Polymerase Chain Reaction Prevalence Research Articles

The Impact of Emerging Plasmodium knowlesi on Accurate Diagnosis by Light Microscopy: A Systematic Review and Modeling Analysis

The five major Plasmodium spp. that cause human malaria appear similar under light microscopy, which raises the possibility that misdiagnosis could routinely occur in clinical settings. Assessing the extent of misdiagnosis is of particular importance for monitoring P. knowlesi, which cocirculates with the other Plasmodium spp. We performed a systematic review and meta-analysis of studies comparing the performance of microscopy and polymerase chain reaction (PCR) for diagnosing malaria in settings with co-circulation of the five Plasmodium spp. We assessed the extent to which co-circulation of Plasmodium parasites affects diagnostic outcomes. We fit a Bayesian hierarchical latent class model to estimate variation in microscopy sensitivity and specificity measured against PCR as the gold standard. Mean sensitivity of microscopy was low, yet highly variable across Plasmodium spp., ranging from 65.7% (95% confidence interval: 48.1-80.3%) for P. falciparum to 0.525% (95% confidence interval 0.0210-3.11%) for P. ovale. Observed PCR prevalence was positively correlated with estimated microscopic sensitivity and negatively correlated with estimated microscopic specificity, though the strength of the associations varied by species. Our analysis suggests that cocirculation of Plasmodium spp. undermines the accuracy of microscopy. Sensitivity was considerably lower for P. knowlesi, P. malariae, and P. ovale. The negative association between specificity and prevalence imply that less frequently encountered species may be misdiagnosed as more frequently encountered species. Together, these results suggest that the burden of P. knowlesi, P. malariae, and P. ovale may be underappreciated in a clinical setting.

SARS-CoV-2 prevalence in an asymptomatic cancer cohort - results and consequences for clinical routine

BackgroundStarting in December 2019, the current pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) confronts the world with an unprecedented challenge. With no vaccine or drug being currently available to control the pandemic spread, prevention and PCR (Polymerase chain reaction) testing becomes a crucial pillar of medical systems. Aim of the present study was to report on the first results of the measures taken in a large German Department of Radiation Oncology, including PCR testing of asymptomatic cancer patients.MethodsPandemic-adapted hygiene regulations and prevention measures for patients and staff were implemented. A visiting ban on both wards was implemented from the beginning and medical staff and patients were required to wear face masks at all times. The waiting rooms were rearranged to ensure distance between patients of at least 1.5 m. Clinical follow up was mainly done by telephone and all patients had to complete a questionnaire regarding symptoms and contacts with COVID-19 patients before entering our department. Educational documents were created for patients to raise awareness of symptoms and avoidance strategies for interactions with other people. Indications for therapy and fractionation schemes were adapted when possible. In a subsequent step, all new asymptomatic patients were tested via nasopharyngeal swab at our screening station shortly before their simulation CT.ResultsAll these measures and implementations have been well accepted semiquantitatively measured by the consent received from patients and staff. Regarding the PCR testing, only 1 out of 139 asymptomatic patients of our cohort so far tested positive for SARS-CoV-2, reflecting a prevalence of 0.72% in this cancer patient population. Up to this point no staff members was tested positive. The start of the treatment for the PCR-positive patient was deferred for 2 weeks.ConclusionDue to the pandemic-adapted implementations, our department seems well prepared during this crisis. The initial screening helps to identify asymptomatic COVID-19 patients in order to protect other patients and our staff from infection and the observed PCR prevalence is in line with comparable studies. A regular PCR testing (e.g. twice a week) of all patients and staff would in principle be desirable but is limited due to testing capacities at present.

Prevalence of Plasmodium spp. in the Amazonian Border Context (French Guiana-Brazil): Associated Factors and Spatial Distribution.

