Resistome and microbial profiling of pediatric patient's gut infected with multidrug-resistant diarrhoeagenic <i>Enterobacteriaceae</i> using next-generation sequencing; the first study from Pakistan.

"consent for publication not applicable availability of data and materials the metagenomic raw reads used for this study were deposited in publicly accessible ncbi's sequence read archive (sra) under the accession number: prjna612780. availability of data and materials the metagenomic raw reads used for this study were deposited in publicly accessible ncbi's sequence read archive (sra) under the accession number: prjna612780"

"Disclosure statement The authors declare that they have no competing interests. Declarations"

"To explore the effect of MDR Enterobacteriaceae on the gut microbiota, each of MDR Enterobacter specie and ESBL producing E. coli strains were selected for gut microbiome and its resistome profiling using NGS. In addition to the diseased children, the gut microbiota of healthy children was also profiled to ascertain how they differ from each other. The resistome analysis of MDR Enterobacteriaceae (Enterobacter specie and ESBL producing E. coli) infected children revealed the high abundance of various ARGs conferring resistance to multiple classes of antibiotics (). Among the various genes identified in the resistome of MDR Enterobacteriaceae infected children, efflux pumps associated ARGs were found most abundantly in both Enterobacter species and ESBL producing E. coli infected pediatric patients. The high prevalence of antibiotic efflux pumps and their association with MDR Enterobactericeae in our study is supported by a recent study indicating its presence in the pediatric population []. The abundant presence of various ARGs in the resistome of MDR Enterobactericeae infected children could be attributed to the use of antibiotics administered routinely during acute gastroenteritis. Parental self-medication is an important factor justifying the high prevalence of MDR genes in pediatric patients []. In Pakistan, antibiotics are commonly administered by children and infant’s mothers without a physician’s prescription []. Furthermore, antibiotics are available over the counter and are freely available to everyone in Pakistan due to the absence of any legislation unlike developed countries []. In contrast to the diseased children, the gut resistome of healthy controls exhibited lower prevalence and diversity of various ARGs (). Tetracyclines associated ARGs were found to be the most abundant genes in the resistome of healthy children. Although, antibiotic therapy potentially acts as a selective pressure for the emergence of various ARGs in the human resistome. However, studies provide evidence for the presence of various ARGs in human resistome even in the absence of any selective pressure []. Furthermore, the presence of various ARGs in the resistome of healthy children in our results are in agreement with a previous study indicating the existence of diverse ARGs in the resistome of healthy infants and children []. Literature provides evidence that ARGs appear as the inherent features of the human microbiome albeit, excessive antibiotic administration upsurges the acquisition, transmission, and dissemination of various ARG types in the different gut resistomes []. The abundance of tetracycline-associated ARGs in healthy controls could be justified by the fact tetracycline has been reported to be the most commonly used group of antibiotics worldwide [,]. Moreover, the use of tetracycline has been reduced in recent years especially its therapeutic usage has been stopped in pregnant women or children aged less than 8 years []. However, in developing countries, it is still commonly used for therapeutic purposes and to promote growth in food animals, and in this way, the intestinal bacteria remained exposing to it."