Resistome composition and dynamics in gut microbiota of humans and animals in rural Bangladesh

Abstract

Background The rise of antimicrobial resistance (AMR) in bacteria is a worldwide problem that causes considerable morbidity and mortality, since infections with resistant pathogens may have no therapeutic treatment. People that live in low- and middle-income countries (LMIC) are especially impacted by antimicrobial resistance. However, data on the emergence and spread of antimicrobial resistance in these countries is lacking. Improved AMR surveillance in LMICs is urgently needed, considering that antimicrobial resistance prevalence is increasing in LMIC. People in rural areas often are in close contact with animals and might have poor sanitation, which are risk factors for transmission of antimicrobial resistance genes (ARGs). In this longitudinal study, we characterised ARGs in humans and animals in households in rural Bangladesh.

Methods Samples were taken at three different timepoints. At the first timepoint, faecal samples from pregnant women, siblings, and household livestock were taken. A week after giving birth, mothers and their infants were sampled. The last timepoint was several months later, and again, mothers, infants, siblings, and household animals were sampled. Using a metagenomics approach allowed for identification of the total pool of ARGs (the resistome) in the gut microbiome of humans and animals.

Results Resistome analysis showed that samples of mothers contained a more diverse set of ARGs around the time of giving birth. The composition of mother resistomes just after giving birth was distinct from mother resistomes while they were pregnant or a several months after giving birth. Moreover, newborn resistomes differed from those of their mothers and siblings, reflecting that their microbiomes and thus, their resistomes are still developing. Differential abundance analysis showed that numerous ARGs were more abundant in mothers and newborns just after birth compared to the other timepoints. These changes in the human resistome were not linked to antibiotic usage. However, a significant correlation was found between the microbiome and the resistome composition, and the microbiome of mothers also changed around the time of giving birth. Thus, cooccurrence networks were made, in which Klebsiella was found to correlate with multiple ARGs.

Discussion The high prevalence of ARGs and possibly pathogenic bacteria in mothers and infants just after birth could increase the risk of people in this study population to obtain difficult to treat infections, or to spread resistant bacteria within their households. Further research could focus on identifying transmission routes of mobile ARGs in rural households, and on determining if the increase in ARGs in mothers and infants is due to exposure to resistant bacteria in the hospitals where the infants were born