Total escape of SARS-CoV-2 from dual monoclonal antibody therapy in an immunocompromised patient.

Monoclonal antibodies (mAbs) directed against the spike of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are effective therapeutic options to combat infections in high-risk patients. Here, we report the adaptation of SARS-CoV-2 to the mAb cocktail REGN-COV in a kidney transplant patient with hypogammaglobulinemia. Following mAb treatment, the patient did not clear the infection. During viral persistence, SARS-CoV-2 acquired three novel spike mutations. Neutralization and mouse protection analyses demonstrate a complete viral escape from REGN-COV at the expense of ACE-2 binding. Final clearance of the virus occurred upon reduction of the immunosuppressive regimen and total IgG substitution. Serology suggests that the development of highly neutralizing IgM rather than IgG substitution aids clearance. Our findings emphasise that selection pressure by mAbs on SARS-CoV-2 can lead to development of escape variants in immunocompromised patients. Thus, modification of immunosuppressive therapy, if possible, might be preferable to control and clearance of the viral infection.

Acute Viral Gastrointestinal (GI) Infections in the Tropics-A Role for Cartridge-Based Multiplex PCR Panels?

Acute gastroenteritis (AGE) contributes to increased morbidity and mortality worldwide. In particular, children in resource-poor settings suffer from frequent episodes of diarrhea. A variety of pathogens, including bacteria, viruses, fungi, and protozoa, can cause AGE. Common viruses associated with AGE are norovirus, rotavirus, astrovirus, adenovirus, and sapovirus. Due to their similar clinical presentation, AGE pathogens cannot be distinguished on clinical grounds rendering the etiological diagnosis challenging. However, reliable diagnosis is essential for individual and public health reasons, e.g., to limit transmission, for appropriate antibiotic use, prognostic appreciation, and vaccination programs. Therefore, high-quality data derived by accurate diagnostics are important to improve global health. In Western industrialized countries, diagnosis relies on microbiological testing, including culture methods, microscopy, immunochromatography, and single-target molecular methods. Recently, multiplex PCR or syndromic panels have been introduced, which simultaneously analyze for multiple pathogens in a very short time. A further technological advancement is cartridge-based syndromic panels, which allow for near patient/point-of-care testing independently from a laboratory. In resource-poor tropical regions, however, laboratory diagnosis is rarely established, and there are little routine laboratory data on the epidemiology of viral AGE pathogens. Limiting factors for the implementation of syndromic panels are high costs, sophisticated equipment, and the need for trained personnel. In addition, pilot studies have shown a large number of viral (co-)detections among healthy controls, thus further challenging their clinical utilization. Hence, there are little evidence-based data on the impact of multiplex syndromic panels from resource-limited regions. Here, we aim to provide a brief overview of what is known about the use of syndromic panels for virus-associated AGE in tropical regions and to address future challenges.

High detection rate of Rickettsia africae in Amblyomma variegatum but low prevalence of anti-rickettsial antibodies in healthy pregnant women in Madagascar.

Tick-borne spotted fever group (SFG) rickettsioses are emerging infectious diseases in Sub-Saharan Africa. In Madagascar, the endemicity of tick-borne rickettsiae and their vectors has been incompletely studied. The first part of the present study was conducted in 2011 and 2012 to identify potential anthropophilic tick vectors for SFG rickettsiae on cattle from seven Malagasy regions, and to detect and characterize rickettsiae in these ticks. Amblyomma variegatum was the only anthropophilic tick species found on 262 cattle. Using a novel ompB-specific qPCR, screening for rickettsial DNA was performed on 111 A. variegatum ticks. Rickettsial DNA was detected in 96 of 111 ticks studied (86.5%). Rickettsia africae was identified as the only infecting rickettsia using phylogenetic analysis of ompA and ompB gene sequences and three variable intergenic spacers from 11 ticks. The second part of the study was a cross-sectional survey for antibodies against SFG rickettsiae in plasma samples taken from healthy, pregnant women at six locations in Madagascar, two at sea level and four between 450 and 1300m altitude. An indirect fluorescent antibody test with Rickettsia conorii as surrogate SFG rickettsial antigen was used. We found R. conorii-seropositives at all altitudes with prevalences between 0.5% and 3.1%. Our results suggest that A. variegatum ticks highly infected with R. africae are the most prevalent cattle-associated tick vectors for SFG rickettsiosis in Madagascar. Transmission of SFG rickettsiosis to humans occurs at different altitudes in Madagascar and should be considered as a relevant cause of febrile diseases.

