Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform

Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish

Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.

HPB-Chip: An accurate high-throughput qPCR-based tool for rapidly profiling waterborne human pathogenic bacteria in the environment

Waterborne pathogens are threatening public health globally, but profiling multiple human pathogenic bacteria (HPBs) in various polluted environments is still a challenge due to the absence of rapid, high-throughput and accurate quantification tools. This work developed a novel chip, termed the HPB-Chip, based on high-throughput quantitative polymerase chain reactions (HT-qPCR). The HPB-Chip with 33-nL reaction volume could simultaneously complete 10,752 amplification reactions, quantifying 27 HPBs in up to 192 samples with two technical replicates (including those for generating standard curves). Specific positive bands of target genes across different species and single peak melting curves demonstrated high specificity of the HPB-Chip. The mixed plasmid serial dilution test validated its high sensitivity with the limit of quantification (LoD) of averaged 82 copies per reaction for 25 target genes. PCR amplification efficiencies and R2 coefficients of standard curves of the HPB-Chip averaged 101 % and 0.996, respectively. Moreover, a strong positive correlation (Pearson' r: 0.961-0.994, P < 0.001) of HPB concentrations (log10 copies/L) between HPB-Chip and conventional qPCR demonstrated high accuracy of the HPB-Chip. Subsequently, the HPB-Chip has been successfully applied to absolutely quantify 27 HPBs in municipal and hospital wastewater treatment plants (WWTPs) after PMA treatment. A total of 17 HPBs were detected in the 6 full-scale WWTPs, with an additional 19 in the hospital WWTP. Remarkably, Acinetobacter baumannii, Legionella pneumophila, and Arcobacter butzler were present in the final effluent of each municipal WWTP. Overall, the HPB-Chip is an efficient and accurate high-throughput quantification tool to comprehensively and rapidly quantify 27 HPBs in the environment.

The Role of Wastewater Treatment Plants in Dissemination of Antibiotic Resistance: Source, Measurement, Removal and Risk Assessment

Antibiotic Resistance Genes (ARGs) are contaminants of emerging concern with marked potential to impact public and environmental health. This review focusses on factors that influence the presence, abundance, and dissemination of ARGs within Wastewater Treatment Plants (WWTPs) and associated effluents. Antibiotic-Resistant Bacteria (ARB) and ARGs have been detected in the influent and the effluent of WWTPs worldwide. Different levels of wastewater treatment (primary, secondary, and tertiary) show different degrees of removal efficiency of ARGs, with further differences being observed when ARGs are captured as intracellular or extracellular forms. Furthermore, routinely used molecular methodologies such as quantitative polymerase chain reaction or whole genome sequencing may also vary in resistome identification and in quantifying ARG removal efficiencies from WWTP effluents. Additionally, we provide an overview of the One Health risk assessment framework, as well as future strategies on how WWTPs can be assessed for environmental and public health impact.

Effect of fertilizer type on antibiotic resistance genes by reshaping the bacterial community and soil properties

Conventional and bio-organic fertilizers play an important role in maintaining soil health and promoting crop growth. However, the effect of organic fertilizers on the prevalence of antibiotic resistance genes (ARGs) in the vegetable cropping system has been largely overlooked. In this study, we investigated the impacts of soil properties and biotic factors on ARG profiles by analyzing ARG and bacterial communities in vegetable copping soils with a long-term history of manure and bio-organic fertilizer application. The ARG abundance in the soil was significantly increased by 116% with manure application compared to synthetic NPK fertilizer application. This finding was corroborated by our meta-analysis that the longer the duration of manure application, the greater the response of increased soil ARG abundance. However, bio-organic fertilizers containing Trichoderma spp. Significantly reduced ARG contamination by 31% compared to manure application. About half of the ARG variation was explained by changes in bacterial abundance and structure, followed by soil properties. The mitigation of ARG by Trichoderma spp. Is achieved by altering the structure of the bacterial community and weakening the close association between bacteria and ARG prevalence. Taken together, these findings shed light on the contribution of bio-organic fertilizers in mitigating ARG contamination in agricultural soils, which can help manage the ecological risk posed by ARG inputs associated with manure application.

Distribution and co-occurrence patterns of antibiotic resistance genes in black soils in Northeast China

Black soils (Mollisols) are among the most important soil resources for crop production and food security. In China, they are mainly distributed in the northeastern region. To investigate soil antibiotic resistance distribution patterns and monitor soil quality, we randomly chose nine corn fields in Northeast China and analyzed the antibiotic resistance gene (ARG) distribution and co-occurrence patterns on the basis of high-throughput approaches and network analyses. High genetic diversity (136 unique genes) and low ARG abundances (10^-5-10^-2 copies/16S rRNA gene copy) were detected, with relatively few interactions among ARGs. Type I integron genes were prevalent in the soil and were positively correlated with ARGs, which may increase the risk of ARG transmission. Most ARGs were strongly associated with microorganisms. Moreover, several ARGs were significantly correlated with antibiotics, nutrients, and metal elements. The generation and dissemination of ARGs, which were most likely mediated by mobile genetic elements (MGEs) and bacteria, were affected by environmental conditions. These results provide insights into the widespread co-occurrence patterns in soil resistomes.

Characterization of Bacteria and Antibiotic Resistance in Commercially Produced Cheeses Sold in China

ABSTRACT

The consumption of cheese in the People's Republic of China is increasing rapidly. Little is known about the microbiota, the presence of antibiotic-resistant bacteria, or the distribution of antibiotic resistance genes (ARGs) in commercially produced cheeses sold in China. This information is important for evaluating quality and safety. This study was conducted using 16S rRNA gene sequencing to assess the metagenomics of 15 types of cheese. Fourteen bacterial genera were detected, and Lactococcus, Lactobacillus, and Streptococcus were dominant based on number of sequence reads. Multidrug-resistant lactic acid bacteria (i.e., resistant to two or more types of antibiotic) were isolated from most of the types of cheese. Of these isolates, 100 and 91.7% were resistant to streptomycin and sulfamethoxazole, respectively, and genes involved in acquired resistance to streptomycin (strB) and sulfonamides (sul2) were detected with high frequency. To analyze the distribution of ARGs in the cheeses overall, 309 ARGs from eight categories and nine transposase genes were profiled. A total of 169 ARGs were detected in the 15 cheeses; their occurrence and abundance varied significantly between cheeses. Our study revealed diverse bacteria and ARGs in cheeses sold in China. The risks associated with multidrug resistance among dominant lactic acid bacteria are of great concern.

