The field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD; http://arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment.A ntibiotic resistance is an increasing crisis as both the range of microbial antibiotic resistance in clinical settings expands and the pipeline for development of new antibiotics contracts (1). This problem is compounded by the global genomic scope of the antibiotic resistome, such that antibiotic resistance spans a continuum from genes in pathogens found in the clinic to those of benign environmental microbes along with their proto-resistance gene progenitors (2, 3). The recent emergence of New Delhi metallo-ß-lactamase (NDM-1) in Gram-negative organisms (4), which can hydrolyze all ␤-lactams with the exception of monobactams, illustrates the capacity of new antibiotic resistance genes to emerge rapidly from as-yet-undetermined reservoirs. Surveys of genes originating from both clinical and environmental sources (microbes and metagenomes) will provide increasing insight into these reservoirs and offer predictive capacity for the emergence and epidemiology of antibiotic resistance.The increasing opportunity to prepare a broader and comprehensive antibiotic resistance gene census is facilitated by the power and falling costs of next-generation DNA sequencing. For example, whole-genome sequencing (WGS) is being increasingly used to examine new antibiotic-resistant isolates discovered in clinical settings (5). Additionally, culture-independent metagenomic surveys are adding tremendously to the pool of known genes and their distribution outside clinical settings (6, 7). These approaches have the advantage of providing a rapid survey of the antibiotic resistome of new strains, the discovery of newly emergent antibiotic resistance genes, the epidemiology of antibiotic resistance genes, and the horizontal gene transfer (HGT) of known antibiotic resistance genes through plasmids and transposable elements. However, despite the existence of tools for general annotation of prokaryotic genomes (see, e.g., reference 8), prediction of an antibiotic resista...

The emergence and spread of carbapenem-resistant Gram-negative pathogens is a global public health problem. The acquisition of metallo-β-lactamases (MBLs) such as NDM-1 is a principle contributor to the emergence of carbapenem-resistant Gram-negative pathogens that threatens the use of penicillin, cephalosporin, and carbapenem antibiotics to treat infections. So far a clinical inhibitor of MBLs that could reverse resistance and re-sensitize resistant Gram-negative pathogens to carbapenems does not exist. Here we have identified a fungal natural product, aspergillomarasmine A (AMA) that is a rapid and potent inhibitor of the NDM-1 enzyme and another clinically relevant MBL, VIM-2. AMA also fully restored the activity of meropenem against Enterobacteriaceae, Acinetobacter spp. and Pseudomonas spp. possessing either VIM or NDM-type alleles. In mice infected with NDM-1-expressing Klebsiella pneumoniae, AMA efficiently restored meropenem activity, demonstrating that a combination of AMA and a carbapenem antibiotic has therapeutic potential to address the clinical challenge of MBL positive carbapenem-resistant Gram-negative pathogens.

The authors screen for compounds that show synergistic antifungal activity when combined with the widely-used fungistatic drug fluconazole. Chemogenomic profiling explains the mode of action of synergistic drugs and allows the prediction of additional drug synergies.

MurM is an aminoacyl ligase that adds L-serine or L-alanine as the first amino acid of a dipeptide branch to the stem peptide lysine of the pneumococcal peptidoglycan. MurM activity is essential for clinical pneumococcal penicillin resistance. Analysis of peptidoglycan from the highly penicillin-resistant Streptococcus pneumoniae strain 159 revealed that in vivo and in vitro, in the presence of the appropriate acyl-tRNA, MurM 159 alanylated the peptidoglycan ⑀-amino group of the stem peptide lysine in preference to its serylation. However, in contrast, identical analyses of the penicillin-susceptible strain Pn16 revealed that MurM Pn16 activity supported serylation more than alanylation both in vivo and in vitro. The stem peptide is constructed in the cytoplasm appended to a UDP nucleotide (Fig.

Solving the antibiotic resistance crisis requires the discovery of new antimicrobial drugs and the preservation of existing ones. The discovery of inhibitors of antibiotic resistance, antibiotic adjuvants, is a proven example of the latter. A major difficulty in identifying new antibiotics is the frequent rediscovery of known compounds, necessitating laborious "dereplication" to identify novel chemical entities. We have developed an antibiotic resistance platform (ARP) that can be used for both the identification of antibiotic adjuvants and for antibiotic dereplication. The ARP is a cell-based array of mechanistically distinct individual resistance elements in an identical genetic background. In dereplication mode, we demonstrate the rapid identification, and thus discrimination, of common antibiotics. In adjuvant discovery mode, we show that the ARP can be harnessed in screens to identify inhibitors of resistance. The ARP is therefore a powerful tool that has broad application in confronting the resistance crisis.