Microbial source tracking leverages a wide range of approaches designed to trace the origins of fecal contamination in aquatic environments. Although source tracking methods are typically employed within the laboratory setting, computational techniques can be leveraged to advance microbial source tracking methodology. Herein, we present a logic regression-based supervised learning approach for the discovery of source-informative genetic markers within intergenic regions across the Escherichia coli genome that can be used for source tracking. With just single intergenic loci, logic regression was able to identify highly source-specific (i.e., exceeding 97.00%) biomarkers for a wide range of host and niche sources, with sensitivities reaching as high as 30.00%-50.00% for certain source categories, including pig, sheep, mouse, and wastewater, depending on the specific intergenic locus analyzed. Restricting the source range to reflect the most prominent zoonotic sources of E. coli transmission (i.e., bovine, chicken, human, and pig) allowed for the generation of informative biomarkers for all host categories, with specificities of at least 90.00% and sensitivities between 12.50% and 70.00%, using the sequence data from key intergenic regions, including emrKY-evgAS, ibsB-(mdtABCD-baeSR), ompC-rcsDB, and yedS-yedR, that appear to be involved in antibiotic resistance. Remarkably, we were able to use this approach to classify 48 out of 113 river water E. coli isolates collected in Northwestern Sweden as either beaver, human, or reindeer in origin with a high degree of consensus-thus highlighting the potential of logic regression modeling as a novel approach for augmenting current source tracking efforts.IMPORTANCEThe presence of microbial contaminants, particularly from fecal sources, within water poses a serious risk to public health. The health and economic burden of waterborne pathogens can be substantial-as such, the ability to detect and identify the sources of fecal contamination in environmental waters is crucial for the control of waterborne diseases. This can be accomplished through microbial source tracking, which involves the use of various laboratory techniques to trace the origins of microbial pollution in the environment. Building on current source tracking methodology, we describe a novel workflow that uses logic regression, a supervised machine learning method, to discover genetic markers in Escherichia coli, a common fecal indicator bacterium, that can be used for source tracking efforts. Importantly, our research provides an example of how the rise in prominence of machine learning algorithms can be applied to improve upon current microbial source tracking methodology.

The recent regulatory spotlight on continuous monitoring (CM) solutions and the rapid development of CM solutions have demanded the characterization of solution performance through regular, rigorous testing using consensus test protocols. This study is the second known implementation of such a protocol involving single-blind controlled testing of 9 CM solutions. Controlled releases of rates (6-7100 g) CH4/h over durations (0.4-10.2 h) under a wind speed range of (0.7-9.9 m/s) were conducted for 11 weeks. Results showed that 4 solutions achieved method detection limits (DL90s) within the tested emission rate range, with all 4 solutions having both the lowest DL90s (3.9 [3.0, 5.5] kg CH4/h to 6.2 [3.7, 16.7] kg CH4/h) and false positive rates (6.9-13.2%), indicating efforts at balancing low sensitivity with a low false positive rate. These results are likely best-case scenario estimates since the test center represents a near-ideal upstream field natural gas operation condition. Quantification results showed wide individual estimate uncertainties, with emissions underestimation and overestimation by factors up to >14 and 42, respectively. Three solutions had >80% of their estimates within a quantification factor of 3 for controlled releases in the ranges of [0.1-1] kg CH4/h and > 1 kg CH4/h. Relative to the study by Bell et al., current solutions performance, as a group, generally improved, primarily due to solutions from the study by Bell et al. that were retested. This result highlights the importance of regular quality testing to the advancement of CM solutions for effective emissions mitigation.

