• Deep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the Gut

      Carroll, M; Haldenby, S; Rickett, N; Pályi, B; Garcia-Dorival, I; Liu, X; Barker, G; Bore, J; Koundouno, F; Williamson, E; et al. (American Society for Microbiology, 2017-08-23)
      In this study, samples from the 2013-2016 West African Ebola virus outbreak from patients in Guinea with Ebola virus disease (EVD) were analyzed to discover and classify what other pathogens were present. Throat swabs were taken from deceased EVD patients, and peripheral blood samples were analyzed that had been taken from patients when they presented at the treatment center with acute illness. High-throughput RNA sequencing (RNA-seq) and bioinformatics were used to identify the potential microorganisms. This approach confirmed Ebola virus (EBOV) in all samples from patients diagnosed as acute positive for the virus by quantitative reverse transcription-PCR in deployed field laboratories. Nucleic acid mapping to Plasmodium was also used on the patient samples, confirming results obtained with an antigen-based rapid diagnostic test (RDT) conducted in the field laboratories. The data suggested that a high Plasmodium load, as determined by sequence read depth, was associated with mortality and influenced the host response, whereas a lower parasite load did not appear to affect outcome. The identifications of selected bacteria from throat swabs via RNA-seq were confirmed by culture. The data indicated that the potential pathogens identified in the blood samples were associated with translocation from the gut, suggesting the presence of bacteremia, which transcriptome data suggested may induce or aggravate the acute-phase response observed during EVD. Transcripts mapping to different viruses were also identified, including those indicative of lytic infections. The development of high-resolution analysis of samples from patients with EVD will help inform care pathways and the most appropriate general antimicrobial therapy to be used in a resource-poor setting. IMPORTANCE Our results highlight the identification of an array of pathogens in the blood of patients with Ebola virus disease (EVD). This has not been done before, and the data have important implications for the treatment of patients with EVD, particularly considering antibiotic stewardship. We show that EVD patients who were also infected with Plasmodium, particularly at higher loads, had more adverse outcomes than patients with lower levels of Plasmodium. However, the presence of Plasmodium did not influence the innate immune response, and it is likely that the presence of EBOV dominated this response. Several viruses other than EBOV were identified, and bacteria associated with sepsis were also identified. These findings were indicative of bacterial translocation across the gut during the acute phase of EVD.
    • Designing HIV Testing Algorithms Based on 2015 WHO Guidelines Using Data from Six Sites in sub-Saharan Africa

      Kosack, C; Shanks, L; Beelaert, G; Benson, T; Savane, A; Ng'ang'a, A; Andre, B; Zahinda, J; Fransen, K; Page, A (American Society for Microbiology, 2017-07-26)
      Our objective was to evaluate the performance of HIV testing algorithms based on WHO recommendations, using data from specimens collected at six HIV testing and counselling sites in sub-Saharan Africa (Guinea, Conakry; Kitgum and Arua, Uganda; Homa Bay, Kenya; Douala, Cameroun; Baraka, Democratic Republic of Congo). A total of 2780 samples, including 1306 HIV-positive, were included in the analysis. HIV testing algorithms were designed using Determine as a first test. Second and third rapid diagnostic tests (RDT) were selected based on site-specific performance, adhering where possible to the WHO-recommended minimum requirements of sensitivity and specificity of ≥99%. The threshold for specificity was reduced to 98% or 96% if necessary. We also simulated algorithms consisting of one RDT followed by a simple confirmatory assay. The positive predictive values (PPV) of the simulated algorithms varied from 75.8%-100% using strategies recommended for high-prevalence settings; 98.7%-100% using strategies recommended for low-prevalence settings; and 98.1%-100% using a rapid test followed by a simple confirmatory assay. Although we were able to design algorithms that met the recommended PPV of ≥99% in five of six sites using the applicable high prevalence strategy, options were often very limited due to sub-optimal performance of individual RDTs and to shared false-reactive results. These results underscore the impact of the sequence of HIV tests and of shared false-reactivity on algorithm performance. Where it is not possible to identify tests that meet WHO-recommended specifications, the low-prevalence strategy may be more suitable.
    • Diagnostic accuracy of two rK39 antigen-based dipsticks and the formol gel test for rapid diagnosis of visceral leishmaniasis in northeastern Uganda.

