Environmental DNA metabarcoding reveals comparable responses to agricultural stressors on different trophic levels of a freshwater community.

Freshwater habitats are under stress from agricultural land use, most notably the influx of neonicotinoid pesticides and increased nutrient pressure from fertilizer. Traditional studies investigating the effects of stressors on freshwater systems are often limited to a narrow range of taxa, depending heavily on morphological expertise. Additionally, disentanglement of multiple simultaneous stressors can be difficult in field studies, whereas controlled laboratory conditions do not accurately reflect natural conditions and food webs. To overcome these drawbacks, we investigated the impacts of two agricultural stressors (the neonicotinoid insecticide thiacloprid and fertilizer) in full-factorial design in a semi-natural research site, using environmental DNA sampling to study three different taxonomic groups representing three trophic levels: bacteria (decomposers), phytoplankton (primary producers), and chironomids (consumers). The results show considerable impact of both stressors across trophic levels, with an additive effect of fertilizer and thiacloprid on community composition at all levels. These findings suggest that agricultural stressors affect the entire food web, either directly or through cascade reactions. They are also consistent with morphological assessments that were performed in the same study site, even at a lower number of replicates. The study presented shows that the use of multimarker environmental DNA provides a more comprehensive assessment of stressor impacts across multiple trophic levels, at a higher taxonomic resolution than traditional surveys. Additionally, many putative novel bioindicators for both agricultural stressors were discovered. We encourage further investigations into stressors impacts at different trophic levels, which will lead to more effective monitoring and management of freshwater systems.

Lactobacillus iners-dominated vaginal microbiota is associated with increased susceptibility to Chlamydia trachomatis infection in Dutch women: a case-control study.

INTRODUCTION: This prospective study aimed to study the composition and structure of the vaginal microbiota prior to Chlamydia trachomatis infection. METHODS: A nested case-control study was performed in 122 women, half of which acquired C. trachomatis within a year after their first visit. At the first visit, the composition and structure of vaginal microbial communities were analysed using 16S rRNA sequencing in the context of the sociodemographic and sexual risk behaviour information using logistic regression. RESULTS: Five vaginal community state types (CSTs) were identified. Four CSTs were dominated by Lactobacillus spp., of which L. crispatus (37%) and L. iners (33%) were the most common. One CST was characterised by the absence of Lactobacillus spp. (25%) and the presence of an array of strict and facultative anaerobes. Multivariate logistic regression analysis revealed that women with a L. iners-dominated CST had an increased risk of C. trachomatis infection (p=0.04; OR: 2.6, 95% CI 1.0 to 6.6). CONCLUSIONS: The distribution of CSTs dominated by Lactobacillus spp. agreed with previous studies. However, the frequency of dysbiosis among Caucasian women was relatively high (24%). Having vaginal microbiota dominated by L. iners was associated with an increased risk for C. trachomatis infection. Therefore, we hypothesise that specific signatures of vaginal microbiota are indicative of increased host predisposition to acquiring STIs.

Earlier Detection of Hepatitis C Virus Infection Through Routine Hepatitis C Virus Antibody Screening of Human Immunodeficiency Virus-Positive Men Who Have Sex With Men Attending A Sexually Transmitted Infection Outpatient Clinic: A Longitudinal Study.