HIGHLIGHTS

Advancements in detection and removal of antibiotic resistance genes in sludge digestion: A state-of-art review

Sludge from wastewater treatment plants can act as a repository and crucial environmental provider of antibiotic resistance genes (ARGs). Over the past few years, people's knowledge regarding the occurrence and removal of ARGs in sludge has broadened remarkably with advancements in molecular biological techniques. Anaerobic and aerobic digestion were found to effectively achieve sludge reduction and ARGs removal. This review summarized advanced detection and removal techniques of ARGs, in the last decade, in the sludge digestion field. The fate of ARGs due to different sludge digestion strategies (i.e., anaerobic and aerobic digestion under mesophilic or thermophilic conditions, and in combination with relevant pretreatment technologies (e.g., thermal hydrolysis pretreatment, microwave pretreatment and alkaline pretreatment) and additives (e.g., ferric chloride and zero-valent iron) were systematically summarized and compared in this review. To date, this is the first review that provides a comprehensive assessment of the state-of-the-art technologies and future recommendations.

Distribution of Metal Resistance Genes in Estuarine Sediments and Associated Key Impact Factors

Currently, little is known about the distribution of metal resistance genes (MRGs) in estuarine sediments. In this study, we used the high-throughput quantitative real-time polymerase chain reaction (HT-qPCR) to determine the distribution of MRGs in the sediments of an estuary system and the associated key impact factors. The relative abundance of the detected MRGs showed a decreasing trend from the river inlet toward the sea and a decrease from the middle area of the estuary to the near-shore areas on both sides; these decreases were higher in the summer than in the winter. In the estuary system during the summer, the abundance of Zn- and Cu-MRGs from the river inlet to the sea decreased by 99.5% and 93.6%, whereas those of Hg- and Cd-Zn-Co-MRGs increased by 51.5% and 16.7%, respectively. Moreover, the abundance of Zn- and Cu-MRGs in the winter decreased by 88.6% and 97.7%, respectively, whereas that of Cd-Bi-Zn-Pb-MRGs increased by 729.6%. Furthermore, the abundances of MRGs and mobile genetic elements (MGEs) were significantly positively correlated with the levels of antibiotic residues and heavy metals as well as with the particle size and total organic carbon content of the sediment; however, they were significantly negatively correlated with seawater salinity and the oxidation and reduction potential (E_h) and pH of the sediment. The abundance of MGEs was significantly positively correlated with the abundance of MRGs in the sediment. Our findings suggest that antibiotic residues facilitated the proliferation and propagation of MRGs by promoting MGEs in estuarine sediments.

Distance dilution of antibiotic resistance genes of sediments in an estuary system in relation to coastal cities

Coastal tourist and industrial cities are most likely to have differential effects on the distance dilution of antibiotic resistance genes (ARGs) in an estuary system. This study used high-throughput fluorescence quantitative polymerase chain reaction to identify sediment ARGs in two typical estuaries of coastal tourist and industrial cities (Xiamen and Taizhou) in China. The distance dilution of ARGs and its relationship with key environmental factors were analysed. The results indicated that along the river inlet towards the sea, the distance dilution effect on ARG abundance in estuary sediments of Taizhou was approximately double that in Xiamen, and the macrolide, lincosamide, and streptogramin B (MLSB) and vancomycin genes were replaced by the fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol (FCA) and β-lactam genes in Taizhou, whereas β-lactam genes succeeded the MLSB and sul genes in Xiamen. The abundance and number of ARGs and mobile genetic elements (MGEs) were positively correlated with the particle size and total organic carbon (TOC) contents of sediments, whereas they were negatively associated with the oxidation and reduction potential (E_h) and pH of sediments, as well as the seawater salinity. The sediment particle size (SPZ) was the dominant physicochemical factor affecting the abundance of ARGs (r = 0.826, p < 0.05) and MGEs (r = 0.850, p < 0.01). These findings suggest that although the distance dilution effect on the ARG abundance of estuary sediments of the industrial city is greater than that of the tourist city, the larger SPZ, higher TOC content, and lower salinity, pH, and E_h in estuary regions adjacent to the industrial city can more significantly facilitate the proliferation and propagation of ARGs in the sediments.

Bacterial community assembly and antibiotic resistance genes in the lettuce-soil system upon antibiotic exposure

Bacteria and antibiotic resistance genes (ARGs) in vegetables may influence human gut microbiome and ultimately human health. However, little is known about how vegetable microbiomes and ARGs respond to exposure of anthropogenic antibiotics from crop irrigation water. This study investigated bacterial community assembly and ARG profiles in lettuce (Lactuca sativa) shoots and roots, rhizosphere soil, and bulk soil irrigated with antibiotics-containing water, using 16S rRNA amplicon sequencing and high throughput real-time qPCR, respectively. With antibiotic exposure alpha diversity values remained unchanged for the rhizosphere soil and lettuce roots, but were significantly decreased for the bulk soil and lettuce shoots (p < 0.05). Based on calculations of normalized stochastic ratio (NST), bacterial community assembly was more stochastic in the rhizosphere soil (83%-86%) and bulk soil (81%-84%) than in the lettuce roots (45%-48%). These results suggest a stronger deterministic control of plant roots in bacterial community assembly. Antibiotic exposure did not substantially change the stochasticity of the bacterial communities, despite the NST values were significantly increased by ~3% (p < 0.05) for the rhizosphere soil and lettuce roots and significantly decreased by ~3% (p < 0.05) for the bulk soil, when comparing treatments with and without antibiotics. The levels of Methylophilaceae and Beijerinckiaceae were significantly different between the antibiotic and antibiotics-free treatments. Antibiotic exposure consistently increased the abundance of mobile genetic elements (MGEs) in the rhizosphere soil, but not in other samples. No consistent changes in ARGs were observed with and without antibiotic exposure. Finally, the correlation network analysis revealed that the rhizosphere soil may be a hotspot for interactions between ARGs, MGEs, bacterial communities, and antibiotic residues.

High-throughput diagnosis of human pathogens and fecal contamination in marine recreational water

Waterborne pathogens and their associated diseases are major threats to public health, and surveillance of pathogens and identification of the sources of pollution are imperative for preventing infections. However, simultaneously quantitative detection of multiple pathogens and pollution sources in water environments is the major challenge. In this study, we developed and validated a highly sensitive (mostly >80%) and highly specific (>99%) high-throughput quantitative PCR (HT-qPCR) approach, which could simultaneously quantify 68 marker genes of 33 human pathogens and 23 fecal markers of 10 hosts. The HT-qPCR approach was then successfully used to investigate pathogens and fecal pollution in marine recreational water samples of Xiamen, China. Totally, seven pathogenic marker genes were found in 13 beach bathing waters, which targeted Acanthamoeba spp., Clostridium perfringens, enteropathogenic Escherichia coli, Klebsiella pneumoniae, Vibrio cholera/V. parahaemolyticus and Legionella spp.. Fecal markers from human and dog were the most frequently detected, indicating human and dog feces were the main contamination in the recreational waters. Nanopore sequencing of full-length 16S rRNA gene revealed that 28 potential human pathogens were detected and electrical conductivity, salinity, oxidation-reduction potential and dissolved oxygen were significantly correlated with the variation in bacterial community. Our results demonstrated that HT-qPCR approach had the potential rapid quantification of microbial contamination, providing useful data for assessment of microbial pathogen associated health risk and development of management practices to protect human health.

