Predicting antibiotic resistance

The treatment of bacterial infections is increasingly complicated because microorganisms can develop resistance to antimicrobial agents. This article discusses the information that is required to predict when antibiotic resistance is likely to emerge in a bacterial population. Indeed, the development of the conceptual and methodological tools required for this type of prediction represents an important goal for microbiological research. To this end, we propose the establishment of methodological guidelines that will allow researchers to predict the emergence of resistance to a new antibiotic before its clinical introduction.

[1]  P. Collignon,et al.  Evolution of multi-resistance plasmids in Australian clinical isolates of Escherichia coli. , 2004, Microbiology.

[2]  F. Baquero,et al.  Acquisition of antibiotic resistance plasmids in vivo by extraintestinal Salmonella spp. , 1987, The Journal of antimicrobial chemotherapy.

[3]  Jehoshua Bruck,et al.  2020 Computing: Can computers help to explain biology? , 2006, Nature.

[4]  Barbara Di Ventura,et al.  From in vivo to in silico biology and back , 2006, Nature.

[5]  Jianping Xu,et al.  INVITED REVIEW: Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances , 2006, Molecular ecology.

[6]  M. Maciá,et al.  Efficacy and Potential for Resistance Selection of Antipseudomonal Treatments in a Mouse Model of Lung Infection by Hypermutable Pseudomonas aeruginosa , 2006, Antimicrobial Agents and Chemotherapy.

[7]  S. Falkow,et al.  Bile-salt-mediated induction of antimicrobial and bile resistance in Salmonella typhimurium. , 2004, Microbiology.

[8]  P. Bork,et al.  Genome evolution reveals biochemical networks and functional modules , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[9]  J. Frère,et al.  Postgenomic Scan of Metallo-β-Lactamase Homologues in Rhizobacteria: Identification and Characterization of BJP-1, a Subclass B3 Ortholog from Bradyrhizobium japonicum , 2006, Antimicrobial Agents and Chemotherapy.

[10]  J. Shapiro A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering. , 2005, Gene.

[11]  Ulf Dieckmann,et al.  Surprising evolutionary predictions from enhanced ecological realism. , 2006, Theoretical population biology.

[12]  P Stoodley,et al.  Survival strategies of infectious biofilms. , 2005, Trends in microbiology.

[13]  D. Vos,et al.  Metronidazole resistance in Helicobacter pylori , 1990, The Lancet.

[14]  O. Berg,et al.  Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[15]  J. Pepper The evolution of evolvability in genetic linkage patterns. , 2003, Bio Systems.

[16]  J. Buer,et al.  Expression Analysis of a Highly Adherent and Cytotoxic Small Colony Variant of Pseudomonas aeruginosa Isolated from a Lung of a Patient with Cystic Fibrosis , 2004, Journal of bacteriology.

[17]  Karin A Remington,et al.  Taking metagenomic studies in context. , 2005, Trends in microbiology.

[18]  E. Denamur,et al.  In Brief , 2006, Nature Reviews Microbiology.

[19]  F. Baquero,et al.  hns mutant unveils the presence of a latent haemolytic activity in Escherichia coli K‐12 , 1996, Molecular microbiology.

[20]  Gerard D. Wright The antibiotic resistome: the nexus of chemical and genetic diversity , 2007, Nature Reviews Microbiology.

[21]  T. Walsh Combinatorial genetic evolution of multiresistance. , 2006, Current opinion in microbiology.

[22]  John W. Beaber,et al.  SOS response promotes horizontal dissemination of antibiotic resistance genes , 2004, Nature.

[23]  O. Berg,et al.  Effects of environment on compensatory mutations to ameliorate costs of antibiotic resistance. , 2000, Science.

[24]  D. Hughes,et al.  Sampling the Antibiotic Resistome , 2006, Science.

[25]  S. Leibler,et al.  Bacterial Persistence , 2005, Genetics.

[26]  I. Wiegand,et al.  β-Lactamase induction and cell wall recycling in gram-negative bacteria , 1998 .

