Metabolic Clusters of Early-Lactating Dairy Cows Based on Blood ß-hydroxybutyrate Trajectories and Predicted from Milk Compounds.

High-yielding dairy cows encounter metabolic challenges in early lactation. Typically, ß-hydroxybutyrate (BHB), measured at a specific time point is employed to diagnose the metabolic status of cows based on a predetermined threshold. However, in early lactation, BHB is highly dynamic, and there is high interindividual variability in its time profile. This could limit the effectiveness of the single measurement and threshold-based diagnosis probably contributing to the disparities in reports linking metabolic status with productive and reproductive outcomes. This research delves into the examination of the trajectories of BHB to unveil inter-cow variations and identify latent metabolic groups. We compiled a data set from 2 observational studies involving a total of 195 lactations from multiparous Holstein Friesian cows. The data set encompasses measurements of BHB, NEFA, and insulin from blood samples collected at 3, 6, 9, and 21 d in milk (DIM), along with weekly determinations of milk composition and fatty acids (FA) proportions in milk fat. In both experiments, milk yield (MY) and feed intake were recorded daily during the first month of lactation. We explored interindividual and intraindividual variations in metabolic responses using the trajectories of blood BHB and evaluated the presence of distinct metabolic groups based on such variations. For this purpose, we employed the growth mixture model (GMM), a trajectory clustering technique. Our findings unveil novel insights into the diverse metabolic responses among cows, encompassing both trajectory patterns and the magnitude of blood BHB concentrations. Specifically, we identified 3 latent metabolic groups: the "QuiBHB" cluster (≈10%) exhibited a higher initial BHB concentration than other clusters, peaking on d 9 (average maximum BHB of 2.4 mM) and then declining by d 21; the "SloBHB" cluster (≈23%) started with a lower BHB concentration, gradually increasing until d 9, and at the highest BHB concentration at d 21 (1.6 mM serum BHB at the end of the experimental period); and the "LoBHB" cluster (≈67%) began with the lowest serum BHB concentration (serum BHB <0.75 mM), remaining relatively stable throughout the sampling period. Notably, the 3 metabolic groups exhibited significant physiological disparities, evident in blood NEFA and insulin concentrations. The QuiBHB and SloBHB cows exhibited higher NEFA and lower insulin concentrations as compared with the LoBHB cows. Interestingly, these metabolic differences extended to MY and DMI during the first month of lactation. The elevated BHB concentrations observed in QuiBHB cows were linked with lower DMI and MY as compared with SloBHB and LoBHB cows. Accordingly, these animals were considered metabolically impaired. Conversely, SloBHB cows displayed higher MY along with increased DMI, and thus the elevated BHB might be indicative of an adaptive response for these cows. The QuiBHB cows also displayed higher proportions of unsaturated FA (UFA), monounsaturated FA (MUFA), and total C18:1 FA in milk during the first week of lactation. Prediction of the QuiBHB cows using these FA and test day variables resulted in moderate predictive accuracy (ROCAUC > 0.7). Given the limited sample size for the development of prediction models, and the variation in DIM among samples in the same week, the result is indicative of the predictive potential of the model and room for model optimization. In summary, distinct metabolic groups of cows could be identified based on the trajectories of blood BHB in early lactation.

Oligosaccharide concentrations in colostrum, transition milk, and mature milk of primi- and multiparous Holstein cows during the first week of lactation.