Source attribution has traditionally involved combining epidemiological data with different pathogen characterisation methods, including 7-gene multi locus sequence typing (MLST) or serotyping, however, these approaches have limited resolution. In contrast, whole genome sequencing data provide an overview of the whole genome that can be used by attribution algorithms. Here, we applied a random forest (RF) algorithm to predict the primary sources of human clinical Salmonella Typhimurium (S. Typhimurium) and monophasic variants (monophasic S. Typhimurium) isolates. To this end, we utilised single nucleotide polymorphism diversity in the core genome MLST alleles obtained from 1,061 laboratory-confirmed human and animal S. Typhimurium and monophasic S. Typhimurium isolates as inputs into a RF model. The algorithm was used for supervised learning to classify 399 animal S. Typhimurium and monophasic S. Typhimurium isolates into one of eight distinct primary source classes comprising common livestock and pet animal species: cattle, pigs, sheep, other mammals (pets: mostly dogs and horses), broilers, layers, turkeys, and game birds (pheasants, quail, and pigeons). When applied to the training set animal isolates, model accuracy was 0.929 and kappa 0.905, whereas for the test set animal isolates, for which the primary source class information was withheld from the model, the accuracy was 0.779 and kappa 0.700. Subsequently, the model was applied to assign 662 human clinical cases to the eight primary source classes. In the dataset, 60/399 (15.0%) of the animal and 141/662 (21.3%) of the human isolates were associated with a known outbreak of S. Typhimurium definitive type (DT) 104. All but two of the 141 DT104 outbreak linked human isolates were correctly attributed by the model to the primary source classes identified as the origin of the DT104 outbreak. A model that was run without the clonal DT104 animal isolates produced largely congruent outputs (training set accuracy 0.989 and kappa 0.985; test set accuracy 0.781 and kappa 0.663). Overall, our results show that RF offers considerable promise as a suitable methodology for epidemiological tracking and source attribution for foodborne pathogens.

Although the concentrations of five basic ambient air pollutants in the Yangtze River Delta (YRD) have been reduced since the implementation of the \"Air Pollution Prevention and Control Action Plan\" in 2013, the ozone concentrations still increase. In order to explore the causes of ozone pollution in YRD, we use the GEOS-Chem and its adjoint model to study the sensitivities of ozone to its precursor emissions from different source regions and emission sectors during heavy ozone pollution events under typical circulation patterns. The Multi-resolution Emission Inventory for China (MEIC) of Tsinghua University and 0.25° × 0.3125° nested grids are adopted in the model. By using the T-mode principal component analysis (T-PCA), the circulation patterns of heavy ozone pollution days (observed MDA8 O3 concentrations ≥160 μg m-3) in Nanjing located in the center area of YRD from 2013 to 2019 are divided into four types, with the main features of Siberian Low, Lake Balkhash High, Northeast China Low, Yellow Sea High, and southeast wind at the surface. The adjoint results show that the contributions of emissions emitted from Jiangsu and Zhejiang are the largest to heavy ozone pollution in Nanjing. The 10 % reduction of anthropogenic NOx and NMVOCs emissions in Jiangsu, Zhejiang and Shanghai could reduce the ozone concentrations in Nanjing by up to 3.40 μg m-3 and 0.96 μg m-3, respectively. However, the reduction of local NMVOCs emissions has little effect on ozone concentrations in Nanjing, and the reduction of local NOx emissions would even increase ozone pollution. For different emissions sectors, industry emissions account for 31 %-74 % of ozone pollution in Nanjing, followed by transportation emissions (18 %-49 %). This study could provide the scientific basis for forecasting ozone pollution events and formulating accurate strategies of emission reduction.

Fundamental to effective Legionnaires\' disease outbreak control is the ability to rapidly identify the environmental source(s) of the causative agent, Legionella pneumophila. Genomics has revolutionized pathogen surveillance, but L. pneumophila has a complex ecology and population structure that can limit source inference based on standard core genome phylogenetics. Here, we present a powerful machine learning approach that assigns the geographical source of Legionnaires\' disease outbreaks more accurately than current core genome comparisons. Models were developed upon 534 L. pneumophila genome sequences, including 149 genomes linked to 20 previously reported Legionnaires\' disease outbreaks through detailed case investigations. Our classification models were developed in a cross-validation framework using only environmental L. pneumophila genomes. Assignments of clinical isolate geographic origins demonstrated high predictive sensitivity and specificity of the models, with no false positives or false negatives for 13 out of 20 outbreak groups, despite the presence of within-outbreak polyclonal population structure. Analysis of the same 534-genome panel with a conventional phylogenomic tree and a core genome multi-locus sequence type allelic distance-based classification approach revealed that our machine learning method had the highest overall classification performance-agreement with epidemiological information. Our multivariate statistical learning approach maximizes the use of genomic variation data and is thus well-suited for supporting Legionnaires\' disease outbreak investigations.IMPORTANCEIdentifying the sources of Legionnaires\' disease outbreaks is crucial for effective control. Current genomic methods, while useful, often fall short due to the complex ecology and population structure of Legionella pneumophila, the causative agent. Our study introduces a high-performing machine learning approach for more accurate geographical source attribution of Legionnaires\' disease outbreaks. Developed using cross-validation on environmental L. pneumophila genomes, our models demonstrate excellent predictive sensitivity and specificity. Importantly, this new approach outperforms traditional methods like phylogenomic trees and core genome multi-locus sequence typing, proving more efficient at leveraging genomic variation data to infer outbreak sources. Our machine learning algorithms, harnessing both core and accessory genomic variation, offer significant promise in public health settings. By enabling rapid and precise source identification in Legionnaires\' disease outbreaks, such approaches have the potential to expedite intervention efforts and curtail disease transmission.