.To implement future malaria elimination strategies in French Guiana, a characterization of the infectious reservoir is recommended. A cross-sectional survey was conducted between October and December 2017 in the French Guianese municipality of St Georges de l’Oyapock, located along the Brazilian border. The prevalence of Plasmodium spp. was determined using a rapid diagnostic test (RDT) and a polymerase chain reaction (PCR). Demographic, house locations, medical history, and biological data were analyzed. Factors associated with Plasmodium spp. carriage were analyzed using logistic regression, and the carriage localization was investigated through spatial cluster analysis. Of the 1,501 samples analyzed with PCR, positive results totaled 90 and 10 for Plasmodium vivax and Plasmodium falciparum, respectively. The general PCR prevalence was 6.6% [5.3–7.9], among which 74% were asymptomatic. Only 13/1,549 were positive by RDT. In multivariate analysis, participants older than 15 years, living in a remote neighborhood, with a prior history of malaria, anemia, and thrombocytopenia were associated with an increased odds of Plasmodium spp. carriage. High-risk clusters of P. vivax carriage were detected in the most remote neighborhoods on the village outskirts and two small foci in the village center. We also detected a hot spot for both P. vivax and P. falciparum symptomatic carriers in the northwestern part of the village. The present study confirms a wide-scale presence of asymptomatic P. falciparum and P. vivax carriers in this area. Although they were more often located in remote areas, their geographic distribution was spatially heterogeneous and complex.

Unbiased Assessment of Abundance of Rhipicephalus sanguineus sensu lato Ticks, Canine Exposure to Spotted Fever Group Rickettsia, and Risk Factors in Mexicali, México.

An epidemic of Rocky Mountain spotted fever (RMSF) is ongoing in Mexicali, México. We visited 100 neighborhoods with diagnosed human cases and 100 control neighborhoods to evaluate knowledge of the epidemic; obtain data on the spatial distribution of dogs, canine seroprevalence and active infection, tick infestations, and presence of rickettsial DNA in ticks; and evaluate risk factors for human cases, seropositivity, and tick infestation within an unbiased study design. The majority (80%) of residents had heard of RMSF, but only 48% used acaricides in the home or on dogs. Case neighborhoods and those with high canine seroprevalence tended to be on the city periphery or in the agricultural valley. No dogs were polymerase chain reaction (PCR) positive for Rickettsia rickettsii, and the overall seroprevalence was 65% (titers from 64 to 1,024). PCR prevalence in ticks was 0.70%, confirmed by DNA sequencing as R. rickettsii; neighborhood prevalence ranged from 0.7% to 6.1%. Twelve percent of dogs had high tick burdens, and all ticks were Rhipicephalus sanguineus. Epidemiologically significant risk factors were ground covering for a neighborhood having a human case; dogs having poor body condition and weighing < 10 kg for canine seropositivity; dogs living at the home for the number of ticks in the environment; and being near canals, having trash on the patio, and a dog being thin for tick burdens on dogs. A One Health approach is crucial to understanding RMSF and brown dog ticks.

Malaria hotspots defined by clinical malaria, asymptomatic carriage, PCR and vector numbers in a low transmission area on the Kenyan Coast.

BackgroundTargeted malaria control interventions are expected to be cost-effective. Clinical, parasitological and serological markers of malaria transmission have been used to detect malaria transmission hotspots, but few studies have examined the relationship between the different potential markers in low transmission areas. The present study reports on the relationships between clinical, parasitological, serological and entomological markers of malaria transmission in an area of low transmission intensity in Coastal Kenya.MethodsLongitudinal data collected from 831 children aged 5–17 months, cross-sectional survey data from 800 older children and adults, and entomological survey data collected in Ganze on the Kenyan Coast were used in the present study. The spatial scan statistic test used to detect malaria transmission hotspots was based on incidence of clinical malaria episodes, prevalence of asymptomatic asexual parasites carriage detected by microscopy and polymerase chain reaction (PCR), seroprevalence of antibodies to two Plasmodium falciparum merozoite antigens (AMA1 and MSP1-19) and densities of Anopheles mosquitoes in CDC light-trap catches.ResultsThere was considerable overlapping of hotspots by these different markers, but only weak to moderate correlation between parasitological and serological markers. PCR prevalence and seroprevalence of antibodies to AMA1 or MSP1-19 appeared to be more sensitive markers of hotspots at very low transmission intensity.ConclusionThese findings may support the choice of either serology or PCR as markers in the detection of malaria transmission hotspots for targeted interventions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12936-016-1260-3) contains supplementary material, which is available to authorized users.