[27]  S. Salipante,et al.  GeneHunter, a Transposon Tool for Identification and Isolation of Cryptic Antibiotic Resistance Genes , 2003, Antimicrobial Agents and Chemotherapy.

[28]  Jake Yue Chen,et al.  A Systems Biology Approach to the Study of cisplatin Drug Resistance in Ovarian cancers , 2007, J. Bioinform. Comput. Biol..

[29]  A. Robicsek,et al.  Fluoroquinolone-modifying enzyme: a new adaptation of a common aminoglycoside acetyltransferase , 2006, Nature Medicine.

[30]  Miriam Barlow,et al.  Predicting evolutionary potential: in vitro evolution accurately reproduces natural evolution of the tem beta-lactamase. , 2002, Genetics.

[31]  I. Matic,et al.  Environmental tuning of mutation rates. , 2006, Environmental microbiology.

[32]  W. Dunne,et al.  Use of Several Inducer and Substrate Antibiotic Combinations in a Disk Approximation Assay Format To Screen for AmpC Induction in Patient Isolates of Pseudomonas aeruginosa, Enterobacter spp., Citrobacter spp., and Serratia spp , 2005, Journal of Clinical Microbiology.

[33]  D. Andersson,et al.  Antibiotic treatment in vitro of phenotypically tolerant bacterial populations. , 2007, The Journal of antimicrobial chemotherapy.

[34]  A. Danchin The bag or the spindle: the cell factory at the time of systems' biology , 2004, Microbial cell factories.

[35]  F. Baquero,et al.  RESISTANCE TO BETA-LACTAM/CLAVULANATE , 1987, The Lancet.

[36]  Ariane Toussaint,et al.  Mobile elements as a combination of functional modules. , 2002, Plasmid.

[37]  F. Baquero,et al.  Mutation Frequencies and Antibiotic Resistance , 2000, Antimicrobial Agents and Chemotherapy.

[38]  B. Spratt,et al.  Role of interspecies transfer of chromosomal genes in the evolution of penicillin resistance in pathogenic and commensal Neisseria species , 1992, Journal of Molecular Evolution.

[39]  O. Sahin,et al.  Enhanced in vivo fitness of fluoroquinolone-resistant Campylobacter jejuni in the absence of antibiotic selection pressure. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[40]  D. Andersson,et al.  Persistence of antibiotic resistant bacteria. , 2003, Current opinion in microbiology.

[41]  F. Baquero,et al.  Haemophilus influenzae bla ROB-1 Mutations in Hypermutagenic ΔampC Escherichia coli Conferring Resistance to Cefotaxime and β-Lactamase Inhibitors and Increased Susceptibility to Cefaclor , 2003, Antimicrobial Agents and Chemotherapy.

[42]  Maria J. Gomez,et al.  Genes Involved in Intrinsic Antibiotic Resistance of Acinetobacter baylyi , 2006, Antimicrobial Agents and Chemotherapy.

[43]  U. Dieckmann,et al.  The evolution of phenotypic plasticity in spatially structured environments: implications of intraspecific competition, plasticity costs and environmental characteristics , 2004, Journal of evolutionary biology.

[44]  A. Robicsek,et al.  Prevalence in the United States of aac(6′)-Ib-cr Encoding a Ciprofloxacin-Modifying Enzyme , 2006, Antimicrobial Agents and Chemotherapy.

[45]  R. Lande,et al.  On the distribution of the mean and variance of a quantitative trait under mutation-selection-drift balance. , 1994, Genetics.

[46]  B. Levin,et al.  Non-inherited antibiotic resistance , 2006, Nature Reviews Microbiology.

[47]  J. Hearst,et al.  Genes acrA and acrB encode a stress‐induced efflux system of Escherichia coli , 1995, Molecular microbiology.

[48]  P. Collignon,et al.  Species differences in plasmid carriage in the Enterobacteriaceae. , 2003, Plasmid.

[49]  G. Wagner,et al.  The topology of the possible: formal spaces underlying patterns of evolutionary change. , 2001, Journal of theoretical biology.

