Application of Luminex Gastrointestinal Pathogen Panel to human stool samples from Côte d'Ivoire.

INTRODUCTION: Gastrointestinal infections caused by viruses, bacteria, and parasites are endemic in most developing countries due to inadequate provision of safe water supplies, sanitation, and hygiene. To investigate the enteric pathogens infecting people living in Côte d'Ivoire, the Luminex Gastrointestinal Pathogen Panel (xTAG GPP) assay was used to analyze 34 human fecal samples. This study represents the first application of this technology to samples from a sub-Saharan African country. METHODOLOGY: Thirty-four stool samples from asymptomatic and symptomatic patients, 1-15 years of age, were analyzed by xTAG GPP. The Luminex assay represents a qualitative bead-based multiplexed molecular diagnostic test able to identify concurrently 15 enteric pathogens, including bacteria, viruses, and parasites. RESULTS: Overall, 22 out of 34 (64.7%) fecal specimens were detected to be positive by xTAG GPP. Sixteen were from asymptomatic subjects, and 10 patients (45.4%) showed co-infections. G. duodenalis was detected in 15 patients, in both mono- and co-infections, representing the most frequent pathogen, followed by enterotoxigenic Escherichia coli (ETEC) LT/ST. Four norovirus isolates were also detected and assigned to genogroups I and II. CONCLUSIONS: Considering the burden of enteric infections in developing countries, particularly among children, and the high rate of co-infections in asymptomatic subjects, this study shows the need for diagnostic tools such as xTAG GPP to improve diagnosis and treatment of these infections in endemic areas.

Detection and characterization of enteroviruses and parechoviruses in healthy people living in the South of Côte d'Ivoire.

BACKGROUND: Human enteroviruses (EVs) and parechoviruses (HPeVs) belong to the family Picornaviridae. Although most EV and HPeV infections remain asymptomatic, both pathogens can cause a wide spectrum of clinical manifestations ranging from respiratory or gastrointestinal symptoms to myocarditis, neonatal sepsis, and infections of the central nervous system. OBJECTIVES: Aim of the present study was to investigate the spectrum of EVs and HPeVs in apparently healthy adults and children living in the South of Côte d'Ivoire. STUDY DESIGN: The study included 105 stool samples obtained from healthy individuals aged 0-53 years between June 2013 and December 2014 in the Sud-Como region of Côte d'Ivoire. After collection and shipment to Germany, the samples were analyzed by real-time PCR for the presence of EVs and HPeVs RNA. Molecular typing and virus isolation of all samples were performed.''é RESULTS: Out of 105 samples, 24 (22.8%) were EV positive and six (5.2%) were HPeV positive. Twenty-one EV positive samples could be characterized with serotypes belonging to EV group A-C, while three could not be further specified. Interestingly, several rarely described serotypes were identified, e.g., EV-C99, EV-B93, EV-C116, and EV-A119. Typing of HPeV positive samples resulted in HPeV-1 and -5 detections, while one isolate could not be assigned to the known HPeV types. CONCLUSIONS: This study showed a large variety of EV strains in healthy people in the South of Côte d'Ivoire and provided the first available data about HPeV infections in a sub-Saharan African country.

Longitudinal comparison of HIV-1 plasma viral load and cellular proviral load.

