BackgroundThe soil transmitted helminths are a group of parasitic worms responsible for extensive morbidity in many of the world’s most economically depressed locations. With growing emphasis on disease mapping and eradication, the availability of accurate and cost-effective diagnostic measures is of paramount importance to global control and elimination efforts. While real-time PCR-based molecular detection assays have shown great promise, to date, these assays have utilized sub-optimal targets. By performing next-generation sequencing-based repeat analyses, we have identified high copy-number, non-coding DNA sequences from a series of soil transmitted pathogens. We have used these repetitive DNA elements as targets in the development of novel, multi-parallel, PCR-based diagnostic assays.Methodology/Principal FindingsUtilizing next-generation sequencing and the Galaxy-based RepeatExplorer web server, we performed repeat DNA analysis on five species of soil transmitted helminths (Necator americanus, Ancylostoma duodenale, Trichuris trichiura, Ascaris lumbricoides, and Strongyloides stercoralis). Employing high copy-number, non-coding repeat DNA sequences as targets, novel real-time PCR assays were designed, and assays were tested against established molecular detection methods. Each assay provided consistent detection of genomic DNA at quantities of 2 fg or less, demonstrated species-specificity, and showed an improved limit of detection over the existing, proven PCR-based assay.Conclusions/SignificanceThe utilization of next-generation sequencing-based repeat DNA analysis methodologies for the identification of molecular diagnostic targets has the ability to improve assay species-specificity and limits of detection. By exploiting such high copy-number repeat sequences, the assays described here will facilitate soil transmitted helminth diagnostic efforts. We recommend similar analyses when designing PCR-based diagnostic tests for the detection of other eukaryotic pathogens.

Successful mass drug administration (MDA) campaigns have brought several countries near the point of Lymphatic Filariasis (LF) elimination. A diagnostic tool is needed to determine when the prevalence levels have decreased to a point that MDA campaigns can be discontinued without the threat of recrudescence. A six-country study was conducted assessing the performance of seven diagnostic tests, including tests for microfilariae (blood smear, PCR), parasite antigen (ICT, Og4C3) and antifilarial antibody (Bm14, PanLF, Urine SXP). One community survey and one school survey were performed in each country. A total of 8,513 people from the six countries participated in the study, 6,443 through community surveys and 2,070 through school surveys. Specimens from these participants were used to conduct 49,585 diagnostic tests. Each test was seen to have both positive and negative attributes, but overall, the ICT test was found to be 76% sensitive at detecting microfilaremia and 93% specific at identifying individuals negative for both microfilariae and antifilarial antibody; the Og4C3 test was 87% sensitive and 95% specific. We conclude, however, that the ICT should be the primary tool recommended for decision-making about stopping MDAs. As a point-of-care diagnostic, the ICT is relatively inexpensive, requires no laboratory equipment, has satisfactory sensitivity and specificity and can be processed in 10 minutes—qualities consistent with programmatic use. Og4C3 provides a satisfactory laboratory-based diagnostic alternative.

Seven rounds of mass drug administration (MDA) have been administered in Leogane, Haiti, an area hyperendemic for lymphatic filariasis (LF). Sentinel site surveys showed that the prevalence of microfilaremia was reduced to <1% from levels as high as 15.5%, suggesting that transmission had been reduced. A separate 30-cluster survey of 2- to 4-year-old children was conducted to determine if MDA interrupted transmission. Antigen and antifilarial antibody prevalence were 14.3% and 19.7%, respectively. Follow-up surveys were done in 6 villages, including those selected for the cluster survey, to assess risk factors related to continued LF transmission and to pinpoint hotspots of transmission. One hundred houses were mapped in each village using GPS-enabled PDAs, and then 30 houses and 10 alternates were chosen for testing. All individuals in selected houses were asked to participate in a short survey about participation in MDA, history of residence in Leogane and general knowledge of LF. Survey teams returned to the houses at night to collect blood for antigen testing, microfilaremia and Bm14 antibody testing and collected mosquitoes from these communities in parallel. Antigen prevalence was highly variable among the 6 villages, with the highest being 38.2% (Dampus) and the lowest being 2.9% (Corail Lemaire); overall antigen prevalence was 18.5%. Initial cluster surveys of 2- to 4-year-old children were not related to community antigen prevalence. Nearest neighbor analysis found evidence of clustering of infection suggesting that LF infection was focal in distribution. Antigen prevalence among individuals who were systematically noncompliant with the MDAs, i.e. they had never participated, was significantly higher than among compliant individuals (p<0.05). A logistic regression model found that of the factors examined for association with infection, only noncompliance was significantly associated with infection. Thus, continuing transmission of LF seems to be linked to rates of systematic noncompliance.