[50]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[51]  B. Levin,et al.  The biological cost of antibiotic resistance. , 1999, Current opinion in microbiology.

[52]  Robert T. Pennock,et al.  The evolutionary origin of complex features , 2003, Nature.

[53]  T. Richmond,et al.  Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori , 2005, Nature Methods.

[54]  Andreas Handel,et al.  The Role of Compensatory Mutations in the Emergence of Drug Resistance , 2006, PLoS Comput. Biol..

[55]  C. Fishwick,et al.  Analysis of Mupirocin Resistance and Fitness in Staphylococcus aureus by Molecular Genetic and Structural Modeling Techniques , 2004, Antimicrobial Agents and Chemotherapy.

[56]  A. Tomasz,et al.  Beta-Lactam antibiotic resistance in gram-positive bacterial pathogens of the upper respiratory tract: a brief overview of mechanisms. , 1995, Microbial drug resistance.

[57]  C. Fishwick,et al.  Molecular Genetic and Structural Modeling Studies of Staphylococcus aureus RNA Polymerase and the Fitness of Rifampin Resistance Genotypes in Relation to Clinical Prevalence , 2006, Antimicrobial Agents and Chemotherapy.

[58]  J. Davies,et al.  Origins, acquisition and dissemination of antibiotic resistance determinants. , 1997, Ciba Foundation symposium.

[59]  D. Andersson The biological cost of mutational antibiotic resistance: any practical conclusions? , 2006, Current opinion in microbiology.

[60]  W. L. Payne,et al.  High Mutation Frequencies Among Escherichia coli and Salmonella Pathogens , 1996, Science.

[61]  J. Roth,et al.  Origin of mutations under selection: the adaptive mutation controversy. , 2006, Annual review of microbiology.

[62]  B. Levin,et al.  Concentration-Dependent Selection of Small Phenotypic Differences in TEM β-Lactamase-Mediated Antibiotic Resistance , 2000, Antimicrobial Agents and Chemotherapy.

[63]  J. Costerton,et al.  Antibiotic resistance of bacteria in biofilms , 2001, The Lancet.

[64]  A. Cloeckaert,et al.  Overexpression of the Multidrug Efflux Operon acrEF by Insertional Activation with IS1 or IS10 Elements in Salmonella enterica Serovar Typhimurium DT204 acrB Mutants Selected with Fluoroquinolones , 2005, Antimicrobial Agents and Chemotherapy.

[65]  Claudia Schmidt-Dannert,et al.  Dealing with complexity: evolutionary engineering and genome shuffling. , 2004, Current opinion in biotechnology.

[66]  Barry G. Hall,et al.  Predicting Evolution by In Vitro Evolution Requires Determining Evolutionary Pathways , 2002, Antimicrobial Agents and Chemotherapy.

[67]  Fernando Baquero,et al.  Interactions among Strategies Associated with Bacterial Infection: Pathogenicity, Epidemicity, and Antibiotic Resistance , 2002, Clinical Microbiology Reviews.

[68]  Thijs J. G. Ettema,et al.  Modularity in the gain and loss of genes: applications for function prediction. , 2001, Trends in genetics : TIG.

[69]  J. Roth,et al.  Multiple pathways of selected gene amplification during adaptive mutation , 2006, Proceedings of the National Academy of Sciences.

[70]  N. Datta,et al.  Plasmids of the same Inc groups in Enterobacteria before and after the medical use of antibiotics , 1983, Nature.

[71]  Fernando Baquero,et al.  Selection of Naturally Occurring Extended-Spectrum TEM β-Lactamase Variants by Fluctuating β-Lactam Pressure , 2000, Antimicrobial Agents and Chemotherapy.

[72]  Barry G. Hall,et al.  Predicting the evolution of antibiotic resistance genes , 2004, Nature Reviews Microbiology.

[73]  Barry G. Hall,et al.  Evolution of the serine β-lactamases: past, present and future , 2004 .

[74]  A. Alonso,et al.  Environmental selection of antibiotic resistance genes. , 2001, Environmental microbiology.