BACKGROUND: In 2007, routine hepatitis C virus (HCV) antibody testing was introduced for men who have sex with men (MSM) with a human immunodeficiency virus (HIV)-positive or unknown status attending a Dutch sexually transmitted infection (STI) outpatient clinic. We evaluated whether this screening resulted in additional and earlier HCV diagnoses among MSM who also attend HIV clinics. METHODS: At first STI consultation, HIV-positive MSM and MSM opting-out of HIV testing (HIV-status-unknown) were tested for HCV antibodies (anti-HCV). During follow-up consultations, only previously HCV-negative men were tested. Retrospectively, STI clinic and HIV clinic HCV diagnosis dates were compared. RESULTS: One hundred twelve (6.4%) of 1742 (95% confidence interval [CI], 5.3-7.6%) HIV-positive and 3 (0.7%) of 446 (95% CI, 0.2-2.0%) HIV-status-unknown MSM tested anti-HCV-positive at first consultation. During follow-up consultations, 32 HIV-positive (incidence HCV-positive: 2.35/100 person years (PY) (95% CI, 1.66-3.33)) and 0 (1-sided, 97.5% CI, 0.0-3.76) HIV-status-unknown MSM became anti-HCV-positive. Four (11.8%) of 34 HIV-positive MSM notified by their sexual partner of HCV tested anti-HCV-positive.Of 163 HIV-positive MSM with HCV antibodies, 78 reported a history of HCV. HCV diagnosis data at the HIV clinic was requested for the remaining 85 MSM and available for 54 MSM. Of these 54 MSM, 28 (51.9%) had their first HCV diagnosis at the STI clinic, of whom 7 concurrently with HIV. At their next scheduled HIV clinic consultation, 3 HCV cases probably would have been missed. CONCLUSIONS: The introduction of routine anti-HCV testing at the STI outpatient clinic resulted in additional and earlier HCV detection among HIV-positive MSM. Testing should be continued among HIV-positive MSM, at least for those not (yet) under the care of an HIV clinic and those notified of HCV by their sexual partner.

Rapid and reliable discrimination between Shigella species and Escherichia coli using MALDI-TOF mass spectrometry.

E. coli-Shigella species are a cryptic group of bacteria in which the Shigella species are distributed within the phylogenetic tree of E. coli. The nomenclature is historically based and the discrimination of these genera developed as a result of the epidemiological need to identify the cause of shigellosis, a severe disease caused by Shigella species. For these reasons, this incorrect classification of shigellae persists to date, and the ability to rapidly characterize E. coli and Shigella species remains highly desirable. Until recently, existing matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) assays used to identify bacteria could not discriminate between E. coli and Shigella species. Here we present a rapid classification method for the E. coli-Shigella phylogroup based on MALDI-TOF MS which is supported by genetic analysis. E. coli and Shigella isolates were collected and genetically characterized by MLVA. A custom reference library for MALDI-TOF MS that represents the genetic diversity of E. coli and Shigella strains was developed. Characterization of E. coli and Shigella species is based on an approach with Biotyper software. Using this reference library it was possible to distinguish between Shigella species and E. coli. Of the 180 isolates tested, 94.4% were correctly classified as E. coli or shigellae. The results of four (2.2%) isolates could not be interpreted and six (3.3%) isolates were classified incorrectly. The custom library extends the existing MALDI-TOF MS method for species determination by enabling rapid and accurate discrimination between Shigella species and E. coli.

Urogenital Chlamydia trachomatis strain types, defined by high-resolution multilocus sequence typing, in relation to ethnicity and urogenital symptoms among a young screening population in Amsterdam, The Netherlands.

INTRODUCTION: Previous studies found conflicting results regarding associations between urogenital Chlamydia trachomatis infections and ethnicity or urogenital symptoms among at-risk populations using either ompA-based genotyping or high-resolution multilocus sequence typing (MLST). This study applied high-resolution MLST on samples of individuals from a selected young urban screening population to assess the relationship of C. trachomatis strain types with ethnicity and self-reported urogenital symptoms. Demographic and sexual risk behaviour characteristics of the identified clusters were also analysed. METHODS: We selected C. trachomatis-positive samples from the Dutch Chlamydia Screening Implementation study among young individuals in Amsterdam, the Netherlands. All samples were typed using high-resolution MLST. Clusters were assigned using minimum spanning tree analysis and were combined with epidemiological data of the participants. RESULTS: We obtained full MLST data for C. trachomatis-positive samples from 439 participants and detected nine ompA genovars. MLST analysis identified 175 sequence types and six large clusters; in one cluster, participants with Surinamese/Antillean ethnicity were over-represented (58.8%) and this cluster predominantly consisted of genovar I. In addition, we found one cluster with an over-representation of participants with Dutch ethnicity (90.0%) and which solely consisted of genovar G. No association was observed between C. trachomatis clusters and urogenital symptoms. CONCLUSIONS: We found an association between urogenital C. trachomatis clusters and ethnicity among young screening participants in Amsterdam, the Netherlands. However, no association was found between C. trachomatis clusters and self-reported urogenital symptoms.

