Multiplex real-time SYBR Green I PCR assay for detection of tetracycline efflux genes of Gram-negative bacteria

Advances in characterization of probiotics and challenges in industrial application

An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.

Natural compound-induced downregulation of antimicrobial resistance and biofilm-linked genes in wastewater Aeromonas species

Addressing the global antimicrobial resistance (AMR) crisis requires a multifaceted innovative approach to mitigate impacts on public health, healthcare and economic systems. In the complex evolution of AMR, biofilms and the acquisition of antimicrobial resistance genes (ARGs) play a pivotal role. Aeromonas is a major AMR player that often forms biofilm, harbors ARGs and is frequently detected in wastewater. Existing wastewater treatment plants (WWTPs) do not have the capacity to totally eliminate antimicrobial-resistant bacteria favoring the evolution of ARGs in wastewater. Besides facilitating the emergence of AMR, biofilms contribute significantly to biofouling process within the activated sludge of WWTP bioreactors. This paper presents the inhibition of biofilm formation, the expression of biofilm-linked genes and ARGs by phytochemicals andrographolide, docosanol, lanosterol, quercetin, rutin and thymohydroquinone. Aeromonas species were isolated and purified from activated sludge samples. The ARGs were detected in the isolated Aeromonas species through PCR. Aeromonas biofilms were quantified following the application of biocompounds through the microtiter plate assay. qPCR analyses of related genes were done for confirmation. Findings showed that the natural compounds inhibited the formation of biofilms and reduced the expression of genes linked to biofilm production as well as ARGs in wastewater Aeromonas. This indicates the efficacy of these compounds in targeting and controlling both ARGs and biofilm formation, highlighting their potential as innovative solutions for combating antimicrobial resistance and biofouling.

Serovar and sequence type distribution and phenotypic and genotypic antimicrobial resistance of Salmonella originating from pet animals in Chongqing, China

A total of 334 Salmonella isolates were recovered from 6,223 pet rectal samples collected at 50 pet clinics, 42 pet shops, 7 residential areas, and 4 plazas. Forty serovars were identified that included all strains except for one isolate that did not cluster via self-agglutination, with Salmonella Typhimurium monophasic variant, Salmonella Kentucky, Salmonella Enteritidis, Salmonella Pomona, and Salmonella Give being the predominant serovars. Fifty-one sequence types were identified among the isolates, and ST198, ST11, ST19, ST451, ST34, and ST155 were the most common. The top four dominant antimicrobials to which isolates were resistant were sulfisoxazole, ampicillin, doxycycline, and tetracycline, and 217 isolates exhibited multidrug resistance. The prevalence of β-lactamase genes in Salmonella isolates was 59.6%, and among these isolates, 185 harbored blaTEM, followed by blaCTX-M (66) and blaOXA (10). Moreover, six PMQR genes, namely, including qnrA (4.8%), qnrB (4.2%), qnrD (0.9%), qnrS (18.9%), aac(6')-Ib-cr (16.5%), and oqxB (1.5%), were detected. QRDR mutations (76.6%) were very common in Salmonella isolates, with the most frequent mutation in parC (T57S) (47.3%). Furthermore, we detected six tetracycline resistance genes in 176 isolates, namely, tet(A) (39.5%), tet(B) (8.1%), tet(M) (7.7%), tet(D) (5.4%), tet(J) (3.3%), and tet(C) (1.8%), and three sulfonamide resistance genes in 303 isolates, namely, sul1 (84.4%), sul2 (31.1%), and sul3 (4.2%). Finally, we found 86 isolates simultaneously harboring four types of resistance genes that cotransferred 2-7 resistance genes to recipient bacteria. The frequent occurrence of antimicrobial resistance, particularly in dogs and cats, suggests that antibiotic misuse may be driving multidrug-resistant Salmonella among pets.IMPORTANCEPet-associated human salmonellosis has been reported for many years, and antimicrobial resistance in pet-associated Salmonella has become a serious public health problem and has attracted increasing attention. There are no reports of Salmonella from pets and their antimicrobial resistance in Chongqing, China. In this study, we investigated the prevalence, serovar diversity, sequence types, and antimicrobial resistance of Salmonella strains isolated from pet fecal samples in Chongqing. In addition, β-lactamase, QRDR, PMQR, tetracycline and sulfonamide resistance genes, and mutations in QRDRs in Salmonella isolates were examined. Our findings demonstrated the diversity of serovars and sequence types of Salmonella isolates. The isolates were widely resistant to antimicrobials, notably with a high proportion of multidrug-resistant strains, which highlights the potential direct or indirect transmission of multidrug-resistant Salmonella from pets to humans. Furthermore, resistance genes were widely prevalent in the isolates, and most of the resistance genes were spread horizontally between strains.

