Every fifth published metagenome is not available to science

Have you ever sought to use metagenomic DNA sequences reported in scientific publications? Were you successful? Here, we reveal that metagenomes from no fewer than 20% of the papers found in our literature search, published between 2016 and 2019, were not deposited in a repository or were simply inaccessible. The proportion of inaccessible data within the literature has been increasing year-on-year. Noncompliance with Open Data is best predicted by the scientific discipline of the journal. The number of citations, journal type (e.g., Open Access or subscription journals), and publisher are not good predictors of data accessibility. However, many publications in high–impact factor journals do display a higher likelihood of accessible metagenomic data sets. Twenty-first century science demands compliance with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly. Data accessibility must become one of the routine and mandatory components of manuscript submissions—a requirement that should be applicable across the increasing number of disciplines using metagenomics. Compliance must be ensured and reinforced by funders, publishers, editors, reviewers, and, ultimately, the authors.info:eu-repo/semantics/publishedVersio

A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants

The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantification methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with extended-spectrum ?-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly (< 0.1% to 38.3%), being positively correlated (p < 0.001) with regional atmospheric temperatures. Although most WWTPs removed large proportions of CTX-R coliforms, loads over 103 colony-forming units per mL were occasionally observed in final effluents. We demonstrate that CTX-R coliform monitoring is a feasible and affordable approach to assess wastewater antibiotic resistance status

[Performance by cytology and hybrid capture II in screening for high-grade squamous intraepithelial lesions in women with HIV].

HIV-infected women are at increased risk of developing high-grade squamous intraepithelial lesions (HSIL), the precursor lesions for cervical cancer. This study estimated and compared the performance of cytology and hybrid capture II in screening for precursor lesions of cervical cancer among HIV-infected women. The study population consisted of women from the open prospective cohort at the Evandro Chagas Clinical Research Institute, Oswaldo Cruz Foundation (IPEC/Fiocruz). Colposcopy and histology were considered jointly in defining the gold standard. Cytology showed 31.8% sensitivity and 95.5% specificity, while hybrid capture II showed higher sensitivity (100%) and lower specificity (52%). The positive likelihood ratio was 7.1 for cytology and 2.1 for hybrid capture II, while the negative likelihood ratio was 0.7 for cytology and 0.0 for hybrid capture II

Absence of effect of menopause status at initiation of first-line antiretroviral therapy on immunologic or virologic responses: a cohort study from Rio de Janeiro, Brazil