Spontaneous pharyngeal Chlamydia trachomatis RNA clearance. A cross-sectional study followed by a cohort study of untreated STI clinic patients in Amsterdam, The Netherlands.

OBJECTIVES: Pharyngeal Chlamydia trachomatis (chlamydia) might contribute to ongoing chlamydia transmission, yet data on spontaneous clearance duration are rare. We examined the prevalence, spontaneous clearance, chlamydial DNA concentration and genotypes of pharyngeal chlamydia among clinic patients with sexually transmitted infection (STI). METHODS: Female patients at high risk for an STI who reported active oral sex and male patients who have sex with men (MSM) were screened for pharyngeal chlamydia RNA using a nucleic acid amplification test. A repeat swab was obtained to evaluate spontaneous clearance in untreated patients with pharyngeal chlamydia. Quantitative chlamydia DNA load was determined by calculating the chlamydia/human cell ratio. RESULTS: Pharyngeal chlamydia was detected in 148/13 111 (1.1%) MSM and in 160/6915 (2.3%) women. 53% of MSM and 32% of women with pharyngeal chlamydia did not have a concurrent anogenital chlamydia infection. In 16/43 (37%) MSM and in 20/55 (36%) women, the repeat pharyngeal swab was negative (median follow-up 10 days, range 4-58 days). Patients with an initial chlamydial DNA concentration above the median were less likely to clear. Of 23 MSM with pharyngeal chlamydia who had sex with a lymphogranuloma venereum (LGV)-positive partner recently or in the past, two were LGV biovar positive (8.7%). CONCLUSIONS: The pharynx is a reservoir for chlamydia and LGV, and may play a role in ongoing transmission. Although delay in ribosomal RNA decline after resolution of the infection might have led to an underestimation of spontaneous clearance, in high-risk STI clinic patients, testing the pharynx for chlamydia should be considered.

Use of Chlamydia trachomatis high-resolution typing: an extended case study to distinguish recurrent or persistent infection from new infection.

OBJECTIVES: Repeated infections of Chlamydia trachomatis may be new infections or persistent infections due to treatment failure or due to unresolved infections in sexual partners. We aimed to establish the value of using high-resolution multilocus sequence typing (CT-MLST) to discriminate repeated C trachomatis infections. METHODS: Paired C trachomatis positive samples (baseline (T0) and after 6 months (T1)) were selected from two Dutch screening implementation studies among young heterosexual people. Typing with six CT-MLST loci included the ompA gene. The uniqueness of strains was assessed using 256 reference CT-MLST profiles. RESULTS: In 27 out of 34 paired cases, full sequence types were obtained. A multilocus (13 cases) or single locus variant (4 cases) was seen, indicating 17 new C trachomatis infections at T1. The ompA genovar was identical for 5 of 17 discordant cases. The 10 cases with concordant typing results were categorised as treatment failure (5 cases) versus persistent or recurrent infections (5 cases). Surprisingly, these concordant cases had C trachomatis strains that were either unique or found in small clusters. The median time between T0 and T1 did not differ between the concordant and discordant cases. CONCLUSIONS: High-resolution typing was superior in discriminating new infections compared with only using ompA genovar typing. Many cases (37%) showed exactly the same C trachomatis strain after 6 months. CT-MLST is not conclusive in distinguishing recurrent infections from treatment failure.

Perceived HIV status is a key determinant of unprotected anal intercourse within partnerships of men who have sex with men in Amsterdam.

The practice of unprotected anal intercourse (UAI) involves at least two partners. We examined the associations between insertive or receptive UAI and perceived HIV seroconcordance and partnership type in self-perceived HIV-negative and self-perceived HIV-positive men who have sex with men (MSM). MSM (age ≥ 18 years) were recruited for a cross-sectional survey at the sexually transmitted infections clinic in Amsterdam, the Netherlands, in 2008-2009. Participants completed a questionnaire concerning partnerships in the preceding 6 months. Associations were quantified via multinomial logistic regression models using generalized estimating equations. The outcomes were 'no, or safe anal intercourse', 'insertive UAI', and 'receptive UAI'. We included 5,456 partnerships from 1,890 self-perceived HIV-negative men and 1,861 partnerships from 558 self-perceived HIV-positive men. Within the partnerships, perceived HIV status of the partner was an important determinant of UAI (p < 0.001). Among HIV-negative men, perceived HIV discordance was negatively associated with receptive UAI compared with no or safe UAI (OR 0.57; 95 % CI 0.36-0.92); when the partners were more familiar with each other, the risk of receptive UAI was increased relative to no or safe anal intercourse. Among HIV-positive men, perceived HIV discordance was negatively associated with insertive UAI (OR 0.05; 95 % CI 0.03-0.08). Within partnerships, perceived HIV status of the partner was one of the strongest determinants of UAI among self-perceived HIV-negative and HIV-positive MSM, and discordant serostatus was negatively associated with UAI. The findings suggest that serosorting is one of the main strategies when engaging in UAI.