Effects of earthworms on antibiotic resistance genes in different soil-plant systems

Earthworms play an important role in the soil environment. To explore the difference in earthworms influence on various media in different soil-plant systems, the abundance of tetracycline, sulfonamide and quinolone resistance genes and the structure of the bacterial community were analysed from five different media including non-rhizosphere soil, rhizosphere soil, phyllosphere, root endophytes and earthworm intestine by real-time quantitative PCR and high-throughput 16S rRNA sequencing. Studies have shown that earthworms can reduce the absolute abundance of antibiotic resistance genes (ARGs) in non-rhizosphere soil. Root endophytes in the soil-cabbage system and rhizosphere soil in the soil-setaria system had the same findings. Earthworms can change the bacterial community structure, especially that of Proteobacteria and Cyanobacteria in the phyllosphere and root endophytes. Redundancy analysis (RDA) results that bacterial community change was the main factor affecting ARGs. In addition, earthworms increased the proportion of Cyanobacteria in root endophytes, and Cyanobacteria was significantly positively correlated with sul3. This study provides a scientific basis for controlling the migration and diffusion of ARGs and reducing environmental risks in soil-plant systems in the future.

Ac2-26 attenuates hepatic ischemia-reperfusion injury in mice via regulating IL-22/IL-22R1/STAT3 signaling

Hepatic ischemia-reperfusion injury (HIRI) is one of the major sources of mortality and morbidity associated with hepatic surgery. Ac2-26, a short peptide of Annexin A1 protein, has been proved to have a protective effect against IRI. However, whether it exerts a protective effect on HIRI has not been reported. The HIRI mice model and the oxidative damage model of H₂O₂-induced AML12 cells were established to investigate whether Ac2-26 could alleviate HIRI by regulating the activation of IL-22/IL-22R1/STAT3 signaling. The protective effect of Ac2-26 was measured by various biochemical parameters related to liver function, apoptosis, inflammatory reaction, mitochondrial function and the expressions of IL-22, IL-22R1, p-STAT3^Tyr705. We discovered that Ac2-26 reduced the Suzuki score and cell death rate, and increased the cell viability after HIRI. Moreover, we unraveled that Ac2-26 significantly decreased the number of apoptotic hepatocytes, and the expressions of cleaved-caspase-3 and Bax/Bcl-2 ratio. Furthermore, HIRI increased the contents of malondialdehyde (MDA), NADP⁺/NADPH ratio and reactive oxygen species (ROS), whereas Ac2-26 decreased them significantly. Additionally, Ac2-26 remarkably alleviated mitochondria dysfunction, which was represented by an increase in the adenosine triphosphate (ATP) content and mitochondrial membrane potential, a decrease in mitochondrial DNA (mtDNA) damage. Finally, we revealed that Ac2-26 pretreatment could significantly inhibit the activation of IL-22/IL22R1/STAT3 signaling. In conclusion, this work demonstrated that Ac2-26 ameliorated HIRI by reducing oxidative stress and inhibiting the mitochondrial apoptosis pathway, which might be closely related to the inhibition of the IL-22/IL22R1/STAT3 signaling pathway.

Oxytetracycline and Streptomycin Resistance Genes in Xanthomonas arboricola pv. pruni, the Causal Agent of Bacterial Spot in Peach