The objective of this study was to characterize the oligosaccharide (OS) profile of colostrum and transition milk from primiparous (Pp, n = 10) and multiparous (Mp, n = 10) Holstein cows. The experiment was conducted on a commercial dairy farm, where cows were assigned to the study at calving. Colostrum (milking 1) was collected at 5.3 ± 0.7 h after parturition, followed by collection of milkings 2 through 6, milkings 8, 10, 12, and 14 at 0500 and 1600 h each day. Samples were analyzed for OS concentrations using liquid chromatography-mass spectrometry and for IgG and milk components. Concentration of IgG was highest in colostrum and milking 2. Colostral IgG concentration was less in Pp cows than in Mp cows (82.1 ± 3.1 vs. 106.1 ± 16.2 mg/mL). Colostrum and milkings 2 and 3 had 3'-sialyllactose and 6'-sialyllactose concentrations greater than those of mature milk (milkings 8+). For colostrum and milking 2, 6'-sialyllactosamine concentrations were higher than all other milkings, while disialyllactose was only higher in colostrum. In addition, 3'-sialyllactose was the most abundant OS in colostrum and milkings 2 and 3 compared with all other OS. A parity difference was observed for 6'-sialyllactosamine, with Mp having a higher concentration over the first 7 d in milk than Pp (46.4 ± 8.7 vs. 16.9 ± 3.2 µg/mL). Similar results were observed between milkings for OS yields. Parity differences were detected for 3'-sialyllactose, 6'-sialyllactose, and 6'-sialyllactosamine yield, with Mp yield being greater than Pp over the first 7 d in milk. These findings demonstrate that colostrum and transition milk contain elevated concentrations of certain OS compared with mature milk and suggest further research should be conducted regarding the potential benefits of OS in colostrum and transition milk when fed to newborn calves.

The effect of partial depopulation on Campylobacter introduction in broiler houses.

Poultry is seen as the main reservoir for Campylobacter. Control of this zoonotic pathogen in primary production could potentially reduce the colonization in broiler flocks and consequently reduce the number of human infections. In the present study, 20 broiler flocks from 10 farms, were sampled immediately before and 5 to 7 d after partial depopulation (thinning) for the presence of Campylobacter using cecal droppings and overshoes. At the time of thinning, the catching crew, transportation vehicles, forklift, and transport containers were sampled for the presence of Campylobacter. Samples were cultivated; presumed positive isolates were confirmed by PCR. The isolates were molecularly typed by flaA restriction analysis and pulsed field gel electrophoresis. Results show that all flocks were thinned using Campylobacter-contaminated equipment and materials. One-third of the broiler flocks became colonized after thinning. In 67% of the colonization cases, identical strains were found matching those of container systems, transport trucks, and/or forklifts. This identifies thinning as an important risk factor for Campylobacter introduction into broiler houses. Setup and compliance with biosecurity practices during thinning is essential to prevent Campylobacter colonization of broiler flocks.

The impact of individual human immunodeficiency virus type 1 protease mutations on drug susceptibility is highly influenced by complex interactions with the background protease sequence.

The requirement for multiple mutations for protease inhibitor (PI) resistance necessitates a better understanding of the molecular basis of resistance development. The novel bioinformatics resistance determination approach presented here elaborates on genetic profiles observed in clinical human immunodeficiency virus type 1 (HIV-1) isolates. Synthetic protease sequences were cloned in a wild-type HIV-1 background to generate a large number of close variants, covering 69 mutation clusters between multi-PI-resistant viruses and their corresponding genetically closely related, but PI-susceptible, counterparts. The vast number of mutants generated facilitates a profound and broad analysis of the influence of the background on the effect of individual PI resistance-associated mutations (PI-RAMs) on PI susceptibility. Within a set of viruses, all PI-RAMs that differed between susceptible and resistant viruses were varied while maintaining the background sequence from the resistant virus. The PI darunavir was used to evaluate PI susceptibility. Single sets allowed delineation of the impact of individual mutations on PI susceptibility, as well as the influence of PI-RAMs on one another. Comparing across sets, it could be inferred how the background influenced the interaction between two mutations, in some cases even changing antagonistic relationships into synergistic ones or vice versa. The approach elaborates on patient data and demonstrates how the specific mutational background greatly influences the impact of individual mutations on PI susceptibility in clinical patterns.

Tipranavir inhibits broadly protease inhibitor-resistant HIV-1 clinical samples.

OBJECTIVE: Although the use of HIV-1 protease inhibitors (PI) has substantially benefited HIV-1-infected individuals, new PI are urgently needed, as broad PI resistance and therapy failure is common. METHODS: The antiviral activity of tipranavir (TPV), a non-peptidic PI, was assessed in in vitro culture for 134 clinical isolates with a wide range of resistance to currently available peptidomimetic PI. The susceptibility of all 134 variants was then re-tested with the four PI simultaneously with TPV, using the Antivirogram assay. RESULTS: Of 105 viruses with more than tenfold resistance to three or four PI and an average of 6.1 PI mutations per sample, 95 (90%) were susceptible to TPV; eight (8%) had four- to tenfold resistance to TPV and only two (2%) had more than tenfold resistance. CONCLUSIONS: The substantial lack of PI cross-resistance to TPV shown by highly PI-resistant clinical isolates makes TPV an attractive new-generation HIV inhibitor.