S u m m a r y :This paper is the first large-scale molecular phylogenetic study on filarial parasites (family Onchocercidae) which includes 16 spe cies of 6 genera : Brugia beaveri Ash et Little, 1 9 6 4 ; B . buckleyi Dissanaike et Paramananthan, 1961 ; B . malayi (Brug, 1927) Buckley, 1 9 6 0 ; B . pahangi (Buckley et Edeson, 1956) Buckley, 1 9 6 0 ; B . p a tei (Buckley, Nelson et Heisch, 1958) Buckley, 1 9 6 0 ; B. timori Partono e t al, 1 9 7 7 ; W uchereria bancrofti (Cobbold, 1877) Seurat, 1 9 2 1 ; W . kalimantani Palmieri , Purnomo, Dennis and Marwoto, 1 9 8 0 ; Mansonella perstans (Manson, 1891 ) Eberhard et Orihel, 1 9 8 4 ; Loa loa, Stiles, 1 9 0 5 ; O nchocerca volvulus (Leuckart, 1983) Railliet et Henry, 1 9 1 0 ; O . ochengi Bwangamoi, 1 9 6 9 ; O . gutturosa Neumann, 1 9 1 0 ; Dirofilaria immitis (Leidy, 1856) Railliet et Henry, 1911 ; A c a nthocheilonema viteae (Krepkogorskaya, 1933) Bain, Baker et Chabaud, 19 8 2 and Litomosoides sigmodontis Chandler, 1 9 3 1 . 5 S rRNA gene spacer region sequence data were collec ted by PCR, cloning and dideoxy sequencing. The 5 S rRNA gene spacer region sequences were aligned and analyzed by maxi mum parsimony algorithms, distance methods and maximum likeli hood methods to construct phylogenetic trees. Bootstrap analysis w as used to test the robustness of the different phylogenetic reconstructions. The data indicated that 5 S spacer region sequences are highly conserved within species yet differ signifi cantly between species. Spliced leader sequences were observed in all of the 5 S rDNA spacers with no sequence variation, although flanking region sequence and length heterogeneity w as observed even within species. All of the various tree-building methods gave very similar results. This study identified four clades which are strongly supported by bootstrap analysis: the Brugia clade; the W uchereria clade; the Brugia-Wuchereria clade and the O nchocerca clade. The analyses indicated that L. sigmodontis and A . viteae may be the most primitive among the 16 species studied. The data did not show any close relationship between Loa loa and D. immitis presently classified in the same subfamily, and the constitution of the Dirofilariinae subfamily is questionable. * P ro g ra m in M o le c u la r a n d C e llu la r B io lo g y , U n iv e rsity o f KEY W O R D S R é s u m é : É t u d e s p h y l o g é n é t iq u e s m o l é c u l a ir e s d e s f il a ir e s à pa r t ir DE SÉQUENCES DU « SPACER-DU 5S RIBOSOMAL