Xanthomonas arboricola pv. pruni (Xap) causes bacterial spot, a major worldwide disease of Prunus species. Very few chemical management options are available for this disease and frequent applications of oxytetracycline (OTC) in the United States peach orchards have raised concerns about resistance development. During 2017-2020, 430 Xap strains were collected from ten peach orchards in South Carolina. Seven OTC-resistant (OTC R ) Xap strains were found in 2017 and 2020 from four orchards about 20-270 km apart. Interestingly, the seven strains were also resistant to streptomycin (STR). Six strains grew on media amended with ≤100 μg/mL OTC, while one strain, R1, grew on ≤250 μg/mL OTC. Genome sequence analysis of four representative OTC R strains revealed a 14-20 kb plasmid carrying tetC, tetR, and strAB in each strain. These three genes were transferable to Xanthomonas perforans via conjugation, and they were PCR confirmed in all seven OTC R Xap strains. When tetC and tetR were cloned and expressed together in a sensitive strain, the transconjugants showed resistance to ≤100 μg/mL OTC. When tetC was cloned and expressed alone in a sensitive strain, the transconjugants showed resistance to ≤250 μg/mL OTC. TetC and tetR expression was inducible by OTC in all six wild-type strains resistant to ≤100 μg/mL OTC. However, in the R1 strain resistant to ≤250 μg/mL OTC, tetR was not expressed, possibly due to the presence of Tn3 in the tetR gene, and in this case tetC was constitutively expressed. These data suggest that tetC confers OTC resistance in Xap strains, and tetR regulates the level of OTC resistance conferred by tetC. To our knowledge, this is the first report of OTC resistance in plant pathogenic xanthomonads.

Increased Antimicrobial and Multidrug Resistance Downstream of Wastewater Treatment Plants in an Urban Watershed

Development and spread of antimicrobial resistance (AMR) and multidrug resistance (MDR) through propagation of antibiotic resistance genes (ARG) in various environments is a global emerging public health concern. The role of wastewater treatment plants (WWTPs) as hot spots for the dissemination of AMR and MDR has been widely pointed out by the scientific community. In this study, we collected surface water samples from sites upstream and downstream of two WWTP discharge points in an urban watershed in the Bryan-College Station (BCS), Texas area, over a period of nine months. E. coli isolates were tested for resistance to ampicillin, tetracycline, sulfamethoxazole, ciprofloxacin, cephalothin, cefoperazone, gentamycin, and imipenem using the Kirby-Bauer disc diffusion method. Antimicrobial resistant heterotrophic bacteria were cultured on R2A media amended with ampicillin, ciprofloxacin, tetracycline, and sulfamethoxazole for analyzing heterotrophic bacteria capable of growth on antibiotic-containing media. In addition, quantitative real-time polymerase chain reaction (qPCR) method was used to measure eight ARG – tetA, tetW, aacA, ampC, mecA, ermA, blaTEM, and intI1 in the surface water collected at each time point. Significant associations (p < 0.05) were observed between the locations of sampling sites relative to WWTP discharge points and the rate of E. coli isolate resistance to tetracycline, ampicillin, cefoperazone, ciprofloxacin, and sulfamethoxazole together with an increased rate of isolate MDR. The abundance of antibiotic-resistant heterotrophs was significantly greater (p < 0.05) downstream of WWTPs compared to upstream locations for all tested antibiotics. Consistent with the results from the culture-based methods, the concentrations of all ARG were substantially higher in the downstream sites compared to the upstream sites, particularly in the site immediately downstream of the WWTP effluent discharges (except mecA). In addition, the Class I integron (intI1) genes were detected in high amounts at all sites and all sampling points, and were about ∼20 times higher in the downstream sites (2.5 × 10⁷ copies/100 mL surface water) compared to the upstream sites (1.2 × 10⁶ copies/100 mL surface water). Results suggest that the treated WWTP effluent discharges into surface waters can potentially contribute to the occurrence and prevalence of AMR in urban watersheds. In addition to detecting increased ARG in the downstream sites by qPCR, findings from this study also report an increase in viable AMR (HPC) and MDR (E. coli) in these sites. This data will benefit establishment of improved environmental regulations and practices to help manage AMR/MDR and ARG discharges into the environment, and to develop mitigation strategies and effective treatment of wastewater.

Escherichia coli Antibiotic Resistance Patterns from Co-Grazing and Non-Co-Grazing Livestock and Wildlife Species from Two Farms in the Western Cape, South Africa