PCR Prevalence of Ranavirus in Free-Ranging Eastern Box Turtles (Terrapene carolina carolina) at Rehabilitation Centers in Three Southeastern US States

Ranaviruses (genus Ranavirus) have been observed in disease epidemics and mass mortality events in free-ranging amphibian, turtle, and tortoise populations worldwide. Infection is highly fatal in turtles, and the potential impact on endangered populations could be devastating. Our objectives were to determine the prevalence of ranavirus DNA in blood and oral swabs, report associated clinical signs of infection, and determine spatial distribution of infected turtles. Blood and oral swabs were taken from 140 eastern box turtles (Terrapene carolina carolina) that were presented to the wildlife centers at the University of Tennessee (UT; n=39), Wildlife Center of Virginia (WCV; n=34), and North Carolina State University (NCSU; n=36), as well as a free-ranging nonrehabilitation population near Oak Ridge, Tennessee (OR; n=39) March-November 2007. Samples were evaluated for ranavirus infection using polymerase chain reaction (PCR) targeting a conserved portion of the major capsid protein. Two turtles, one from UT and one from NCSU, had evidence of ranavirus infection; sequences of PCR products were 100% homologous to Frog Virus 3. Prevalence of ranavirus DNA in blood was 3, 0, 3, and 0% for UT, WCV, NCSU, and OR, respectively. Prevalence in oral swab samples was 3, 0, and 0% for UT, WCV, and NCSU, respectively. Wildlife centers may be useful in detection of Ranavirus infection and may serve as a useful early monitoring point for regional disease outbreaks.

Submicroscopic Infection inPlasmodium falciparum–Endemic Populations: A Systematic Review and Meta‐Analysis

Light microscopy examination of blood slides is the main method of detecting malaria infection; however, it has limited sensitivity. Low-density infections are most likely to be missed, but they contribute to the infectious reservoir. Quantifying these submicroscopic infections is therefore key to understanding transmission dynamics and successfully reducing parasite transmission. We conducted a systematic review of endemic population surveys in which P. falciparum prevalence had been measured by both microscopy and a more-sensitive polymerase chain reaction (PCR)-based technique. The combined microscopy:PCR prevalence ratio was estimated by random-effects meta-analysis, and the effect of covariates was determined by meta-regression. Seventy-two pairs of prevalence measurements were included in the study. The prevalence of infection measured by microscopy was, on average, 50.8% (95% confidence interval [CI], 45.2%-57.1%) of that measured by PCR. For gametocyte-specific detection, the microscopy prevalence was, on average, 8.7% (95% CI, 2.8%-26.6%) of the prevalence measured by PCR. A significantly higher percentage of total infections was detected by microscopy in areas of high, compared with low, transmission (74.5% when the prevalence determined by PCR was >75% versus 12.0% when the prevalence determined by PCR was <10%). Microscopy can miss a substantial proportion of P. falciparum infections in surveys of endemic populations, especially in areas with low transmission of infection. The extent of the submicroscopic reservoir needs to be taken into account for effective surveillance and control.