Aquaculture located in urban river estuaries, where other anthropogenic activities may occur, has an impact on and may be affected by the environment where they are inserted, namely by the exchange of antimicrobial resistance genes. The latter may ultimately, through the food chain, represent a source of resistance genes to the human resistome. In an exploratory study of the presence of resistance genes in aquaculture sediments located in urban river estuaries, two machine learning models were applied to predict the source of 34 resistome observations in the aquaculture sediments of oysters and gilt-head sea bream, located in the estuaries of the Sado and Lima Rivers and in the Aveiro Lagoon, as well as in the sediments of the Tejo River estuary, where Japanese clams and mussels are collected. The first model included all 34 resistomes, amounting to 53 different antimicrobial resistance genes used as source predictors. The most important antimicrobial genes for source attribution were tetracycline resistance genes tet(51) and tet(L); aminoglycoside resistance gene aadA6; beta-lactam resistance gene blaBRO-2; and amphenicol resistance gene cmx_1. The second model included only oyster sediment resistomes, amounting to 30 antimicrobial resistance genes as predictors. The most important antimicrobial genes for source attribution were the aminoglycoside resistance gene aadA6, followed by the tetracycline genes tet(L) and tet(33). This exploratory study provides the first information about antimicrobial resistance genes in intensive and semi-intensive aquaculture in Portugal, helping to recognize the importance of environmental control to maintain the integrity and the sustainability of aquaculture farms.

Campylobacteriosis causes a significant disease burden in humans worldwide and is the most common type of zoonotic gastroenteritis in Finland. To identify infection sources for domestic Campylobacter infections, we analyzed Campylobacter case data from the Finnish Infectious Disease Register (FIDR) in 2004-2021 and outbreak data from the National Food- and Waterborne Outbreak Register (FWO Register) in 2010-2021, and conducted a pilot case-control study (256 cases and 756 controls) with source attribution and patient sample analysis using whole-genome sequencing (WGS) in July-August 2022. In the FIDR, 41% of the cases lacked information on travel history. Based on the case-control study, we estimated that of all cases, 39% were of domestic origin. Using WGS, 22 clusters of two or more cases were observed among 185 domestic cases, none of which were reported to the FWO register. Based on this case-control study and source attribution, poultry is an important source of campylobacteriosis in Finland. More extensive sampling and comparison of patient, food, animal, and environmental isolates is needed to estimate the significance of other sources. In Finland, campylobacteriosis is more often of domestic origin than FIDR notifications indicate. To identify the domestic cases, travel information should be included in the FIDR notification, and to improve outbreak detection, all domestic patient isolates should be sequenced.

