Sampling the Antibiotic Resistome

Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario, Canada, L8N 3Z5.
Science (Impact Factor: 33.61). 02/2006; 311(5759):374-7. DOI: 10.1126/science.1120800
Source: PubMed


Microbial resistance to antibiotics currently spans all known classes of natural and synthetic compounds. It has not only hindered our treatment of infections but also dramatically reshaped drug discovery, yet its origins have not been systematically studied. Soil-dwelling bacteria produce and encounter a myriad of antibiotics, evolving corresponding sensing and evading strategies. They are a reservoir of resistance determinants that can be mobilized into the microbial community. Study of this reservoir could provide an early warning system for future clinically relevant antibiotic resistance mechanisms.

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    • "It is not yet clear and arguments among scientists increase daily about the involvement of man and his many anthropogenic activities in the spread of resistance elements in microorganisms . Several studies have reported lack of tangible relationship between anthropogenic activities and antibiotic resistance in bacteria and many believe that the elements that selects for resistance are naturally present within microbial genome (Davis and Anandan, 1970; Hughes and Datta, 1983; Barlow and Hall, 2002; Hall and Barlow, 2004; D'Costa et al., 2006, 2011; Wright, 2007, 2010; Baltz, 2008; Brown and Balkwill, 2009; Thaller et al., 2010; Toth et al., 2010; Bhullar et al., 2012; Cox and Wright, 2013). On the other hand, evidence abound that increased bacterial resistance to antibiotics and the transfer of resistance elements is a modern phenomenon having a strong link with anthropogenic activities (Knapp et al., 2010; Bhullar et al., 2012). "
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    ABSTRACT: Antibiotics are emerging environmental contaminants, causing both short-term and long-term alterations of natural microbial communities due to their high biological activities. The antibiotic resistance pattern of bacteria from anthropogenic polluted Oluwa River, Nigeria was carried out. Microbial profiling and antibiotic sensitivity tests were carried out on water and sediment samples using 13 different antibiotics. Microorganisms isolated include those in the genera Bacillus, Micrococcus, Pseudomonas, Streptococcus, Proteus and Staphylococcus. The microbial count of isolates from water samples ranged between 94.10 × 102 Cfu/100 ml and 156.20 × 102 Cfu/100 ml while that of sediment samples ranged from 2.55 × 104 Cfu g−1 to 14.30 × 104 Cfu g−1. From the water isolates, 100% resistance to antibiotics was found in Micrococcus spp. and Pseudomonas spp. while another Micrococcus, Streptococcus, Staphylococcus and Bacillus spp. showed between 40% and 90% resistances. From the sediment isolates, 100% resistance to antibiotics was found in a Bacillus spp. and Pseudomonas spp. while another Bacillus, Micrococcus, Staphylococcus, Streptococcus and Proteus spp. showed between 70% and 90% resistances. Multiple antibiotic resistance (MAR) was shown by all the isolates and Bacillus, Micrococcus and Pseudomonas spp. showed the highest resistances (100%) to all antibiotics. Thus, Oluwa River is not safe for public consumption.
    Egyptian Journal of Aquatic Research 10/2014; 40(3). DOI:10.1016/j.ejar.2014.09.002
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    • "For this reason, it is not unexpected that their microbial community possesses specialized mechanisms to respond to and metabolize small molecules, including antibiotics (Knapp et al., 2010), indicating that the environment is a massive reservoir in which to search for novel resistant organisms (Allen et al., 2010). Indeed, the concept of the resistome on a global scale consists of antibiotic resistance genes detected either free living or as commensals in the environment (D’Costa et al., 2006). "
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    ABSTRACT: In recent years a major worldwide problem has arisen with regard to infectious diseases caused by resistant bacteria. Resistant pathogens are related to high mortality and also to enormous healthcare costs. In this field, cultured microorganisms have been commonly focused in attempts to isolate antibiotic resistance genes or to identify antimicrobial compounds. Although this strategy has been successful in many cases, most of the microbial diversity and related antimicrobial molecules have been completely lost. As an alternative, metagenomics has been used as a reliable approach to reveal the prospective reservoir of antimicrobial compounds and antibiotic resistance genes in the uncultured microbial community that inhabits a number of environments. In this context, this review will focus on resistance genes as well as on novel antibiotics revealed by a metagenomics approach from the soil environment. Biotechnology prospects are also discussed, opening new frontiers for antibiotic development.
    Frontiers in Microbiology; 09/2014
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    • "The environment is both the main receptor for animal wastes containing AMR determinants, particularly those on MGEs (Heuer et al., 2011), and the locus of the natural resistome (D'Costa et al., 2006, 2007) and mobilome (Siefert, 2009; Gillings, 2013) which together constitute the genetic resources available to microbial communities for surviving antimicrobial stress and the genetic machinery to transfer these genetic resources among bacteria within and among different microbial communities. The environmental resistome, which encompasses both natural constituents as well as inputs from anthropogenic activities like agriculture, is relevant to human health as it can be a source of resistance determinants found in human pathogens, particularly through the mobilome (Forsberg et al., 2012; Perry and Wright, 2013). "
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    ABSTRACT: Antimicrobial resistance is a growing public health challenge worldwide, with agricultural use of antimicrobials being one major contributor to the emergence and dissemination of antimicrobial resistance (AMR). Globally, most antimicrobials are used in industrial food animal production, a major context for microbiomes encountering low-doses or subtherapeutic-levels of antimicrobial agents from all mechanistic classes. This modern practice exerts broad eco-evolutionary effects on the gut microbiome of food animals, which is subsequently transferred to animal waste. This waste contains complex constituents that are challenging to treat, including AMR determinants and low-dose antimicrobials. Unconfined storage or land deposition of a large volume of animal waste causes its wide contact with the environment and drives the expansion of the environmental resistome through mobilome facilitated horizontal genet transfer. The expanded environmental resistome, which encompasses both natural constituents and anthropogenic inputs, can persist under multiple stressors from agriculture and may re-enter humans, thus posing a public health risk to humans. For these reasons, this review focuses on agricultural antimicrobial use as a laboratory for understanding low-dose antimicrobials as drivers of resistome expansion, briefly summarizes current knowledge on this topic, highlights the importance of research specifically on environmental microbial ecosystems considering AMR as environmental pollution, and calls attention to the needs for longitudinal studies at the systems level.
    Frontiers in Microbiology 06/2014; 5:284. DOI:10.3389/fmicb.2014.00284 · 3.99 Impact Factor
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Vanessa D'Costa