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.

Baseline HIV drug resistance profile predicts response to ritonavir-saquinavir protease inhibitor therapy in a community setting.

OBJECTIVE: To determine whether baseline drug resistance assays could help to predict treatment failure with the protease inhibitor combination ritonavir-saquinavir. METHODS: Baseline HIV-1 drug resistance was determined for 76 consecutive patients who started treatment with the dual protease inhibitor combination ritonavir-saquinavir between September 1996 and June 1997 either alone or in combination with other antiviral agents. Resistance to 10 different antiviral agents was assessed by both phenotype (Virco Antivirogram) and genotype (Vircogen). RESULTS: Resistance inferred from viral genotype was similar to measured phenotypic resistance for both ritonavir and saquinavir (P<0.01). Baseline drug resistance phenotype was predictive of poor virological response to this dual protease inhibitor combination, despite the confounding effects of other antivirals. Patients were at least four times less likely to achieve a 0.5 log10 decrease in plasma HIV RNA viral load if their viral isolates were resistant to ritonavir or saquinavir. Patients classified as resistant to either drug using either method had median decreases in plasma viral load of 0.05 log10 HIV RNA copies/ml or less, compared to >0.8 log10 for those with sensitive virus. Patients resistant to both drugs never achieved plasma viral loads <100000 copies/ml. As little as fourfold increases in baseline resistance appeared to be sufficient to compromise even dual protease inhibitor therapy. CONCLUSION: Baseline resistance to ritonavir or saquinavir or both was associated with a poor antiviral response. Our data suggest that the measurement of drug resistance may assist in optimizing antiretroviral therapy in the clinic.

Virological and immunological effects of treatment interruptions in HIV-1 infected patients with treatment failure.

OBJECTIVE: To analyse the immunological and virological effects of treatment interruptions in HIV-1-infected patients with treatment failure and multidrug-resistant virus. METHODS: Drug susceptibility was assessed using Antivirogram and genotypic analysis was based on population and clonal sequencing for 48 patients who had interrupted treatment (> or = 2 months). RESULTS: Treatment interruption resulted in viral load increases (mean 0.7 log 10 copies/ ml; P = 0.0001) and CD4 cell count decreases (mean 89 x 10(6) cells/l; P = 0.0001). A complete shift to wild-type virus at the phenotypic, genotypic and clonal level was observed in 28/45 patients. These patients differed from those that did not show a shift to wild type in baseline CD4 cell counts (192 versus 59 x 10(6) cells/l; P= 0.007) and in the relationship between baseline viral load and CD4 cell count (no correlation versus a significant negative correlation; P= 0.008). Response to re-initiation of treatment fell with increasing viral load [relative hazard (RH) 0.33; P= 0.001] and with increasing total number of drugs with reduced susceptibility (RH 0.51; P = 0.0003); it improved with the number of new drugs received (RH 2.12; P = 0.0002) and a shift to wild type (RH 5.22, P = 0.006). CONCLUSIONS: Changes in surrogate markers suggest that treatment provided benefit in spite of virological failure and resistant virus. Although patients with a shift to wildtype virus responded better in the short term to treatment re-initiation, the long-term effects are not known and the risk of immune deterioration needs to be carefully considered.

Non-nucleoside reverse transcriptase inhibitor resistance among patients failing a nevirapine plus protease inhibitor-containing regimen.