      Chappuis, F; Mueller, Y; Nguimfack, A; Rwakimari, J; Couffignal, S; Boelaert, M; Cavailler, P; Loutan, L; Piola, P; Travel and Migration Medicine Unit, Geneva University Hospital, Rue Micheli-du-Crest 24, 1211 Geneva 14, Switzerland. francois.chappuis@hcuge.ch (American Society for Microbiology, 2005-12)
      The development of an accurate, practical, and affordable diagnostic test is essential to improve the management of visceral leishmaniasis (VL) in remote health centers. We evaluated the Formol Gel test (FGT) and two rK39 antigen-based dipsticks, the DUAL-IT L/M, and the Kalazar Detect for VL diagnosis in Amudat Hospital in Uganda. The DUAL-IT L/M was also evaluated for the diagnosis of malaria. All patients clinically suspect of VL were prospectively included in the study between October 2003 and March 2004. The gold standard used to define a VL case was a positive spleen aspirate or a direct agglutination test titer of >1:12,800 with an appropriate clinical response to antileishmanial therapy. A total of 131 VL and 112 non-VL patients were included in the analysis. The DUAL IT L/M was found to be more sensitive than the Kalazar Detect: 97% (95% confidence interval [95%CI] = 92 to 99%) versus 82% (95%CI = 74 to 87%). The Kalazar Detect and the DUAL IT L/M were highly specific (99% [95%CI = 95 to 100%] and 97% [95%CI = 92 to 99%], respectively). The FGT lacked both sensitivity (66% [95%CI = 57 to 73%]) and specificity (90% [95%CI = 83 to 94%]). The sensitivity of the DUAL IT L/M for malaria was only 57% (95%CI = 37 to 76%). The two rK39 dipsticks can be used for diagnostic confirmation of VL in this region. The DUAL-IT L/M without its malaria diagnostic component (DiaMed-IT LEISH) will be adopted as first-line test for VL in Uganda.
    • Evaluation of OMNIgene® SPUTUM and ethanol reagent for preservation of sputum prior to Xpert and culture testing in Uganda.

      Ardizzoni, E; Orikiriza, P; Ssuuna, C; Nyehangane, D; Gumsboga, M; Taremwa, IM; Turyashemererwa, E; Mwanga-Amumpaire, J; Langendorf, C; Bonnet, M (American Society for Microbiology, 2019-10-16)
      Background: Xpert MTB/RIF (Xpert) and culture are the most reliable methods for tuberculosis diagnosis but are still poorly accessible in many low resource countries. We aimed to assess the effect of OMNIgene® SPUTUM (OM-S) and ethanol in preserving sputum for Xpert and OM-S for mycobacteria growth indicator tube (MGIT) testing over a period of 15 and 8 days respectively. Methods: Sputum were collected from newly diagnosed smear-positive patients. For Xpert, pooled samples were split into 5 aliquots: 3 for Xpert on day 0, 7 and 15 days without additive and 2 with either OM-S or ethanol at day 15. For MGIT, 2 aliquots were tested without preservative and 2 with OM-S at 0 and 8 days. Results: A total of 48 and 47 samples were included in the analysis for Xpert and culture. With Xpert, using Day 0 as reference, untreated samples stored for 7 and 15 days showed concordance of 45/46 (97.8%) and 46/48 (95.8%). For samples preserved with OM-S or ethanol for 15 days compared with untreated samples processed at day 0 or after 15 days, OM-S concordance was 46/48(95.8%) and 47/48(97.9%), while ethanol was 44/48 (91.7%) and 45/48 (93.8%). With MGIT, concordance between untreated and OM-S treated samples was 21/41(51.2%) at Day 0 and 21/44(47.7%) at day8. Conclusions: Xpert equally detected TB in OM-S treated and untreated samples up to 15 days but showed slightly lower detection in ethanol treated samples. Among OM-S treated samples, MGIT positivity was significantly lower compared to untreated samples at both time-points.
    • Field evaluation of a rapid immunochromatographic assay for detection of Trypanosoma cruzi infection by use of whole blood