[75]  Yipeng Wang,et al.  Selective Silencing of Foreign DNA with Low GC Content by the H-NS Protein in Salmonella , 2006, Science.

[76]  A. Oliver,et al.  High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. , 2000, Science.

[77]  F. Baquero From pieces to patterns: evolutionary engineering in bacterial pathogens , 2004, Nature Reviews Microbiology.

[78]  F. Baquero,et al.  Beta-lactam-fosfomycin antagonism involving modification of penicillin-binding protein 3 in Pseudomonas aeruginosa , 1990, Antimicrobial Agents and Chemotherapy.

[79]  Peter L Lee,et al.  The SOS response regulates adaptive mutation. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[80]  U. Alon,et al.  Spontaneous evolution of modularity and network motifs. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[81]  H. Ceri,et al.  The Calgary Biofilm Device: New Technology for Rapid Determination of Antibiotic Susceptibilities of Bacterial Biofilms , 1999, Journal of Clinical Microbiology.

[82]  B. Hall,et al.  Experimental prediction of the evolution of cefepime resistance from the CMY-2 AmpC beta-lactamase. , 2003, Genetics.

[83]  C. Dorman H-NS: a universal regulator for a dynamic genome , 2004, Nature Reviews Microbiology.

[84]  G. Archer,et al.  Related Clones Containing SCCmec Type IV Predominate among Clinically Significant Staphylococcus epidermidis Isolates , 2003, Antimicrobial Agents and Chemotherapy.

[85]  V. Souza,et al.  Bacteria gone native vs. bacteria gone awry?: plasmidic transfer and bacterial evolution. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[86]  A. Oliver,et al.  Hypermutation Is a Key Factor in Development of Multiple-Antimicrobial Resistance in Pseudomonas aeruginosa Strains Causing Chronic Lung Infections , 2005, Antimicrobial Agents and Chemotherapy.

[87]  F. Baquero,et al.  Polymorphic Mutation Frequencies in Escherichia coli: Emergence of Weak Mutators in Clinical Isolates , 2004, Journal of bacteriology.

[88]  F. Baquero Low-level antibacterial resistance: a gateway to clinical resistance. , 2001, Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy.

[89]  J. Handelsman Metagenomics: Application of Genomics to Uncultured Microorganisms , 2004, Microbiology and Molecular Biology Reviews.

[90]  F. Baquero,et al.  H-NS and RpoS regulate emergence of Lac Ara+ mutants of Escherichia coli MCS2 , 1997, Journal of bacteriology.

[91]  Valeria Souza,et al.  Stress-Induced Mutagenesis in Bacteria , 2003, Science.

[92]  P. Bennett,et al.  Evidence of Antibiotic Resistance Gene Silencing in Escherichia coli , 2006, Antimicrobial Agents and Chemotherapy.

[93]  Michael Lynch,et al.  The Origin of Subfunctions and Modular Gene Regulation , 2005, Genetics.

[94]  J. Hinton H-NS mediates the silencing of laterally acquired genes in bacteria (vol 2, pg 746, 2006) , 2007 .

[95]  Miriam Barlow,et al.  Experimental prediction of the natural evolution of antibiotic resistance. , 2003, Genetics.

[96]  J. Costerton,et al.  Bacterial biofilms: a common cause of persistent infections. , 1999, Science.

[97]  F. Taddei,et al.  Highly variable mutation rates in commensal and pathogenic Escherichia coli. , 1997, Science.

[98]  I. Matic,et al.  Environmental tuning of mutation rates: Environmental tuning of mutation rates , 2006 .

[99]  F. Baquero,et al.  Fosfomycin and Rifampin Disk Diffusion Tests for Detection of Escherichia coli Mutator Strains , 2004, Journal of Clinical Microbiology.

[100]  M. Maciá,et al.  Detection and Susceptibility Testing of Hypermutable Pseudomonas aeruginosa Strains with the Etest and Disk Diffusion , 2004, Antimicrobial Agents and Chemotherapy.

[101]  R. Skurray,et al.  Regulation of Bacterial Drug Export Systems , 2002, Microbiology and Molecular Biology Reviews.