Real-time PCR for detection of Strongyloides stercoralis in human stool samples from Côte d'Ivoire: diagnostic accuracy, inter-laboratory comparison and patterns of hookworm co-infection.

Human infections with the helminth species Strongyloides stercoralis encompass a wide clinical spectrum, ranging from asymptomatic carriage to life-threatening disease. The diagnosis of S. stercoralis is cumbersome and the sensitivity of conventional stool microscopy is low. New molecular tools have been developed to increase sensitivity. We compared the diagnostic accuracy of real-time PCR with microscopy for the detection of S. stercoralis and hookworm in human stool samples, and investigated the inter-laboratory agreement of S. stercoralis-specific real-time PCR in two European laboratories. Stool specimens from 256 randomly selected individuals in rural Côte d'Ivoire were examined using three microscopic techniques (i.e. Kato-Katz, Koga agar plate (KAP) and Baermann (BM)). Additionally, ethanol-fixed stool aliquots were subjected to molecular diagnosis. The prevalence of S. stercoralis and hookworm infection was 21.9% and 52.0%, respectively, whilst co-infections were detected in 35 (13.7%) participants. The diagnostic agreement between real-time PCR and microscopy was excellent when both KAP and BM tested positive for S. stercoralis, but was considerably lower when only one microscopic technique was positive. The sensitivity of KAP, BM and real-time PCR for detection of S. stercoralis as compared to a combination of all diagnostic techniques was 21.4%, 37.5% and 76.8%, respectively. The inter-laboratory agreement of S. stercoralis-specific PCR was substantial (κ=0.63, p<0.001). We conclude that a combination of real-time PCR and stool microscopy shows high accuracy for S. stercoralis diagnosis. Besides high sensitivity, PCR may also enhance specificity by reducing microscopic misdiagnosis of morphologically similar helminth larvae (i.e. hookworm and S. stercoralis) in settings where both helminth species co-exist.

Safety and immunogenicity of a candidate bioconjugate vaccine against Shigella dysenteriae type 1 administered to healthy adults: A single blind, partially randomized Phase I study.

BACKGROUND: Shigellae cause severe disease in endemic countries, especially in children. Several efficacy trials have been conducted with candidate vaccines against Shigellae, but the lack of protection, the safety concerns, or manufacturing challenges hindered successful market approval. Conjugated vaccines have been shown to be safe and effective for different pathogens (i.e., Neisseria meningitidis, Shigella pneumonia, Haemophilus influenzae). The bio-conjugation technology, exploited here for the Shigella dysenteriae candidate vaccine, offers a novel and potentially simpler way to develop and produce vaccines against one of the major causes of morbidity and mortality in developing countries. METHODS: A novel S. dysenteriae bioconjugate vaccine (GVXN SD133) made of the polysaccharide component of the Shigella O1 lipopolysaccharide, conjugated to the exotoxin protein A of Pseudomonas aeruginosa (EPA), was evaluated for immunogenicity and safety in healthy adults in a single blind, partially randomized Phase I study. Forty subjects (10 in each dose group; 2 µg or 10 µg with or without aluminium adjuvant) received two injections 60 days apart and were followed-up for 150 days. RESULTS: Both doses and formulations were well tolerated; the safety and reactogenicity profiles were consistent with that of other conjugated vaccines, adjuvanted or not, independent of the dose and the number of injections. The GVXN SD133 vaccine elicited statistically significant O1 specific humoral responses at all time points in all vaccination groups. Between-group comparisons did not show statistically significant differences in geometric mean titers of immunoglobulin G and A at any post-vaccination time point. CONCLUSIONS: This study demonstrated that the GVXN SD133 vaccine has a satisfactory safety profile. It elicited a significant humoral response to Shigella O1 polysaccharides at all doses tested. The protein carrier also elicited functional antibodies, showing the technology's advantages in preserving both sugar and conjugated protein epitopes. This trial is registered at ClinicalTrials.gov (NCT01069471).