      Roddy, P; Goiri, J; Flevaud, L; Palma, P; Morote, S; Lima, N; Villa, L; Torrico, F; Albajar-Vinas, P; Médecins Sans Frontières – Spain, Barcelona, Spain; Centro Universitario de Medicina Tropical - Facultad de Medicina, Universidad Mayor de San Simon, Cochabamba, Bolivia; Laboratório de Doenças Parasitárias, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil. (American Society for Microbiology, 2008-06)
      Laboratory and clinical diagnostic classification of seropositive individuals, followed by treatment and supportive therapy, is an established component of Chagas disease control in endemic areas. However, most Chagas-infected patients live in remote areas where neither equipped laboratories nor skilled human resources are widely available. Employing a rapid diagnostic test (RDT), when using whole blood samples, is the best-option for Chagas disease control. A high sensitivity and specificity for the Chagas Stat-Pak(TM) RDT (Chembio Diagnostic Systems, Inc., Medford, NY) has been reported when assayed with serum and plasma but its validity for the detection of antibodies to Trypanosoma cruzi infection in whole blood is unknown. This cross-sectional study measured the sensitivity and specificity of the Chagas Stat-Pak(TM) when using whole blood and conventional serological assays as a comparison. The inter-observer reliability in the interpretation of the Chagas Stat-Pak(TM) results and 'ease of use' criterion needed to perform the Chagas Stat-Pak(TM) and conventional assays were also measured. The Chagas Stat-Pak(TM) yielded a high specificity [99.0%, (95%CI: 98.4%-99.4%)] but a relatively low sensitivity [93.4%, (95%CI: 87.4%-97.1%)]. The inter-observer reliability was excellent [kappa(n=1,913)= .999,(p<.0001)] and quantified 'ease of use' criterion suggested that the RDT is simple to perform. Despite the distinguished attributes of the Chagas Stat-Pak(TM), it is not an ideal diagnostic test for the population investigated in this study due to its relatively low sensitivity and high cost. The RDT manufacturer is called upon to improve the test if the international community hopes to make progress in controlling Chagasic infections in endemic areas.
    • Improving the Specificity of Plasmodium falciparum Malaria Diagnosis in High-Transmission Settings with a Two-Step Rapid Diagnostic Test and Microscopy Algorithm

      Murungi, M; Fulton, T; Reyes, R; Matte, M; Ntaro, M; Mulogo, E; Nyehangane, D; Juliano, J; Siedner, M; Boum, Y; et al. (American Society for Microbiology, 2017-05)
      Poor specificity may negatively impact rapid diagnostic test (RDT)-based diagnostic strategies for malaria. We performed real-time PCR on a subset of subjects who had undergone diagnostic testing with a multiple-antigen (histidine-rich protein 2 and pan-lactate dehydrogenase pLDH [HRP2/pLDH]) RDT and microscopy. We determined the sensitivity and specificity of the RDT in comparison to results of PCR for the detection of Plasmodium falciparum malaria. We developed and evaluated a two-step algorithm utilizing the multiple-antigen RDT to screen patients, followed by confirmatory microscopy for those individuals with HRP2-positive (HRP2+)/pLDH-negative (pLDH-) results. In total, dried blood spots (DBS) were collected from 276 individuals. There were 124 (44.9%) individuals with an HRP2+/pLDH+ result, 94 (34.1%) with an HRP2+/pLDH- result, and 58 (21%) with a negative RDT result. The sensitivity and specificity of the RDT compared to results with real-time PCR were 99.4% (95% confidence interval [CI], 95.9 to 100.0%) and 46.7% (95% CI, 37.7 to 55.9%), respectively. Of the 94 HRP2+/pLDH- results, only 32 (34.0%) and 35 (37.2%) were positive by microscopy and PCR, respectively. The sensitivity and specificity of the two-step algorithm compared to results with real-time PCR were 95.5% (95% CI, 90.5 to 98.0%) and 91.0% (95% CI, 84.1 to 95.2), respectively. HRP2 antigen bands demonstrated poor specificity for the diagnosis of malaria compared to that of real-time PCR in a high-transmission setting. The most likely explanation for this finding is the persistence of HRP2 antigenemia following treatment of an acute infection. The two-step diagnostic algorithm utilizing microscopy as a confirmatory test for indeterminate HRP2+/pLDH- results showed significantly improved specificity with little loss of sensitivity in a high-transmission setting.
    • Population Pharmacokinetics of Piperaquine after Two Different Treatment Regimens with Dihydroartemisinin-Piperaquine in Patients with Plasmodium falciparum Malaria in Thailand.