Understanding the causes and sources responsible for severe fine particulate matter (PM2.5) pollution episodes that occur under conducive synoptic weather patterns (SWPs) is essential for regional air quality management. The Yangtze River Delta (YRD) region in eastern China has experienced recurrent severe PM2.5 episodes during the winters from 2013 to 2017. In this study, we employed an objective classification approach, the self-organizing map, to investigate the underlying impact of predominant SWPs on PM2.5 pollution in the YRD. We further conducted a series of source apportionment simulations using the Particulate Source Apportionment Technology (PSAT) tool integrated within the Comprehensive Air Quality Model with Extensions (CAMx) to quantify the source contributions to PM2.5 pollution under different SWPs. Here we identified six predominant SWPs over the YRD that are robustly connected to the evolution of the Siberian High. Considering the regional average PM2.5 anomalies, our results show that polluted SWPs favourable for the occurrence of regional PM2.5 pollution account for 61-78 %. The most conducive SWP, associated with the highest regional exceedance (46 %) of PM2.5 levels, is characterized by noticeable cyclonic anomalies at 850 hPa and stagnant surface weather conditions. Our source apportionment analysis emphasizes the pivotal role of local emissions and intra-regional transport within the YRD in shaping PM2.5 pollution in representative cities. Local emissions have the most significant impact on PM2.5 levels in Shanghai (32-48 %), while PM2.5 pollution in Nanjing, Hangzhou, and Hefei is more influenced by intra-regional transport (33-61 %). Industrial and residential emissions are the dominant sources, contributing 32-41 % and 24-38 % to PM2.5, respectively. Under specific SWPs associated with a stronger influence of inter-regional transport from northern China, there is a synchronously remarkable enhancement in the contribution of residential emissions. Our study pinpoints the opportunities for future air quality planning that would benefit from quantitative source attribution linked to prevailing SWPs.

Based on the ISAM module in the WRF-CMAQ model, this study analyzed the source contribution(both regional and sectoral) of O3 and its precursors(NO2 and VOCs) in Zibo in June 2021. Days with a maximum daily 8-h average(MDA8) O3 higher(lower) than 160 μg·m-3 were defined as polluted(clean) days. Differences in the source contribution between clean days and polluted days were compared, and a typical pollution period was selected for further process analysis. The results showed that NO2 in Zibo mainly came from local emissions in summer, with a relative contribution of 45.1%. Vehicle emissions(33.8%) and natural sources(20.7%) were the primary NO2 sources. VOC contributions from natural sources, solvent usage, and the petrochemical industry were significant, with a total contribution of 78.5%. The MDA8 contribution from local sources was 21.4%, whereas the impact of regional transport(32%) and surrounding cities(26.8%) was also substantial. Among local emission sources, vehicle emissions, the power industry, and the building materials industry contributed 10.9%-18.8% to local MDA8. On O3 pollution days, the MDA8 contribution from local emissions and surrounding cities increased. However, the relative contributions from local sources were similar under different pollution conditions.

Snowpack, which serves as a natural archive of atmospheric deposition of multiple pollutants, is a practical environmental media that can be used for assessing atmospheric records and input of the pollutants to the surface environments and ecosystems. A total of 29 snowpack samples were collected at 20 sampling sites covering three different functional areas of a major city (Harbin) in Northeast China. Two samples at the \"snow layer\" and one or two samples at the \"particulate layer\" were collected at each sampling site in the industrial areas characterized by multi-layer snowpack, and only one sample at the \"snow layer\" was collected at each sampling site in the cultural and recreational as well as agricultural areas. The snow contents of 31 elements (Na, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Y, Cd, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, and Pb) and six major water-soluble inorganic ions (WSIIs, NH4+, K+, Ca2+, NO2-, NO3-, and SO42-) were analyzed. The total mass of the measured elements is dominated (95.8%-99.2%) by crustal elements. Heavy metals only account for 0.77%-4.07% of the total mass of the elements, but are occasionally close to or even above the standard limit in the \"Environmental Quality Standards for Surface Water\" of China (GB3838-2002). SO42- and Ca2+ are the main anion and cation, accounting for 34.9%-81.1% and 1.43%-29.9%, respectively, of the measured total ions. Total atmospheric deposition of crustal elements and heavy metals is dominated by wet deposition in areas near the petrochemical plant and by dry deposition in areas near the cement plant. Coal combustion, industrial emissions, and traffic-related activities lead to the enrichment of heavy metals in the snowpacks of urban and suburban areas, while coal combustion and biomass burning contribute to pollution in rural areas. The cities and regions situated in the western, northwestern, northern, and northeastern directions from Harbin are potential source regions of these pollutant species.