INTRODUCTION: The goal of antiretroviral treatment (ART) in HIV-1 infection is the permanent suppression of plasma viral load (pVL) below the currently existing limit of detection of 50 copies/mL (DAIG HIV-therapy guidelines). Therefore, treatment effectiveness is based on pVL. pVL measurements however do not give any information about the viral reservoir in peripheral blood mononuclear cells (PBMCs). Therefore, the proviral DNA of HIV-1 could be a useful marker for the investigation of viral reservoirs and monitoring ART in patients showing undetectable pVL. MATERIALS AND METHODS: Seventy-seven treatment-experienced HIV-1 infected patients with pVL <50 copies/mL were randomly selected. pVL and proviral DNA load were measured using the Roche COBAS TaqMan HIV-1 v2.0 assay. Additionally, CD4+ cell count per mL and the total white blood cell (wbc) count per mL were determined for each patient. Follow-up data were collected 24 weeks after the time point of the first measurement. Proviral DNA load per mL, CD4+ cell count per mL as well as wbc count per mL were observed over time and differences were estimated using the Mann-Whitney U test. Additionally, correlations between the clinical parameters were analyzed using the two-sided Pearson correlation analysis. RESULTS: Out of the 77 patients, 38 show a significant increase in proviral load per mL over time (p=0,001), whereas 39 patients show a significant decrease (p=0,001). No differences became visible in the CD4+ cell count per mL comparing week 0 and week 24 data. Thirty five patients show a significant increase in wbc count per mL over time (p<0,001), while 42 patients show a significant decrease (p<0,001). A significant correlation of increasing proviral load per mL and wbc count per mL for data of the first (p<0.001) and the second measurement (p<0.001) can be detected, while there are no correlations found between proviral load per mL and CD4+ cell count per mL. CONCLUSIONS: Our data show that the presence of viral reservoirs in other cell types and not only CD4+ cells is most probable. HIV-1 proviral DNA seems to be an interesting marker in patients with undetectable pVL and allows the assessment of replication under ART. Nevertheless, further longitudinal studies are needed to assess the usefulness and the clinical significance of this marker.

Extraction of viral nucleic acids: comparison of five automated nucleic acid extraction platforms.

BACKGROUND: Nucleic acid extraction has a major impact on the reliability of results in routine molecular diagnostics. Optimal isolation of nucleic acids and removal of inhibitors are essential. OBJECTIVES: This study compares five different automated extraction platforms for the extraction of norovirus RNA from stool and cytomegalovirus (CMV) DNA from plasma samples. STUDY DESIGN: Norovirus positive stool samples and CMV positive plasma samples were aliquoted and analyzed using five different automated platforms (easyMAG, bioMerieux; m2000sp, Abbott; MagNA Pure LC 2.0, Roche; QiaSymphony, Qiagen; sample preparation module of the VERSANT kPCR Molecular System, Siemens). Similar sample input and output volumes, the identical real-time PCR cycler, and the identical assays for amplification and detection for norovirus RNA and CMV DNA, respectively, were chosen. RESULTS: Of 39 stool samples, 36 tested positive for norovirus RNA with all extraction platforms. The three discrepant samples showed inhibition after extraction with at least one platform. Only with the VERSANT platform all samples tested positive for both the target RNA and the internal controls. Of 42 plasma samples, 27 gave quantifiable results for CMV DNA with all extraction platforms. There was significant variance between viral concentrations when different extraction platforms were compared. The majority of the 15 discrepant samples showed low viral concentrations. The internal control of the CMV assay gave positive results for all samples tested below the limit of quantification. CONCLUSIONS: The five automated extraction platforms yielded comparable results. However, the extraction performance was found to be impaired by inhibitory substances in stool samples.

Detection of adenoviruses and rotaviruses in drinking water sources used in rural areas of Benin, West Africa.

Diseases associated with viruses also found in environmental samples cause major health problems in developing countries. Little is known about the frequency and pattern of viral contamination of drinking water sources in these resource-poor settings. We established a method to analyze 10 liters of water from drinking water sources in a rural area of Benin for the presence of adenoviruses and rotaviruses. Overall, 541 samples from 287 drinking water sources were tested. A total of 12.9% of the sources were positive for adenoviruses and 2.1% of the sources were positive for rotaviruses at least once. Due to the temporary nature of viral contamination in drinking water sources, the probability of virus detection increased with the number of samples taken at one test site over time. No seasonal pattern for viral contaminations was found after samples obtained during the dry and wet seasons were compared. Overall, 3 of 15 surface water samples (20%) and 35 of 247 wells (14.2%) but also 2 of 25 pumps (8%) tested positive for adenoviruses or rotaviruses. The presence of latrines within a radius of 50 m in the vicinity of pumps or wells was identified as being a risk factor for virus detection. In summary, viral contamination was correlated with the presence of latrines in the vicinity of drinking water sources, indicating the importance of appropriate decision support systems in these socioeconomic prospering regions.