Balancing agriculture and environment: Andrew Sharpley's nutrient, soil, and water management legacy.

Managing agricultural phosphorus (P) to balance food security and water quality priorities is a massive challenge fraught with uncertainty and competing interests. Throughout his career, Andrew Sharpley addressed this challenge by building our understanding of the fundamental principles and processes that control P behavior in agricultural land, developing tools to assess P losses, and then evaluating and refining nutrient, soil, and water beneficial management practices (BMPs). Together with an exceptionally large and diverse group of collaborators, Sharpley developed, tested, refined, calibrated, and validated management practices and risk assessment tools to develop site-specific recommendations for the right practices, in the right places, and at the right times. This approach has resonated globally, with the strategic use of BMPs in "critical source areas" widely implemented in an effort to improve the effectiveness of BMPs while reducing implementation costs. Additional contributions to nutrient management include determining environmental thresholds for soil test P and measuring the risk of P loss from different sources of P (e.g., various manures and commercial fertilizers). Sharpley's work was also distinctly realistic, ensuring that strategies for mitigating P loss were critically evaluated so that not only were the benefits highlighted, but also that trade-offs were measured. Nowhere is this better illustrated than with trade-offs in particulate P loss and dissolved P loss with conservation tillage. This review summarizes Sharpley's enormous contributions to our knowledge of agricultural P stewardship as well as his model of collaborative, multi-disciplinary leadership, helping the world to maintain agricultural productivity and protect water quality.

A Simulation-Based Training Program in Rapid Sequence Induction for Novice Anesthesiology Trainees Using a Novel Checklist.

Background: The novice anesthesiology trainee is required to assimilate the technical and nontechnical skills required to safely perform a rapid sequence induction (RSI). Acquisition of this core competency is traditionally achieved using operating room-based experiential learning, which may be associated with significant gaps in early trainee preparation. We conducted a study to explore the role of a new, customized, high-fidelity simulation-based training program designed to address this gap in RSI training. We then assessed mean performance scores of participants in the simulator and 4 weeks later. Methods: This observational study assessed participants' performance in the simulator on the day of training and in the workplace 4 weeks later. There is no universally agreed checklist or cognitive aid incorporating nontechnical skills and planning for unanticipated difficult airway management in RSI, so we applied a new scoring checklist developed by 6 experts using the modified Delphi technique. Results: Our task scoring checklist included nontechnical skills and consisted of 37 weighted parameters with a maximum performance score of 171. On the day of training, mean performance score was 105 (SD of 16). At the workplace evaluation 4 weeks after simulation training, the mean performance score of participants had increased to 140 (SD of 14.5; P = .001). The 95% confidence intervals for the simulator and workplace participant scores were 92 to 118 and 128 to 152, respectively. Conclusions: The results suggest that this simulation-based training in RSI was associated with an improvement in RSI performance in novice trainees and may complement the current system of workplace-based training.

Why soil testing is not enough: A mixed methods study of farmer nutrient management decision-making among U.S. producers.

Understanding farmers' nutrient management decision-making is critical to minimizing nutrient loss to water resources. This research examines farmer decision-making in the United States surrounding nutrients (primarily nitrogen and phosphorus) and water quality among 105 farmers in Missouri, North Carolina, and Ohio. Data were collected between 2015 and 2016 using a mixed-methods approach of in-person farmer interviews and accompanying quantitative surveys with demographic and Likert ranking questions. This work presents findings regarding 1) how farmers made decisions, 2) who and what they consult with when making decisions, and 3) how their views on local water quality and regional pollution impact their choices. Farmers reported many resources for information when making nutrient management decisions including yield data, market prices, weather, product availability, prior experience, risk management/avoidance, university research reports, soil and tissue sampling, and social networks. Location also shaped how farmers made nutrient management decisions both because of differences in the structure and types of professional and informal support available to farmers as well as how individuals perceived the severity of local water problems. Younger farmers saw more room for improvement in their nutrient management practices while older farmers were more likely to be satisfied with current practices and decisions. Ultimately, our findings suggest we need to tailor programs and education to regional economic, social norm, and environmental contexts with recognition that past experiences and long-term knowledge shape how farmers receive new interventions. Constructing multifaceted approaches to address these diverse conditions is a critical step in improving water quality when it comes to nutrient management choices.