      Tarning, J; Ashley, E A; Lindegardh, N; Stepniewska, K; Phaiphun, L; Day, N P J; McGready, R; Ashton, M; Nosten, F; White, N J; et al. (American Society for Microbiology, 2008-03)
      The population pharmacokinetics of piperaquine in adults and children with uncomplicated Plasmodium falciparum malaria treated with two different dosage regimens of dihydroartemisinin-piperaquine were characterized. Piperaquine pharmacokinetics in 98 Burmese and Karen patients aged 3 to 55 years were described by a two-compartment disposition model with first-order absorption and interindividual random variability on all parameters and were similar with the three- and four-dose regimens. Children had a lower body weight-normalized oral clearance than adults, resulting in longer terminal elimination half-lives and higher total exposure to piperaquine (area under the concentration-time curve from 0 to 63 days [AUC(day 0-63)]). However, children had lower plasma concentrations in the therapeutically relevant posttreatment prophylactic period (AUC(day 3-20)) because of smaller body weight-normalized central volumes of distribution and shorter distribution half-lives. Our data lend further support to a simplified once-daily treatment regimen to improve treatment adherence and efficacy and indicate that weight-adjusted piperaquine doses in children may need to be higher than in adults.
    • Prospective Evaluation of the Diagnostic Accuracy of Dried Blood Spots from Finger-Prick for the Determination of HIV-1 Viral Load with the NucliSENS Easy-Q HIV-1 v2.0 in Malawi

      Fajardo, Emmanuel; Metcalf, Carol A; Chaillet, Pascale; Aleixo, Lucia; Pannus, Pieter; Panunzi, Isabella; Triviño, Laura; Ellman, Tom; Likaka, Andrew; Mwenda, Reuben (American Society for Microbiology, 2014-02-05)
      HIV-1 viral load (VL) testing is not widely available in resource-limited settings. Use of finger-prick dried blood spot (FP-DBS) samples could remove barriers related to sample collection and transport. Measurement of VL using DBS from EDTA venous blood (VB-DBS) in place of plasma has previously been validated using the NucliSENS EasyQ HIV-1 v2.0 assay, but information on the accuracy of FP-DBS samples for measuring VL is limited. This prospective study, conducted at Thyolo District Hospital in Southern Malawi, compared VL levels measured on FP-DBS samples and plasma, using the NucliSENS EasyQ HIV-1 v2.0 assay. Comparability was assessed by means of agreement and correlation (131 patients with VLs ≥100 copies/ml), and sensitivity and specificity (612 patients on ART). Samples of EDTA venous blood and FP-DBS from 1,009 HIV-infected individuals were collected and prepared in the laboratory. Bland-Altman analysis found good agreement between plasma and FP-DBS VL levels, with a mean difference of -0.35 log10, and 95% limits of agreement from -1.26 to 0.55 log10. FP-DBS had a sensitivity of 88.7% (95% confidence interval [CI]: 81.1 - 94.4%) and specificity of 97.8% (95% CI: 96.1 - 98.9%) using a 1,000 copies/ml cut-point; and a sensitivity of 83.0% (95% CI: 73.4 - 90.1%) and specificity of 100% (95% CI: 99.3-100%) using a 5,000 copies/ml cut-point. This study shows that FP-DBS is an acceptable alternative to plasma for measuring VL using the NucliSENS EasyQ HIV-1 v2.0. We are conducting a second study to assess the proficiency of health workers at preparing FP-DBS in primary healthcare clinics.
    • Real-Time PCR for the Evaluation of Treatment Response in Clinical Trials of Adult Chronic Chagas Disease: Usefulness of Serial Blood Sampling and qPCR Replicates

