Maternal Microbiota Contribution to Antibiotic Resistance Development in Infants

Project goal: Purpose of the study: To determine the contribution of vertical transmission of antibiotic resistance genes to the infant resistome from the mother and to characterize the factors influencing their accumulation in early childhood.

Project description: The global threat of antibiotic resistance requires urgent action, the effectiveness of which depends on understanding the transmission and accumulation of corresponding genes. These processes remain particularly poorly understood at the critically important stage of early childhood microbiome development. This longitudinal cohort study aims to elucidate the role of the maternal microbiota as a source of infant gut resistome formation using metagenomic sequencing. Recruitment of 100 mother-infant pairs will be carried out followed by collection of fecal samples from birth to 3 years of age. Comparison of resistomes dynamically will establish common genes indicating vertical transmission of antibiotic resistance. Key microbial carriers and trajectories of resistome changes under the influence of environmental factors and gut development will also be determined. The project results will expand fundamental understanding of the origins and evolution of the early-life resistome and serve as a basis for optimizing antibiotic use in pediatrics. Continuing our laboratory’s program of dynamic monitoring of microbiota development in children, the project will contribute to establishing links between the resistome and long-term health outcomes. Hypothesis: Maternal transmission is a key source of antibiotic resistance genes in the infant gut that shape resistance trajectories over the first 3 years of life.

Project facilitators:
PI: Samat Kozhakhmetov
Marina Morenko
Zharkyn Jarmukhanov
Nurislam Mukhanbetzhanov
Laura Chulenbayeva
Arailym Duisebayeva

Project partners:
Astana Medical University

Realisation period:
2024-2026

Expected results: As part of the study, recruitment will be carried out and at least 1000 samples will be collected from 100 children dynamically and once from their mothers. The samples collected in this study will replenish the biobank of samples, metagenomic, clinical data as part of the laboratory's efforts to track dynamic changes in the formation of the microbiome of Kazakh children from birth to 15 years of age. The main results of the study will also be the determination of inheritance of resistance genes from mother to child, which will expand knowledge of the mechanisms of early resistome formation. We expect to establish the transmission of specific resistance gene variants from mothers to newborn children, which will indicate vertical transmission. A deeper understanding of this process is critical for predicting and preventing the emergence and spread of inadequate antibiotic resistance at the earliest stages of human microbiome development. The data obtained within the framework of the project will not only supplement fundamental knowledge in this area, but will also serve as the basis for developing science-based recommendations for optimizing the use of antibiotics in pregnant women and young children. During the implementation of the project, scientific data will be obtained, which, after preliminary coding, will be deposited in open databases for subsequent analysis by the international scientific community. This will expand global knowledge on the formation of the resistome in the early stages of human development and serve as the basis for the development of personalized prevention and treatment approaches. This project will seamlessly integrate into the research already underway in our laboratory to study the microbiome of children from birth to adolescence. It is planned to continue dynamic monitoring of the health and microbiota of participants for 15 years. This will establish long-term correlations between the features of the early microbiome and subsequent health status, as well as put forward hypotheses about possible corrective interventions. In addition, young scientists and student volunteers will be involved in the work on the project, which will increase their qualifications in the field of studying the human microbiome using modern methods of metagenomics and bioinformatics. The results of the research will be published in peer-reviewed journals that meet the requirements of the competition documentation. The data on transmission of antibiotic resistance genes from mother to infant obtained in this study will contribute to fundamental knowledge on gut microbiome and resistome formation in early stages of human development. The research will provide new mechanistic insights into microbiota ecology, succession and resistance evolution. Knowledge gained in this study will aid in developing recommendations for optimizing antibiotic use that could impact related fields like pediatrics, neonatology, and clinical microbiology. Findings will form a basis for advancing approaches in prevention of dysbioses and infections in newborns and young infants. Longitudinal infant microbiome data will be demanded in personalized pediatrics and gastroenterology, allowing new hypotheses on the microbiota's role in health maintenance and disease.

Methodology: The research methodology includes recruiting participants through parent surveys with informed consent and assigning unique codes for confidentiality. Fecal samples are self-collected using DNA/RNA Shield tubes. Samples are delivered to the laboratory within 1-2 days, stored at +4°C for up to 7 days and partially at -80°C for future research. DNA is extracted using ZymoBIOMICS kit, quality control is performed by electrophoresis and spectrophotometry. Shotgun sequencing is performed on Illumina NovaSeq 6000 platform using QIAseq FX DNA Library. Bioinformatic analysis includes microbial signature identification (MetaPhlAn 4), metabolic pathway profiling (HUMAnN 3.6), and annotation of resistance genes (RGI, CARD). Statistical processing is carried out using Python 3.9 and specialized libraries. The study was approved by the Ethics Committee of Nazarbayev University (No.05-2023 dated 11/21/2023), sequencing results will be deposited in the international SRA database

Contacts: Samat Kozhakhmetov, Email: skozhakhmetov@nu.edu.kz