P-FLUX: A phosphorus budget dataset spanning diverse agricultural production systems in the United States and Canada.

Quantifying spatial and temporal fluxes of phosphorus (P) within and among agricultural production systems is critical for sustaining agricultural production while minimizing environmental impacts. To better understand P fluxes in agricultural landscapes, P-FLUX, a detailed and harmonized dataset of P inputs, outputs, and budgets, as well as estimated uncertainties for each P flux and budget, was developed. Data were collected from 24 research sites and 61 production systems through the Long-term Agroecosystem Research (LTAR) network and partner organizations spanning 22 U.S. states and 2 Canadian provinces. The objectives of this paper are to (a) present and provide a description of the P-FLUX dataset, (b) provide summary analyses of the agricultural production systems included in the dataset and the variability in P inputs and outputs across systems, and (c) provide details for accessing the dataset, dataset limitations, and an example of future use. P-FLUX includes information on select site characteristics (area, soil series), crop rotation, P inputs (P application rate, source, timing, placement, P in irrigation water, atmospheric deposition), P outputs (crop removal, hydrologic losses), P budgets (agronomic budget, overall budget), uncertainties associated with each flux and budget, and data sources. Phosphorus fluxes and budgets vary across agricultural production systems and are useful resources to improve P use efficiency and develop management strategies to mitigate environmental impacts of agricultural systems. P-FLUX is available for download through the USDA Ag Data Commons (https://doi.org/10.15482/USDA.ADC/1523365).

GLP-2 Is Locally Produced From Human Islets and Balances Inflammation Through an Inter-Islet-Immune Cell Crosstalk.

Glucagon-like peptide-1 (GLP-1) shows robust protective effects on ß-cell survival and function and GLP-1 based therapies are successfully applied for type-2 diabetes (T2D) and obesity. Another cleavage product of pro-glucagon, Glucagon-like peptide-2 (GLP-2; both GLP-1 and GLP-2 are inactivated by DPP-4) has received little attention in its action inside pancreatic islets. In this study, we investigated GLP-2 production, GLP-2 receptor (GLP-2R) expression and the effect of GLP-2R activation in human islets. Isolated human islets from non-diabetic donors were exposed to diabetogenic conditions: high glucose, palmitate, cytokine mix (IL-1ß/IFN-γ) or Lipopolysaccharide (LPS) in the presence or absence of the DPP4-inhibitor linagliptin, the TLR4 inhibitor TAK-242, the GLP-2R agonist teduglutide and/or its antagonist GLP-2(3-33). Human islets under control conditions secreted active GLP-2 (full-length, non-cleaved by DPP4) into the culture media, which was increased by combined high glucose/palmitate, the cytokine mix and LPS and highly potentiated by linagliptin. Low but reproducible GLP-2R mRNA expression was found in all analyzed human islet isolations from 10 donors, which was reduced by pro-inflammatory stimuli: the cytokine mix and LPS. GLP-2R activation by teduglutide neither affected acute or glucose stimulated insulin secretion nor insulin content. Also, teduglutide had no effect on high glucose/palmitate- or LPS-induced dysfunction in cultured human islets but dampened LPS-induced macrophage-dependent IL1B and IL10 expression, while its antagonist GLP-2(3-33) abolished such reduction. In contrast, the expression of islet macrophage-independent cytokines IL6, IL8 and TNF was not affected by teduglutide. Medium conditioned by teduglutide-exposed human islets attenuated M1-like polarization of human monocyte-derived macrophages, evidenced by a lower mRNA expression of pro-inflammatory cytokines, compared to vehicle treated islets, and a reduced production of itaconate and succinate, marker metabolites of pro-inflammatory macrophages. Our results reveal intra-islet production of GLP-2 and GLP-2R expression in human islets. Despite no impact on ß-cell function, local GLP-2R activation reduced islet inflammation which might be mediated by a crosstalk between endocrine cells and macrophages.

A novel glycosidase plate-based assay for the quantification of galactosylation and sialylation on human IgG.