Chlamydophila species in dairy farms: Polymerase chain reaction prevalence, disease association, and risk factors identified in a cross-sectional study in western Germany

The prevalence of Chlamydophila spp. was determined in a cross-sectional study carried out in 2007 using 100 randomly selected dairy herds in the western part of Germany. Ten dairy cows per herd were sampled in herds with fewer than 100 cows; in bigger herds, 10% of the cows were sampled. For the detection of Chlamydophila spp., vaginal swabs from early lactating dairy cows were analyzed using an established highly sensitive genus-specific real-time PCR. In consideration of the discontinuous shedding of the pathogen, a herd was classified as positive if at least 1 animal per herd tested positive for Chlamydophila spp. By use of these methods and definitions, 61% of the dairy herds and 13.5% of the cows were detected as PCR-positive for Chlamydophila spp., which is indicative for ongoing infections. To compare herd health and herd performance between herds testing positive or negative and to identify risk factors for the presence of Chlamydophila spp., a questionnaire was designed to evaluate farm characteristics and management practices. In addition, the performance recordings of the state dairy recording organization were used for these purposes. Milk yield, number of lactations, and calving to first-service interval were lower in herds testing positive for Chlamydophila spp. compared with negative herds. For all these variables, there was no interaction between Chlamydophila status and lactation number. Replacement of animals from outside sources, use of breeding bulls, lack of separate calving pens, and low scores for cleanliness of beddings, walkways, and cows were identified as the main risk factors for Chlamydophila spp.

Reptile Infection with Anaplasma phagocytophilum, the Causative Agent of Granulocytic Anaplasmosis

Granulocytic anaplasmosis (GA) is a potentially fatal tick-borne rickettsial disease that occurs sporadically in the far western United States. We evaluated the prevalence of Anaplasma phagocytophilum in multiple species of lizards and snakes from enzootic sites in northern California, described the infestation prevalence of its tick vector Ixodes pacificus on reptiles, and conducted an experimental challenge of western fence lizards (Sceloporus occidentalis) and Pacific gopher snakes (Pituophis catenifer) with A. phagocytophilum delivered via needle inoculation or tick bite. Both serologically and polymerase-chain reaction (PCR)-positive lizards (seroprevalence = 10.8%, PCR prevalence = 10.2%) and snakes (seroprevalence = 5.8%, PCR prevalence = 11.7%) were detected among wild-caught animals. A DNA sequence of the A. phagocytophilum groESL gene from a PCR-positive snake was 100% homologous to that of the human-derived A. phagocytophilum. Experimental attempts to infect naïve animals were unsuccessful for snakes (n = 2), but 1 of 12 lizards became infected for 1 wk only by tick bite. Xenodiagnostic I. pacificus larvae that fed on a PCR-positive lizard did not acquire or transmit rickettsiae. Our findings suggest that lizards and snakes are exposed to A. phagocytophilum by infected ticks, but that they do not serve as primary reservoir hosts of this rickettsia.

Evaluation of Squirrels (Rodentia: Sciuridae) as Ecologically Significant Hosts for &lt;I&gt;Anaplasma phagocytophilum&lt;/I&gt; in California

Granulocytic anaplasmosis (GA), caused by Anaplasma phagocytophilum, is a potentially fatal, emerging rickettsial disease of humans, domestic animals, and wildlife. The purpose of this study was to determine whether sciurids from multiple areas of northern California were infested with ticks or exposed to or infected with A. phagocytophilum using polymerase chain reaction (PCR) and indirect-fluorescent antibody (IFA) serology. Sciurids of nine different tree- and ground-dwelling species were assessed: arboreal squirrels (western and eastern gray squirrels, Sciurus griseus and S. carolinensis, and Douglas squirrels, Tamiasciurus douglasii) but not northern flying squirrels (Glaucomys sabrinus) had greater evidence of exposure and current infection than did semiarboreal or ground dwelling sciurids (California ground squirrels, Spermophilus beecheyi, and chipmunks, Tamias spp.). Western gray squirrels had the most extensive exposure (70.7% seroprevalence and 12.1% PCR prevalence). Positive squirrels were identified in all regions where squirrels were collected. A logistic regression identified being a western gray squirrel (OR = 20.5, P = 2.95 X 10(-8)) and from the north coastal region of California (OR = 9.052, P = 1.41 X 10(-6)) as having the highest risk of exposure to A. phagocytophilum. Five of nine sciurid species had evidence of infestation with Ixodes pacificus or I. spinipalpis that could vector A. phagocytophilum. Extensive exposure from multiple areas suggests sciurids may be important in the maintenance of GA in California and indicates that studies of reservoir competence of these species are warranted.