Although limited, studies have found conflicting results on whether co-grazing results in significant antibiotic resistance transfer between species. This type of farming system can act as a vector in the geographical spread of antibiotic-resistant bacteria in the environment. The aim of this study was to determine the antibiotic-resistant patterns between co-grazing and non-co-grazing livestock and wildlife species in South Africa. Escherichia coli was isolated from the faeces of various wildlife and livestock species from two farms in South Africa and was tested for antibiotic resistance using the Kirby–Bauer disk diffusion method against chloramphenicol, nalidixic acid, ampicillin, streptomycin, sulphafurazole, and tetracycline. A selection of some common antibiotic-resistant genes (blaCMY, aadA1, sul1, sul2, tetA, and tetB) were detected using PCR. The E. coli isolates from wildlife and livestock that co-grazed showed no significant differences in antibiotic resistance patterns. However, this was not the case for tetracycline resistance as the livestock isolates were significantly more resistant than the co-grazing wildlife isolates. The E. coli isolates from the non-co-grazing livestock and wildlife had significant differences in their antibiotic susceptibility patterns; the wildlife E. coli isolates were significantly more resistant to sulphafurazole and streptomycin than the livestock isolates, whilst those isolated from the cattle were significantly more resistant to ampicillin than the wildlife and sheep isolates. The results of this study suggest that there could be an exchange of antibiotic-resistant bacteria and genes between livestock and wildlife that co-graze.

Using the heat generated from electrically conductive concrete slabs to reduce antibiotic resistance in beef cattle manure

Proper treatment is necessary to reduce antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in livestock manure before land application. Conventional stockpiling suffers unreliable removal efficiency, while composting can be complicated and expensive. The objective of this study was to test the feasibility of a novel heat-based technology, i.e., stockpiling manure on conductive concrete slabs, to inactivate ARB and ARGs in beef cattle manure. In this study, two independent bench-scale trials were conducted. In both trials, samples were taken from manure piles on conductive concrete slabs and regular slabs (i.e., heated and unheated piles). In the heated pile of the first trial, 25.9% and 83.5% of the pile volume met the EPA Class A and Class B biosolids standards, respectively. For the heated pile of the second trial, the two values were 43.9% and 74.2%. In both trials, nearly all forms of the total and resistant Escherichia coli and enterococci were significantly lower in the heated piles than in the unheated piles. Besides, significant reduction of ARGs in heated piles was observed in the first trial. Through this proof-of-concept study, the new technology based on conductive concrete slabs offers an alternative manure storage method to conventional stockpiling and composting with respect to reduce ARB and ARGs in manure.

Multiplex real-time SYBR Green I PCR assays for simultaneous detection of 15 common enteric pathogens in stool samples

Diarrheal diseases account for more than 50% of foodborne diseases worldwide, the majority of which occur in infants and young children. The traditional bacterial detection method is complex and time-consuming; therefore, it is necessary to establish a rapid and convenient detection method that can detect multiple pathogens simultaneously. In this study, we developed a set of five multiplex real-time SYBR Green I PCR assays to simultaneously detect 15 common enteric pathogens based on the Homo-Tag Assisted Non-Dimer system. These assays effectively reduced primer-dimer formation and improved the stability, uniformity, and amplification efficiency of multiplex PCR. The detection limit of the multiplex SYBR Green I PCR system was approximately 10⁴-10⁶ CFU/mL for stool specimens. Furthermore, we vitrified heat-unstable components on the cap of a reaction tube, showing that Taq DNA polymerase, dNTPs, primers, and SYBR Green I remained stable at 25 °C. In summary, we developed multiplex SYBR Green I PCR assays that can simultaneously detect 15 enteric pathogens. This method is comprehensive, rapid, inexpensive, accurate, and simple and displays high specificity.

Removal of Antibiotic Resistance Genes at Two Conventional Wastewater Treatment Plants of Louisiana, USA

Wastewater treatment plants (WWTPs) represent all known types of antibiotic resistance mechanisms and are considered as the critical points for the spread of antibiotic resistance genes (ARGs). The purpose of this study is to investigate the removal of a Class 1 integrase gene (intI1) and a selected set of ARGs (blaTEM, ermF, mecA, and tetA) at two conventional WWTPs by using chlorination in Louisiana, USA. We collected 69 wastewater samples (23 each from influent, secondary effluent, and final effluent) and determined the concentrations of ARGs by using quantitative polymerase chain reaction. All tested ARGs, except for mecA, were detected in 83–96% and 30–65% of influent and final effluent samples, respectively. Although the ARGs underwent approximately 3-log10 reduction, two WWTPs on an average still released 3.3 ± 1.7 log10 copies/mL of total ARGs studied in the effluents. Chlorination was found to be critical in the significant reduction of total ARGs (p < 0.05). Correlation analysis and the ability of intI1 to persist through the treatment processes recommend the use of intI1 as a marker of ARGs in effluents to monitor the spread of antibiotic resistance in effluents. Our study suggests that conventional WWTPs using chlorination do not favor the proliferation of antibiotic resistance bacteria and ARGs during wastewater treatment.