Changes in human IgG galactosylation and sialylation have been associated with several inflammatory diseases which are a major burden on the health care system. A large body of work on well-established glycomic and glycopeptidomic assays has repeatedly demonstrated inflammation-induced changes in IgG glycosylation. However, these assays are usually based on specialized analytical instrumentation which could be considered a technical barrier for uptake by some laboratories. Hence there is a growing demand for simple biochemical assays for analyzing these glycosylation changes. We have addressed this need by introducing a novel glycosidase plate-based assay for the absolute quantification of galactosylation and sialylation on IgG. IgG glycoproteins are treated with specific exoglycosidases to release the galactose and/or sialic acid residues. The released galactose monosaccharides are subsequently used in an enzymatic redox reaction that produces a fluorescence signal that is quantitative for the amount of galactosylation and, in-turn, sialylation on IgG. The glycosidase plate-based assay has the potential to be a simple, initial screening assay or an alternative assay to the usage of high-end analytical platforms such as HILIC-FLD-MSn when considering the analysis of galactosylation and sialylation on IgG. We have demonstrated this by comparing our assay to an industrial established HILIC-FLD-MSn glycomic analysis of 15 patient samples and obtained a Pearson's r correlation coefficient of 0.8208 between the two methods.

A Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Assay for the Relative Quantitation of Antennary Fucosylated N-Glycans in Human Plasma.

Changes in the abundance of antennary fucosylated glycans in human total plasma N-glycome (TPNG) have been associated with several diseases ranging from diabetes to various forms of cancer. However, it is challenging to address this important part of the human glycome. Most commonly, time-consuming chromatographic separations are performed to differentially quantify core and antenna fucosylation. Obtaining sufficient resolution for larger, more complex glycans can be challenging. We introduce a matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) assay for the relative quantitation of antennary fucosylation in TPNG. N-linked glycans are released from plasma by PNGase F and further treated with a core fucosidase before performing a linkage-informative sialic acid derivatization. The core fucosylated glycans are thus depleted while the remaining antennary fucosylated glycans are quantitated. Simultaneous quantitation of α2,3-linked sialic acids and antennary fucosylation allows an estimation of the sialyl-Lewis x motif. The approach is feasible using either ultrahigh-resolution Fourier-transform ion cyclotron resonance mass spectrometry or time-of-flight mass spectrometry. The assay was used to investigate changes of antennary fucosylation as clinically relevant marker in 14 colorectal cancer patients. In accordance with a previous report, we found elevated levels of antennary fucosylation pre-surgery which decreased after tumor resection. The assay has the potential for revealing antennary fucosylation signatures in various conditions including diabetes and different types of cancer.

Increasing the Effectiveness and Adoption of Agricultural Phosphorus Management Strategies to Minimize Water Quality Impairment.

Phosphorus (P) is essential for optimum agricultural production, but it also causes water quality degradation when lost through erosion (sediment-attached P), runoff (soluble reactive P; SRP), or leaching (sediment-attached P or SRP). Implementation of conservation practices (CP) affects P at the source (avoiding), during transport (controlling), or at the water resource edge (trapping). Trade-offs often occur with CP implementation. For instance, multiple researchers have shown that conservation tillage reduces total P by over 50%, while increasing SRP by upward of 40%. Conservation tillage may increase water quality degradation as SRP is more bioavailable than is particulate P. Conservation practices must be implemented as a system of practices to increase redundancy and to address all loss pathways, such as P management with conservation tillage and a riparian buffer. Further, planning and adoption must be at a watershed scale to ensure practices are placed in critical source areas, thereby providing the most treatment for the least price. Farmers must be involved in watershed planning, which should include financial backstopping and educational outreach. It is imperative that CPs be used more effectively to reduce and retard off-site P losses. New and innovative CPs are needed to improve control of P leaching, address legacy stores of soil test P, and mitigate increased P losses expected with climate change. Without immediate changes to CP implementation, P losses will increase due to climate change, with a concomitant degradation of water quality. These changes must be made at a watershed scale and in an intentional and transparent manner.

Magnitude of Mycobacterium tuberculosis transmission among household and non-household contacts of TB patients.

