Nitrogen and oxygen isotopes in nitrate in the groundwater and surface water discharge from two rural catchments: implications for nitrogen loading to coastal waters

In Prince Edward Island, Canada, widespread intensive potato production has contributed to elevated nitrate concentrations in groundwater and streams, and eutrophic or anoxic conditions occur regularly in several estuarine systems. In this research, the stable isotopes of nitrogen and oxygen in nitrate in intertidal groundwater discharge and stream water were used, in conjunction with water quality and quantity data and land use information, to better understand the characteristics of nitrate delivered to two small estuaries with contrasting land use in their contributory catchments. Most of the water samples collected during the two-year study had isotopic signatures that fell in the range expected for nitrate derived from ammonium-based fertilizers (26.5 % of the samples) or in the overlapping range formed between ammonium-based fertilizers and nitrate derived from soil (64 % of the samples). Overall, isotopic signatures spanned over relatively narrow ranges, and correlations with other water quality parameters, or catchment characteristics, were weak. Nitrate in groundwater discharge and surface water in the Trout River catchment exhibited significantly different isotopic signatures only for the nitrogen isotope, while in the McIntyre Creek catchment groundwater discharge and surface water had similar isotopic signatures. When the isotopic results for the waters from the two catchments were compared, the surface waters were found to be similar, while the isotopic signatures of nitrate in groundwater were distinct only for the nitrogen isotope. Denitrification in the two study catchments was not evident based on the isotopic results for nitrate; however, in the case of the Trout River catchment, where a small freshwater pond exists, an average nitrate load reduction of 14 % was inferred based on a comparison of nitrate loads entering and leaving the pond. Overall, it appears that natural attenuation processes, occurring either in the streams or groundwater flow systems, do not significantly reduce nitrate loading to these estuaries.     

Learning from the COVID-19 pandemic to strengthen routine immunization systems

Kate Causey and Jonathan F Mosser discuss what can be learnt from the observed impacts of the COVID-19 pandemic on routine immunisation systems.

In the final months of 2021, deaths due to the Coronavirus Disease 2019 (COVID-19) surpassed 5 million globally [1]. Available data suggest that even this staggering figure may be a substantial underestimate of the true toll of the pandemic [2]. Beyond mortality, it may take years to fully quantify the direct and indirect impacts of the COVID-19 pandemic such as disruptions in preventive care services. In an accompanying research study in PLOS Medicine, McQuaid and colleagues report on the uptake of routine childhood immunizations in 2020 in Scotland and England during major pandemic-related lockdowns [3]. This adds to a growing body of literature quantifying the impact of the COVID-19 pandemic on routine health services and childhood immunization [4,5], which provides important opportunities to learn from early pandemic experiences as immunization systems face ongoing challenges.McQuaid and colleagues compared weekly or monthly data on vaccine uptake in Scotland and England from January to December of 2020 to the rates observed in 2019 to estimate the changes in uptake before, during, and after COVID-19 pandemic lockdowns in each country. The authors included 2 different preschool immunizations, each with multiple doses. They found significantly increased uptake within 4 weeks of eligibility during the lockdown and postlockdown periods in Scotland for all 5 vaccine dose combinations examined: During lockdown, percentage point increases ranged from 1.3% to 14.3%. In England, there were significant declines in uptake during the prelockdown, lockdown, and postlockdown periods for all 4 vaccine dose combinations examined. However, declines during lockdown were small, with percentage point decreases ranging from −0.5% to −2.1%. Due to the nature of the data available, the authors were unable to account for possible seasonal variation in vaccine delivery, control for important individual-level confounders or effect modifiers such as child sex and parental educational attainment, or directly compare outcomes across the 2 countries.These findings stand in contrast to the documented experience of many other countries, where available data suggest historic disruptions in routine childhood vaccination coverage, particularly during the first months of pandemic-related lockdowns [5,6]. Supply side limitations such as delayed shipments of vaccines and supplies [7], inadequate personal protective equipment [8], staff shortages [9], and delayed or canceled campaigns and introductions [9] threatened vaccine delivery. Furthermore, fear of exposure to COVID-19 at vaccination centers [10], misinformation about vaccine safety [8], and lockdown-related limitations on travel to facilities [9,10] reduced demand. In polls of country experts conducted by WHO, UNICEF, and Gavi, the Vaccine Alliance throughout the second quarter of 2020, 126 of 170 countries reported at least some disruption to routine immunization programs [10,11]. Global estimates suggest that millions more children missed doses of important vaccines than would have in the absence of the COVID-19 pandemic [5,6]. While many vaccine programs showed remarkable resilience in the second half of 2020, with rates of vaccination returning to or even exceeding prepandemic levels [5,6], disruptions to immunization services persisted into 2021 in many countries [12].As the authors discuss, it is critical to pinpoint the specific program policies and strategies that contributed to increased uptake in Scotland and only small declines in England and, more broadly, to the rapid recovery of vaccination rates observed in many other countries. McQuaid and colleagues cite work suggesting that increased flexibility in parental working patterns during lockdowns, providing mobile services or public transport to vaccine centers, and sending phone- and mail-based reminders are strategies that may have improved uptake of timely vaccination in Scotland during this period [13]. Similarly, immunization programs around the world have employed a broad range of strategies to maintain or increase vaccination during the pandemic. Leaders in Senegal, Paraguay, and Sri Lanka designed and conducted media campaigns to emphasize the importance of childhood immunization even during lockdown [8,14,15]. Although many programs delayed mass campaigns in the spring of 2020, multiple countries were able to implement campaigns by the summer of 2020 [8,16–20]. In each of these examples, leaders responded quickly to meet the unique challenges presented by the COVID-19 pandemic in their communities.Increased data collection and tracking systems are essential for efficient and effective responses as delivery programs face challenges. When concern arose for pandemic-related disruptions to immunization services, public health decision-makers in Scotland and England responded by increasing the frequency and level of detail in reports of vaccine uptake and by making these data available for planning and research. The potential for robust data systems to inform real-time decision-making is not limited to high-income countries. For instance, the Nigerian National Health Management Information System released an extensive online dashboard shortly after the onset of the pandemic, documenting the impact of COVID-19 on dozens of indicators of health service uptake, including 16 related to immunization [21]. Vaccination data systems that track individual children and doses, such as the reminder system in Scotland, allow for highly targeted responses. Similarly, in Senegal, Ghana, and in Karachi, Pakistan, healthcare workers have relied on existing or newly implemented tracking systems to identify children who have missed doses and provide text message and/or phone call reminders [8,22,23]. Investing in robust routine data systems allows for rapid scale-up of data collection, targeted services to those who miss doses, and a more informed response when vaccine delivery challenges arise.Policy and program decision-makers must learn from the observed impacts of the COVID-19 pandemic on health systems and vaccine delivery. The study by McQuaid and colleagues provides further evidence that vaccination programs in England and Scotland leveraged existing strengths and identified novel strategies to mitigate disruptions and deliver vaccines in the early stages of the pandemic. However, the challenges posed by the pandemic to routine immunization services continue. To mitigate the risk of outbreaks of measles and other vaccine-preventable diseases, strategies are needed to maintain and increase coverage, while ensuring that children who missed vaccines during the pandemic are quickly caught up. The accompanying research study provides important insights into 2 countries where services were preserved—and even increased—in the early pandemic. To meet present and future challenges, we must learn from early pandemic successes such as those in Scotland and England, tailor solutions to improve vaccine uptake, and strengthen data systems to support improved decision-making.     

