HIV resistance testing: methods, utility, and limitations.

Widespread use of combination antiretroviral therapy for HIV has led to increased incidence of HIV resistance and a need for antiretroviral resistance testing to optimize therapeutic choices. Antiretroviral resistance analysis is performed using either genotypic or phenotypic assays. Genotypic assays identify resistance-associated mutations in the HIV genome. They are faster and less technically demanding than phenotypic assays; however, the associations between mutations and resistance patterns are often complicated, making interpretation difficult. Phenotypic assays directly measure the ability of antiviral compounds to inhibit replication of patient-derived virus. Phenotypic assays provide results that are easier to interpret; however, there is little data that relates the degree of resistance detected in phenotypic assays to patient clinical response. Despite limitations, the improved therapeutic outcome of therapies guided by resistance testing is leading to incorporation of resistance testing into the standard of care for HIV treatment.

Phenotypic and genotypic analysis of clinical HIV-1 isolates reveals extensive protease inhibitor cross-resistance: a survey of over 6000 samples.

OBJECTIVE: To evaluate in HIV-1 the extent of phenotypic and genotypic antiretroviral drug resistance and cross-resistance towards the protease inhibitors (PIs) saquinavir, ritonavir, indinavir and nelfinavir among a set of patient samples originating from European and US routine clinical practice and submitted for phenotypic drug resistance testing and/or genotypic analysis. The mutational pattern(s) underlying both resistance and cross-resistance to PIs was investigated. METHOD: Over 6000 patient isolates with plasma viral load greater than 1000 copies/ml plasma were analysed. Phenotypic resistance was evaluated by a recombinant virus assay. Phenotypic resistance is expressed as the fold-increase of the 50% inhibitory concentration (IC50) value of a compound for a patient-derived recombinant virus isolate compared with that for a wild-type laboratory virus. Genotypic analysis is reported as amino acid changes at positions in the HIV-1 protease compared to a wild-type reference. RESULTS: Phenotypic resistance to any single PI was observed in 17 to 25% of the clinical isolates investigated. Phenotypic cross-resistance among PIs (> 10-fold increase in IC50 value) was detected in 59 to 80% of the samples resistant (> 10-fold increase in IC50 value) to at least one PI. The prevalent mutations in PI-resistant isolates involved substitutions at codons 10, 36, 46, 54, 71, 77, 82 and 90. The most frequent mutational pattern in samples with PI cross-resistance involved combined substitutions at positions 10 and 90, extended with substitutions at positions 54, 71, 77, 82 or 84. CONCLUSIONS: Extensive use of first-generation PIs leads to the emergence of HIV-1 isolates possessing cross-resistance to all members of this class. Identification of particular mutational profiles among these isolates may assist in the design of new generation inhibitors with specific activity against protease-mutant HIV strains.

A novel human immunodeficiency virus type 1 reverse transcriptase mutational pattern confers phenotypic lamivudine resistance in the absence of mutation 184V.

We describe a new human immunodeficiency virus type 1 (HIV-1) mutational pattern associated with phenotypic resistance to lamivudine (3TC) in the absence of the characteristic replacement of methionine by valine at position 184 (M184V) of reverse transcriptase. Combined genotypic and phenotypic analyses of clinical isolates revealed the presence of moderate levels of phenotypic resistance (between 4- and 50-fold) to 3TC in a subset of isolates that did not harbor the M184V mutation. Mutational cluster analysis and comparison with the phenotypic data revealed a significant correlation between moderate phenotypic 3TC resistance and an increased incidence of replacement of glutamic acid by aspartic acid or alanine and of valine by isoleucine at residues 44 and 118 of reverse transcriptase, respectively. This occurred predominantly in those isolates harboring zidovudine resistance-associated mutations (41L, 215Y). The requirement of the combination of mutations 41L and 215Y with mutations 44D and 44A and/or 118I for phenotypic 3TC resistance was confirmed by site-directed mutagenesis experiments. These data support the assumption that HIV-1 may have access to several different genetic pathways to escape drug pressure or that the increase in the frequency of particular mutations may affect susceptibility to drugs that have never been part of a particular regimen.