OBJECTIVE: To determine the rate of nevirapine resistance in patients failing a nevirapine plus protease inhibitor (PI)-based regimen, and whether these isolates remain susceptible to other non-nucleoside reverse transcriptase inhibitors (NNRTI). DESIGN AND SETTING: A retrospective cohort study in two tertiary university hospitals. PATIENTS: Eighty-eight HIV-infected, NNRTI-naive patients receiving nevirapine plus PI as a rescue regimen after PI treatment failure. MAIN OUTCOME MEASURES: Genotypic and phenotypic resistance data at inclusion (73 and 60 plasma samples, respectively) and after 24 weeks (53 and 42 samples). RESULTS: Baseline phenotypic susceptibility to nevirapine was found in 70% of patients, and similar data were observed for efavirenz (91%) and delavirdine (71%). NNRTI resistance-associated mutations were found in 11 patients (12.5%). At 24 weeks, resistant isolates to nevirapine were found in 92% of patients, and correlated with similar resistance to efavirenz (68%) and delavirdine (73%). In the genotypic analysis, the Y181 C mutation was observed in 76% of mutants, and the most common changes were a combination of mutations at positions Y181C/K103N (23%) and the single mutation Y181C (15%). The development of nevirapine resistance was associated with baseline resistance to PI included in the regimen (P= 0.01). For isolates containing the single amino acid substitution Y181C, 29% remained fully susceptible to efavirenz, whereas 14% showed intermediate resistance to efavirenz and delavirdine. CONCLUSION: The failure of a nevirapine plus PI-containing regimen is associated with nevirapine resistance in most patients, with the most common mutation occurring at amino acid residue 181. Although there is a high degree of cross-resistance among NNRTI, nearly one third of resistant isolates carrying the single Y181C mutation remain susceptible to efavirenz.

The M184V mutation in HIV-1 reverse transcriptase (RT) conferring lamivudine resistance does not result in broad cross-resistance to nucleoside analogue RT inhibitors.

OBJECTIVE: To investigate the prevalence and magnitude of M184V-mediated changes in susceptibility to zalcitabine, didanosine, stavudine and abacavir (1592U89 succinate) in a cohort of lamivudine-treated patients. DESIGN AND METHODS: A total of 255 samples from patients treated with lamivudine and zidovudine with or without other nucleoside reverse transcriptase inhibitors (NRTI) were analysed for susceptibility to zidovudine, lamivudine, zalcitabine, didanosine and stavudine using a recombinant virus assay. Seventy-three samples originated from patients exposed to zidovudine and lamivudine only. A subset of 27 samples was investigated for cross-resistance to abacavir. Resistance was defined as a change in median inhibitory concentration more than fivefold compared with wild-type (high-level resistance, > 10-fold). A genotypic analysis of plasma-derived reverse transcriptase coding regions was carried out in samples with cross-resistance. RESULTS: The majority of samples displayed wild-type or greater than wild-type sensitivity to zalcitabine, didanosine and stavudine: resistance was seen in 17.2, 9 and 6.3% of the total sample population, respectively. Of these, 1.2, 2.7 and 2.4%, respectively, showed high-level resistance. The prevalence of resistance to a particular NRTI was lower in samples from patients not pretreated with that NRTI and in samples from patients exposed to zidovudine-lamivudine only. Cross-resistance was more prevalent in samples with high ZDV resistance. There was no obvious correlation between cross-resistance and genotype; all but two samples were mutant at codon 184. There were no consistent changes at positions associated with zidovudine resistance. The majority of samples from a subset (n=27) were four- to eightfold less sensitive to abacavir. There were no other genotypic changes in addition to M184V known to be associated with abacavir resistance. CONCLUSIONS: Cross-resistance was not commonly observed in this lamivudine-treated cohort. M184V per se is not expected to compromise subsequent treatment with NRTI such as didanosine-stavudine or combinations containing abacavir.

Prevalence of genotypic and phenotypic resistance to anti-retroviral drugs in a cohort of therapy-naïve HIV-1 infected US military personnel.

OBJECTIVE: While transmission of drug-resistant HIV-1 has been reported, estimates of prevalence of resistance in drug-naïve populations are incomplete. We investigated the prevalence of genotypic mutations and phenotypic antiretroviral resistance in a cohort of HIV-1 infected U.S. military personnel prior to the institution of antiretroviral therapy. DESIGN: Cross-sectional cohort study. METHODS: Plasma was obtained from 114 recently HIV-1 infected subjects enrolled in an epidemiological study. Genotypic resistance was determined by consensus sequencing of a PCR product from the HIV-1 pol gene. Sequences were interpreted by a phenotypic-genotypic correlative database. Resistance phenotypes were determined by a recombinant virus cell culture assay. RESULTS: Genotypic mutations and phenotypic resistance were found at a higher than expected frequency. Resistance to non-nucleoside reverse transcriptase inhibitors was most common, with a prevalence of 15% of 95 subjects by genotype and 26% of 91 subjects by phenotype. Genotypic and phenotypic resistance respectively were found in 4% and 8% of subjects for nucleoside reverse transcriptase inhibitors and in 10% and 1% for protease inhibitors. One subject harbored virus with resistance to all three drug classes. CONCLUSIONS: A substantial frequency of resistance to antiretroviral drugs was identified in a therapy-naïve U.S. cohort. In most cases, the genotypic and phenotypic assays yielded similar results, although the genotypic assay could detect some protease inhibitor resistance-associated mutations in the absence of phenotypic resistance. These data suggest the need for optimization of treatment guidelines based on current estimates of the prevalence of drug resistance in HIV-1 seroconverters.