Route of sexual exposure is independently associated with seropositivity to HPV-16 and HPV-18 among clients of an STI clinic in the Netherlands.

We investigated the route of sexual exposure as a determinant for human papillomavirus (HPV)-16 and HPV-18 seropositivity. At the Amsterdam sexually transmitted infections clinic we recruited 4 risk groups: (1) men who have sex with women only (MSW; n = 751); (2) women who have sex with men (WSM; n = 749); (3) men who have sex with men (MSM) reporting insertive anal sex only (insMSM; n = 156); and (4) MSM reporting receptive anal sex (recMSM; n = 415). In multivariable analyses, HPV-16 seropositivity was significantly more common in WSM vs MSW, recMSM vs MSW, and recMSM vs insMSM. HPV-18 results were similar. Route of sexual exposure is independently associated with HPV seropositivity.

Urethral lymphogranuloma venereum infections in men with anorectal lymphogranuloma venereum and their partners: the missing link in the current epidemic?

Urethral lymphogranuloma venereum (LGV) is not screened routinely. We found that in 341 men having sex with men with anorectal LGV, 7 (2.1%) had concurrent urethral LGV. Among 59 partners, 4 (6.8%) had urethral LGV infections. Urethral LGV is common, probably key in transmission, and missed in current routine LGV screening algorithms.

Screening for hepatitis B and C in first-generation Egyptian migrants living in the Netherlands.

BACKGROUND: Egypt has high prevalence of hepatitis C virus (HCV) infection and intermediate prevalence of hepatitis B virus (HBV) infection; however, infection prevalence among Egyptian migrants is unknown. Considering the asymptomatic onset and development of disease in chronically-infected patients, many may remain undiagnosed. AIMS: To evaluate an HCV- and HBV-screening programme designed to identify undetected infections among first-generation Egyptian migrants in Amsterdam, the Netherlands. METHODS: In 2009 and 2010, viral hepatitis educational and screening sessions were established at Egyptian meeting places. Data regarding demographics and HCV risk factors were collected. Chronically infected participants were referred and followed up. Phylogenetic analyses were used to ascertain the geographic origin of infections. RESULTS: Eleven of 465 (2.4%; 95% CI = 1.3-4.2%) migrants had HCV antibodies; 10/11 were HCV RNA positive. All had genotype 4a, and strains were typical of those of Egypt and the Middle East. Older age and exposure to parenteral antischistosomal therapy (PAT) were significantly associated with HCV. Anti-HBc prevalence was 16.8% (95% CI = 13.7-20.4%); HBsAg prevalence was 1.1% (95% CI = 0.5-2.5%). All had genotype D, typical of those of the Middle East. Most (9/10 HCV; 3/5 HBV) chronic infections were newly diagnosed; four of the HCV-infected individuals started treatment. CONCLUSIONS: Anti-HCV and HBsAg prevalence among Egyptian migrants was lower compared with the general Egyptian population, but higher than the general population of Western countries. Phylogenetic analyses suggest that all infections were from the region of origin. HCV-screening programmes should target first-generation Egyptian migrants, especially those of older age and those who received PAT.

Translational characterization of the temporal dynamics of metabolic dysfunctions in liver, adipose tissue and the gut during diet-induced NASH development in Ldlr-/-.Leiden mice.