High prevalence of large trematode eggs in schoolchildren in Cambodia.

Large trematode eggs (LTE) resembling Fasciola spp. eggs were reportedly found in the stools of schoolchildren in Kandal province, Cambodia. This study aimed to assess the prevalence of LTE in the stools of children attending the affected school, identify potential risk factors for infection and ascertain the trematode species. We performed a cross-sectional study involving an in-depth questionnaire administered to schoolchildren at the affected school, and examined cattle droppings in the surrounding area and the livers of slaughtered cattle. Three stool samples were examined per child, using Kato-Katz and formalin-ether concentration techniques. In addition, blood serum enzyme-linked immunosorbent assay (ELISA) and coprological polymerase chain reaction (PCR) was conducted for species clarification. Cattle droppings were examined by cup sedimentation and coprological ELISA. LTE were observed in the stools of 106 schoolchildren (46.5%). Two blood serum samples from schoolchildren were positive for Fasciola hepatica in a first ELISA but were negative in a confirmation immunofluorescence antibody test. Out of 221 PCR samples, only one tested positive for Fasciola spp. and none for Fasciolopsis buski. The consumption of raw aquatic plants (odds ratio (OR)=3.3) and fermented fish sauce (OR=2.1) were significantly associated with LTE in the stool. Fasciola spp. flukes were observed in 18.3% of 191 cattle livers. The prevalence of fascioliasis in cattle droppings was 88.8%. The low prevalence of schoolchildren that tested positive for Fasciola spp. with specific molecular diagnostics and who had no diagnostic evidence of F. buski strongly indicates that the majority of microscopically observed LTE are from Echinostoma spp. Fasciola spp. transmission from cattle to human is possible and public health services need to be alerted accordingly.

Evaluation of real-time PCR for Strongyloides stercoralis and hookworm as diagnostic tool in asymptomatic schoolchildren in Cambodia.

Diagnosis of soil-transmitted helminths such as Strongyloides stercoralis and hookworms (Ancylostoma duodenale and Necator americanus) is challenging due to irregular larval and egg output in infected individuals and insensitive conventional diagnostic procedures. Sensitive novel real-time PCR assays have been developed. Our study aimed to evaluate the real-time PCR assays as a diagnostic tool for detection of Strongyloides spp. and hookworms in a random stool sample of 218 asymptomatic schoolchildren in Cambodia. Overall prevalence of 17.4% (38/218) and 34.9% (76/218) were determined by real-time PCR for S. stercoralis and hookworms, respectively. Sensitivity and specificity of S. stercoralis specific real-time PCR as compared to the combination of Baermann/Koga Agar as gold standard were 88.9% and 92.7%, respectively. For hookworm specific real-time PCR a sensitivity of 78.9% and specificity of 78.9% were calculated. Co-infections were detectable by PCR in 12.8% (28/218) of individuals. S. stercoralis real-time PCR applied in asymptomatic cases showed a lower sensitivity compared to studies undertaken with symptomatic patients with the same molecular tool, yet it proved to be a valid supplement in the diagnosis of STH infection in Cambodia.

Novel real-time PCR for the universal detection of Strongyloides species.

Strongyloidiasis is a neglected disease that is prevalent mainly in tropical and subtropical regions. It is caused by intestinal nematodes of the genus Strongyloides. Due to the rise in worldwide travel, infections are increasingly encountered in non-endemic regions. Diagnosis is hampered by insensitive and laborious detection methods. A universal Strongyloides species real-time PCR was developed with an internal competitive control system. The 95% limit of detection as determined by probit analysis was one larva per PCR equivalent to 100 larvae per 200 mg stool. The assay proved to be 100% specific as assessed using a panel of parasites and bacteria and thus might be useful in the diagnostic setting as well as for Strongyloides research.

Diagnosing schistosomiasis by detection of cell-free parasite DNA in human plasma.