HIV drug susceptibility and treatment response to mega-HAART regimen in patients from the Frankfurt HIV cohort.

OBJECTIVE: To assess the relationship between viral susceptibility at baseline and virological response in human immunodeficiency virus (HIV)-infected patients treated with multi-drug salvage regimens after multiple previous treatment failures. DESIGN: Retrospective analysis of 50 patients from the Frankfurt HIV cohort who had received treatment with a minimum of six drugs, and for whom a sample for baseline viral phenotyping was available. METHODS: Viral drug susceptibility was measured retrospectively from stored samples using the Antivirogram, a recombinant virus assay based method. Virological response was defined as a viral load of < 400 copies/ml at week 24. For analysis of treatment response, drop-outs were dealt with in two ways, either as failures (DAF) or censored (DAC). Several logistical regression models were applied to identify predictors of response, including baseline virus load, number of new drugs and phenotypic sensitivity scores. RESULTS: At baseline, drug resistance was extensive: 96% of patients had viruses resistant to at least one drug class and 32% had viruses resistant to all three drug classes. In the DAF analysis, 39 patients experienced virological failure. In the DAC analysis, eight were censored and 31 patients experienced virological failure. In multivariate models that adjust for baseline viral load, the number of new drugs and total phenotypic sensitivity scores, the baseline viral load and phenotypic sensitivity score remained significantly associated with virological outcome, whereas in those adjusted for baseline viral load, the number of new drugs, NRTI phenotypic sensitivity score and PI phenotypic sensitivity score, only the latter remained significantly associated with virological outcome. Both the DAF and DAC analyses produced similar results. In all models used, virological failure was shown to be significantly associated with baseline viral load and phenotypic sensitivity score. CONCLUSIONS: In this retrospective analysis based on a small number of patients, viral drug susceptibility at baseline was strongly associated with virological outcome at 24 weeks, independent of covariates such as baseline viral load and treatment history. Baseline viral load also maintained a significant, independent association with virological outcome in most models.

Laboratory guidelines for the practical use of HIV drug resistance tests in patient follow-up.

HIV drug resistance is one of the major limitations in the successful treatment of HIV-infected patients using currently available antiretroviral combination therapies. When appropriate, drug susceptibility profiles should be taken into consideration in the choice of a specific combination therapy. Guidelines recommending resistance testing in certain circumstances have been issued. Many clinicians have access to resistance testing and will increasingly use these results in their treatment decisions. In this document, we comment on the different methods available, and the relevant issues relating to the clinical application of these tests. Specifically, the following recommendations can be made: (i) genotypic and phenotypic HIV-1 drug resistance analyses can yield complementary information for the clinician. However, insufficient information currently exists as to which approach is preferable in any particular clinical setting; (ii) when HIV-1 drug resistance testing is required, it is recommended that testing be performed on plasma samples obtained before starting, stopping or changing therapy, on samples that have a viral load above the detection limit of the resistance test; (iii) the panel recommends that genotypic and phenotypic HIV-1 drug resistance testing for clinical purposes be performed in a certified laboratory under strict quality control and quality assurance standards; and (iv) the panel recommends that resistance testing laboratories provide clinicians with resistance reports that include a list of drug-related resistance mutations (genotype) and/or a list of drug-related fold resistance values (phenotype), with interpretations of each by an experienced virologist. The interpretation of genotypic and phenotypic analysis is a complex and developing science, and in order to understand HIV-1 drug resistance reports, communication between the requesting clinician and the expert that interpreted the resistance report is recommended.