The incidence of antibiotic resistance within and beyond the agricultural ecosystem: A concern for public health

The agricultural ecosystem creates a platform for the development and dissemination of antimicrobial resistance, which is promoted by the indiscriminate use of antibiotics in the veterinary, agricultural, and medical sectors. This results in the selective pressure for the intrinsic and extrinsic development of the antimicrobial resistance phenomenon, especially within the aquaculture‐animal‐manure‐soil‐water‐plant nexus. The existence of antimicrobial resistance in the environment has been well documented in the literature. However, the possible transmission routes of antimicrobial agents, their resistance genes, and naturally selected antibiotic‐resistant bacteria within and between the various niches of the agricultural environment and humans remain poorly understood. This study, therefore, outlines an overview of the discovery and development of commonly used antibiotics; the timeline of resistance development; transmission routes of antimicrobial resistance in the agro‐ecosystem; detection methods of environmental antimicrobial resistance determinants; factors involved in the evolution and transmission of antibiotic resistance in the environment and the agro‐ecosystem; and possible ways to curtail the menace of antimicrobial resistance.

High-Throughput Multiparallel Enteropathogen Detection via Nano-Liter qPCR

Quantitative molecular diagnostic methods can effectively detect pathogen-specific nucleic acid sequences, but costs associated with multi-pathogen panels hinder their widespread use in research trials. Nano-liter qPCR (nL-qPCR) is a miniaturized tool for quantification of multiple targets in large numbers of samples based on assay parallelization on a single chip, with potentially significant cost-savings due to rapid throughput and reduced reagent volumes. We evaluated a suite of novel and published assays to detect 17 enteric pathogens using a commercially available nL-qPCR technology. Amplification efficiencies ranged from 88 to 98% (mean 91%) and were reproducible across four operators at two separate facilities. When applied to fecal material, assays were sensitive and selective (99.8% of DNA amplified were genes from the target organism). Due to nanofluidic volumes, detection limits were 1-2 orders of magnitude less sensitive for nL-qPCR than an enteric TaqMan Array Card (TAC). However, higher detection limits do not hinder detection of diarrhea-causing pathogen concentrations. Compared to TAC, nL-qPCR displayed 99% (95% CI 0.98, 0.99) negative percent agreement and 62% (95% CI 0.59, 0.65) overall positive percent agreement for presence of pathogens across diarrheal and non-diarrheal fecal samples. Positive percent agreement was 89% among samples with concentrations above the nL-qPCR detection limits. nL-qPCR assays showed an underestimation bias of 0.34 log₁₀ copies/gram of stool [IQR -0.40, -0.28] compared with TAC. With 12 times higher throughput for a sixth of the per-sample cost of the enteric TAC, the nL-qPCR chip is a viable alternative for enteropathogen quantification for studies where other technologies are cost-prohibitive.

Fate and abundance of antibiotic resistance genes on microplastics in facility vegetable soil

Microplastics (MPs) and antibiotic resistance genes (ARGs) coexist widely in farmland soils, but the fate and abundance of ARGs on MPs is rarely explored. In this study, high-throughput fluorescent quantitative polymerase chain reaction was used to determine ARGs on MPs in facility vegetable soil. The results indicated that when the particle size of the MPs was larger, the weathering was more serious, or the MPs came from soils with a long vegetable cultivation period, the levels of antibiotics and heavy metals on the MPs were higher. The distribution of the detected ARGs types on distinct MPs showed changes. Compared with weakly weathered MPs, the detected beta lactamase and aminoglycoside resistance genes on strongly weathered MPs were decreased by 2.6% and 1.7%, while the detected sul-ARGs and Macrolide-Lincosamide-Streptogramin B (MLSB) resistance genes were increased by 1.5% and 2.8%. Compared with smaller MPs, the detected MLSB and vancomycin resistance genes on larger MPs were decreased by 2.0% and 1.4%, while the detected fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol (FCA) resistance genes and sul-ARGs were increased by 1.2% and 1.0%. Compared with MPs in soil after three years of vegetable cultivation, the detected FCA resistance genes and sul-ARGs on MPs in soil after ten years of vegetable cultivation were decreased by 1.3% and 1.6%, while the detected beta lactamase and aminoglycoside resistance genes were increased by 1.0% and 1.7%. This study suggests that MPs with larger size, stronger weathering or from soil after long-term vegetable cultivation adsorb more antibiotics and heavy metals and cause more mobile genetic elements, which can contribute to antibiotic resistance on the MPs.

TCR Convergence in Individuals Treated With Immune Checkpoint Inhibition for Cancer

Tumor antigen-driven selection may expand T cells having T cell receptors (TCRs) of shared antigen specificity but different amino acid or nucleotide sequence in a process known as TCR convergence. Substitution sequencing errors introduced by TCRβ (TCRB) repertoire sequencing may create artifacts resembling TCR convergence. Given the anticipated differences in substitution error rates across different next-generation sequencing platforms, the choice of platform could be consequential. To test this, we performed TCRB sequencing on the same peripheral blood mononuclear cells (PBMC) from individuals with cancer receiving anti-CTLA-4 or anti-PD-1 using an Illumina-based approach (Sequenta) and an Ion Torrent-based approach (Oncomine TCRB-LR). While both approaches found similar TCR diversity, clonality, and clonal overlap, we found that Illumina-based sequencing resulted in higher TCR convergence than with the Ion Torrent approach. To build upon this initial observation we conducted a systematic comparison of Illumina-based TCRB sequencing assays, including those employing molecular barcodes, with the Oncomine assay, revealing differences in the frequency of convergent events, purportedly artifactual rearrangements, and sensitivity of detection. Finally, we applied the Ion Torrent-based approach to evaluate clonality and convergence in a cohort of individuals receiving anti-CTLA-4 blockade for cancer. We found that clonality and convergence independently predicted response and could be combined to improve the accuracy of a logistic regression classifier. These results demonstrate the importance of the sequencing platform in assessing TCRB convergence.

Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce

New classes of emerging contaminants such as pharmaceuticals, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs) have received increasing attention due to rapid increases of their abundance in agroecosystems. As food consumption is a direct exposure pathway of pharmaceuticals, ARB, and ARGs to humans, it is important to understand changes of bacterial communities and ARG profiles in food crops produced with contaminated soils and waters. This study examined the level and type of ARGs and bacterial community composition in soil, and lettuce shoots and roots under soil-surface or overhead irrigation with pharmaceuticals-contaminated water, using high throughput qPCR and 16S rRNA amplicon sequencing techniques, respectively. In total 52 ARG subtypes were detected in the soil, lettuce shoot and root samples, with mobile genetic elements (MGEs), and macrolide-lincosamide-streptogramin B (MLSB) and multidrug resistance (MDR) genes as dominant types. The overall abundance and diversity of ARGs and bacteria associated with lettuce shoots under soil-surface irrigation were lower than those under overhead irrigation, indicating soil-surface irrigation may have lower risks of producing food crops with high abundance of ARGs. ARG profiles and bacterial communities were sensitive to pharmaceutical exposure, but no consistent patterns of changes were observed. MGE intl1 was consistently more abundant with pharmaceutical exposure than in the absence of pharmaceuticals. Pharmaceutical exposure enriched Proteobacteria (specifically Methylophilaceae) and decreased bacterial alpha diversity. Finally, there were significant interplays among bacteria community, antibiotic concentrations, and ARG abundance possibly involving hotspots including Sphingomonadaceae, Pirellulaceae, and Chitinophagaceae, MGEs (intl1 and tnpA_1) and MDR genes (mexF and oprJ).

