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New Strategies to Discover Non-Ribosomal Peptides as a Source of Antibiotics Molecules
Published in Peter Grunwald, Pharmaceutical Biocatalysis, 2019
Mario Alberto Martínez-Núñez, Zuemy Rodríguez-Escamilla, Víctor López y López
Through molecular elements such as enzymes or efflux pumps, bacteria have been able to contend against the antibiotics of other bacteria, which allows them to increase their population in the different environments they inhabit, i.e., land, water, or be associated to other organisms. Being able to compete for the colonization of the same or different ecological niches as an adaptive strategy, antibiotic resistance is an ancient, diverse, and widely distributed mechanism (Pawlowski et al., 2016). This group of molecular elements that allow bacteria to resist antibiotics is now known as the resistome, and its presence in ancient natural environments has been proven, for example, in frozen sediments of 30,000 years old, predating the modern use of antibiotics as drugs (D’Costa et al., 2011). The resistome comprises all genes present in a bacterial genome or in a group of bacterial genomes (pan-genome) that live in a given environment and confer antibiotic resistance to the bacterial population not only to clinical pathogenic bacteria, but also to the non-pathogenic species (Wright, 2007; Perry et al., 2014). This collection of resistance genes encompasses both intrinsic and acquired resistance genes, as well as proto-resistance genes and silent or cryptic resistance genes that have moved across environment and bacterial species through mobile elements such as plasmids or transposons that facilitate the horizontal gene transfer of the resistome (Perry et al., 2014; Hu et al., 2016). The resistome profile can vary between different environments, for example, in water environments, including sewage, hospital and animal production wastewaters, ground water, surface water, drinking water, and so on. The most frequently genes are tet genes encoding resistance to tetracyclines, aac, aph, and ant genes to aminoglycosides, and a variety of bla genes to β-lactams. In marine environments, resistome profile changes, with an abundance of genes that confer resistance to ampicillin, tetracycline, nitrofurantoin, and sulfadimethoxine (Hu et al., 2017). The host- associated environments such as gut microbiota in humans and farm animals, have a more complex resistome profile because to the more frequent exposure to antibiotics. In farm pigs from different countries the genes coding for resistance to bacitracin, cephalosporin, macrolide, streptogramin B and tetracycline are prevalent (Xiao et al., 2016), while in the human gut microbiota of Chinese individuals, the tetracycline resistance gene tet showed the highest abundance (Hu et al., 2014). An analysis of resistome present in more than 600 bacterial genomes found that the environmental and human-associated microbial communities harbor distinct antibiotic-resistant genes; therefore resistome profile may be clustered by ecology (Gibson et al., 2015), while transfer of mobile resistome in bacteria is mainly controlled by phylogeny (Hu et al., 2016).
Antibiotics and antibiotic resistance genes in agricultural soils: A systematic analysis
Published in Critical Reviews in Environmental Science and Technology, 2023
Jie Wu, Jinyang Wang, Zhutao Li, Shumin Guo, Kejie Li, Pinshang Xu, Yong Sik Ok, Davey L. Jones, Jianwen Zou
Antibiotics are used worldwide to treat human diseases and animals in agricultural production systems (Martinez, 2009; Sarmah et al., 2006; Wang, Li, et al., 2020; Wang, Wang, Zhu, et al., 2020; Wang, Wang, Wang, et al., 2020). As antibiotics are not fully absorbed by the body, they ultimately lead to the loss of large amounts of antibiotics and their degradation products into the soil environment, such as through animal excreta, livestock wastes, human-derived biosolids, and irrigation water (Du & Liu, 2012; Jechalke et al., 2014; Kuppusamy et al., 2018; Zhao et al., 2021). This has been put increased selective pressure on the environmental resistome and consequently, agricultural-derived antibiotics are now widely considered to be a key driver of the global increase in antibiotic resistance genes (ARGs) (Berendonk et al., 2015; Kuppusamy et al., 2018; Pruden et al., 2006).
The perinatal period, the developing intestinal microbiome and inflammatory bowel diseases: What links early life events with later life disease?
Published in Journal of the Royal Society of New Zealand, 2020
Fathalla Ali, Kei Lui, Alex Wang, Andrew S. Day, Steven T. Leach
Duration of exposure to antibiotics may be an important factor with regards to infant microbial composition. Duration of antibiotics exposure during the first month of life correlates with a decline in the microbiota diversity (Magne et al. 2005). Chernikova et al. (Chernikova et al. 2016) observed a downward linear trend in microbial diversity with an increase in the days of antibiotic exposure. Dardas et al. (Dardas et al. 2014) hypothesised that neonatal gut microbiota colonisation is influenced by the duration of antibiotic therapy and that the diversity of the intestinal microbiota of premature infants inversely correlates with the duration of antibiotic exposure. Compared with full-term infants, preterm infants have excessive exposure to antibiotics, which is administrated both intra-partum to the mother and post-partum to the newborn (DiGiulio 2015). Extensive exposure to antibiotics can lead to long term overrepresentation of antimicrobial resistance (AMR) genes (Rose et al. 2017) which is also referred to as the resistome (Penders et al. 2013). The resistome is highly evident in the microbiota of premature infants who are also cared for in an environment that is potentially contaminated with multi-resistant bacteria (DiGiulio 2015).