Intracellular Cytokine Staining and Flow Cytometry: Considerations for Application in Clinical Trials of Novel Tuberculosis Vaccines

Intracellular cytokine staining combined with flow cytometry is one of a number of assays designed to assess T-cell immune responses. It has the specific advantage of enabling the simultaneous assessment of multiple phenotypic, differentiation and functional parameters pertaining to responding T-cells, most notably, the expression of multiple effector cytokines. These attributes make the technique particularly suitable for the assessment of T-cell immune responses induced by novel tuberculosis vaccines in clinical trials. However, depending upon the particular nature of a given vaccine and trial setting, there are approaches that may be taken at different stages of the assay that are more suitable than other alternatives. In this paper, the Tuberculosis Vaccine Initiative (TBVI) TB Biomarker Working group reports on efforts to assess the conditions that will determine when particular assay approaches should be employed. We have found that choices relating to the use of fresh whole blood or peripheral blood mononuclear cells (PBMC) and frozen PBMC; use of serum-containing or serum-free medium; length of stimulation period and use of co-stimulatory antibodies can all affect the sensitivity of intracellular cytokine assays. In the case of sample material, frozen PBMC, despite some loss of sensitivity, may be more advantageous for batch analysis. We also recommend that for multi-site studies, common antibody panels, gating strategies and analysis approaches should be employed for better comparability.     

Mechanistic studies of agmatine deiminase from multiple bacterial species

One subfamily of guanidino group-modifying enzymes (GMEs) consists of the agmatine deiminases (AgDs). These enzymes catalyze the conversion of agmatine (decarboxylated arginine) to N-carbamoyl putrescine and ammonia. In plants, viruses, and bacteria, these enzymes are thought to be involved in energy production, biosynthesis of polyamines, and biofilm formation. In particular, we are interested in the role that this enzyme plays in pathogenic bacteria. Previously, we reported the initial kinetic characterization of the agmatine deiminase from Helicobacter pylori and described the synthesis and characterization the two most potent AgD inactivators. Herein, we have expanded our initial efforts to characterize the catalytic mechanisms of AgD from H. pylori as well as Streptococcus mutans and Porphyromonas gingivalis. Through the use of pH rate profiles, pK(a) measurements of the active site cysteine, solvent isotope effects, and solvent viscosity effects, we have determined that the AgDs, like PADs 1 and 4, utilize a reverse protonation mechanism.     