A Preliminary Study: Antibiotic Resistance Patterns of Escherichia coli and Enterococcus Species from Wildlife Species Subjected to Supplementary Feeding on Various South African Farms

Simple Summary

Supplementary feeding of wildlife allows more opportunity for disease and antibiotic resistant genes to be transferred directly between species due to increased herd density, more frequent direct contact at feeding and water points and increased human contact. The feed itself can also be a direct source of antibiotic compounds and of antibiotic resistant bacteria. This study aimed to determine whether the practice of wildlife supplementary feeding could have an influence on the antibiotic resistance of the bacteria harboured by the supplementary fed wildlife, and thus play a potential role in the dissemination of antibiotic resistance throughout nature. Overall, the E. coli and Enterococcus isolates from the supplementary fed wildlife were found to be more frequently resistant to the selection of antibiotics than from those which were not supplementary fed. Game farmers should be knowledgeable of the ingredients that are used in the game feed that is used to feed both their livestock and wildlife, as certain feed ingredients, such as antibiotics or bone meal, can have a detrimental effect on health and safety. Game farmers should also be aware that farm history can have an impact on the animals which graze on the pastures with regards to antibiotic resistance transfer.

Abstract

Studies have shown that antibiotic resistance among wild animals is becoming a public health concern, owing to increased contact and co-habitation with domestic animals that, in turn, results in increased human contact, indirectly and directly. This type of farming practice intensifies the likelihood of antibiotic resistant traits in microorganisms transferring between ecosystems which are linked via various transfer vectors, such as rivers and birds. This study aimed to determine whether the practice of wildlife supplementary feeding could have an influence on the antibiotic resistance of the bacteria harboured by the supplementary fed wildlife, and thus play a potential role in the dissemination of antibiotic resistance throughout nature. Escherichia coli and Enterococcus were isolated from the faeces of various wildlife species from seven different farms across South Africa. The Kirby-Bauer disk diffusion method was used according to the Clinical and Laboratory Standards Institute 2018 guidelines. The E. coli (F: 57%; N = 75% susceptible) and Enterococcus (F: 67%; N = 78% susceptible) isolates from the supplementary fed (F) wildlife were in general, found to be more frequently resistant to the selection of antibiotics than from those which were not supplementary fed (N), particularly towards tetracycline (E. coli F: 56%; N: 71%/Enterococcus F: 53%; N: 89% susceptible), ampicillin (F: 82%; N = 95% susceptible) and sulphafurazole (F: 68%; N = 98% susceptible). Interestingly, high resistance towards streptomycin was observed in the bacteria from both the supplementary fed (7% susceptible) and non-supplementary fed (6% susceptible) wildlife isolates. No resistance was found towards chloramphenicol and ceftazidime.

The Occurrence of Antibiotic Resistance Genes in an Urban River in Nepal

Urban rivers affected by anthropogenic activities can act as reservoirs of antibiotic resistance genes (ARGs). This study aimed to describe the occurrence of selected ARGs (blaTEM, ermF, mecA, and tetA) and a class 1 integron (intI1) in an urban river in Nepal. A total of 18 water samples were collected periodically from upstream, midstream, and downstream sites along the Bagmati River over a 1-year period. All ARGs except mecA and intI1 were consistently detected by a quantitative polymerase chain reaction in the midstream and downstream sites, with concentrations ranging from 3.1 to 7.8 log copies/mL. ARG abundance was significantly lower at the upstream site (p < 0.05), reflecting the impact of anthropogenic activities on increasing concentrations of ARGs at midstream and downstream sites. Our findings demonstrate the presence of clinically relevant ARGs in the urban river water of Nepal, suggesting a need for mitigating strategies to prevent the spread of antibiotic resistance in the environment.

