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Volume 7, Number 2—April 2001
4th Decennial International Conference on Nosocomial and Healthcare-Associated Infections

State of the Art

Molecular Approaches to Diagnosing and Managing Infectious Diseases: Practicality and Costs

Michael A. PfallerComments to Author 
Author affiliation: University of Iowa College of Medicine, Iowa City, Iowa, USA

Main Article

Table 3

Molecular methods for detecting antimicrobial resistancea

Organism(s) Antimicrobial agent(s) Gene Detection method
Staphylococci Methicillin
Oxacillin mec Ab Standard DNA probe
Branched chain DNA probe
Enterococci Vancomycin van A, B, C, Dc Standard DNA probe
Haemophilus influenzae
Neisseria gonorrhoeae Beta-lactams blaTEM
blaSHVd Standard probe
PCR and sequencing
Enterobacteriaceae and gram-positive cocci Quinolones Point mutations in gyr A, gyr B, par C and par E PCR and sequencing
Mycobacterium tuberuclosise Rifampin
Streptomycin Point mutations in rpo B
Point mutations in kat G, inh A, and ahp C
Point mutations in emb B
Point mutations in rps L and rrs PCR and SSCP
PCR and sequencing
PCR and sequencing
Herpes virusesf Acyclovir and related drugs
Foscarnet Mutations or deletions in the TK gene
Point mutations in DNA polymerase gene PCR and sequencing
PCR and sequencing
HIVg Nucleoside reverse transcriptase inhibitors
Protease inhibitors Point mutations in RT gene
Point mutations in PROT gene PCR and sequencing
PCR and sequencing

aAdapted from Pfaller (2). bmecA encodes for the altered penicillin binding protein PBP2a'; phenotypic methods may require 48 hours incubation or more to detect resistance and are less than 100% sensitive. Detection of mecA has potential for clinical application in specific circumstances.
cVancomycin resistance in enterococci may be related to one of four distinct resistance genotypes of which vanA and vanB are most important. Genotypic detection of resistance is useful in validation of phenotypic methods.
dThe genetic basis of resistance to beta-lactam antibiotics is extremely complex. The blaTEM and blaSHV genes are the two most common sets of plasmid encoded beta-lactamases. The presence of either a blaTEM or blaSHV gene implies ampicillin resistance. Variants of the blaTEM and blaSHV genes (extended spectrum beta-lactamases) may also encode for resistance to a range of third-generation cephalosporins and to monobactams.
eM. tuberculosis is very slow growing. Four weeks or more may be required to obtain phenotypic susceptibility test results. Detection of resistance genes in M. tuberculosis has potential for clinical application in the short term.
fThere are no phenotypic methods sufficiently practical for routine clinical detection of resistance to antiviral agents. Genotypic methods represent a practical method for routine detection of antiviral resistance.
gAbbreviations not defined in text: RFLP, restriction fragment length polymorphism; SSCP, single-stranded conformational polymorphism; LIPA, line probe assay; TK, thymidine kinase; RT, reverse transcriptase; PROT, protease.

Main Article