Detection of presumed genes encoding beta-lactamases by sequence based screening of metagenomes derived from Antarctic microbial mats

Analysis of environmental samples for bacterial antibiotic resistance genes may have different objectives and analysis strategies. In some cases, the purpose was to study diversity and evolution of genes that could be grouped within a mechanism of antibiotic resistance. Different protocols have been designed for detection and confirmation that a functional gene was found. In this study, we present a sequence-based screening of candidate genes encoding beta-lactamases in 14 metagenomes of Antarctic microbial mats. The samples were obtained from different sites, representing diverse biogeographic regions of maritime and continental Antarctica. A protocol was designed based on generation of Hidden Markov Models from the four beta-lactamase classes by Ambler classification,using sequences from the Comprehensive Antibiotic Resistance Database (CARD). The models were used as queries for metagenome analysis and recovered contigs were subsequently annotated using RAST. According to our analysis, 14 metagenomes analyzed contain A, B and C beta-lactamase genes.Class D genes, however, were identified in 11 metagenomes. The most abundant was class C (46.8%), followed by classes B (35.5%), A (14.2%) and D (3.5%). A considerable number of sequences formed clusters which included, in some cases, contigs from different metagenomes. These assemblies are clearly separated from reference clusters, previously identified using CARD beta-lactamase sequences.While bacterial antibiotic resistance is a major challenge of public health worldwide, our results suggest that environmental diversity of beta-lactamase genes is higher than that currently reported, although this should be complemented with gene function analysis.Fil: Azziz, Gastón. Universidad de la República; UruguayFil: Gimentz, Matìas. Universidad de la República; UruguayFil: Romero, Hèctor. Universidad de la República; UruguayFil: Valdespino Castillo, P.. Lawrence Berkeley National Laboratory; Estados UnidosFil: Falcòn, Luisa I.. Universidad Nacional Autónoma de México; MéxicoFil: Ruberto, Lucas Adolfo Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; ArgentinaFil: Mac Cormack, Walter Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; ArgentinaFil: Batista, Silvia. Universidad de la República; Urugua

Metagenomic strategies identify diverse integron-integrase and antibiotic resistance genes in the Antarctic environment

The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.Fil: Antelo, Verónica. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Giménez, Matías. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Azziz, Gastón. Universidad de la Republica. Facultad de Agricultura; UruguayFil: Valdespino Castillo, Patricia. Lawrence Berkeley National Laboratory; Estados UnidosFil: Falcón, Luisa I.. Universidad Nacional Autónoma de México; MéxicoFil: Ruberto, Lucas Adolfo Mauro. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; ArgentinaFil: MacCormack, Walter P.. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Nanobiotecnología. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Nanobiotecnología; ArgentinaFil: Mazel, Didier. Institut Pasteur de Paris.; FranciaFil: Batista, Silvia. Instituto de Investigaciones Biológicas "Clemente Estable"; Urugua

Nitrogen and Phosphorous Retention in Tropical Eutrophic Reservoirs with Water Level Fluctuations: A Case Study Using Mass Balances on a Long-Term Series

Nitrogen and phosphorous loading drives eutrophication of aquatic systems. Lakes and reservoirs are often effective N and P sinks, but the variability of their biogeochemical dynamics is still poorly documented, particularly in tropical systems. To contribute to the extending of information on tropical reservoirs and to increase the insight on the factors affecting N and P cycling in aquatic ecosystems, we here report on a long-term N and P mass balance (2003–2018) in Valle de Bravo, Mexico, which showed that this tropical eutrophic reservoir lake acts as a net sink of N (−41.7 g N m y) and P (−2.7 g P m y), mainly occurring through net sedimentation, equivalent to 181% and 68% of their respective loading (23.0 g N m y and 4.2 g P m y). The N mass balance also showed that the Valle de Bravo reservoir has a high net N atmospheric influx (31.6 g N m y), which was 1.3 times the external load and likely dominated by N fixation. P flux was driven mainly by external load, while in the case of N, net fixation also contributed. During a period of high water level fluctuations, the net N atmospheric flux decreased by 50% compared to high level years. Our results outlining water regulation can be used as a useful management tool of water bodies, by decreasing anoxic conditions and net atmospheric fluxes, either through decreasing nitrogen fixation and/or promoting denitrification and other microbial processes that alleviate the N load. These findings also sustain the usefulness of long-term mass balances to assess biogeochemical dynamics and its variability.This research was funded by UNAM, PAPIIT-IN207702 and CONACYT-SEMARNAT, C01-1125 projects to M.M-

Vertical Boundary Mixing Events during Stratification Govern Heat and Nutrient Dynamics in a Windy Tropical Reservoir Lake with Important Water-Level Fluctuations: A Long-Term (2001–2021) Study

hysical processes play important roles in controlling eutrophication and oligotrophication. In stratified lakes, internal waves can cause vertical transport of heat and nutrients without breaking the stratification, through boundary mixing events. Such is the case in tropical Valle de Bravo (VB) reservoir lake, where strong diurnal winds drive internal waves, boundary mixing, and hypolimnetic warming during stratification periods. We monitored VB during 21 years (2001–2021) when important water-level fluctuations occurred, affecting mixing and nutrient flux. Stability also varied as a function of water level. Hypolimnetic warming (0.009–0.028 °C day−1) occurred in all the stratifications monitored. We analyzed temperature distributions and modeled the hypolimnion heat budget to assess vertical mixing between layers (0.639–3.515 × 10−6 m3 day−1), vertical diffusivity coefficient KZ (2.5 × 10−6–13.6 × 10−6 m2 s−1), and vertical nutrient transport to the epilimnion. Nutrient flux from the metalimnion to the epilimnion ranged 0.42–5.99 mg P m−2day−1 for soluble reactive phosphorus (SRP) and 5.8–101.7 mg N m−2day−1 for dissolved inorganic nitrogen (DIN). Vertical mixing and the associated nutrient fluxes increase evidently as the water level decreases 8 m below capacity, and they can increase up to fivefold if the water level drops over 12 m. The observed changes related to water level affect nutrient recycling, ecosystemic metabolic balance, and planktonic composition of VB.This research was funded by UNAM (PAPIIT-IN207702 and PAPIIT-IN111321) and by CONACYT-SEMARNAT (C01-1125) projects to M.M.-I.Peer reviewe

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Early transmission dynamics, spread, and genomic characterization of SARS-CoV-2 in Panama.

We report an epidemiologic analysis of 4,210 cases of infection with severe acute respiratory syndrome coronavirus 2 and genetic analysis of 313 new near-complete virus genomes in Panama during March 9-April 16, 2020. Although containment measures reduced R0 and Rt, they did not interrupt virus spread in the country