Synergistic effects of key parameters on the fate of antibiotic resistance genes during swine manure composting

Livestock manure is a reservoir of antibiotic resistance genes (ARGs), posing a potential risk to environment and human health. However, there has been no optimization study about the comprehensive composting treatment for livestock manure ARGs based on multiple operation factors. In this study, anaerobic composting of swine manure in light was conducted under different combined conditions of composting time, temperature, water content, pH, heavy metal passivators and wheat straw. The diversity and relative abundance of ARGs in the compost were detected using high throughput quantitative real-time PCR, and the concentrations of antibiotics and heavy metals were determined. The results showed that under the optimized conditions (composting time, 30 d; temperature, 50 °C; water content, 50%; pH 9.0; heavy metal passivators and wheat straw), compared with the control, the detected number of ARGs and mobile genetic elements in the compost was reduced by 45% and 27.3%, and their relative abundance decreased by 33.9% and 36.9%, respectively. Moreover, the exchangeable heavy metal content of the compost declined by 34.7-57.1%, and the antibiotic level decreased by 28.8-77.8%. This study proposes that synergistic effects of key parameters can effectively mitigate the combined contamination of ARGs, antibiotics, and heavy metals in swine manure. MAIN FINDING: Optimized parameters (anaerobic composting time 30 d, temperature 50 °C, water content 50%, pH 9.0) effectively mitigated the combined pollution of ARGs, antibiotics, and heavy metals in swine manure.

Microfluidic-Based Nucleic Acid Amplification Systems in Microbiology

Rapid, sensitive, and selective bacterial detection is a hot topic, because the progress in this research area has had a broad range of applications. Novel and innovative strategies for detection and identification of bacterial nucleic acids are important for practical applications. Microfluidics is an emerging technology that only requires small amounts of liquid samples. Microfluidic devices allow for rapid advances in microbiology, enabling access to methods of amplifying nucleic acid molecules and overcoming difficulties faced by conventional. In this review, we summarize the recent progress in microfluidics-based polymerase chain reaction devices for the detection of nucleic acid biomarkers. The paper also discusses the recent development of isothermal nucleic acid amplification and droplet-based microfluidics devices. We discuss recent microfluidic techniques for sample preparation prior to the amplification process.

Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent

Wastewater treatment plants (WWTPs) collect wastewater from various sources for a multi-step treatment process. By mixing a large variety of bacteria and promoting their proximity, WWTPs constitute potential hotspots for the emergence of antibiotic resistant bacteria. Concerns have been expressed regarding the potential of WWTPs to spread antibiotic resistance genes (ARGs) from environmental reservoirs to human pathogens. We utilized epicPCR (Emulsion, Paired Isolation and Concatenation PCR) to detect the bacterial hosts of ARGs in two WWTPs. We identified the host distribution of four resistance-associated genes (tetM, int1, qacEΔ1and bla_OXA-58) in influent and effluent. The bacterial hosts of these resistance genes varied between the WWTP influent and effluent, with a generally decreasing host range in the effluent. Through 16S rRNA gene sequencing, it was determined that the resistance gene carrying bacteria include both abundant and rare taxa. Our results suggest that the studied WWTPs mostly succeed in decreasing the host range of the resistance genes during the treatment process. Still, there were instances where effluent contained resistance genes in bacterial groups not carrying these genes in the influent. By permitting exhaustive profiling of resistance-associated gene hosts in WWTP bacterial communities, the application of epicPCR provides a new level of precision to our resistance gene risk estimates.

Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence

Integrated antibiotic resistance (AR) surveillance is one of the objectives of the World Health Organization global action plan on antimicrobial resistance. Urban wastewater treatment plants (UWTPs) are among the most important receptors and sources of environmental AR. On the basis of the consistent observation of an increasing north-to-south clinical AR prevalence in Europe, this study compared the influent and final effluent of 12 UWTPs located in seven countries (Portugal, Spain, Ireland, Cyprus, Germany, Finland, and Norway). Using highly parallel quantitative polymerase chain reaction, we analyzed 229 resistance genes and 25 mobile genetic elements. This first trans-Europe surveillance showed that UWTP AR profiles mirror the AR gradient observed in clinics. Antibiotic use, environmental temperature, and UWTP size were important factors related with resistance persistence and spread in the environment. These results highlight the need to implement regular surveillance and control measures, which may need to be appropriate for the geographic regions.

AsChip: A High-Throughput qPCR Chip for Comprehensive Profiling of Genes Linked to Microbial Cycling of Arsenic

Arsenic (As) is a ubiquitous toxic element adversely affecting human health. Microbe-mediated cycling of As is largely mediated by detoxification and energy metabolism in microorganisms. We here report the development of a novel high-throughput qPCR (HT-qPCR) chip (AsChip) for comprehensive profiling of genes involved in microbial As cycling (here collectively termed "As genes"). AsChip contained 81 primer sets targeting 19 As genes and the 16S rRNA gene as a reference gene. Gene amplicon sequencing showed high identity (>96%) of newly designed primers corresponding to their targets. AsChip displayed high sensitivity (plasmid template serial dilution test; r = -0.99), with more than 96% of all PCR assays yielding true positive signals. R² coefficients for standard curves and PCR amplification efficiencies averaged 0.98 and 0.99, respectively. A high correlation between C_T values obtained by AsChip and conventional qPCR was obtained ( r = 0.962, P < 0.001). Finally, we successfully applied AsChip on soil samples from a chromium-copper-arsenic-contaminated field site and identified diverse As genes with total abundance average of 0.4 As gene copies per 16S rRNA. Our results indicate that AsChip constitutes a robust tool for comprehensive quantitative profiling of As genes in environmental samples.

Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review

Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGen^TM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.