The household and non-household contacts of patients with tuberculosis (TB) face varying degrees of risk of infection by Mycobacterium tuberculosis. To quantify new infection and to determine the risk factors associated with new infection among named contacts in San Francisco, CA, USA. We performed a cohort study in patients with culture-positive pulmonary TB. We analyzed patient, contact, environmental and bacterial characteristics. Of the 2422 contacts named by 256 patients, 149 (6.2%) had new infection due to recent transmission from 79 (30.9%) patients. Of the 149 new infections, 87 (58.4%) occurred among household contacts and 62 (41.6%) among non-household contacts. Numerous acid-fast bacilli in sputum (odds ratio [OR] 2.64, 95%CI 1.32-5.25) and contacts being named by more than one patient (OR 2.90, 95%CI 1.23-6.85) were associated with new infection among household contacts. Being older than 50 years (OR 1.93, 95%CI 1.09-3.41) and an Asian/Pacific Islander (OR 3.09, 95%CI 1.50-6.37) were associated with new infection among non-household contacts. Fewer than one third of patients caused new infection to his/her contacts. A substantial proportion of transmission resulting in new infection occurred outside of the household. The risk factors for infection among household and non-household contacts are different and should be considered when prioritizing control interventions. .

Interplay of strain and race/ethnicity in the innate immune response to M. tuberculosis.

BACKGROUND: The roles of host and pathogen factors in determining innate immune responses to M. tuberculosis are not fully understood. In this study, we examined host macrophage immune responses of 3 race/ethnic groups to 3 genetically and geographically diverse M. tuberculosis lineages. METHODS: Monocyte-derived macrophages from healthy Filipinos, Chinese and non-Hispanic White study participants (approximately 45 individuals/group) were challenged with M. tuberculosis whole cell lysates of clinical strains Beijing HN878 (lineage 2), Manila T31 (lineage 1), CDC1551 (lineage 4), the reference strain H37Rv (lineage 4), as well as with Toll-like receptor 2 agonist lipoteichoic acid (TLR2/LTA) and TLR4 agonist lipopolysaccharide (TLR4/LPS). Following overnight incubation, multiplex assays for nine cytokines: IL-1ß, IL-2, IL-6, IL-8, IL-10, IL-12p70, IFNγ, TNFα, and GM-CSF, were batch applied to supernatants. RESULTS: Filipino macrophages produced less IL-1, IL-6, and more IL-8, compared to macrophages from Chinese and Whites. Race/ethnicity had only subtle effects or no impact on the levels of IL-10, IL-12p70, TNFα and GM-CSF. In response to the Toll-like receptor 2 agonist lipoteichoic acid (TLR2/LTA), Filipino macrophages again had lower IL-1 and IL-6 responses and a higher IL-8 response, compared to Chinese and Whites. The TLR2/LTA-stimulated Filipino macrophages also produced lower amounts of IL-10, TNFα and GM-CSF. Race/ethnicity had no impact on IL-12p70 levels released in response to TLR2/LTA. The responses to TLR4 agonist lipopolysaccharide (TLR4/LPS) were similar to the TLR2/LTA responses, for IL-1, IL-6, IL-8, and IL-10. However, TLR4/LPS triggered the release of less IL-12p70 from Filipino macrophages, and less TNFα from White macrophages. CONCLUSIONS: Both host race/ethnicity and pathogen strain influence the innate immune response. Such variation may have implications for the development of new tools across TB therapeutics, immunodiagnostics and vaccines.

Clinical and bacteriological characteristics associated with clustering of multidrug-resistant tuberculosis.

SETTING: The impact of the genetic characteristics of Mycobacterium tuberculosis on the clustering of multidrug-resistant tuberculosis (MDR-TB) has not been analyzed together with clinical and demographic characteristics. OBJECTIVE: To determine factors associated with genotypic clustering of MDR-TB in a community-based study. DESIGN: We measured the proportion of clustered cases among MDR-TB patients and determined the impact of clinical and demographic characteristics and that of three M. tuberculosis genetic characteristics: lineage, drug resistance-associated mutations, and rpoA and rpoC compensatory mutations. RESULTS: Of 174 patients from California and Texas included in the study, the number infected by East-Asian, Euro-American, Indo-Oceanic and East-African-Indian M. tuberculosis lineages were respectively 70 (40.2%), 69 (39.7%), 33 (19.0%) and 2 (1.1%). The most common mutations associated with isoniazid and rifampin resistance were respectively katG S315T and rpoB S531L. Potential compensatory mutations in rpoA and rpoC were found in 35 isolates (20.1%). Hispanic ethnicity (OR 26.50, 95%CI 3.73-386.80), infection with an East-Asian M. tuberculosis lineage (OR 30.00, 95%CI 4.20-462.40) and rpoB mutation S531L (OR 4.03, 95%CI 1.05-23.10) were independent factors associated with genotypic clustering. CONCLUSION: Among the bacterial factors studied, East-Asian lineage and rpoB S531L mutation were independently associated with genotypic clustering, suggesting that bacterial factors have an impact on the ability of M. tuberculosis to cause secondary cases.