PCR detection and prevalence of α-, β-, β2-, ε-, ι- and enterotoxin genes in Clostridium perfringens isolated from lambs with clostridial dysentery

Clostridium perfringens isolated from lambs with dysentery ( n=117) were analysed by a DNA amplification technique, the polymerase chain reaction (PCR), in order to determine the prevalence of the α-, β-, β2-, ε-, ι- and enterotoxin genes. The most prevalent toxin type of C. perfringens found was type B, containing the α-, β-, and ε-toxin genes, representing 46% of the cases with clostridial dysentery. C. perfringens type C containing the α-, and β-toxin genes was isolated in 20% and type D, which is characterized by the α- and ε-toxin genes, was isolated in 28% of all isolates. The recently discovered, not yet assigned β2-toxigenic type of C. perfringens was represented in 6% of all isolates. No C. perfringens type A containing the α-toxin alone and no type E, which harbours the ADP-ribosylating ι-toxin, were found in the diseased animals. None of the samples contained the enterotoxin gene. Only one type of C. perfringens was found in a given herd, revealing the epidemiological use of PCR toxin gene typing of C. perfringens. The animals originated from 79 different herds with sizes ranging from 30 to 250 animals, bred in the area of northern Greece.

Frequent umbilical cord-blood and maternal-blood infections with Plasmodium falciparum, P. malariae, and P. ovale in Kenya.

The prevalence of malaria infection in 102 paired maternal-blood and umbilical cord-blood samples was assessed by microscopy and polymerase chain reaction (PCR) in a holoendemic area in Kenya. Plasmodium falciparum single-species infection was detected in maternal peripheral blood (3.4%), whereas microscopy indicated that no Plasmodium species were in cord blood. In contrast, maternal-blood samples showed a PCR prevalence of 48% for P. falciparum, 25% for P. malariae, and 24% for P. ovale, and cord-blood samples showed a PCR prevalence of 32%, 23%, and 21%, respectively. Although mothers with mixed-species infections were more likely to have offspring infected with mixed species, the specific malaria species were discordant in paired maternal- and cord-blood samples. Triple-species infections were observed in 11 cord- and maternal-blood samples at a 5.5-fold greater frequency than expected. These findings indicate that Plasmodium species infections in cord blood are common, occur at lower densities, and may be acquired before parturition.

Ehrlichia spp. in cervids from California.

Blood samples from six mule deer (Odocoileus hemionus hemionus), 15 black-tailed deer (O. hemionus columbianus), and 29 elk (Cervus elaphus nannodes) were assayed for human monocytic and human granulocytic ehrlichiosis (HGE) by polymerase chain reaction (PCR), DNA sequencing, and serology to determine whether or not cervids are involved in the maintenance of these potential human pathogens in California (USA). The deer were sampled in August to October 1992-95. The 29 tule elk from Point Reyes National Seashore were sampled in August 1997. All deer were seronegative for antibodies to HGE/Ehrlichia equi, while the E. equi seroprevalence among elk was 17%. The 16S rDNA PCR prevalence in deer was 38% (in mule deer and black-tailed deer) for Ehrlichia-like sp. of white-tailed deer, 5% (one black-tailed deer only) for E. equi, and 0% for E. chaffeensis. The PCR prevalence in elk was 0% for Ehrlichia-like sp. of white-tailed deer, 31% for E. equi, and 0% for E. chaffeensis. The E. equi from two positive elk samples was successfully propagated in HL-60 cell cultures. DNA sequencing confirmed that the Ehrlichia-like sp. sequences from deer in California were closely related to sequences reported from white-tailed deer from Oklahoma and Georgia. The E. equi strain from deer and elk resembled other E. equi strains from California. These results suggest that cervids may be important in the natural maintenance of E. equi in California.