Assessing the safety of thermally processed penicillin mycelial dreg following the soil application: Organic matter's maturation and antibiotic resistance genes

To degrade the residual penicillin G in penicillin mycelial dreg (PMD), thermal treatment was used as a pretreatment for practical disposal. Given that the characteristics of treated-PMD aren't adequately clear, a lab-scale experiment was conducted to verify its safety assessment for land application under the following points: (i) variation of penicillin G residue (ii) maturity of organic matter (OM) (iii) phytotoxicity (iv) abundance of antibiotic resistance genes (ARGs). A high-throughput quantitative polymerase chain reaction (HT-qPCR) method was used to perform an overall investigation of soil ARGs. The results show that heat treatment effectively degrades 98% of penicillin in PMD within 120 min. After thermal treatment, the treated-PMD was applied to soil. The original penicillin level was considerably lower and completely degraded within 4 days. Variation of germination index (GI) implied that the created phytotoxicity was significantly reduced. Furthermore, compared with PMD, the addition of treated-PMD didn't cause enrichment of soil ARGs in diversity and abundance. Therefore, heat treatment can be considered as an effective pretreatment for PMD practical application.

Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements

The high-throughput antibiotic resistance gene (ARG) qPCR array, initially published in 2012, is increasingly used to quantify resistance and mobile determinants in environmental matrices. Continued utility of the array; however, necessitates improvements such as removing or redesigning questionable primer sets, updating targeted genes and coverage of available sequences. Towards this goal, a new primer design tool (EcoFunPrimer) was used to aid in identification of conserved regions of diverse genes. The total number of assays used for diverse genes was reduced from 91 old primer sets to 52 new primer sets, with only a 10% loss in sequence coverage. While the old and new array both contain 384 primer sets, a reduction in old primer sets permitted 147 additional ARGs and mobile genetic elements to be targeted. Results of validating the updated array with a mock community of strains resulted in over 98% of tested instances incurring true positive/negative calls. Common queries related to sensitivity, quantification and conventional data analysis (e.g. Ct cutoff value, and estimated genomic copies without standard curves) were also explored. A combined list of new and previously used primer sets is provided with a recommended set based on redesign of primer sets and results of validation.

Integrating omics to unravel the stress-response mechanisms in probiotic bacteria: Approaches, challenges, and prospects

Identifying the stress-response mechanism of probiotic bacteria has always captivated the interest of food producers. It is crucial to identify probiotic bacteria that have increased stress tolerance to survive during production, processing, and storage of food products. However, in order to achieve high resistance to environmental factors, there is a need to better understand stress-induced responses and adaptive mechanisms. With advances in bacterial genomics, there has been an upsurge in the application of other omic platforms such as transcriptomics, proteomics, metabolomics, and some more recent ones such as interactomics, fluxomics, and phenomics. These omic technologies have revolutionized the functional genomics and their application. There have been several studies implementing various omic technologies to investigate the stress responses of probiotic bacteria. Integrated omics has the potential to provide in-depth information about the mechanisms of stress-induced responses in bacteria. However, there remain challenges in integrating information from different omic platforms. This review discusses current omic techniques and challenges faced in integrating various omic platforms with focus on their use in stress-response studies.

Antibiotic-Resistance Genes in Waste Water

Waste water and waste water treatment plants can act as reservoirs and environmental suppliers of antibiotic resistance. They have also been proposed to be hotspots for horizontal gene transfer, enabling the spread of antibiotic resistance genes between different bacterial species. Waste water contains antibiotics, disinfectants, and metals which can form a selection pressure for antibiotic resistance, even in low concentrations. Our knowledge of antibiotic resistance in waste water has increased tremendously in the past few years with advances in the molecular methods available. However, there are still some gaps in our knowledge on the subject, such as how active is horizontal gene transfer in waste water and what is the role of the waste water treatment plant in the environmental resistome? The purpose of this review is to briefly describe some of the main methods for studying antibiotic resistance in waste waters and the latest research and main knowledge gaps on the issue. In addition, some future research directions are proposed.

Characterization and quantification of antibiotic resistance genes in manure of piglets and adult pigs fed on different diets

Studies have shown that pig manure is a reservoir of antibiotic resistance genes (ARGs). However, little is known about the characteristics of ARGs in the manure of piglets and adult pigs fed on different diets. In the present study, the ARG characteristics of the manure of piglets and adult pigs fed on different diets (feed, grain) were analyzed using high-throughput fluorescence quantitative PCR. Correlations between heavy metals, antibiotics, and ARGs in pig manure were analyzed. The results showed that the heavy metal and antibiotic contents in the manure of pigs receiving feed significantly exceeded those in the manure of pigs receiving grain. The heavy metal and antibiotic contents were higher in manure of piglets than in that of adult pigs. Feed significantly increased the ARG diversity in the pig manure. The ARG diversity was higher in manure of piglets than in that of adult pigs. In the manure of pigs receiving feed, 25 (from piglets), 12 (from adult pigs) ARGs were enriched significantly compared with pig fed with grain. In particular, sat4 (in piglets) and vatE-01 (in adult pigs) showed the highest enrichment, being increased by 59 and 19-fold, respectively. The ARG diversity correlated positively with the concentrations of antibiotics and heavy metals in the manure.

Modulatory Influence of Segmented Filamentous Bacteria on Transcriptomic Response of Gnotobiotic Mice Exposed to TCDD

Environmental toxicants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AhR), are known to induce host toxicity and structural shifts in the gut microbiota. Key bacterial populations with similar or opposing functional responses to AhR ligand exposure may potentially help regulate expression of genes associated with immune dysfunction. To examine this question and the mechanisms for AhR ligand-induced bacterial shifts, C57BL/6 gnotobiotic mice were colonized with and without segmented filamentous bacteria (SFB) – an immune activator. Mice were also colonized with polysaccharide A producing Bacteroides fragilis – an immune suppressor to serve as a commensal background. Following colonization, mice were administered TCDD (30 μg/kg) every 4 days for 28 days by oral gavage. Quantified with the nCounter^® mouse immunology panel, opposing responses in ileal gene expression (e.g., genes associated with T-cell differentiation via the class II major histocompatibility complex) as a result of TCDD dosing and SFB colonization were observed. Genes that responded to TCDD in the presence of SFB did not show a significant response in the absence of SFB, and vice versa. Regulatory T-cells examined in the mesenteric lymph-nodes, spleen, and blood were also less impacted by TCDD in mice colonized with SFB. TCDD-induced shifts in abundance of SFB and B. fragilis compared with previous studies in mice with a traditional gut microbiome. With regard to the mouse model colonized with individual populations, results indicate that TCDD-induced host response was significantly modulated by the presence of SFB in the gut microbiome, providing insight into therapeutic potential between AhR ligands and key commensals.

TCDD administered on activated carbon eliminates bioavailability and subsequent shifts to a key murine gut commensal

Activated carbon (AC) is an increasingly attractive remediation alternative for the sequestration of dioxins at contaminated sites globally. However, the potential for AC to reduce the bioavailability of dioxins in mammals and the residing gut microbiota has received less attention. This question was partially answered in a recent study examining 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced hallmark toxic responses in mice administered with TCDD sequestered by AC or freely available in corn oil by oral gavage. Results from that study support the use of AC to significantly reduce the bioavailability of TCDD to the host. Herein, we examined the bioavailability of TCDD sequestered to AC on a key murine gut commensal and the influence of AC on the community structure of the gut microbiota. The analysis included qPCR to quantify the expression of segmented filamentous bacteria (SFB) in the mouse ileum, which has responded to TCDD-induced host toxicity in previous studies and community structure via sequencing the 16S ribosomal RNA (rRNA) gene. The expression of SFB 16S rRNA gene and functional genes significantly increased with TCDD administered with corn oil vehicle. Such a response was absent when TCDD was sequestered by AC. In addition, AC appeared to have a minimal influence on murine gut community structure and diversity, affecting only the relative abundance of Lactobacillaceae and two other groups. Results of this study further support the remedial use of AC for eliminating bioavailability of TCDD to host and subsequent influence on the gut microbiome.

Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers

Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R² = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively "untrained" personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.

Influence of Manure Application on the Environmental Resistome under Finnish Agricultural Practice with Restricted Antibiotic Use

The co-occurrence of antibiotic-resistance genes (ARGs) and mobile genetic elements (MGEs) in farm environments can potentially foster the development of antibiotic-resistant pathogens. We studied the resistome of Finnish dairy and swine farms where use of antibiotics is limited to treating bacterial infections and manure is only applied from April to September. The resistome of manure, soil, and tile drainage water from the ditch was investigated from the beginning of the growing season until forage harvest. The relative ARG and MGE abundance was measured using a qPCR array with 363 primer pairs. Manure samples had the highest abundance of ARGs and MGEs, which increased during storage. Immediately following land application, the ARGs abundant in manure were detected in soil, but their abundance decreased over time with many becoming undetectable. This suggests that increases in ARG abundances after fertilizing are temporary and occur annually under agricultural practices that restrict antibiotic use. A few of the ARGs were detected in the ditch water, but most of them were undetected in the manure. Our results document the dissipation and dissemination off farm of ARGs under Finnish limited antibiotic use and suggest that such practices could help reduce the load of antibiotic-resistance genes in the environment.

Virulence factor activity relationships (VFARs): a bioinformatics perspective

Virulence factor activity relationships (VFARs) - a concept loosely based on quantitative structure-activity relationships (QSARs) for chemicals was proposed as a predictive tool for ranking risks due to microorganisms relevant to water safety. A rapid increase in sequencing capabilities and bioinformatics tools has significantly increased the potential for VFAR-based analyses. This review summarizes more than 20 bioinformatics databases and tools, developed over the last decade, along with their virulence and antimicrobial resistance prediction capabilities. With the number of bacterial whole genome sequences exceeding 241 000 and metagenomic analysis projects exceeding 13 000 and the ability to add additional genome sequences for few hundred dollars, it is evident that further development of VFARs is not limited by the availability of information at least at the genomic level. However, additional information related to co-occurrence, treatment response, modulation of virulence due to environmental and other factors, and economic impact must be gathered and incorporated in a manner that also addresses the associated uncertainties. Of the bioinformatics tools, a majority are either designed exclusively for virulence/resistance determination or equipped with a dedicated module. The remaining have the potential to be employed for evaluating virulence. This review focusing broadly on omics technologies and tools supports the notion that these tools are now sufficiently developed to allow the application of VFAR approaches combined with additional engineering and economic analyses to rank and prioritize organisms important to a given niche. Knowledge gaps do exist but can be filled with focused experimental and theoretical analyses that were unimaginable a decade ago. Further developments should consider the integration of the measurement of activity, risk, and uncertainty to improve the current capabilities.

Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils

Soil is an important environmental reservoir of antibiotic resistance genes (ARGs), which are increasingly recognized as environmental contaminants. Methods to assess the risks associated with the acquisition or transfer of resistance mechanisms are still underdeveloped. Quantification of background levels of antibiotic resistance genes and what alters those is a first step in understanding our environmental resistome. Toward this goal, 62 samples were collected over 3 years from soils near the 30-year old Gondwana Research Station and for 4 years before and during development of the new Jang Bogo Research Station, both at Terra Nova Bay in Antarctica. These sites reflect limited and more extensive human impact, respectively. A qPCR array with 384 primer sets targeting antibiotic resistance genes and mobile genetic elements (MGEs) was used to detect and quantify these genes. A total of 73 ARGs and MGEs encompassing eight major antibiotic resistance gene categories were detected, but most at very low levels. Antarctic soil appeared to be a common reservoir for seven ARGs since they were present in most samples (42%-88%). If the seven widespread genes were removed, there was a correlation between the relative abundance of MGEs and ARGs, more typical of contaminated sites. There was a relationship between ARG content and distance from both research stations, with a significant effect at the Jang Bogo Station especially when excluding the seven widespread genes; however, the relative abundance of ARGs did not increase over the 4 year period. Silt, clay, total organic carbon, and SiO₂ were the top edaphic factors that correlated with ARG abundance. Overall, this study identifies that human activity and certain soil characteristics correlate with antibiotic resistance genes in these oligotrophic Antarctic soils and provides a baseline of ARGs and MGEs for future comparisons.

Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens

An antibiotic resistance (AR) Dashboard application is being developed regarding the occurrence of antibiotic resistance genes (ARG) and bacteria (ARB) in environmental and clinical settings. The application gathers and geospatially maps AR studies, reported occurrence and antibiograms, which can be downloaded for offline analysis. With the integration of multiple data sets, the database can be used on a regional or global scale to identify hot spots for ARGs and ARB; track and link spread and transmission, quantify environmental or human factors influencing presence and persistence of ARG harboring organisms; differentiate natural ARGs from those distributed via human or animal activity; cluster and compare ARGs connections in different environments and hosts; and identify genes that can be used as proxies to routinely monitor anthropogenic pollution. To initially populate and develop the AR Dashboard, a qPCR ARG array was tested with 30 surface waters, primary influent from three waste water treatment facilities, ten clinical isolates from a regional hospital and data from previously published studies including river, park soil and swine farm samples. Interested users are invited to download a beta version (available on iOS or Android), submit AR information using the application, and provide feedback on current and prospective functionalities.

Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens - A Review

Chicken is a major food source for humans, hence it is important to understand the mechanisms involved in nutrient absorption in chicken. In the gastrointestinal tract (GIT), the microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, thereby affecting both growth and health of chicken. There is little information on the diversity and functions of chicken GIT microbiota, its impact on the host, and the interactions between the microbiota and host. Here, we review the recent metagenomic strategies to analyze the chicken GIT microbiota composition and its functions related to improving metabolism and health. We summarize methodology of metagenomics in order to obtain bacterial taxonomy and functional inferences of the GIT microbiota and suggest a set of indicator genes for monitoring and manipulating the microbiota to promote host health in future.