INTRODUCTION: Schistosomiasis (bilharzia), one of the most relevant parasitoses of humans, is confirmed by microscopic detection of eggs in stool, urine, or organ biopsies. The sensitivity of these procedures is variable due to fluctuation of egg shedding. Serological tests on the other hand do not distinguish between active and past disease. In patients with acute disease (Katayama syndrome), both serology and direct detection may produce false negative results. To overcome these obstacles, we developed a novel diagnostic strategy, following the rationale that Schistosoma DNA may be liberated as a result of parasite turnover and reach the blood. Cell-free parasite DNA (CFPD) was detected in plasma by PCR. METHODOLOGY/PRINCIPAL FINDINGS: Real-time PCR with internal control was developed and optimized for detection of CFPD in human plasma. Distribution was studied in a mouse model for Schistosoma replication and elimination, as well as in human patients seen before and after treatment. CFPD was detectable in mouse plasma, and its concentration correlated with the course of anti-Schistosoma treatment. Humans with chronic disease and eggs in stool or urine (n = 14) showed a 100% rate of CFPD detection. CFPD was also detected in all (n = 8) patients with Katayama syndrome. Patients in whom no viable eggs could be detected and who had been treated for schistomiasis in the past (n = 30) showed lower detection rates (33.3%) and significantly lower CFPD concentrations. The duration from treatment to total elimination of CFPD from plasma was projected to exceed one year. CONCLUSIONS/SIGNIFICANCE: PCR for detection of CFPD in human plasma may provide a new laboratory tool for diagnosing schistosomiasis in all phases of clinical disease, including the capacity to rule out Katayama syndrome and active disease. Further studies are needed to confirm the clinical usefulness of CFPD quantification in therapy monitoring.

Orientia tsutsugamushi bacteremia and cytokine levels in Vietnamese scrub typhus patients.

Scrub typhus, caused by the intracellular bacterium Orientia tsutsugamushi, is a major cause of febrile illness in the Asia/Pacific region. Here, we implemented a novel real-time PCR and determined the relation of DNA target gene concentration with serum cytokine levels. The limit of detection of the novel real-time PCR was 1,062 DNA copies per ml of EDTA whole blood. Specificity was excellent as determined on a panel of blood- and skin-borne bacteria, including Rickettsia spp. as well as healthy Vietnamese blood donors. Bacterial DNA concentrations after 9 to 12 days from symptoms onset were significantly higher than in earlier or later periods (P<0.05). Significantly higher concentrations of gamma interferon (IFN-gamma) and interleukin-10 (IL-10) occurred during the acute phase of disease (<10 days from onset) as opposed to the convalescent phase (P<0.05). No significant differences were observed between the acute and the convalescent phases for tumor necrosis factor alpha (TNF-alpha) and IL-1beta concentrations. Regression analysis of DNA concentrations and cytokine levels identified a significant positive relationship for IL-10 (P<0.0182) but not for IFN-gamma, TNF-alpha, and IL-1beta. In conclusion, proinflammatory cytokines and IL-10 were differentially related to human bacteremia. They may thus be induced by different constituents of O. tsutsugamushi. As a future prospect in a clinical diagnostic laboratory, quantitative real-time PCR may serve as a reliable tool to monitor therapy and to detect treatment failure.

High throughput detection of Coxiella burnetii by real-time PCR with internal control system and automated DNA preparation.