Efficacy, tolerance, and pharmacokinetics of the combination of stavudine, nevirapine, nelfinavir, and saquinavir as salvage regimen after ritonavir or indinavir failure.

The high rate of protease inhibitor treatment failure in clinical cohorts makes it necessary to define novel salvage therapies. In a prospective study of 31 HIV-infected patients included in a salvage regimen with stavudine, nevirapine, nelfinavir, and saquinavir, viral load decreased a median of 1.65 log(10) and 1.95 log(10) after 6 and 12 months of treatment, respectively, and 35 and 56% of patients had an HIV RNA level below 50 copies/ml at the same time points. At baseline, the mean number of mutations in the protease gene was 10 (2-19), and the V82A and L90M mutations were present in 54 and 21% of patients. The presence of the V82A mutation did not affect significantly the rate of response (36 vs. 38%), whereas the L90M mutation was associated with treatment failure (0 vs. 43%). Plasma trough levels of nelfinavir (NFV) and saquinavir (SQV), in a twice daily dosing regimen, were above the protein-corrected IC(95) in most patients despite the addition of an enzymatic inducer such as nevirapine, and peak levels were 2- and 5-fold increased with respect to standard doses. However, pharmacokinetics of saquinavir-hard gel capsule (SQV-hgc) did not improve significantly in the three times daily dosing regimen. In conclusion, the combination of stavudine, nevirapine, nelfinavir, and saquinavir increased plasma drug levels and produced an adequate virological response in patients who had failed indinavir or ritonavir therapy. This degree of response is not significantly decreased in the presence of genotypic mutations associated with indinavir/ritonavir (IDV/RTV) resistance.

Phenotypic cross-resistance to nelfinavir: the role of prior antiretroviral therapy and the number of mutations in the protease gene.

Cross-resistance to nelfinavir (NFV) is observed in patients failing protease inhibitor (PI)-containing therapies. We performed a study with 111 patients who started an NFV-based salvage regimen after failing PI-based therapy to evaluate genotypic changes and to identify factors associated with resistance to NFV. Genotypic and phenotypic resistance data at entry (111 and 51 samples) and after NFV failure (74 and 31 samples) were available. Median CD4(+) cell count was 208 x 10(6)/liter, HIV RNA level was 4.6 log(10) copies/ml, and median number of mutations in the protease was 9. At baseline, 51 and 14% of viral isolates showed high or intermediate phenotypic resistance to NFV. Phenotypic data correlated with virological outcome, reaching undetectability at the third month in 40, 14, and 0% of those patients with susceptible, intermediate, or resistant viral isolates, respectively. Phenotypic resistance to NFV was associated with the presence of the L90M mutation: 46% for resistant vs. 6% in susceptible strains. The number of mutations in the protease correlated with the fold-increase in the IC(50)-NFV. The D30N mutation was detected in only 1 of 74 patients who failed. In a logistic regression analysis, the number of mutations in the protease was associated with NFV cross-resistance (RR, 2.09 per each additional mutation; 95% CI 1.23-3.55; p < 0.01). In conclusion, phenotypic cross-resistance to NFV for PI-experienced patients can be predicted by the number of mutations in the protease. The L90M mutation is significantly associated with the subsequent failure of NFV-containing regimens. The presence of the D30N mutation was rare and not useful in identifying NFV-resistant isolates.

Impact of HIV type 1 drug resistance mutations and phenotypic resistance profile on virologic response to salvage therapy.

This study examines the association between presence of drug resistance mutations and phenotypic resistance at baseline to virologic response to salvage therapy in a community setting. The study population consisted of 58 antiretroviral drug-experienced patients with HIV-1 infection who had recently switched therapy because of virologic failure. Drug resistance mutations in the reverse transcriptase- and protease-coding regions and phenotypic susceptibility to 13 antiretroviral drugs were assessed at baseline. Plasma HIV-1 RNA levels were assessed at baseline and at subsequent clinic visits. Results showed that three variables were significant in predicting virologic response: HIV-1 levels at baseline, number of protease mutations, and phenotypic sensitivity score for the regimen at baseline. For four drugs there was a significant association between the presence of specific drug resistance mutations and >10-fold phenotypic resistance to that drug. With phenotypic resistance defined as >4-fold resistance, the association between specific drug resistance mutations and phenotypic resistance was significant for seven drugs. Overall, these data show that phenotypic susceptibility and absence of drug resistance mutations, particularly protease mutations, are significant predictors of virologic response. For several drugs, specific combinations of drug resistance mutations are associated with decreased phenotypic susceptibility and might provide useful clinical guidelines in selecting therapeutic options.