Background: NAFLD progression, from steatosis to inflammation and fibrosis, results from an interplay of intra- and extrahepatic mechanisms. Disease drivers likely include signals from white adipose tissue (WAT) and gut. However, the temporal dynamics of disease development remain poorly understood. Methods: High-fat-diet (HFD)-fed Ldlr-/-.Leiden mice were compared to chow-fed controls. At t = 0, 8, 16, 28 and 38w mice were euthanized, and liver, WAT depots and gut were analyzed biochemically, histologically and by lipidomics and transcriptomics together with circulating factors to investigate the sequence of pathogenic events and organ cross-talk during NAFLD development. Results: HFD-induced obesity was associated with an increase in visceral fat, plasma lipids and hyperinsulinemia at t = 8w, along with increased liver steatosis and circulating liver damage biomarkers. In parallel, upstream regulator analysis predicted that lipid catabolism regulators were deactivated and lipid synthesis regulators were activated. Subsequently, hepatocyte hypertrophy, oxidative stress and hepatic inflammation developed. Hepatic collagen accumulated from t = 16 w and became pronounced at t = 28-38 w. Epididymal WAT was maximally hypertrophic from t = 8 w, which coincided with inflammation development. Mesenteric and subcutaneous WAT hypertrophy developed slower and did not appear to reach a maximum, with minimal inflammation. In gut, HFD significantly increased permeability, induced a shift in microbiota composition from t = 8 w and changed circulating gut-derived metabolites. Conclusion: HFD-fed Ldlr-/-.Leiden mice develop obesity, dyslipidemia and insulin resistance, essentially as observed in obese NAFLD patients, underlining their translational value. We demonstrate that marked epididymal-WAT inflammation, and gut permeability and dysbiosis precede the development of NAFLD stressing the importance of a multiple-organ approach in the prevention and treatment of NAFLD.

Unexpectedly high proportion of drug users and men having sex with men who develop chronic hepatitis B infection.

BACKGROUND & AIMS: In low endemic countries, most hepatitis B virus (HBV) infections are found in adult behavioural risk groups, such as drug users (DU) and men having sex with men (MSM). These risk groups are frequently exposed to HBV, which might induce a different rate of viral clearance compared with the general adult population, in whom the chronicity rate is estimated to be 5-10%. Our aim was to obtain insights into the proportion of MSM and DU developing chronic infection after a primary HBV infection, and the underlying risk factors. METHODS: From 1984 to 2002, sera of 1862 MSM and 1268 DU of the Amsterdam Cohort Studies were retrospectively tested for anti-HBc, HBsAg, and HBV DNA. As of 2003, all of the cohort participants were vaccinated, making further testing redundant. RESULTS: Hundred and forty seven participants seroconverted for anti-HBc during follow-up. The median age at the moment of the acute infection was 31 years. The proportion of those becoming chronically infected was 23% and 28% for MSM and DU, respectively. In both cohorts, being younger was a risk factor for developing chronic infection (OR: 0.9; 95% CI: 0.82-0.99). HIV/HCV co-infection was associated with developing chronic HBV infection in the DU cohort (OR: 32.1, 95% CI: 3.1-334.5). CONCLUSIONS: Compared with the general population, MSM and DU had an unanticipated high rate of developing chronic HBV infections. HIV/HCV co-infection proved to be an important risk factor for developing chronic HBV infections in DU. The reason for the high rate of MSM becoming chronically infected remains unclear.

Recreational drug use during sex and sexually transmitted infections among clients of a city sexually transmitted infections clinic in Amsterdam, the Netherlands.

BACKGROUND: Recreational drug use is associated with high-risk sexual behavior and sexually transmitted infections (STIs). We assessed the prevalence of drug use during sex and the associations between such use and STI (chlamydia, gonorrhea, or syphilis). METHODS: During 3 periods in 2008 and 2009, attendees of an STI clinic in Amsterdam were interviewed about sexual behavior and drug use during sex and tested for STI. Associations between sex-related drug use and STI were assessed separately for heterosexual men, men who have sex with men (MSM), and women. We examined whether drug use was associated with STI after adjusting for high-risk sexual behavior. RESULTS: Nine hundred sixty-one heterosexual men, 673 MSM, and 1188 women participated in this study. Of these, 11.9% had chlamydia, 3.4% gonorrhea, and 1.2% syphilis. Sex-related drug use in the previous 6 months was reported by 22.6% of heterosexual men, 51.6% of MSM, and 16.0% of women. In multivariable analyses, adjusting for demographics (and high-risk sexual behavior in MSM), sex-related drug use was associated with STI in MSM (any drugs and poppers) and women (GHB and XTC) but not in heterosexual men. Stratified analysis in MSM showed that sex-related use of poppers was associated with STI in HIV-negative MSM but not in HIV-infected MSM. CONCLUSION: Clients reported frequent sex-related drug use, which was associated with STI in MSM and women. In MSM, sex-related drug use was associated with STI after adjusting for high-risk sexual behavior but only in HIV-negative MSM. Prevention measures targeted at decreasing sex-related drug use could reduce the incidence of STI.