Submitted by Rodrigo Senorans ([email protected]) on 2015-06-26T15:31:26Z No. of bitstreams: 1 Absence of effect of menopause status at initiation of first-line antiretroviral therapy on immunologic or virologic responses A cohort study from Rio de Janeiro, Brazil.pdf: 104692 bytes, checksum: 5af38dd1e354452d045751ee4890aa9e (MD5)Approved for entry into archive by Anderson Silva ([email protected]) on 2015-07-03T12:57:17Z (GMT) No. of bitstreams: 1 Absence of effect of menopause status at initiation of first-line antiretroviral therapy on immunologic or virologic responses A cohort study from Rio de Janeiro, Brazil.pdf: 104692 bytes, checksum: 5af38dd1e354452d045751ee4890aa9e (MD5)Approved for entry into archive by Anderson Silva ([email protected]) on 2015-07-03T12:57:26Z (GMT) No. of bitstreams: 1 Absence of effect of menopause status at initiation of first-line antiretroviral therapy on immunologic or virologic responses A cohort study from Rio de Janeiro, Brazil.pdf: 104692 bytes, checksum: 5af38dd1e354452d045751ee4890aa9e (MD5)Made available in DSpace on 2015-07-06T13:06:45Z (GMT). No. of bitstreams: 1 Absence of effect of menopause status at initiation of first-line antiretroviral therapy on immunologic or virologic responses A cohort study from Rio de Janeiro, Brazil.pdf: 104692 bytes, checksum: 5af38dd1e354452d045751ee4890aa9e (MD5) Previous issue date: 2014Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, Brasil / Universidade Federal do Estado do Rio de Janeiro. Departamento de Matemática e Estatística. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilFundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas. Laboratório de Pesquisa Clínica em DST e AIDS. Rio de Janeiro, RJ, BrasilObjective: To compare the effectiveness of first-line combination antiretroviral therapy (cART) between premenopausal and postmenopausal women. Methods: ART-naı¨ve women initiating cART between January 2000/June 2010 at the Instituto de Pesquisa Clı´nica Evandro Chagas Cohort were studied. Women were defined as postmenopausal after 12 consecutive months of amenorrhea. CD4 cell counts and HIV-1 RNA viral load (VL) measurements were compared between pre- and postmenopausal at 6, 12 and 24 months after cART initiation. Women who modified/discontinued a drug class or died due to an AIDS defining illness were classified as ART-failures. Variables were compared using Wilcoxon test, x2 or Fisher’s exact test. The odds of cART effectiveness (VL,400 copies/mL and/or no need to change cART) were compared using logistic regression. Linear model was used to access relationship between CD4 change and menopause. Results: Among 383 women, 328 (85%) were premenopausal and 55 (15%) postmenopausal. Median pre cART CD4 counts were 231 and 208 cells/mm3 (p=0.14) in pre- and postmenopausal women, respectively. No difference in the median pre cART VL was found (both 4.8 copies/mL). Median CD4 changes were similar at 6 and 12 months. At 24 months after cART initiation, CD4 changes among postmenopausal women were significantly lower among premenopausal women (p=0.01). When the analysis was restricted to women with VL,400 copies/mL, no statistical difference was observed. Overall, 63.7% achieved cART effectiveness at 24 months without differences between groups at 6, 12 and 24 months. Conclusion: Menopause status at the time of first-line cART initiation does not impact CD4 cell changes at 24 months among women with a virologic response. No relationship between menopause status and virologic response was observed

Most frequent first cART regimens stratified by menopausal status at the initiation of antiretroviral therapy (baseline).

<p>3TC, lamivudine; ATV/r, atazanavir/ritonavir; d4T, stavudine; ddI, didanosine; EFV, efavirenz;</p><p>FTC, emtricitabine; IDV/r, indinavir/ritonavir; LOP/r, lopinavir/ritonavir; SQV/r, saquinavir/ritonavir;</p><p>NFV, nelfinavir; TDF, tenofovir; ZDV, zidovudine;</p><p>cART: combination antiretroviral therapy; PI: Protease inhibitor;</p><p>NNRTI: Non-Nucleoside Reverse Transcriptase Inhibitors.</p

cART effectiveness at 6, 12, and 24 months and the median change in CD4 cell count for premenopausal and postmenopausal antiretroviral-naïve women.

<p>IQR, interquartile interval;</p><p>cART: Combination Antiretroviral Therapy;</p

A global multinational survey of cefotaxime-resistant coliforms in urban wastewater treatment plants

The World Health Organization Global Action Plan recommends integrated surveillance programs as crucial strategies for monitoring antibiotic resistance. Although several national surveillance programs are in place for clinical and veterinary settings, no such schemes exist for monitoring antibiotic-resistant bacteria in the environment. In this transnational study, we developed, validated, and tested a low-cost surveillance and easy to implement approach to evaluate antibiotic resistance in wastewater treatment plants (WWTPs) by targeting cefotaxime-resistant (CTX-R) coliforms as indicators. The rationale for this approach was: i) coliform quantification methods are internationally accepted as indicators of fecal contamination in recreational waters and are therefore routinely applied in analytical labs; ii) CTX-R coliforms are clinically relevant, associated with extended-spectrum β-lactamases (ESBLs), and are rare in pristine environments. We analyzed 57 WWTPs in 22 countries across Europe, Asia, Africa, Australia, and North America. CTX-R coliforms were ubiquitous in raw sewage and their relative abundance varied significantly