Current Levels of Drug Resistance Among Therapy-Naive HIV-Infected Patients Have Significant Impact on Treatment Response

Outcome Impacts Due to Pathogen-Specific Antimicrobial Resistance: A Narrative Review of Published Literature

Antimicrobial resistance (AMR) has become a global threat to not only public health impacts but also clinical and economic outcomes. During the past decades, there have been many studies focusing on surveillance, mechanisms, and diagnostics of AMR in infectious diseases but the impacts on public health, clinical and economic outcomes due to emergence of these AMRs are rarely studied and reported. This review was aimed to summarize the findings from published studies to report the outcome impacts due to AMR of malaria, tuberculosis and HIV and briefly discuss the implications for application to other infectious diseases. PubMed/Medline and Google Scholar databases were used for search of empirical and peer-reviewed papers reporting public health, clinical and economic outcomes due to AMR of malaria, tuberculosis and HIV. Papers published through 1 December 2019 were included in this review. A total of 76 studies were included for this review, including 16, 49 and 11 on public health, clinical and economic outcomes, respectively. The synthesized data indicated that the emergence and spread of AMR of malaria, tuberculosis and HIV have resulted in adverse public health, clinical and economic outcomes. AMR of malaria, tuberculosis and HIV results in significant adverse impacts on public health, clinical and economic outcomes. Evidence from this review suggests the needs to consider the similar studies for other infectious diseases.

The urgent need for more potent antiretroviral therapy in low-income countries to achieve UNAIDS 90-90-90 and complete eradication of AIDS by 2030

Background

Over 90% of Human Immunodeficiency Virus (HIV) infected individuals will be on treatment by 2020 under UNAIDS 90–90-90 global targets. Under World Health Organisation (WHO) “Treat All” approach, this number will be approximately 36.4 million people with over 98% in low-income countries (LICs).

Main body

Pretreatment drug resistance (PDR) largely driven by frequently use of non-nucleoside reverse transcriptase inhibitors (NNRTIs), efavirenz and nevirapine, has been increasing with roll-out of combined antiretroviral therapy (cART) with 29% annual increase in some LICs countries. PDR has exceeded 10% in most LICs which warrants change of first line regimen to more robust classes under WHO recommendations. If no change in regimens is enforced in LICs, it’s estimated that over 16% of total deaths, 9% of new infections, and 8% of total cART costs will be contributed by HIV drug resistance by 2030. Less than optimal adherence, and adverse side effects associated with currently available drug regimens, all pose a great threat to achievement of 90% viral suppression and elimination of AIDS as a public health threat by 2030. This calls for urgent introduction of policies that advocate for voluntary and compulsory drug licensing of new more potent drugs which should also emphasize universal access of these drugs to all individuals worldwide.

Conclusions

The achievement of United Nations Programme on HIV and AIDS 2020 and 2030 targets in LICs depends on access to active cART with higher genetic barrier to drug resistance, better safety, and tolerability profiles. It’s also imperative to strengthen quality service delivery in terms of retention of patients to treatment, support for adherence to cART, patient follow up and adequate drug stocks to help achieve a free AIDS generation.

Electronic supplementary material

The online version of this article (10.1186/s40249-019-0573-1) contains supplementary material, which is available to authorized users.

Trends and predictors of transmitted drug resistance (TDR) and clusters with TDR in a local Belgian HIV-1 epidemic

We aimed to study epidemic trends and predictors for transmitted drug resistance (TDR) in our region, its clinical impact and its association with transmission clusters. We included 778 patients from the AIDS Reference Center in Leuven (Belgium) diagnosed from 1998 to 2012. Resistance testing was performed using population-based sequencing and TDR was estimated using the WHO-2009 surveillance list. Phylogenetic analysis was performed using maximum likelihood and Bayesian techniques. The cohort was predominantly Belgian (58.4%), men who have sex with men (MSM) (42.8%), and chronically infected (86.5%). The overall TDR prevalence was 9.6% (95% confidence interval (CI): 7.7-11.9), 6.5% (CI: 5.0-8.5) for nucleoside reverse transcriptase inhibitors (NRTI), 2.2% (CI: 1.4-3.5) for non-NRTI (NNRTI), and 2.2% (CI: 1.4-3.5) for protease inhibitors. A significant parabolic trend of NNRTI-TDR was found (p = 0.019). Factors significantly associated with TDR in univariate analysis were male gender, Belgian origin, MSM, recent infection, transmission clusters and subtype B, while multivariate and Bayesian network analysis singled out subtype B as the most predictive factor of TDR. Subtype B was related with transmission clusters with TDR that included 42.6% of the TDR patients. Thanks to resistance testing, 83% of the patients with TDR who started therapy had undetectable viral load whereas half of the patients would likely have received a suboptimal therapy without this test. In conclusion, TDR remained stable and a NNRTI up-and-down trend was observed. While the presence of clusters with TDR is worrying, we could not identify an independent, non-sequence based predictor for TDR or transmission clusters with TDR that could help with guidelines or public health measures.