First Evaluation after Implementation of a Quality Control System for the Second Line Drug Susceptibility Testing of Mycobacterium tuberculosis Joint Efforts in Low and High Incidence Countries

Three networks/projects involving 27 European countries were established to investigate the quality of second-line drug (SLD) susceptibility testing with conventional and molecular methods. 1. The “Baltic-Nordic TB-Laboratory Network” comprised 11 reference laboratories in the Baltic-Nordic States. They performed SLD testing in the first phase with a panel of 20 Mycobacterium tuberculosis strains. After several laboratories made technical changes a second panel of 10 strains with a higher proportion of resistant strains were tested. Although the concordance for Ofloxacin, Kanamycin, and Capreomycin was consistently high, the largest improvements in performance were achieved for the analysis of Ofloxacin resistant (from 88.9 to 95.0%), and Capreomycin resistant (from 71.0 to 88.9%) strains. 2. Within the FP7 TB PAN-NET project (EU Grant agreement 223681) a quality control panel to standardize the EQA (External Quality Assurance) for first-line drugs (FLD) and SLD testing for phenotypic and molecular methods was established. The strains were characterized by their robustness, unambiguous results when tested, and low proportion of secondary drug resistances. 3. The (European Reference Laboratory Network-TB) ERLN-TB network analyzed four different panels for drug resistance testing using phenotypic and molecular methods; in two rounds in 2010 the 31 participating laboratories began with 5 strains, followed by 10 strains and 6 additional crude DNA extracts in 2011 and 2012 were examined by conventional DST and molecular methods. Overall, we demonstrated the importance of developing inter-laboratory networks to establish quality assurance and improvement of SLD testing of M. tuberculosis.     

Metal accumulation in two contiguous eutrophic peri-urban lakes,Chivero and Manyame,Zimbabwe

Concentrations of aluminium, cadmium, chromium, cobalt, copper, iron, lead, nickel and zinc were determined in surface water, benthic sediments, and the gills, liver and stomach muscle tissues of Oreochromis niloticus and Clarias gariepinus in peri-urban lakes Chivero and Manyame, Zimbabwe. Five sites were sampled in each lake once per month in November 2015, February, May, August and November 2016. Pollution load index detected no metal contamination, whereas the geo-accumulation index reflected heavy to extreme sediment pollution, with Fe, Cd, Zn, Cr, Ni and Cu present in both lakes. Significant spatial temporal variations were detected for Al, Cr, Cu and Pb across sites within and between the two lakes. High Fe, Al and Cr concentrations in water and sediments in lakes Chivero and Manyame derive from geogenic background sources in addition to anthropogenic loads and intensity. Elevated concentrations of Al, Pb, Cu, Cd, Fe and Zn detected in gills, liver and stomach tissue of catfish corroborate concentrations in water and sediments, and pose the highest ecological and health risk for hydrobionts in lakes Chivero and Manyame. Contiguity of peri-urban lakes exposes them to similar threats, necessitating creative water management strategies, which ensure ecological continuity.     

Two African Viruses Serologically and Morphologically Related to Rabies Virus

Lagos bat virus and an isolate from shrews (IbAn 27377), both from Nigeria, were found to be bullet-shaped and to mature intracytoplasmically in association with a distinct matrix. They were related to, but readily distinguishable from, rabies virus and each other by complement fixation and neutralization tests. The three viruses, including rabies, form a subgrouping within the rhabdoviruses.     

Mitochondrial DNA phylogeography of least cisco Coregonus sardinella in Alaska

This study presents the first detailed analysis of the mitochondrial DNA diversity of least cisco Coregonus sardinella in Alaska using a 678 bp segment of the control region (D‐loop) of the mitochondrial genome. Findings suggest that the history of C. sardinella in Alaska differs from that of other species of Coregonus present in the state and surrounding regions. The examined populations of C. sardinella are genetically diverse across Alaska. Sixty‐eight distinct mitochondrial haplotypes were identified among 305 individuals sampled from nine locations. The haplotype minimum spanning network and phylogeny showed a modest level of geographic segregation among haplotypes, suggesting high levels of on‐going or recent connectivity among distant populations. Observed Φ_ST values and the results of homogeneity and AMOVAs indicate incipient genetic differentiation between aggregations in three broad regional groups. Sites north of the Brooks Range formed one group, sites in the Yukon and Selawik Rivers formed a second group and sites south of the Yukon drainage formed the third group. Overall, the sequence data showed that a large proportion of mtDNA genetic variation in C. sardinella is shared across Alaska, but this variation is not homogeneously distributed across all regions and for all haplotype groups.