Antibiotic resistome and its association with bacterial communities during sewage sludge composting

Composting is widely used for recycling of urban sewage sludge to improve soil properties, which represents a potential pathway of spreading antibiotic resistant bacteria and genes to soils. However, the dynamics of antibiotic resistance genes (ARGs) and the underlying mechanisms during sewage sludge composting were not fully explored. Here, we used high-throughput quantitative PCR and 16S rRNA gene based illumina sequencing to investigate the dynamics of ARGs and bacterial communities during a lab-scale in-vessel composting of sewage sludge. A total of 156 unique ARGs and mobile genetic elements (MGEs) were detected encoding resistance to almost all major classes of antibiotics. ARGs were detected with significantly increased abundance and diversity, and distinct patterns, and were enriched during composting. Marked shifts in bacterial community structures and compositions were observed during composting, with Actinobacteria being the dominant phylum at the late phase of composting. The large proportion of Actinobacteria may partially explain the increase of ARGs during composting. ARGs patterns were significantly correlated with bacterial community structures, suggesting that the dynamic of ARGs was strongly affected by bacterial phylogenetic compositions during composting. These results imply that direct application of sewage sludge compost on field may lead to the spread of abundant ARGs in soils.

Increased levels of antibiotic resistance in urban stream of Jiulongjiang River, China

The rapid global urbanization and other extensive anthropogenic activities exacerbated the worldwide human health risks induced by antibiotic resistance genes (ARGs). Knowledge of the origins and dissemination of ARGs is essential for understanding modern resistome, while little information is known regarding the overall resistance levels in urban river. In this study, the abundance of multi-resistant bacteria (MRB) and ARGs was investigated using culture-based method and high-throughput qPCR in water samples collected from urban stream and source of Jiulongjiang River, China, respectively. The abundance of MRB (conferring resistance to three combinations of antibiotics and vancomycin) was significantly higher in urban samples. A total of 212 ARGs were detected among all the water samples, which encoded resistance to almost all major classes of antibiotics and encompassed major resistant mechanisms. The total abundance of ARGs in urban samples (ranging from 9.72 × 10(10) to 1.03 × 10(11) copies L(-1)) was over two orders of magnitude higher than that in pristine samples (7.18 × 10(8) copies L(-1)), accompanied with distinct ARGs structures, significantly higher diversity, and enrichment of ARGs. Significant correlations between the abundance of ARGs and mobile genetic elements (MGEs) were observed, implicating the potential of horizontal transfer of ARGs. High abundance and enrichment of diverse ARGs and MGEs detected in urban river provide evidence that anthropogenic activities are responsible for the emergence and dissemination of ARGs to the urban river and management options should be taken into account for minimizing the spread of ARGs.

Microfluidic quantitative PCR for simultaneous quantification of multiple viruses in environmental water samples

To secure food and water safety, quantitative information on multiple pathogens is important. In this study, we developed a microfluidic quantitative PCR (MFQPCR) system to simultaneously quantify 11 major human viral pathogens, including adenovirus, Aichi virus, astrovirus, enterovirus, human norovirus, rotavirus, sapovirus, and hepatitis A and E viruses. Murine norovirus and mengovirus were also quantified in our MFQPCR system as a sample processing control and an internal amplification control, respectively. River water contaminated with effluents from a wastewater treatment plant in Sapporo, Japan, was collected and used to validate our MFQPCR system for multiple viruses. High-throughput quantitative information was obtained with a quantification limit of 2 copies/μl of cDNA/DNA. Using this MFQPCR system, we could simultaneously quantify multiple viral pathogens in environmental water samples. The viral quantities obtained using MFQPCR were similar to those determined by conventional quantitative PCR. Thus, the MFQPCR system developed in this study can provide direct and quantitative information for viral pathogens, which is essential for risk assessments.

Nanoliter qPCR platform for highly parallel, quantitative assessment of reductive dehalogenase genes and populations of dehalogenating microorganisms in complex environments

Idiosyncratic combinations of reductive dehalogenase (rdh) genes are a distinguishing genomic feature of closely related organohalogen-respiring bacteria. This feature can be used to deconvolute the population structure of organohalogen-respiring bacteria in complex environments and to identify relevant subpopulations, which is important for tracking interspecies dynamics needed for successful site remediation. Here we report the development of a nanoliter qPCR platform to identify organohalogen-respiring bacteria and populations by quantifying major orthologous reductive dehalogenase gene groups. The qPCR assays can be operated in parallel within a 5184-well nanoliter qPCR (nL-qPCR) chip at a single annealing temperature and buffer condition. We developed a robust bioinformatics approach to select from thousands of computationally proposed primer pairs those that are specific to individual rdh gene groups and compatible with a single amplification condition. We validated hundreds of the most selective qPCR assays and examined their performance in a trichloroethene-degrading bioreactor, revealing population structures as well as their unexpected shifts in abundance and community dynamics.

High throughput profiling of antibiotic resistance genes in urban park soils with reclaimed water irrigation

Reclaimed water irrigation (RWI) in urban environments is becoming popular, due to rapid urbanization and water shortage. The continuous release of residual antibiotics and antibiotic resistance genes (ARGs) from reclaimed water could result in the dissemination of ARGs in the downstream environment. This study provides a comprehensive profile of ARGs in park soils exposed to RWI through a high-throughput quantitative PCR approach. 147 ARGs encoding for resistance to a broad-spectrum of antibiotics were detected among all park soil samples. Aminoglycoside and beta-lactam were the two most dominant types of ARGs, and antibiotic deactivation and efflux pump were the two most dominant mechanisms in these RWI samples. The total enrichment of ARGs varied from 99.3-fold to 8655.3-fold compared to respective controls. Six to 60 ARGs were statistically enriched among these RWI samples. Four transposase genes were detected in RWI samples. TnpA-04 was the most enriched transposase gene with an enrichment was up to 2501.3-fold in Urumqi RWI samples compared with control soil samples. Furthermore, significantly positive correlation was found between ARGs and transposase abundances, indicating that transposase might be involved in the propagation of ARGs. This study demonstrated that RWI resulted in the enrichment of ARGs in urban park soils.

Simultaneous quantification of multiple food- and waterborne pathogens by use of microfluidic quantitative PCR

The direct quantification of multiple pathogens has been desired for diagnostic and public health purposes for a long time. In this study, we applied microfluidic quantitative PCR (qPCR) technology to the simultaneous detection and quantification of multiple food- and waterborne pathogens. In this system, multiple singleplex qPCR assays were run under identical detection conditions in nanoliter-volume chambers that are present in high densities on a chip. First, we developed 18 TaqMan qPCR assays that could be run in the same PCR conditions by using prevalidated TaqMan probes. Specific and sensitive quantification was achieved by using these qPCR assays. With the addition of two previously validated TaqMan qPCR assays, we used 20 qPCR assays targeting 10 enteric pathogens, a fecal indicator bacterium (general Escherichia coli), and a process control strain in the microfluidic qPCR system. We preamplified the template DNA to increase the sensitivity of the qPCR assays. Our results suggested that preamplification was effective for quantifying small amounts of the template DNA without any major impact on the sensitivity, efficiency, and quantitative performance of qPCR. This microfluidic qPCR system allowed us to detect and quantify multiple pathogens from fecal samples and environmental water samples spiked with pathogens at levels as low as 100 cells/liter. These results suggest that the routine monitoring of multiple pathogens in food and water samples is now technically feasible. This method may provide more reliable information for risk assessment than the current fecal contamination indicator approach.