HIV-1 resistance and trend analysis in newly diagnosed patients in Belgium

A total of 1055 nucleotide sequences obtained from HIV patients diagnosed in 2008 and 2009 in Belgium were included in this prevalence study. The study population is a group of patients whose visit was considered by the clinician as the first contact with a Belgian AIDS reference centre or with another clinical centre experienced in HIV care. Prevalences of surveillance drug resistance mutations (SDRM) of 11·7% (47/394) and 11·0% (73/661) were observed in 2008 and 2009, respectively. The highest level of SDRM was observed towards nucleoside reverse transcriptase inhibitors (NRTIs) (7·8%), followed by the non-nucleoside reverse transcriptase inhibitors (NNRTIs) (4·2%) and Protease inhibitors (PIs) (2·3%). A potential clinical impact of the SDRM was demonstrated when using the current first-line therapy. A particularly high prevalence of SDRM was observed among intravenous drug users (IDUs) (29·4%). Reanalysis and comparing the data from previous Belgian studies using similar interpretation algorithms could not reveal a significant trend in SDRM prevalence over the last 5 years.

Transmitted HIV-1 drug resistance among young men of color who have sex with men: a multicenter cohort analysis

BACKGROUND

Given the elevated potential for primary or transmitted drug resistance (TDR) among newly HIV-infected individuals, there is a need for a deeper understanding of the baseline resistance patterns present in young men of color who have sex with men.

METHODS

Genotypic data were collected for participants aged 13-24 who were enrolled from seven sites. Univariate and bivariate methods were used to describe the prevalence of TDR and characteristics associated with TDR.

RESULTS

Of the 296 individuals participating in the substudy, 145 (49%) had baseline genotypes. The majority of the individuals were African American (65%) and gay-identified (70%). There was significant variation in genotype availability by site (p < .001). Major surveillance drug resistance mutations were present in 28 subjects (19.3%); the majority were non-nucleoside reverse transcriptase inhibitor mutations (12.4%). Subjects with TDR were less likely to have used alcohol on 1 or more days in the prior 2 weeks. Location was not associated with acquisition of TDR.

CONCLUSIONS

There was a high rate of TDR in a geographically and racially diverse sample of HIV-infected young men of color who have sex with men. This represents a serious public health concern given the young age of this sample and the potential need for long-term antiretroviral therapy. These findings underscore the critical roles of both early case identification and secondary prevention.

Monitoring HIV drug resistance in treatment-naive individuals: molecular indicators, epidemiology and clinical implications

Transmitted drug resistance (TDR) has been documented to occur soon after the introduction of HAART. The purpose of this review is to summarize the current knowledge regarding the epidemiology, the clinical implications and the trends in the research field of TDR. Until now, there have been different approaches for monitoring TDR, however, the surveillance drug resistance-associated mutations list seems fairly advantageous for TDR surveillance compared with other methods. The prevalence of TDR is approximately 10% in Europe and North America among recently or newly infected individuals sampled over the last few years. TDR was found to be higher among patients infected in Europe and North America compared with those in geographic areas with a high prevalence of HIV-1, reflecting the differences in the access to HAART in the two populations. Resistant viruses show different reversal rates to wild-type depending on the fitness cost of particular mutations. TDR in treatment-naive individuals is of major importance in HIV clinical practice and for this reason British–European and USA guideline panels recommend drug-resistance testing prior to treatment.

The Status of HIV-1 Resistance to Antiretroviral drugs in Sub-Saharan Africa

Access to highly active antiretroviral therapy (HAART) for persons infected with HIV in sub-Saharan Africa has greatly improved over the past few years. However, data on long-term clinical outcomes of Africans receiving HAART, patterns of HIV resistance to antiretroviral drugs and implications of HIV type-1 (HIV-1) subtype diversity in Africa for resistance, are limited. In resource-limited settings, concerns have been raised that deficiencies in health systems could create the conditions for accelerated development of resistance. Coordinated surveillance systems are being established to assess the emergence of resistance and the factors associated with resistance development, and to create the possibility for adjusting treatment guidelines as necessary. The purpose of this report is to review the literature on HIV-1 resistance to antiretroviral drugs in sub-Saharan Africa, in relation to the drug regimens used in Africa, HIV-1 subtype diversity and overall prevalence of resistance. The report focuses on resistance associated with treatment, prevention of mother-to-child transmission and transmitted resistance. It also outlines priorities for public health action and research.