      Parrado, R; Ramirez, JC; de la Barra, A; Alonso-Vega, C; Juiz, N; Ortiz, L; Illanes, D; Torrico, F; Gascon, J; Alves, F; et al. (American Society for Microbiology, 2018-12-03)
      This work evaluated a serial blood sampling procedure to enhance the sensitivity of duplex real-time PCR (qPCR) for baseline detection and quantification of parasitic loads and post-treatment identification of failure in the context of clinical trials for treatment of chronic Chagas disease, namely DNDi-CH-E1224-001 (NCT01489228) and MSF-DNDi PCR sampling optimization study (NCT01678599). Patients from Cochabamba (N= 294), Tarija (N= 257), and Aiquile (N= 220) were enrolled. Three serial blood samples were collected at each time-point and qPCR triplicates were tested per sample. The first two samples were collected during the same day and the third one seven days later.A patient was considered PCR positive if at least one qPCR replicate was detectable. Cumulative results of multiple samples and qPCR replicates enhanced the proportion of pre-treatment sample positivity from 54.8 to 76.2%, 59.5 to 77.8%, and 73.5 to 90.2% in Cochabamba, Tarija, and Aiquile cohorts, respectively. This strategy increased the detection of treatment failure from 72.9 to 91.7%, 77.8 to 88.9%, and 42.9 to 69.1% for E1224 low, short, and high dosage regimens, respectively; and from 4.6 to 15.9% and 9.5 to 32.1% for the benznidazole arm in the DNDi-CH-E1224-001 and MSF-DNDi studies, respectively. The addition of the third blood sample and third qPCR replicate in patients with non-detectable PCR results in the first two samples, gave a small, non-statistically significant improvement in qPCR positivity. No change in clinical sensitivity was seen with a blood volume increase from 5 to 10 ml. The monitoring of patients treated with placebo in the DNDi-CH-E1224-001 trial revealed fluctuations in parasitic loads and occasional non-detectable results. In conclusion, serial sampling strategy enhanced PCR sensitivity to detecting treatment failure during follow-up and has the potential for improving recruitment capacity in Chagas disease trials, which require an initial positive qPCR result for patient admission.
    • Transmission of ebola viruses: what we know and what we do not know

      Osterholm, Michael T; Moore, Kristine A; Kelley, Nicholas S; Brosseau, Lisa M; Wong, Gary; Murphy, Frederick A; Peters, Clarence J; LeDuc, James W; Russell, Phillip K; Van Herp, Michel; et al. (American Society for Microbiology, 2015-02-19)
      Available evidence demonstrates that direct patient contact and contact with infectious body fluids are the primary modes for Ebola virus transmission, but this is based on a limited number of studies. Key areas requiring further study include (i) the role of aerosol transmission (either via large droplets or small particles in the vicinity of source patients), (ii) the role of environmental contamination and fomite transmission, (iii) the degree to which minimally or mildly ill persons transmit infection, (iv) how long clinically relevant infectiousness persists, (v) the role that "superspreading events" may play in driving transmission dynamics, (vi) whether strain differences or repeated serial passage in outbreak settings can impact virus transmission, and (vii) what role sylvatic or domestic animals could play in outbreak propagation, particularly during major epidemics such as the 2013-2015 West Africa situation. In this review, we address what we know and what we do not know about Ebola virus transmission. We also hypothesize that Ebola viruses have the potential to be respiratory pathogens with primary respiratory spread.
    • Use of filter paper as a transport medium for laboratory diagnosis of cholera under field conditions

      Page, Anne-Laure; Alberti, Kathryn P; Guénolé, Alain; Mondongue, Vital; Lonlas Mayele, Sylvaine; Guerin, Philippe J; Quilici, Marie-Laure; Epicentre, Paris, France; Institut Pasteur, Centre National de Reference des Vibrions et du Cholera, Unite des Bacteries Pathogenes Enteriques, Paris, France; Ministry of Health, Kinshasa, Democratic Republic of Congo; Medecins Sans Frontieres, Brussels, Belgium; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom (American Society for Microbiology, 2011-06-22)
      Confirmation of a cholera epidemic is based on bacteriological identification of the agent and requires the sending of samples to a culture laboratory, often in countries with limited resources. Comparison of the use of filter paper with the use of Cary-Blair reference medium for stool transport showed that this simple transport medium is appropriate for the recovery of Vibrio cholerae.