Gene-Z: a device for point of care genetic testing using a smartphone

By 2012, point of care (POC) testing will constitute roughly one third of the $59 billion in vitro diagnostics market. The ability to carry out multiplexed genetic testing and wireless connectivity are emerging as key attributes of future POC devices. In this study, an inexpensive, user-friendly and compact device (termed Gene-Z) is presented for rapid quantitative detection of multiple genetic markers with high sensitivity and specificity. Using a disposable valve-less polymer microfluidic chip containing four arrays of 15 reaction wells each with dehydrated primers for isothermal amplification, the Gene-Z enables simultaneous analysis of four samples, each for multiple genetic markers in parallel, requiring only a single pipetting step per sample for dispensing. To drastically reduce the cost and size of the real-time detector necessary for quantification, loop-mediated isothermal amplification (LAMP) was performed with a high concentration of SYTO-81, a non-inhibiting fluorescent DNA binding dye. The Gene-Z is operated using an iPod Touch, which also receives data and carries out automated analysis and reporting via a WiFi interface. This study presents data pertaining to performance of the device including sensitivity and reproducibility using genomic DNA from Escherichia coli and Staphylococcus aureus. Overall, the Gene-Z represents a significant step toward truly inexpensive and compact tools for POC genetic testing.

In-feed antibiotic effects on the swine intestinal microbiome

Antibiotics have been administered to agricultural animals for disease treatment, disease prevention, and growth promotion for over 50 y. The impact of such antibiotic use on the treatment of human diseases is hotly debated. We raised pigs in a highly controlled environment, with one portion of the littermates receiving a diet containing performance-enhancing antibiotics [chlortetracycline, sulfamethazine, and penicillin (known as ASP250)] and the other portion receiving the same diet but without the antibiotics. We used phylogenetic, metagenomic, and quantitative PCR-based approaches to address the impact of antibiotics on the swine gut microbiota. Bacterial phylotypes shifted after 14 d of antibiotic treatment, with the medicated pigs showing an increase in Proteobacteria (1-11%) compared with nonmedicated pigs at the same time point. This shift was driven by an increase in Escherichia coli populations. Analysis of the metagenomes showed that microbial functional genes relating to energy production and conversion were increased in the antibiotic-fed pigs. The results also indicate that antibiotic resistance genes increased in abundance and diversity in the medicated swine microbiome despite a high background of resistance genes in nonmedicated swine. Some enriched genes, such as aminoglycoside O-phosphotransferases, confer resistance to antibiotics that were not administered in this study, demonstrating the potential for indirect selection of resistance to classes of antibiotics not fed. The collateral effects of feeding subtherapeutic doses of antibiotics to agricultural animals are apparent and must be considered in cost-benefit analyses.

Detection of pathogens in water: from phylochips to qPCR to pyrosequencing

Waterborne pathogens pose a significant threat to human health and a proper assessment of microbial water quality is important for decision making regarding water infrastructure and treatment investments and eventually to provide early warning of disease, particularly given increasing global disasters associated with severe public health risks. Microbial water quality monitoring has undergone tremendous transition in recent years, with novel molecular tools beginning to offer rapid, high-throughput, sensitive and specific detection of a wide spectrum of microbial pathogens that challenge traditional culture-based techniques. High-density microarrays, quantitative real-time PCR (qPCR) and pyrosequencing which are considered to be breakthrough technologies borne out of the ‘molecular revolution’ are at present emerging rapidly as tools of pathogen detection and discovery. Future challenges lie in integrating these molecular tools with concentration techniques and bioinformatics platforms for unbiased guide of pathogen surveillance in water and developing standardized protocols.

A universal multiplex PCR strategy for 100-plex amplification using a hydrophobically patterned microarray

Both basic research and clinical medicine have urgent demands for highly efficient strategies to simultaneously identify many different DNA sequences within a single tube. Effective and simultaneous amplification of multiple target sequences is a prerequisite for any successful multiple nucleic acid detection method. Multiplex PCR is one of the best choices for this purpose. However, due to the intrinsic interference and competition among primer pairs in the same tube, multiple rounds of highly empirical optimization procedures are usually required to establish a successful multiplex PCR reaction. To address this challenge, we report here a universal multiplex PCR strategy that is capable of over 100-plex amplification using a specially designed microarray in which hydrophilic microwells are patterned on a hydrophobic chip. On such an array, primer pairs tagged with a universal sequence are physically separated in individual hydrophilic microwells on an otherwise hydrophobic chip, enabling many unique PCR reactions to be proceeded simultaneously during the first step of the procedure. The PCR products are then isolated and further amplified from the universal sequences, producing a sufficient amount of material for analysis by conventional gel electrophoresis or DNA microarray technology. This strategy is abbreviated as "MPH&HPM" for "Multiplex PCR on a Hydrophobically and Hydrophilically Patterned Microarray". The feasibility of this method is first demonstrated by a multiplex PCR reaction for the simultaneous detection of eleven pneumonia-causing pathogens. Further, we demonstrate the power of this strategy with a highly successful 116-plex PCR reaction that required only little prior optimization. The effectiveness of the MPH&HPM strategy with clinical samples is then illustrated with the detection of deleted exons of the Duchenne Muscular Dystrophy (DMD) gene, the results are in excellent agreement with the clinical records. Because of its generality, simplicity, flexibility, specificity and capacity of more than 100-plex amplification, the MPH&HPM strategy should have broad applications in both laboratory research and clinical applications when multiplex nucleic acid analysis is required.

Digital PCR on a SlipChip

This paper describes a SlipChip to perform digital PCR in a very simple and inexpensive format. The fluidic path for introducing the sample combined with the PCR mixture was formed using elongated wells in the two plates of the SlipChip designed to overlap during sample loading. This fluidic path was broken up by simple slipping of the two plates that removed the overlap among wells and brought each well in contact with a reservoir preloaded with oil to generate 1280 reaction compartments (2.6 nL each) simultaneously. After thermal cycling, end-point fluorescence intensity was used to detect the presence of nucleic acid. Digital PCR on the SlipChip was tested quantitatively by using Staphylococcus aureus genomic DNA. As the concentration of the template DNA in the reaction mixture was diluted, the fraction of positive wells decreased as expected from the statistical analysis. No cross-contamination was observed during the experiments. At the extremes of the dynamic range of digital PCR the standard confidence interval determined using a normal approximation of the binomial distribution is not satisfactory. Therefore, statistical analysis based on the score method was used to establish these confidence intervals. The SlipChip provides a simple strategy to count nucleic acids by using PCR. It may find applications in research applications such as single cell analysis, prenatal diagnostics, and point-of-care diagnostics. SlipChip would become valuable for diagnostics, including applications in resource-limited areas after integration with isothermal nucleic acid amplification technologies and visual readout.