Prevalence and epidemiology of HIV type 1 drug resistance among newly diagnosed therapy-naive patients in Belgium from 2003 to 2006

This study is the first prospective study to assess the prevalence, epidemiology, and risk factors of HIV-1 drug resistance in newly diagnosed HIV-infected patients in Belgium. In January 2003 it was initiated as part of the pan-European SPREAD program, and continued thereafter for four inclusion rounds until December 2006. Epidemiological, clinical, and behavioral data were collected using a standardized questionnaire and genotypic resistance testing was done on a sample taken within 6 months of diagnosis. Two hundred and eighty-five patients were included. The overall prevalence of transmitted HIV-1 drug resistance in Belgium was 9.5% (27/285, 95% CI: 6.6-13.4). Being infected in Belgium, which largely coincided with harboring a subtype B virus, was found to be significantly associated with transmission of drug resistance. The relatively high rate of baseline resistance might jeopardize the success of first line treatment as more than 1 out of 10 (30/285, 10.5%) viruses did not score as fully susceptible to one of the recommended first-line regimens, i.e., zidovudine, lamivudine, and efavirenz. Our results support the implementation of genotypic resistance testing as a standard of care in all treatment-naive patients in Belgium.

Transmission of multidrug-resistant HIV-1: 5 years of immunological and virological survey

Multidrug resistant HIV-1 acquired at the time of primary infection in two patients persisted for at least 5 years with and without treatment. In each patient, only one back mutation to wild-type codon in the protease gene occurred, and that was concomitantly associated with a marked CD4 cell count decrease. In both cases, infection was caused by CCR5 viruses and no rapid clinical progression to AIDS after primary infection was observed.

No response to first-line tenofovir+lamivudine+efavirenz despite optimization according to baseline resistance testing: impact of resistant minority variants on efficacy of low genetic barrier drugs

BACKGROUND

Resistance testing has been implemented into clinical guidelines as it has shown some beneficial effect on subsequent therapy response.

CASE REPORT

Routine population-based genotypic resistance testing for a newly diagnosed HIV-1 patient revealed the presence of resistance mutations M41L, V179D and T215E within reverse transcriptase and no mutations within protease. Four weeks after initiation of the combination tenofovir+lamivudine+efavirenz, no response was observed despite good adherence to therapy and efavirenz drug levels in the therapeutic range. Retrospective single genome sequencing of the baseline sample revealed the presence of minority viral variants with additional mutations: a mutation conferring resistance to lamivudine (M184IV), a thymidine associated mutation (K219R) and mutations possibly associated with non-nucleoside reverse transcriptase resistance (F227S, M230IV).

CONCLUSIONS

This case illustrates that undetected drug-resistant minority variants can reduce the efficacy of a normally very potent first-line regimen tenofovir+lamivudine+efavirenz. The presence of drug-resistance mutations at diagnosis should be considered as a warning sign against the use of low genetic barrier drugs in first-line regimens, even when these drugs are considered to be active according to routine resistance testing.

Genotypic resistance in plasma and peripheral blood lymphocytes in a group of naive HIV-1 patients

BACKGROUND

Since HIV infection cannot be completely eliminated due to the establishment of latently infected CD4+ T cell reservoirs, there is an urgent need for a clearer understanding of comparative resistance profiles between plasma and PBMC in HIV-1 patients.

OBJECTIVES

To assess the prevalence of mutations associated with drug resistance and to compare cell free and cell-associated strains.

STUDY DESIGN

Genotypic resistance analysis on viral DNA and plasma was performed in 31 therapy naive patients with chronic infection to check reverse transcriptase (RT) and protease resistance associated mutations before beginning antiretroviral therapy.

RESULTS

Direct sequencing of DNA provirus disclosed key mutations (such as G190A/S, V106A, K103N and T215F) to RT inhibitors more frequently (7 patients out 31) than in plasma RNA (2 out of 31). In addition, major mutations (D30N, M46I, I50V, I84V) associated with drug resistance in the PR region were only found in PBMCs.

CONCLUSIONS

Despite the small number of patients, our results show a different resistance profile between plasma and PBMC compartments and may yield additional information for first-line antiretroviral regimens. Further investigations on larger series followed-up for a longer period of time are required to obtain in-depth information on the meaning of the mutations detectable in plasma and/or in PBMCs.