Human blood samples and indoor-resting Culex pipiens were collected in 33 randomly selected houses from different sectors of a village in the Nile Delta of Egypt which was endemic for Wuchereria bancrofti. Blood was also collected from subjects with no history of living in filarial endemic areas. Human blood samples were divided and assessed by both membrane filtration and polymerase chain reaction (PCR). Similarly, mosquito samples were assessed by both dissection and PCR. Blood pools representing each household were tested by PCR. If a pool gave a positive result, then individual blood specimens were also tested by PCR. Of the 33 houses tested, both membrane filtration and blood pools assayed by PCR identified 14 (42.4%) 'infected houses'. PCR detected parasite deoxyribonucleic acid (DNA) in blood pools from an additional 3 households that gave negative results by membrane filtration. Of 178 endemic blood samples tested by membrane filtration, 22 (12.3%) had microfilariae and all were individually positive by PCR. Although microfilaria counts were lower in blood collected during the day than in night-collected blood, the PCR results were consistent, regardless of time of collection. All non-endemic blood samples were negative by PCR. Among the 33 houses rested, mosquito pools assayed by PCR identified 17 (51.5%) as 'infected households'. Of these, 8 houses (47%) contained at least one microfilaraemic resident. One 'infected household' was identified by mosquito dissection. We concluded that PCR is a powerful epidemiological tool for screening villages for the prevalence of W. bancrofti. PCR detection of W. bancrofti DNA in blood-fed mosquitoes could be used initially to locate endemic areas with transmission of bancroftian filariasis. PCR detection of W. bancrofti DNA in blood collected during the day could then be used to assess W. bancrofti infection rates.

BackgroundThis study employed various monitoring methods to assess the impact of repeated rounds of mass drug administration (MDA) on bancroftian filariasis in Papua New Guinea, which has the largest filariasis problem in the Pacific region.Methodology/Principal FindingsResidents of rural villages near Madang were studied prior to and one year after each of three rounds of MDA with diethylcarbamazine plus albendazole administered per World Health Organization (WHO) guidelines. The mean MDA compliance rate was 72.9%. Three rounds of MDA decreased microfilaremia rates (Mf, 1 ml night blood by filter) from 18.6% pre-MDA to 1.3% after the third MDA (a 94% decrease). Mf clearance rates in infected persons were 71%, 90.7%, and 98.1% after 1, 2, and 3 rounds of MDA. Rates of filarial antigenemia assessed by card test (a marker for adult worm infection) decreased from 47.5% to 17.1% (a 64% decrease) after 3 rounds of MDA. The filarial antibody rate (IgG4 antibodies to Bm14, an indicator of filarial infection status and/or exposure to mosquito-borne infective larvae) decreased from 59.3% to 25.1% (a 54.6% decrease). Mf, antigen, and antibody rates decreased more rapidly in children <11 years of age (by 100%, 84.2%, and 76.8%, respectively) relative to older individuals, perhaps reflecting their lighter infections and shorter durations of exposure/infection prior to MDA. Incidence rates for microfilaremia, filarial antigenemia, and antifilarial antibodies also decreased significantly after MDA. Filarial DNA rates in Anopheles punctulatus mosquitoes that had recently taken a blood meal decreased from 15.1% to 1.0% (a 92.3% decrease).Conclusions/SignificanceMDA had dramatic effects on all filariasis parameters in the study area and also reduced incidence rates. Follow-up studies will be needed to determine whether residual infection rates in residents of these villages are sufficient to support sustained transmission by the An. punctulatus vector. Lymphatic filariasis elimination should be feasible in Papua New Guinea if MDA can be effectively delivered to endemic populations.