DNA metabarcoding using nrITS2 provides highly qualitative and quantitative results for airborne pollen monitoring.

Airborne pollen monitoring is of global socio-economic importance as it provides information on presence and prevalence of allergenic pollen in ambient air. Traditionally, this task has been performed by microscopic investigation, but novel techniques are being developed to automate this process. Among these, DNA metabarcoding has the highest potential of increasing the taxonomic resolution, but uncertainty exists about whether the results can be used to quantify pollen abundance. In this study, it is shown that DNA metabarcoding using trnL and nrITS2 provides highly improved taxonomic resolution for pollen from aerobiological samples from the Netherlands. A total of 168 species from 143 genera and 56 plant families were detected, while using a microscope only 23 genera and 22 plant families were identified. NrITS2 produced almost double the number of OTUs and a much higher percentage of identifications to species level (80.1%) than trnL (27.6%). Furthermore, regressing relative read abundances against the relative abundances of microscopically obtained pollen concentrations showed a better correlation for nrITS2 (R2 = 0.821) than for trnL (R2 = 0.620). Using three target taxa commonly encountered in early spring and fall in the Netherlands (Alnus sp., Cupressaceae/Taxaceae and Urticaceae) the nrITS2 results showed that all three taxa were dominated by one or two species (Alnus glutinosa/incana, Taxus baccata and Urtica dioica). Highly allergenic as well as artificial hybrid species were found using nrITS2 that could not be identified using trnL or microscopic investigation (Alnus × spaethii, Cupressus arizonica, Parietaria spp.). Furthermore, perMANOVA analysis indicated spatiotemporal patterns in airborne pollen trends that could be more clearly distinguished for all taxa using nrITS2 rather than trnL. All results indicate that nrITS2 should be the preferred marker of choice for molecular airborne pollen monitoring.

The mitochondrial genome of Nemalecium lighti (Hydrozoa, Leptothecata).

The hydrozoan species Nemalecium lighti (Hargitt, 1924) is widely distributed in tropical marine waters around the world. Here we report the complete linear mitochondrial genome of N. lighti from Sint Eustatius (Lesser Antilles). The mitochondrial genome with a length of 14,320 bp encodes for 13 protein-coding genes, two tRNA genes, and two rRNA genes. Gene arrangement differs from that found in other species of the same taxonomic order and a phylogenetic analysis shows that based on mitochondrial genes, N. lighti clusters outside of the Leptothecata, rendering the order paraphyletic.

Microbiome and environment explain the absence of correlations between consumers and their diet in Bornean microsnails.

Classical ecological theory posits that species partition resources such that each species occupies a unique resource niche. In general, the availability of more resources allows more species to co-occur. Thus, a strong relationship between communities of consumers and their resources is expected. However, correlations may be influenced by other layers in the food web, or by the environment. Here we show, by studying the relationship between communities of consumers (land snails) and individual diets (from seed plants), that there is in fact no direct, or at most a weak but negative, relationship. However, we found that the diversity of the individual microbiome positively correlates with both consumer community diversity and individual diet diversity in three target species. Moreover, these correlations were affected by various environmental variables, such as anthropogenic activity, habitat island size, and a possibly important nutrient source, guano runoff from nearby caves. Our results suggest that the microbiome and the environment explain the absence of correlations between diet and consumer community diversity. Hence, we advocate that microbiome inventories are routinely added to any community dietary analysis, which our study shows can be done with relatively little extra effort. Our approach presents the tools to quickly obtain an overview of the relationships between consumers and their resources. We anticipate our approach to be useful for ecologists and environmentalists studying different communities in a local food web.

