Can landscape ecology untangle the complexity of antibiotic resistance?

New trends in pharmacogenomic strategies against resistance development in microbial infections

This review summarizes some of the new trends in the fight against drug resistant bacteria. We review Gram-positive (e.g., S.aureus) and Gram-negative (e.g., Pseudomonas aeruginosa, Helicobacter pylori) bacteria, the current antibiotic resistance situation, as well as resistance spread and some recently discovered resistance mechanisms, such as those based on integrons and complex transposons. We then summarize several current routes to identify new drugs such as cationic antimicrobial peptides, novel acyldepsipeptides, RNA aptamers and lipopeptides. New drug strategies to treat resistant pathogens include eliciting growth in dormant bacteria, or a new way to attack efflux systems. Typical approaches from pharmacogenomics combined with systems biology and bioinformatics support these routes (simulations, metagenomics and metabolic network modeling), as well as the patient treatment (e.g., haplotyping and immune response).

Functional metagenomics reveals diverse beta-lactamases in a remote Alaskan soil

Despite the threat posed by antibiotic resistance in infectious bacteria, little is known about the diversity, distribution and origins of resistance genes, particularly among the as yet unculturable environmental bacteria. One potentially rich but largely unstudied environmental reservoir is soil. The complexity of its microbial community coupled with its high density of antibiotic-producing bacteria makes the soil a likely origin for diverse antibiotic resistance determinants. To investigate antibiotic resistance genes among uncultured bacteria in an undisturbed soil environment, we undertook a functional metagenomic analysis of a remote Alaskan soil. We report that this soil is a reservoir for beta-lactamases that function in Escherichia coli, including divergent beta-lactamases and the first bifunctional beta-lactamase. Our findings suggest that even in the absence of selective pressure imposed by anthropogenic activity, the soil microbial community in an unpolluted site harbors unique and ancient beta-lactam resistance determinants. Moreover, despite their evolutionary distance from previously known genes, the Alaskan beta-lactamases confer resistance on E. coli without manipulating its gene expression machinery, demonstrating the potential for soil resistance genes to compromise human health, if transferred to pathogens.

Identification and network of outer membrane proteins regulating streptomysin resistance in Escherichia coli

Bacterial Outer membrane (OM) proteins involved in antibiotic resistance have been reported. However, little is known about the OM proteins and their interaction network regulating streptomycin (SM) resistance. In the present study, a subproteomic approach was utilized to characterize OM proteins of Escherichia coli with SM resistance. TolC, OmpT and LamB were found to be up-regulated, and FadL, OmpW and a location-unknown protein Dps were down-regulated in the SM-resistant E. coli strain. These changes at the level of protein expression were validated using Western blotting. The possible roles of the altered proteins involved in the SM resistance were investigated using genetic modified strains with the deletion of these altered genes. It is found that decreased and elevated minimum inhibitory concentrations and survival capabilities of the gene deleted strains and their resistant strains, Delta tolC, Delta ompT, Delta dps, Delta tolC-R, Delta ompT-R, Delta dps-R and Delta fadL-R, were correlated with the changes of TolC, OmpT, Dps and FadL at the protein expression levels detected by 2-DE gels, respectively. The results may suggest that these proteins are the key OM proteins and play important roles in the regulation of SM resistance in E. coli. Furthermore, an interaction network of altered OM proteins involved in the SM resistance was proposed in this report. Of the six altered proteins, TolC may play a central role in the network. These findings may provide novel insights into mechanisms of SM resistance in E. coli.

Effect of subtherapeutic administration of antibiotics on the prevalence of antibiotic-resistant Escherichia coli bacteria in feedlot cattle

Antibiotic-resistant Escherichia coli in 300 feedlot steers receiving subtherapeutic levels of antibiotics was investigated through the collection of 3,300 fecal samples over a 314-day period. Antibiotics were selected based on the commonality of use in the industry and included chlortetracycline plus sulfamethazine (TET-SUL), chlortetracycline (TET), virginiamycin, monensin, tylosin, or no antibiotic supplementation (control). Steers were initially fed a barley silage-based diet, followed by transition to a barley grain-based diet. Despite not being administered antibiotics prior to arrival at the feedlot, the prevalences of steers shedding TET- and ampicillin (AMP)-resistant E. coli were >40 and <30%, respectively. Inclusion of TET-SUL in the diet increased the prevalence of steers shedding TET- and AMP-resistant E. coli and the percentage of TET- and AMP-resistant E. coli in the total generic E. coli population. Irrespective of treatment, the prevalence of steers shedding TET-resistant E. coli was higher in animals fed grain-based compared to silage-based diets. All steers shed TET-resistant E. coli at least once during the experiment. A total of 7,184 isolates were analyzed for MIC of antibiotics. Across antibiotic treatments, 1,009 (13.9%), 7 (0.1%), and 3,413 (47.1%) E. coli isolates were resistant to AMP, gentamicin, or TET, respectively. In addition, 131 (1.8%) and 143 (2.0%) isolates exhibited potential resistance to extended-spectrum beta-lactamases, as indicated by either ceftazidime or cefpodoxime resistance. No isolates were resistant to ciprofloxacin. The findings of the present study indicated that subtherapeutic administration of tetracycline in combination with sulfamethazine increased the prevalence of tetracycline- and AMP-resistant E. coli in cattle. However, resistance to antibiotics may be related to additional environmental factors such as diet.

Evaluating the effects of chlortetracycline on the proliferation of antibiotic-resistant bacteria in a simulated river water ecosystem

Antibiotics and antibiotic metabolites have been found in the environment, but the biological activities of these compounds are uncertain, especially given the low levels that are typically detected in the environment. The objective of this study was to estimate the selection potential of chlortetracycline (CTC) on the antibiotic resistance of aerobic bacterial populations in a simulated river water ecosystem. Six replicates of a 10-day experiment using river water in continuous flow chemostat systems were conducted. Each replicate used three chemostats, one serving as a control to which no antibiotic was added and the other two receiving low and high doses of CTC (8 microg/liter and 800 microg/liter, respectively). The addition of CTC to the chemostats did not impact the overall level of cultivable aerobic bacteria (P = 0.51). The high-CTC chemostat had significantly higher tetracycline-resistant bacterial colony counts than both the low-CTC and the control chemostats (P < 0.035). The differences in resistance between the low-CTC and control chemostats were highly nonsignificant (P = 0.779). In general a greater diversity of tet resistance genes was detected in the high-CTC chemostat and with a greater frequency than in the low-CTC and control chemostats. Low levels of CTC in this in vitro experiment did not select for increased levels of tetracycline resistance among cultivable aerobic bacteria. This finding should not be equated with the absence of environmental risk, however. Low concentrations of antibiotics in the environment may select for resistant bacterial populations once they are concentrated in sediments or other locations.

The role of ecological theory in microbial ecology

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.