Longitudinal human immunodeficiency virus type 1 load in the italian seroconversion study: correlates and temporal trends of virus load.

A prospective study of 149 human immunodeficiency virus type 1 (HIV-1) seroconverters was conducted to describe trends and correlates of HIV-1 load after seroconversion and over time. HIV-1 load was quantified from frozen sera by reverse transcriptase-polymerase chain reaction. High early virus load was associated with lower CD4 cell counts and male sex but not with age at seroconversion or injection drug use. Early virus load predicted progression to clinical AIDS and AIDS/<200 CD4 cells/microL. Virus load exhibited a decline of 52% by 18 months after seroconversion then increased 23% annually (95% confidence interval, 13%-33%). Men and those developing AIDS during follow-up had higher virus loads over the course of disease. Persons who developed AIDS had a steeper virus load slope than those who were AIDS-free (P=.01). In long-term follow-up, virus load exhibited a gradual and sustained increase over time. Virus load and annual increase are strong predictors of disease progression.

An epidemiological evaluation of the use of microbiological tools for identifying gonorrhoea infection networks.

We aimed to assess the utility of various techniques for identifying gonorrhoea infection networks. All residents of a non-metropolitan North Carolina county visiting a sexually transmitted disease (STD) clinic during a 17-month period were screened for gonorrhoea. Infection networks were estimated by serovar type combined with antibiotic resistance, arbitrarily primed polymerase chain reaction (AP-PCR), or temporal clustering. The residential addresses of infected patients were geocoded and mapped. Among 2 serovar types, the presence of distinguishing characteristics of a network, based on questionnaire data, was assessed with prevalence ratios and 95% confidence intervals (CIs) relative to those not in the network. Twenty-five serovar types were identified among 759 gonorrhoea infections. In one serovar, the networks further delineated by temporal clusters correlated with particular AP-PCR types. In most instances, however, different typing techniques painted different network pictures. No refined serovar network stood out as having a particular set of characteristics that could be used to shape intervention. Teasing out an individual infection network with unique characteristics will require the development and use of other microbiological tools.

Molecular typing of Neisseria gonorrhoeae causing repeated infections: evolution of porin during passage within a community.

Thirty-three Neisseria gonorrhoeae isolates from 15 persons infected multiple times with the same serovar were compared using por gene sequencing, opa-typing, and arbitrarily primed-polymerase chain reaction. All three molecular techniques were more discriminatory than serotyping and identified differences between some isolates belonging to the same serovar. Although there were differences among Por sequences within some serovars, 10 of 15 subjects became reinfected with gonococci expressing identical Por proteins. Sequence analysis of por genes revealed evidence of horizontal genetic exchange and point mutations in potential surface-exposed regions during passage in the community.

Resistance of HIV-1 to antiretroviral agents in blood and seminal plasma: implications for transmission.

OBJECTIVES: To evaluate blood and genital secretions from HIV-infected men for HIV-1 resistant to antiretroviral agents. DESIGN: A longitudinal study of 11 men with HIV infection and persistent detectable HIV RNA levels in blood and semen on antiretroviral therapy. METHODS: HIV-1 from the blood and seminal plasma, obtained before the initiation of a new therapeutic regimen and on therapy, were evaluated by population-based sequencing of reverse transcriptase (RT) and protease RNA for the development of resistance to antiretroviral therapy. The genetic relatedness of sequences over time was compared. RESULTS: RT genotypic resistance markers were present in seminal plasma at baseline in three out of six individuals with previous RT inhibitor experience. Eight out of 10 men, from whom the viral sequence was available on new therapy, demonstrated the evolution of new resistance mutations in the blood or seminal plasma, or both. The evolution of resistance mutations in blood and semen were frequently discordant, although over time similar patterns were seen. In two individuals, protease inhibitor resistance mutations evolved in the blood but not in the major variant in seminal plasma. Comparisons of the viral sequences between blood and seminal plasma from six men revealed two patterns. Three men showed a clustering of sequences from blood and semen. Three had sequences that appeared to evolve separately in the two compartments. CONCLUSIONS: HIV-1 variants with genotypic resistance markers are present in the male genital tract and evolve over time on incompletely suppressive antiretroviral therapy. The absence of genotypic changes consistent with protease inhibitor resistance in the semen, despite their presence in blood plasma, suggests the possibility of limited penetration of these agents into the male genital tract. Sexual transmission of resistant variants may have a negative impact on treatment outcome in newly infected individuals and on the spread of the diseases within a population. Therapeutic strategies that fully suppress HIV-1 in the genital tract should be a public health priority.