A novel filarial serine protease inhibitor (SPI) from the human parasitic nematode Onchocerca volvulus, Ov-SPI-1, was identified through the analysis of a molting third-stage larvae expressed sequence tag dataset. Subsequent analysis of the expressed sequence tag datasets of O. volvulus and other filariae identified four other members of this family. These proteins are related to the low molecular weight SPIs originally isolated from Ascaris suum where they are believed to protect the parasite from host intestinal proteases. The two Ov-spi transcripts are up-regulated in the molting larvae and adult stages of the development of the parasite. Recombinant Ov-SPI-1 is an active inhibitor of serine proteases, specifically elastase, chymotrypsin, and cathepsin G. Immunolocalization of the Ov-SPI proteins demonstrates that the endogenous proteins are localized to the basal layer of the cuticle of third-stage, molting third-stage, and fourth-stage larvae, the body channels and multivesicular bodies of third-stage larvae and the processed material found between the two cuticles during molting. In O. volvulus adult worms the Ov-SPI proteins are localized to the sperm and to eggshells surrounding the developing embryos. RNA interference targeting the Ov-spi genes resulted in the specific knockdown of the transcript levels of both Ov-spi-1 and Ov-spi-2, a loss of native proteins, and a significant reduction in both molting and viability of third-stage larvae. We suggest the Ov-SPI proteins play a vital role in nematode molting by controlling the activity of an endogenous serine protease(s). The localization data in adults also indicate that these inhibitors may be involved in other processes such as embryogenesis and spermatogenesis.The cuticle is an extracellular hydroskeleton that overlays the hypodermis of all nematodes. Most nematodes molt their cuticles four times during pre-adult development. Although being fairly inert and structurally robust, the cuticle is also permeable to small compounds and expands during growth periods between molts (1). A number of enzymes have been implicated in the shedding of old cuticles and the remodeling process that occurs as the new cuticle develops (2-8). Proteolytic enzymes have been shown to play a vital role in these processes, and inhibitor studies and rational cloning strategies have identified several nematode proteases whose functions are required for molting (9 -11).To identify novel filarial proteins involved in the molting process, we adopted a transcriptomics approach. Thousands of expressed sequence tags (ESTs) 4 have been sequenced from cDNA libraries constructed from the infective third-stage larvae (L3) and molting L3 (mL3) of the human filarial nematode Onchocerca volvulus (12, 13). Analysis of these datasets identified novel cysteine proteases involved in the molting process (14,15). Also identified in these analyses was an O. volvulus small molecular weight serine protease inhibitor (SPI) with similarities to other nematode SPI; Ascaris suum chymotrypsin/elastase in...

A total of 688 isolates of Campylobacter jejuni and Campylobacter coli were screened for the presence of plasmid DNA by agarose gel electrophoresis and were tested for susceptibility to ampicillin, chloramphenicol, erythromycin, streptomycin, and tetracycline. Of the isolates examined, 32% were noted to harbor plasmid DNA, ranging in size from 2.0 to 162 kilobases. Only tetracycline resistance was noted to correlate with the presence of plasmids. Plasmids capable of transferring tetracycline resistance via conjugation ranged in size from 42 to 100 kilobases. The BglII and BcII restriction endonuclease profiles of 31 plasmids examined showed marked diversity in their banding patterns. Although a high degree of DNA-DNA homology was noted among the Campylobacter spp. plasmids, no homology was noted between these plasmids and tetracycline R factors commonly found in the family Enterobacteriaceae.Campylobacter jejuni and Campylobacter coli now have been established as agents of acute diarrheal disease in both animals and humans worldwide (3,5,19). Although there have been many reports describing the epidemiology and clinical aspects of campylobacter infections (for reviews, see references 3 and 4), little has been reported about the extrachromosomal gene pool of the organisms.The first report of plasmids in the genus Campylobacter and their possible association with antibiotic resistance was published by Austen and Trust (1). Of the 29 strains of "related vibrios" they screened for extrachromosomal DNA, 6 harbored plasmids. No attempt was made to determine whether specific antibiotic resistance genes were plasmid encoded.The first plasmid shown to mediate antibiotic resistance in C. jejuni was described by Taylor and associates (21). This 38-megadalton R factor was capable of transferring tetracycline resistance via conjugation to other Campylobacter strains including C. jej'uni and Campylobacter fetus but not to Escherichia coli. A similar replicon was noted by Tenover and associates in isolates of C. jejuni recovered from simians (23).More recent studies by Taylor and co-workers (22) have demonstrated a high degree of homology among six Campylobacter R factors obtained from strains isolated in Canada, Belgium, and the United States, despite differences in their restriction endonuclease profiles. These same R factors shared no DNA homology with tetracycline R plasmids common to the family Enterobacteriaceae.The goals of this study were three: first, to establish the prevalence of plasmids within isolates of C. jejuni and C. coli in King County, Wash.; second, to determine whether these plasmids carried antibiotic resistance genes; and third, to characterize the R factors that were identified.(This study was presented in part at the 23rd Interscience