BACKGROUND: Coxiella burnetii is the causative agent of Q-fever, a widespread zoonosis. Due to its high environmental stability and infectivity it is regarded as a category B biological weapon agent. In domestic animals infection remains either asymptomatic or presents as infertility or abortion. Clinical presentation in humans can range from mild flu-like illness to acute pneumonia and hepatitis. Endocarditis represents the most common form of chronic Q-fever. In humans serology is the gold standard for diagnosis but is inadequate for early case detection. In order to serve as a diagnostic tool in an eventual biological weapon attack or in local epidemics we developed a real-time 5'nuclease based PCR assay with an internal control system. To facilitate high-throughput an automated extraction procedure was evaluated. RESULTS: To determine the minimum number of copies that are detectable at 95% chance probit analysis was used. Limit of detection in blood was 2,881 copies/ml [95%CI, 2,188-4,745 copies/ml] with a manual extraction procedure and 4,235 copies/ml [95%CI, 3,143-7,428 copies/ml] with a fully automated extraction procedure, respectively. To demonstrate clinical application a total of 72 specimens of animal origin were compared with respect to manual and automated extraction. A strong correlation between both methods was observed rendering both methods suitable. Testing of 247 follow up specimens of animal origin from a local Q-fever epidemic rendered real-time PCR more sensitive than conventional PCR. CONCLUSION: A sensitive and thoroughly evaluated real-time PCR was established. Its high-throughput mode may show a useful approach to rapidly screen samples in local outbreaks for other organisms relevant for humans or animals. Compared to a conventional PCR assay sensitivity of real-time PCR was higher after testing samples from a local Q-fever outbreak.

Travel-associated Coxiella burnetii infections: three cases of Q fever with different clinical manifestation.

BACKGROUND: Certain activities expose travellers to Coxiella burnetii, the causative agent of acute human Q fever. Awareness of Q fever must be improved, also as a potential imported disease, but delayed seroconversion and serological cross-reactivity complicate the diagnosis. Granulomatous inflammation of liver and bone marrow can be typical histopathological findings. CASE PRESENTATIONS: We present three imported cases of Q fever with different clinical presentations, in which the travel history identified the sources of infection. CONCLUSIONS: Q fever should be suspected in any imported febrile disease of unknown origin. Clinical manifestations are variable and repeated serological testing is mandatory. In some cases diagnostic biopsies might help to establish early diagnosis.

High throughput screening for spores and vegetative forms of pathogenic B. anthracis by an internally controlled real-time PCR assay with automated DNA preparation.

Human infections with Bacillus anthracis have become rare but in cases of intentional release, masses of samples would have to be expected. Current PCR assays for anthrax are appropriate for use in single cases, but they have not been formulated for high throughput screening. This article describes a high throughput real-time PCR for anthrax, including automated sample preparation without the need for pre-culturing of samples. The assay detects single copies of target gene. An internal control monitors the whole assay including sample preparation. The limit of detection in blood was 1,066 (95%CI, 741-1,739) copies/ml, corresponding to 4.4-32.3 organisms/ml. Using spore preparations, 20 colony-forming units (CFU) per sample could be detected reliably (0.8 CFU per PCR). The extraction procedures depleted viable spores from solution by factors of 10,000 (automated procedure) and >100,000 (conventional column procedure). One hundred and ten clinical and environmental specimens were retested, 50 of them sampled during a period of heightened anthrax awareness in 2001. A widely used assay yielded two false positive results (cross-reaction with B. cereus), while the new assay tested all samples negative. The internal control operated stable in all clinical samples. The assay is capable of testing for anthrax in the high throughput mode.

Host range of 14 mycobacteriophages in Mycobacterium ulcerans and seven other mycobacteria including Mycobacterium tuberculosis--application for identification and susceptibility testing.

The host range of well-characterized mycobacteriophages, such as D29 and TM4, has been determined, together with that of more recently isolated mycobacteriophages, in Mycobacterium ulcerans, Mycobacterium tuberculosis, Mycobacterium bovis BCG, Mycobacterium avium, Mycobacterium marinum, Mycobacterium scrofulaceum, Mycobacterium fortuitum and Mycobacterium chelonae. Here, a set of virulent phages for M. ulcerans, a pathogen with a dramatic increase of incidence over the last decade, is demonstrated. In this work, a mycobacteriophage replication assay was adapted for the identification and rifampicin-susceptibility testing of M. ulcerans. Mycobacteriophages have generated a number of useful tools and enabled insights into mycobacterial genetics. With regard to the neglected pathogen M. ulcerans, the findings presented in this work allow the application of a large range of phage-based vectors and markers. The potential of phage therapy can now be evaluated for this extracellular pathogen.

Evaluation of advanced reverse transcription-PCR assays and an alternative PCR target region for detection of severe acute respiratory syndrome-associated coronavirus.