Characterisation of Neisseria gonorrhoeae in semen during urethral infection in men.

OBJECTIVE: To determine the number of Neisseria gonorrhoeae organisms in urine and semen in men with gonococcal urethritis, and to compare selected phenotypic characteristics of organisms harvested from the urethra and semen. DESIGN: Samples from two groups of subjects were examined. Patients with symptomatic urethritis receiving treatment at an STD clinic, as well as six subjects with experimental urethritis. Semen and urine specimens were obtained after the urethral exudate was sampled. RESULTS: Using quantitative cultures, we found an average of 6 x 10(6) gonococci in urine or semen of 17 men with symptomatic urethritis seeking treatment at an STD clinic, and 2 x 10(4) gonococci in secretions of six male subjects with early experimental infection. Gonococcal outer membrane opacity (Opa) proteins and lipo-oligosaccharide (LOS) recovered from urine and semen of these subjects were very similar. CONCLUSIONS: Men with symptomatic gonorrhoea excrete a large number of gonococci in semen which is not affected by the duration of symptoms. The similar phenotype of organisms in urine and semen suggests the bacteria come from the same compartment. These data help to explain the efficiency of gonococcal transmission from men to their partners, and identify an appropriate target for a preventative vaccine or immunotherapy designed to reduce the inoculum in infected patients.

Effects of H2O2-producing lactobacilli on Neisseria gonorrhoeae growth and catalase activity.

In the vagina and endocervix, Neisseria gonorrhoeae must interact with complex microflora. Among these are lactobacilli, which may inhibit the growth of gonococci. Lactobacillus acidophilus, which produce H2O2 (LB+), and L. acidophilus and Lactobacillus casei, which do not produce H2O2 (LB-), were coincubated with catalase-positive and -deficient strains of N. gonorrhoeae. When the incubation medium was maintained at pH 7.3, neither LB+ nor LB- affected gonococcal growth. However, LB+ caused a significant increase in expression of gonococcal catalase, which could be offset by exposure of the bacteria to exogenous catalase. When coincubation medium was at lower pH (4.8-5.0), there was a significant decrease in gonococcal survival and catalase activity, which was only partly reversed by exogenous catalase. Lysates of LB+ also effectively inhibited gonococcal catalase. This inhibition was retained upon heating of the lysate to 100 degrees C for 15 min but was lost with proteinase K treatment. Thus, LB+ may inhibit growth of gonococci by acidification of the environment, secretion of H2O2, and production of protein inhibitors.

Variation in hydrogen peroxide sensitivity between different strains of Neisseria gonorrhoeae is dependent on factors in addition to catalase activity.

Catalase, which catalyzes the reduction of hydrogen peroxide to oxygen and water, is considered the primary defense of Neisseria gonorrhoeae against exogenous hydrogen peroxide. Recent reports have demonstrated drastically different sensitivities of the organism to hydrogen peroxide ranging from greater than 80% survival after challenge with 30 mM hydrogen peroxide to less than 0.001% survival after challenge with 10 mM hydrogen peroxide. In this study, we have examined the hydrogen peroxide sensitivities of six clinical gonococcal isolates. The study demonstrates that the variations in gonococcal hydrogen peroxide sensitivities previously reported can be attributed to (i) differences in experimental methods employed or (ii) variation among different gonococcal strains. All of the gonococcal isolates examined generated similar concentrations of catalase, implying that the differences in the H2O2 sensitivity observed may depend on factors in addition to catalase.