Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers' breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load

Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence

Integrated antibiotic resistance (AR) surveillance is one of the objectives of the World Health Organization global action plan on antimicrobial resistance. Urban wastewater treatment plants (UWTPs) are among the most important receptors and sources of environmental AR. On the basis of the consistent observation of an increasing north-to-south clinical AR prevalence in Europe, this study compared the influent and final effluent of 12 UWTPs located in seven countries (Portugal, Spain, Ireland, Cyprus, Germany, Finland, and Norway). Using highly parallel quantitative polymerase chain reaction, we analyzed 229 resistance genes and 25 mobile genetic elements. This first trans-Europe surveillance showed that UWTP AR profiles mirror the AR gradient observed in clinics. Antibiotic use, environmental temperature, and UWTP size were important factors related with resistance persistence and spread in the environment. These results highlight the need to implement regular surveillance and control measures, which may need to be appropriate for the geographic regions.This work was financed by the Water JPI through the national funding agencies supporting the consortium WaterJPI/0001/2013 STARE—“Stopping Antibiotic Resistance Evolution” (Cyprus, RPF; Germany, BMBF; Spain, MINECO; Finland, AKA; Ireland, EPA; Norway, RCN; Portugal, FCT). I.V.-M. was supported by the FCT grant SFRH/BPD/87360/2012, C.N.-d.-R. by the FCT grant SFRH/BD/97131/2013, and I.H. by the FCT contract IF/00492/2013. Other funders: A grant from the Michigan State University Center for Health Impacts of Agriculture (CHIA) and the National Natural Science Foundation of China (21677149)

Community-led, integrated, reproducible multi-omics with anvi'o

International audienceBig data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi’o was first published, this community-led multi-omics platform is maturing into an open software ecosystem that reduces constraints in ‘omics data analyses

A review on Antibiotic Resistance Gene (ARG) occurrence and detection in WWTP in Ishikawa, Japan and Colombo, Sri Lanka

In this chapter, we give a brief overview on occurrence of antibiotic resistance gene in WWTP based on previous studies conducted in several countries. Then, we describe our initial effort in antibiotic resistance gene screening from samples collected in four WWTP in Ishikawa Prefecture, Japan, employing the activated sludge process, and wastewater samples collected from WWTPs in Colombo, Sri Lanka, Bangkok, Thailand, and Can Tho, Vietnam.by Sulfikar Sorn, Sovannlaksmy, Ryo Honda, Tushara Chaminda and Manish Kuma