Acquired antibiotic resistance: are we born with it?

Abstract

The rapid emergence of antibiotic resistance (AR) is a major public health concern. Recent findings on the prevalence of food-borne antibiotic-resistant (ART) commensal bacteria in ready-to-consume food products suggested that daily food consumption likely serves as a major avenue for dissemination of ART bacteria from the food chain to human hosts. To properly assess the impact of various factors, including the food chain, on AR development in hosts, it is important to determine the baseline of ART bacteria in the human gastrointestinal (GI) tract. We thus examined the gut microbiota of 16 infant subjects, from the newborn stage to 1 year of age, who fed on breast milk and/or infant formula during the early stages of development and had no prior exposure to antibiotics. Predominant bacterial populations resistant to several antibiotics and multiple resistance genes were found in the infant GI tracts within the first week of age. Several ART population transitions were also observed in the absence of antibiotic exposure and dietary changes. Representative AR gene pools including tet(M), ermB, sul2, and bla(TEM) were detected in infant subjects. Enterococcus spp., Staphylococcus spp., Klebsiella spp., Streptococcus spp., and Escherichia coli/Shigella spp. were among the identified AR gene carriers. ART bacteria were not detected in the infant formula and infant foods examined, but small numbers of skin-associated ART bacteria were found in certain breast milk samples. The data suggest that the early development of AR in the human gut microbiota is independent of infants' exposure to antibiotics but is likely impacted by exposure to maternal and environmental microbes during and after delivery and that the ART population is significantly amplified within the host even in the absence of antibiotic selective pressure.

Fig. 1.

Assessment of tetracycline resistance in fecal samples from infant subjects. Black bars, total bacterial counts on CBA plates; gray bars, Tet^r bacterial counts on CBA plates; white bars, copy numbers for tet(M) gene by real-time PCR. Real-time PCR was performed on two independent DNA extract replicates, and the coefficients of variation for log copy numbers of the resistance gene were <0.05.

Fig. 2.

Assessment of AR in fecal samples from baby Q between the newborn stage and 4 months of age. (A) Black bars, total bacterial counts on CBA plates; gray bars, total bacterial counts on MAC plates. (B) Black bars, Erm^r bacterial counts on CBA plates; white bars, Erm^r bacterial counts on MAC plates; gray bars, copy numbers for ermB gene by real-time PCR. (C) Black bars, Tet^r bacterial counts on CBA plates; white bars, Tet^r bacterial counts on MAC plates; gray bars, copy numbers for tet(M) gene by real-time PCR. Real-time PCR was performed on two independent DNA extract replicates, and the coefficients of variation for log copy numbers of resistance genes were <0.05.

Fig. 3.

Predominant ART bacteria during infant (baby Q) development, assessed by DGGE analysis. (A) Tet^r bacteria on CBA plates. (B) Erm^r bacteria on CBA plates. Data are presented in a time-lapse manner (D, day; W, week; M, month). L, DNA ladder. a to e, Staphylococcus sp.; f, Streptococcus sp.; g to i, Veillonella sp.; j, Peptoniphilus sp.; k, Enterococcus sp.; l and n, Staphylococcus sp.; m, Streptococcus sp.; o to q, Klebsiella sp.; r, Enterobacteriaceae.

Fig. 4.

AR gene pools in infant subjects and corresponding mothers. Total DNA from infants was collected when the subjects were 4 months old. Black bars, tet(M) gene pool; gray bars, ermB gene pool; white bars, sul2 gene pool; hatched bars, bla_TEM gene pool. Data represent means for two independent replicates, and coefficients of variations for log copy numbers of resistance genes were <0.05.