OMICS. 2014 Aug;18(8):513-23.

Mid-ATR-FTIR spectroscopic profiling of HIV/AIDS sera for novel systems diagnostics in global health.

Lungile Sitole1, Francois Steffens2, Tjaart .P.J Krüger3 and Debra Meyer1*

 1Department of Biochemistry, University of Pretoria, Pretoria 0028, South Africa

2 Department of Statistics, University of Pretoria, Pretoria 0028, South Africa

3Department of Physics, University of Pretoria, Pretoria 0028, South Africa



Global health, whether in developed or developing countries, is in need of robust systems diagnostics for major diseases such as HIV/AIDS impacting the world populations. Fourier transform Infrared (FTIR) spectroscopy of serum is a quick and reagent-free methodology with which to analyse metabolic alterations such as those caused by disease or treatment. In this study, Attenuated Total Reflectance Fourier-Transform (ATR-FTIR) spectroscopy, was investigated as a means of distinguishing HIV-infected treatment-experienced (HIVpos ARTpos, n=39) and HIV-infected-treatment-naïve (HIVpos ARTneg, n=16) subjects from uninfected control subjects (n=30). Multivariate pattern recognition techniques including partial least squares discriminant analysis (PLS-DA) and orthogonal partial least squares discriminant analysis (OPLS-DA) successfully distinguished sample classes while univariate approaches identified significant differences (p< 0.05) after Benjamini-Hochberg corrections. OPLS-DA discriminated between all groups with sensitivity, specificity and accuracy of > 90%. Compared to uninfected controls, HIVpos ARTpos and HIVpos ARTneg subjects displayed significant differences in spectral regions linked to lipids/fatty acids (3010cm-1), carbohydrates (1299cm-1; 1498cm-1), glucose (1035cm-1) and proteins (1600cm-1; 1652cm-1). These are all molecules shown by conventional biochemical analysis to be affected by HIV/ART interference. The biofluid metabolomics approach applied here successfully differentiated global metabolic profiles of HIV-infected patients and uninfected controls and detected potential biomarkers for development into indicators of host response to treatment and/or disease progression. Our findings therefore contribute to ongoing efforts for capacity-building in global health for robust omics science and systems diagnostics towards major diseases impacting population health.

PMID: 24937213



The acquired immune deficiency syndrome (AIDS) continues to be the leading cause of death worldwide. There is a reported 35 million people currently living with HIV worldwide (UNAIDS, 2012) and the Sub-Saharan Africa region is the most severely affected, accounting for 70% of all global infections (UNAIDS 2012).

HIV infection disrupts the immune system and also interferes with host metabolism causing metabolic disorders such as dyslipidemia, hyperglycaemia, insulin resistance and diabetes.

The introduction of highly active antiretroviral therapy (HAART) brought about a change in HIV/AIDS mortality and improved disease management. Though successful, long-term use of HAART has also been linked to the development of metabolic complications. HIV infected individuals (treated and untreated) must therefore be monitored constantly for the onset of metabolic complications in order to initiate interventions to delay and/or prevent the development of severe metabolic diseases.

Several biochemical methodologies are used to diagnose or monitor metabolic complications associated with HIV/AIDS but these can be expensive, labour intensive, lack both sensitivity and specificity and mainly detect one metabolite at a time. It is therefore imperative to develop methods can analyze a wide range of metabolites simultaneously.

Previous studies from our group described the potential of both nuclear magnetic resonance (NMR) spectroscopy (Hewer et al., 2006; Philippeos et al., 2009; McKnight et al., 2014) and mass spectrometry (MS) (Williams et al., 2012) in HIV/AIDS metabolomics. Here, ATR-FTIR-based metabonomics was explored for the identification of metabolites that could serve as markers of HIV infection and response to treatment. Metabolomics is advantageous in that it allows the detection of multiple metabolites in a single analysis.


f1Figure 1: Representative scatter plot of ATR-FTIR spectra obtained from HIV infected (treated and untreated) and uninfected controls. The three experimental groups’ discriminant functions are: 30 uninfected controls, 39 HIVpos ARTpos and 16 HIVpos   ARTneg.


As expected, results from this study showed for the first time that mid-ATR-FTIR spectroscopy could discriminate between HIV-infected (treated and untreated) and uninfected sera (Figure 1). The separation was improved by the depiction of a two-group discrimination alongside loading plots (Figure 2). The identified functional groups are structural components of metabolites detected using other HIV-metabolomics spectroscopic techniques. These metabolites include lipids, carbohydrates and proteins. Irregularities in the metabolic pathways involving these molecules have been implicated in the development of adverse metabolic effects in HIV-infected individuals using conventional biochemical analysis as well.



f2Figure 2: Multivariate statistical analysis of ATR-FTIR-based serum spectra obtained from HIV uninfected patients and uninfected controls. Scores plots (right panel) and loadings coefficient plots (left panel) generated from: (A) uninfected control vs. HIVpos ARTpos patients, (B) HIV uninfected control vs. HIVpos ARTneg and (C) HIVpos ARTneg vs. HIVpos ARTneg patients.


Even though ATR-FTIR spectroscopy is less sensitive than NMR and MS, results presented here provide relevant insights for novel systems diagnostics for HIV/AIDS. This work also demonstrates the reliability, simplicity and predictive ability of ATR-FTIR-based metabolomics in discriminating between diseases and non-diseased sera.



  1. UNAIDS, 2012. UNAIDS World AIDS Day Report | 2012. Geneva, Switzerland.
  2. Hewer, R., Vorster, J., Steffens, F.E., Meyer, D., 2006. Applying biofluid 1H NMR-based metabonomic techniques to distinguish between HIV-1 positive/AIDS patients on antiretroviral treatment and HIV-1 negative individuals. J. Pharm. Biomed. Anal. 41, 1442–6.
  3. Philippeos, C., Steffens, F.E., Meyer, D., 2009. Comparative 1H NMR-based metabonomic analysis of HIV-1 sera. J. Biomol. NMR 44, 127–37.
  4. Williams, A., Koekemoer, G., Lindeque, Z., Reinecke, C., Meyer, D., 2011. Qualitative serum organic acid profiles of HIV-infected individuals not on antiretroviral treatment. Metabolomics 8, 804–818.
  5. McKnight, T.R., Yoshihara, H. a I., Sitole, L.J., Martin, J.N., Steffens, F., Meyer, D., 2014. A combined chemometric and quantitative NMR analysis of HIV/AIDS serum discloses metabolic alterations associated with disease status. Mol. Biosyst. 10, 2889–2897.



Debra Meyer, PhD

Professor and Head of Department

Department of Biochemistry

Lynwood Road and Roper Street, Hatfield

University of Pretoria, 0002

Pretoria, South Africa


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