of birth [
60]. Epidemiological research has also shown an association between exposure to antibiotics during pregnancy and infant birth weight, and epigenetic analysis has demonstrated altered DNA methylation in these circumstances, which has been associated with obesity as well as other disorders later on in life [
21]. Antibiotics have been shown to trigger altered gene expression and changes in gut microbes in rats. This has been found to influence immune system development and function [
61,
62]. Fetal and/or neonatal exposure to antibiotics may lead to a dysfunctional development of the immune system initiating a cascade of events associated with future health conditions. Csoka and Szyf [
63] hypothesized that pharmaceuticals create a gene-environment interaction which prompts cells to adapt through methylation and that such epigenetic changes may persist after the drug has ceased. As an alternative explanation, a recent study has suggested that maternal antibiotic use may be a surrogate marker of a mother’s general propensity for infections, and that this might be the underlying link between a mothers use of antibiotics and the risk of asthma in the offspring [
64]. This indicates the aetiology is complex and confounded by other pregnancy and intrapartum practices. Long term studies are needed to determine the aetiology and inter-generational outcomes of the current high rates of antibiotic administration during labour and birth [
10].