Anal lymphogranuloma venereum infection screening with IgA anti-Chlamydia trachomatis-specific major outer membrane protein serology.

BACKGROUND: Anal lymphogranuloma venereum (LGV) infections, caused by Chlamydia trachomatis biovar L (Ct+/LGV+), are endemic among men who have sex with men (MSM). Anal non-LGV biovar Ct infections (Ct+/LGV-) can be eradicated with 1 week doxycycline, whereas Ct+/LGV+ infections require 3-week doxycycline. To differentiate Ct+/LGV+ from Ct+/LGV- infections, biovar-specific Nucleic Acid Amplification Test (NAAT) are standard, but also expensive and laborious. A chlamydia-specific serological assay could serve as an alternative test. METHODS: MSM were screened for anal Ct+/LGV+ and Ct+/LGV- infections with a commercial nonspecific NAAT and an in house biovar L-specific NAAT. Serum samples were evaluated with chlamydia-specific anti-Major Outer Membrane Protein (MOMP) and antilipopolysaccharide assays of IgA and IgG classes. Asymptomatic patients were identified as: (1) no anal complaints or (2) no microscopic inflammation (i.e., <10 leucocytes per high power field in anal smears). The best differentiating assay was subsequently evaluated in 100 Ct+/LGV+ and 100 Ct+/LGV- MSM using different cut-off points. RESULTS: The anti-MOMP IgA assay was the most accurate to differentiate Ct+/LGV+ (n = 42) from Ct+/LGV- (n = 19) with 85.7% sensitivity (95% confidence interval [CI], 72.2-93.3) and 84.2% specificity (95% CI, 62.4-94.5), even among asymptomatic patients. In a population comprising 98 Ct+/LGV+ and 105 Ct+/LGV- patients, the anti-MOMP IgA assay scored most accurate when the cut-off point was set to 2.0 with 75.5% (95% CI, 65.8-83.6) sensitivity and 74.3% (95% CI, 64.8-82.3) specificity. CONCLUSIONS: The IgA anti-MOMP assay can identify a considerable proportion of the (asymptomatic) anal LGV infections correctly. Yet, biovar L-specific NAAT are still the preferred diagnostic tests in clinical settings.

Microbiota in Dung and Milk Differ Between Organic and Conventional Dairy Farms.

Organic farming is increasingly promoted as a means to reduce the environmental impact of artificial fertilizers, pesticides, herbicides, and antibiotics in conventional dairy systems. These factors potentially affect the microbial communities of the production stages (soil, silage, dung, and milk) of the entire farm cycle. However, understanding whether the microbiota representative of different production stages reflects different agricultural practices - such as conventional versus organic farming - is unknown. Furthermore, the translocation of the microbial community across production stages is scarcely studied. We sequenced the microbial communities of soil, silage, dung, and milk samples from organic and conventional dairy farms in the Netherlands. We found that community structure of soil fungi and bacteria significantly differed among soil types, but not between organic versus conventional farming systems. The microbial communities of silage also did not differ among conventional and organic systems. Nevertheless, the dung microbiota of cows and the fungal communities in the milk were significantly structured by agricultural practice. We conclude that, while the production stages of dairy farms seem to be disconnected in terms of microbial transfer, certain practices specific for each agricultural system, such as the content of diet and the use of antibiotics, are potential drivers of shifts in the cow's microbiota, including the milk produced. This may reflect differences in farm animal health and quality of dairy products depending on farming practices.

Delayed microbial cure of lymphogranuloma venereum proctitis with doxycycline treatment.

Microbial cure of chlamydia proctitis (lymphogranuloma venereum [LGV] and non-LGV) with doxycycline treatment was evaluated by chlamydia DNA and RNA persistence in anal swab specimens. In LGV proctitis, RNA persisted for up to 16 days. In non-LGV chlamydia proctitis, DNA was undetectable after 7 days. These findings support the Centers for Disease Control and Prevention's treatment recommendation of a 21-day doxycycline regimen for LGV proctitis and a 7-day regimen for non-LGV chlamydia proctitis. Delayed microbial cure of LGV proctitis should be considered in improved treatment regimens.