Impact of Euro-American sublineages of Mycobacterium tuberculosis on new infections among named contacts.

BACKGROUND: The impact of demographic, clinical, and bacterial factors on new infection by Euro-American lineage Mycobacterium tuberculosis among contacts of patients with tuberculosis (TB) has not been evaluated. OBJECTIVE: To describe the risk factors for new infection by Euro-American M. tuberculosis sublineages in San Francisco, California. DESIGN: We included contacts of patients with TB due to Euro-American M. tuberculosis. Sublineages were determined by large-sequence polymorphisms. We used tuberculin skin testing or QuantiFERON®-TB Gold In-Tube to identify contacts with new infection. Regression models with generalized estimating equations were used to determine the risk factors for new infection. RESULTS: We included 1488 contacts from 134 patients with TB. There were 79 (5.3%) contacts with new infection. In adjusted analyses, contacts of patients with TB due to region of difference 219 M. tuberculosis sublineage were less likely to have new infection (OR 0.23, 95%CI 0.06-0.84) than those with other sublineages. Other risk factors for new infection were contacts exposed to more than one patient with TB, contacts exposed for 30 days, or contacts with a history of smoking or excessive alcohol consumption. CONCLUSIONS: In addition to well-known exposure and clinical characteristics, bacterial characteristics independently contribute to the transmissibility of TB in San Francisco.

Evaluation of factors affecting soil carbon sequestration services of stormwater wet retention ponds in varying climate zones.

The carbon sequestration services of stormwater wet retention ponds were investigated in four different climates: U.S., Northern Sweden, Southern Sweden, and Singapore, representing a range of annual mean temperatures, growing season lengths and rainfall depths: geographic factors that were not statistically compared, but have great effect on carbon (C) accumulation. A chronosequence was used to estimate C accumulations rates; C accumulation and decomposition rates were not directly measured. C accumulated significantly over time in vegetated shallow water areas (0-30cm) in the USA (78.4gCm-2yr-1), in vegetated temporary inundation zones in Sweden (75.8gCm-2yr-1), and in all ponds in Singapore (135gCm-2yr-1). Vegetative production appeared to exert a stronger influence on relative C accumulation rates than decomposition. Comparing among the four climatic zones, the effects of increasing rainfall and growing season lengths (vegetative production) outweighed the effects of higher temperature on decomposition rates. Littoral vegetation was a significant source to the soil C pool relative to C sources draining from watersheds. Establishment of vegetation in the shallow water zones of retention ponds is vital to providing a C source to the soil. Thus, the width of littoral shelves containing this vegetation along the perimeter may be increased if C sequestration is a design goal. This assessment establishes that stormwater wet retention ponds can sequester C across different climate zones with generally annual rainfall and lengths of growing season being important general factors for C accumulation.

The Promise, Practice, and State of Planning Tools to Assess Site Vulnerability to Runoff Phosphorus Loss.

Over the past 20 yr, there has been a proliferation of phosphorus (P) site assessment tools for nutrient management planning, particularly in the United States. The 19 papers that make up this special section on P site assessment include decision support tools ranging from the P Index to fate-and-transport models to weather-forecast-based risk calculators. All require objective evaluation to ensure that they are effective in achieving intended benefits to protecting water quality. In the United States, efforts have been underway to compare, evaluate, and advance an array of P site assessment tools. Efforts to corroborate their performance using water quality monitoring data confirms previously documented discrepancies between different P site assessment tools but also highlights a surprisingly strong performance of many versions of the P Index as a predictor of water quality. At the same time, fate-and-transport models, often considered to be superior in their prediction of hydrology and water quality due to their complexity, reveal limitations when applied to site assessment. Indeed, one consistent theme from recent experience is the need to calibrate highly parameterized models. As P site assessment evolves, so too do routines representing important aspects of P cycling and transport. New classes of P site assessment tools are an opportunity to move P site assessment from general, strategic goals to web-based tools supporting daily, operational decisions.