First-generation reverse transcription-PCR (RT-PCR) assays for severe acute respiratory syndrome-associated coronavirus (SARS-CoV) gave false-negative results in a considerable fraction of patients. In the present study, we evaluated two second-generation, replicase (R) gene-based, real-time RT-PCR test kits--the RealArt HPA coronavirus LC kit (Artus, Hamburg, Germany) and the LightCycler SARS-CoV quantification kit (Roche, Penzberg, Germany)--and a real-time RT-PCR assay for the nucleocapsid (N) gene. Detecting the N-gene RNA might be advantageous due to its high abundance in cells. The kits achieved sensitivities of 70.8% (Artus) and 67.1% (Roche) in 66 specimens from patients with confirmed SARS (samples primarily from the upper and lower respiratory tract and stool). The sensitivity of the N-gene assay was 74.2%. The differences in all of the sensitivities were not statistically significant (P = 0.680 [analysis of variance]). Culture cells initially contained five times more N- than R-gene RNA, but the respective levels converged during 4 days of virus replication. In clinical samples the median concentrations of R- and N-gene RNA, respectively, were 1.2 x 10(6) and 2.8 x 10(6) copies/ml (sputum and endotracheal aspirates), 4.3 x 10(4) and 5.5 x 10(4) copies/ml (stool), and 5.5 x 10(2) and 5.2 x 10(2) copies/sample (throat swabs and saliva). Differences between the samples types were significant but not between the types of target RNA. All (n = 12) samples from the lower respiratory tract tested positive in all tests. In conclusion, the novel assays are more sensitive than the first-generation tests, but they still do not allow a comprehensive ruling out of SARS. Methods for the routine sampling of sputum without infection risk are needed to improve SARS RT-PCR.

Rapid detection and differentiation of human pathogenic orthopox viruses by a fluorescence resonance energy transfer real-time PCR assay.

BACKGROUND: The orthopox viruses that are pathogenic for humans include variola major virus (VAR), monkeypox virus (MPV), cowpox virus (CPV), and to a lesser extent, camelpox virus (CML) and vaccinia virus (VAC). PCR is a powerful tool to detect and differentiate orthopox viruses, and real-time PCR has the further advantages of rapid turnaround time, low risk of contamination, capability of strain differentiation, and use of multiplexed probes. METHODS: We used real-time PCR with fluorescence resonance energy transfer technology to simultaneously detect and differentiate VAR, MPV, CPV/VAC, and CML. An internal control generated by cloning and mutating the PCR target gene facilitated monitoring of PCR inhibition in each individual test reaction. RESULTS: Strain differentiation results showed little interassay variability (CV, 0.4-0.6%), and the test was 100-fold more sensitive than virus culture on Vero cells. Low copy numbers of DNA could be detected with > or =95% probability (235-849 genome copies/mL of plasma). CONCLUSIONS: The real-time PCR assay can detect and differentiate human pathogenic orthopox viruses. The use of an internal control qualifies the assay for high sample throughput, as is likely to be needed in situations of suspected acts of biological terrorism, e.g., use of VAR.

Detection and quantification of Mycobacterium leprae in tissue samples by real-time PCR.

Real-time PCR technology has improved molecular diagnostics of many pathogens, but no such test is available for Mycobacterium leprae. In this report we describe the establishment and the pre-clinical evaluation of such an assay. The test achieved a theoretical analytical sensitivity limit of 194 M. leprae cells per skin biopsy specimen and facilitated quantification of mycobacteria in tissue over a range of 54-54,000,000 cells per sample. In punch skin biopsies from 39 untreated Ugandan patients with newly diagnosed leprosy, the clinical diagnosis could be confirmed in 88.9% of multibacillary and 33.3% of paucibacillary (microscopically negative) patients. Real-time detection thus did not increase the clinical sensitivity of PCR as compared to conventional protocols, in spite of its evidently high analytical sensitivity. On the other hand, as still no culture system exists for M. leprae, the assay appears to be a robust tool for detection of the bacterium in selected clinical situations, as well as for quantitation in experimental settings.