Prevalence of antiretroviral drug resistance mutations and HIV-1 non-B subtypes in newly diagnosed drug-naïve patients in Slovenia, 2000–2004

In order to estimate the prevalence and patterns of antiretroviral drug resistance mutations in drug-naïve HIV-1 infected patients in Slovenia, and the prevalence of non-B subtypes, a retrospective study was conducted on a cohort, representing 87% of the total of newly diagnosed HIV-1 infected patients, in a 5 year period (2000-2004). Protease (PR) and reverse transcriptase (RT) sequences were determined in 77 newly diagnosed HIV-1 patients. Non-B subtypes were present in 18% of the population tested. Transmitted drug resistance was identified as in the CATCH study: the presence of primary PR and RT gene mutations according to the IAS-USA mutation list including the revertant mutations in codon 215 and excluding mutations on the RT positions 44 and 118. The estimated prevalence of transmitted resistance mutations was 3.9%. Namely, three out of 77 patients had mutations associated with resistance to NRTIs: one patient carried M184V in association with A62V, while a revertant mutation T215D was found in two patients. No transmitted drug resistance to NNRTIs or PIs was detected. However, to score the expected response to therapy using the REGA and the Stanford algorithms, we also took into account secondary PR mutations and additional RT mutations. Reduced response to some therapeutic options was predicted in five patients (6.5%). In conclusion, testing the vast majority of all newly diagnosed HIV-1 patients in the last 5 years in Slovenia uncovered a relatively high prevalence of non-B subtypes and a low prevalence of transmitted drug resistance.

Drug-resistance mutations in antiretroviral-naive patients with established HIV-1 infection in Mexico

OBJECTIVES

To describe the prevalence of baseline drug-resistance mutations, resistance to antiretroviral drugs, and the subsequent virological response to therapy in treatment-naïve patients from Mexico with established HIV-1 infection.

METHODS

Resistance testing was performed on plasma samples from antiretroviral-naïve patients. Data on mutations associated with antiretroviral drug resistance were obtained using Stanford software (http://hivdb.stanford.edu).

RESULTS

Ninety-six treatment-naïve individuals were enrolled in the study during 2002-2003. Of these, 83 patients (86%) had at least one resistance mutation and 15 (16%) had drug resistance. At baseline, the mean plasma viral load was 299 834 HIV-1 RNA copies/mL, and at follow-up it was 37 620 copies/mL (P<0.0001). Primary mutations in the reverse transcriptase region were observed in 15% of patients. For nucleoside inhibitors, mutations T215Y/C and F77L (3%) and D67N/S, T69N and M184V (2%), were detected. For nonnucleoside inhibitors, mutations K103N/R (6%), Y181C (3%) and G190A (2%) were detected. Overall, 6% of patients showed resistance to delavirdine and nevirapine, 4% to efavirenz, and 2% to lamivudine and nelfinavir. Twelve patients showed no response to treatment and three of these patients had antiretroviral drug resistance.

CONCLUSIONS

The prevalence of baseline drug-resistance mutations found in this study was similar to that found in previous reports for newly HIV-infected individuals, although access to and management of antiretrovirals in Mexico are different.

Prevalence of resistance-associated mutations in newly diagnosed HIV-1 patients in Greece

The prevalence of HIV-1 drug resistance mutations in naïve patients has been previously shown to differ greatly with the geographic origin. The purpose of this study was to prospectively estimate the prevalence of HIV-1 drug resistance in Greece by analyzing a representative sample of newly HIV-1 diagnosed patients, as part of the SPREAD collaborative study. Protease (PR) and partial reverse transcriptase (RT) sequences were determined from 101 newly diagnosed HIV-1 patients, in Greece, during the period September 2002--August 2003, representing one-third of the total newly diagnosed HIV-1 patients in the same time period. The prevalence of HIV-1 drug resistance was estimated according to the IAS-USA mutation table taking into account all mutations in RT and only major mutations in PR region. The overall prevalence of resistance was 9% [95% confidence interval (CI): 4.2--16.2%]. The prevalence of mutations associated with resistance to NRTIs was 5% (95% CI: 1.6--11.2%), for NNRTIs was 4% (95% CI: 1.1--9.8%), while no major resistance mutations were found in PR. No multi-class resistance was detected in the study population. The prevalence of resistant mutations in the recent seroconverters was 22%. For two individuals, there was clear evidence for transmitted resistance based on epidemiological information for a known source of HIV-1 transmission. The prevalence of the HIV-1 non-B subtypes and recombinants was 52%.