Effects of Riparian Buffer Vegetation and Width: A 12-Year Longitudinal Study.

Agricultural contributions of nitrogen are a serious concern for many water resources and have spurred the implementation of riparian buffer zones to reduce groundwater nitrate (NO). The optimum design for buffers is subject to debate, and there are few long-term studies. The objective of this project was to determine the effectiveness over time (12 yr) of buffer types (trees, switchgrass, fescue, native, and a control) and buffer widths (8 and 15 m) by measuring groundwater NO-N and dissolved organic carbon (DOC) trends. At the intermediate groundwater depth (1.5-2.1 m), NO-N reduction effectiveness was 2.5 times greater (46 vs. 16%) for the wider buffer, and, regardless of width, buffer effectiveness increased 0.62% yr. Buffer vegetative type was never statistically significant. In the deep-groundwater depth (2.1-3.5 m), there was no change in NO-N removal over time, although the statistical interaction of width and vegetative type indicated a wide range of removal rates (19-82%). The DOC concentrations were analyzed at the field/buffer and buffer/stream sampling locations. Depending on location position and groundwater sampling depth, DOC concentrations ranged from 1.6 to 2.8 mg L at Year 0 and increased at a rate of 0.13 to 0.18 mg L yr but always remained low (≤5.0 mg L). Greater DOC concentrations in the intermediate-depth groundwater did not increase NO-N removal; redox measurements indicated intermittent reduced soil conditions may have been limiting. This study suggests that riparian buffer width, not vegetation, is more important for NO-N removal in the middle coastal plain of North Carolina for a newly established buffer.

Comparison of Surface Water Quality and Yields from Organically and Conventionally Produced Sweet Corn Plots with Conservation and Conventional Tillage.

Organic agricultural systems are often assumed to be more sustainable than conventional farming, yet there has been little work comparing surface water quality from organic and conventional production, especially under the same cropping sequence. Our objective was to compare nutrient and sediment losses, as well as sweet corn ( L. var. ) yield, from organic and conventional production with conventional and conservation tillage. The experiment was located in the Appalachian Mountains of North Carolina. Four treatments, replicated four times, had been in place for over 18 yr and consisted of conventional tillage (chisel plow and disk) with conventional production (CT/Conven), conservation no-till with conventional production (NT/Conven), conventional tillage with organic production (CT/Org), and conservation no-till with organic production (NT/Org). Water quality (surface flow volume; nitrogen, phosphorus, and sediment concentrations) and sweet corn yield data were collected in 2011 and 2012. Sediment and sediment-attached nutrient losses were influenced by tillage and cropping system in 2011, due to higher rainfall, and tillage in 2012. Soluble nutrients were affected by the nutrient source and rate, which are a function of the cropping system. Sweet corn marketable yields were greater in conventional systems due to high weed competition and reduced total nitrogen availability in organic treatments. When comparing treatment efficiency (yield kg ha /nutrient loss kg ha ), the NT/Conven treatment had the greatest sweet corn yield per unit of nutrient and sediment loss. Other treatment ratios were similar to each other; thus, it appears the most sustainably productive treatment was NT/Conven.

Reduced sensitivity of the QuantiFERON(®) test in diabetic patients with smear-negative tuberculosis.

SETTING: Immunosuppressive conditions have been associated with low sensitivity of interferon-gamma release assays (IGRAs) and the tuberculin skin test (TST) for the diagnosis of tuberculosis (TB). However, no systematic analysis of patient and bacterial characteristics has been performed before. OBJECTIVE: To determine the sensitivity and the risk factors for false-negative QuantiFERON(®)-TB (QFT) assay and TST in TB patients. DESIGN: We performed a retrospective analysis of data collected in a community-based study of TB in San Francisco, CA, USA. We included 300 TB patients who underwent QFT and TST. RESULTS: The risk factors for false-negative QFT were human immunodeficiency virus infection and the use of QuantiFERON(®)-TB Gold. In patients with sputum smear-negative TB, diabetes mellitus (DM) was associated with false-negative QFT (OR 2.85, 95%CI 1.02-7.97, P = 0.045). TST sensitivity was higher than QFT sensitivity in DM patients (OR 9.46, 95%CI 2.53-35.3). CONCLUSIONS: In San Francisco, QFT sensitivity was lower than that of TST, especially in patients with DM. Stratified analysis by sputum smear results showed that this association was specific to smear-negative TB. In contrast, TST was not affected by the presence of DM.