Performance of drug resistance assays in testing HIV-1 non-B subtypes.

Antiretroviral susceptibility analyses were performed in plasma samples collected from 32 HIV-1 non-B-infected individuals, most of whom had received antiretroviral drugs. Reverse transcriptase (RT) and protease gene sequences were obtained, and 15 anti-HIV drugs were tested in a recombinant virus phenotypic assay. Phenotypic results were obtained in 25 (78.1%) samples, while genotypic data were recorded in 19 (59.4%). In seven samples (21.9%), neither genotypic nor phenotypic results were obtained. Ten of 13 samples with plasma HIV RNA below 2000 copies/mL did not yield genotypic results. Resistance assays work accurately when testing HIV-1 non-B subtypes. However, as for subtype B variants, a low viral load is the most important factor limiting the application of these tests.

Low prevalence of antiretroviral drug resistance among HIV-1 seroconverters in London, 1984-1991.

OBJECTIVES: To examine the prevalence of resistance mutations and natural polymorphisms to reverse transcriptase (RT) and protease inhibitors in a cohort of patients with defined seroconversion dates. METHODS: Eligible patients were those attending an HIV centre in North London who seroconverted from HIV negative to positive status between 01/01/85 and 31/12/91 (n=104). Genotypic resistance analysis was performed on the first positive serum sample after seroconversion and before use of antiretroviral therapy using population-based sequencing of RT-PCR fragments and rule-based sequence interpretation (Vircogen). RESULTS: Protease and RT sequences were successfully amplified from only 37 (35.6%) of the 104 seroconverters. Only one patient who seroconverted in August 1991 showed any evidence of significant mutations in the RT region, and this was associated with resistance to zidovudine (ZDV) (215Y and 210W). An additional patient who seroconverted in July 1991 had a TOR mutation and was classified as having intermediate resistance to ZDV. No spontaneous mutations were detected in the protease region. CONCLUSIONS: Overall only 2 (5%) of these treatment-naïve individuals were infected with HIV variants resistant to ZDV. Although the data at present do not support the need for pretreatment genotyping, there is a need for continued surveillance of the frequency of resistance mutations in antiretroviral naïve patients since the introduction of highly active antiretroviral therapy.

RT-PCR for Amplification of Specific Fragments of HIV-1 Genome.

HIV, the etiologic agent of AIDS, is a retrovirus of the family Lentiviridae, first isolated in 1983 by the group of Luc Montagnier at the Pasteur Institute of Paris (1). In the following years, much effort has been, and still is, focused on the search for antiviral drugs that would help to control the course of the disease in infected individuals. To assess the efficacy of those drugs, in vivo clinical markers of virus replication needed to be defined. These markers were for some years, surrogate, e.g., CD4 cell numbers, one of the main target cell types in the HIV replication cycle. More cumbersome methods were also used, such as the in vitro culture of plasma virus on donor peripheral blood lymphocytes (PBMC), with variable results. None of these techniques, however, could provide an accurate measure of virus replication. A major breakthrough in this field was the advent of methods that would allow for a direct quantification of circulating HIV. Viral load determinations soon proved to be an invaluable tool both in the clinical management of HIV-infected individuals and in the monitoring of therapeutic efficacy for commercially available or experimental antiviral drugs (2).

Antiviral activity of tenofovir (PMPA) against nucleoside-resistant clinical HIV samples.

The presence of the lamivudine-associated M184V RT mutation increases tenofovir susceptibility in multiple HIV genotypes. Tenofovir is uniquely active against multinucleoside-resistant HIV expressing the Q151M mutation, but shows reduced susceptibility to the T69S insertion mutations. HIV with common forms of zidovudine and lamivudine resistance are susceptible to tenofovir, corroborating phase II clinical results demonstrating the activity of tenofovir DF in treatment-experienced patients.