Sublineages of lineage 4 (Euro-American) Mycobacterium tuberculosis differ in genotypic clustering.

SETTING: Mycobacterium tuberculosis is classified into six phylogenetic lineages, each of which can be divided into sublineages. Sublineages of the same lineage have phenotypic differences, including their capacity to cause disease (pathogenicity). OBJECTIVE: 1) To test the hypothesis that different sublineages of lineage 4, which causes most of the tuberculosis (TB) in the United States, have varying ability to cause secondary cases as determined by genotypic clustering, a proxy for pathogenicity; and 2) to determine if spoligotype and mycobacterial interspersed repetitive units (MIRU) typing could infer sublineage. DESIGN: We included TB cases caused by lineage 4 strains from our community-based study in San Francisco. Sublineage was determined by regions of difference. Genotypic clustering was determined by insertion sequence 6110 and polymorphic guanine-cytosine-rich sequence. Associations between sublineages and patient characteristics were evaluated with adjusted and unadjusted analyses. RESULTS: The most frequent sublineage was H37Rv-like. In the adjusted analysis, sublineage 183 was associated with clustering and homelessness. We found that strains from different sublineages had convergent spoligotype and MIRU types. CONCLUSIONS: Sublineage 183 is associated with genotypic clustering, evidence of its being more able to cause secondary cases than the other lineage 4 sublineages. This finding suggests that bacterial factors contribute to the pathogenesis of TB. Spoligotype and MIRU type cannot be used to infer sublineage.

Comparing phosphorus indices from twelve southern U.S. states against monitored phosphorus loads from six prior southern studies.

Forty-eight states in the United States use phosphorus (P) indices to meet the requirements of their Natural Resources Conservation Service (NRCS) Code 590 Standard, which provides national guidance for nutrient management of agricultural lands. The majority of states developed these indices without consultation or coordination with neighboring states to meet specific local conditions and policy needs. Using water quality and land treatment data from six previously published articles, we compared P loads with P-Index values and ratings using the 12 southern P indices. When total measured P loads were regressed with P-Index rating values, moderate to very strong relationships (0.50 to 0.97) existed for five indices (Arkansas, Florida, Georgia, North Carolina, and South Carolina) and all but one index was directionally correct. Regressions with dissolved P were also moderate to very strong ( of 0.55 to 0.95) for the same five state P indices (Arkansas, Florida, Georgia, North Carolina, and South Carolina); directionality of the Alabama Index was negative. When total measured P loads were transformed to current NRCS 590 Standard ratings (Low [<2.2 kg P ha], Moderate, [2.2-5.5 kg P ha], and High [>5.5 kg P ha]) and these ratings were then compared to the southern-Index ratings, many of the P indices correctly identified Low losses (77%), but most did not correctly identify Moderate or High loss situations (14 and 31%, respectively). This study demonstrates that while many of the P indices were directionally correct relative to the measured water quality data, there is a large variability among southern P indices that may result in different P management strategies being employed under similar conditions.

Differences among sublineages of the East-Asian lineage of Mycobacterium tuberculosis in genotypic clustering.

SETTING: The East-Asian lineage of Mycobacterium tuberculosis is composed of five sublineages, and includes the strains from the Beijing spoligotype family. In some studies these strains were highly pathogenic, although other studies did not support this finding. OBJECTIVE: To determine if the sublineages of the East-Asian lineage of M. tuberculosis differ in their capacity to cause secondary cases, as assessed by genotypic clustering of isolates. DESIGN: In a population-based study of 545 patients with M. tuberculosis from the East-Asian lineage in San Francisco, we used DNA-based fingerprinting to identify genotypic clustering, which was compared among the different sublineages defined by large sequence polymorphism. RESULTS: Strains from sublineage 207 had the highest frequency of genotypic clustering. In the multivariate analysis, only patients born in the United States were associated with clustering. CONCLUSIONS: We found evidence in a univariate analysis that the different East-Asian sublineages of M. tuberculosis have different frequencies of genotypic clustering. The effect size for this difference was unchanged in multivariate analysis, although loss of observations due to missing data resulted in a non-significant P value. It is tantalizing to hypothesize that the different East-Asian sublineages may differ in their capacity to cause secondary cases.