A preliminary investigation of wild pig (Sus scrofa) impacts in water quality

The United States, particularly the southern portion, has recently suffered drastic population expansion of wild pigs causing destruction of prime farmland. An associated concern, which has been understudied, is the potential transfer of nutrients and pathogens to surface water. This study aimed to identify the abiotic and biotic impacts of captive wild pigs on water quality, including nutrients, fecal indicator and pathogenic bacteria, and antimicrobial resistance. Overall, the study demonstrated that wild pigs harbored Salmonella spp., Campylobacter spp., Escherichia coli, and Clostridium perfringens, which were found in water runoff collected directly beneath the hog paddock, often 2 log₁₀ greater than above-paddock levels. However, the impacts to downstream water quality were limited, perhaps because of a relatively large riparian buffer between the paddock and surface water. A higher rate of ammonium concentration changes over time was detected in the runoff water below the paddock; additionally, microbial releases detected in runoff were also time dependent, possibly associated with increasing pig numbers. Antibiotic resistance was generally not associated with the wild pigs. Antibiotic resistance genes were found in upstream as well as downstream surface water, suggesting that nonpoint sources of microbial contamination were present. Interestingly, intI1 levels were greater in below-paddock runoff by nearly 2 log₁₀ . Overall, it appears that wild pigs potentially pose a threat to water quality but only if they have direct access to the water. Pathogen, fecal indicator bacteria, and some nutrient release were significantly associated with wild pigs, but riparian buffers limited water quality impairment.

Antibiotic-Resistant Bacteria in Greywater and Greywater-Irrigated Soils

This study represents the first systematic attempt to evaluate antibiotic-resistant bacteria (ARB) occurrence in treated greywater and the potential spread of these bacteria from the greywater to greywater-irrigated soil. Treated greywater from three recirculating vertical flow constructed wetlands, each located in a household in the central Negev Desert, Israel, was surveyed. The presence of antibiotic-resistant bacteria in raw and treated greywater was investigated with culture and molecular methods, as well as their presence in the corresponding treated-greywater-irrigated soils. Additionally, the effectiveness of chlorination to prevent the spread of ARB was tested. The total count of tetracycline-resistant bacteria significantly increased in the treated greywater, likely due to their concentration on the filter matrix of the treatment systems. Twenty-four strains of tetracycline-resistant bacteria were isolated and identified at the genus level by 16Sr RNA gene sequencing. All the tetracycline-resistant bacteria showed high resistance traits, and some of them presented multiple antibiotic resistances. Six tetracycline resistance genes (coding for efflux and ribosomal resistance mechanisms) and five β-lactamase genes were detected. In 14 of the isolated strains, the gene tet39, which is phylogenetically related to both environmental and clinical strains, was identified. All the tet39 resistant bacteria were positive to at least one of the β-lactamase genes tested. Chlorination was found to be an efficient method to reduce ARB in treated greywater. We concluded that disinfection of treated greywater may reduce the risks not only from the potential presence of pathogens but also from the presence of ARB and antibiotic resistance genes.

Inputs, source apportionment, and transboundary transport of pesticides and other polar organic contaminants along the lower Red River, Manitoba, Canada

The Red River originates in the U.S., drains into Lake Winnipeg, and is a significant pathway for nutrients. We investigate its role as a source for pesticides, pharmaceuticals, per- and polyfluoroalkyl substances (PFASs), and microbes bearing antibiotic resistance genes (ARGs). We delineate agricultural, urban, and rural land-use for organic contaminants to determine the extent of chemical transboundary riverine fluxes, and characterize levels and trends of organic contaminants and ARGs between spring and fall 2014 and 2015. The herbicide atrazine peaked at over 500 ng/L (14-day time-weighted average) near the border, indicating that the U.S. represents the major source into Canada from the Red River. Neonicotinoid insecticides had relatively constant concentrations, suggesting more widespread agricultural use in both countries. Pesticide concentrations were greatest post-application in June and July. Mass loadings of pesticides over the sampling periods, from the river to Lake Winnipeg, ranged from approximately 800 kg of atrazine, to 120 kg of thiamethoxam and clothianidin, to 40 kg of imidacloprid. Exposure distributions for atrazine exceeded benchmark water quality guidelines for protection of aquatic life (0.2% probability of exceeding chronic benchmark) with no exceedances for neonicotinoids. Seven pharmaceuticals were detected, mostly at low ng/L levels downstream of the City of Winnipeg wastewater treatment plant. Carbamazepine, the only pharmaceutical detected consistently at all sites, contributed on average 20 kg each year into Lake Winnipeg. While minor inputs were observed all along the river, city inputs represented the greatest source of pharmaceuticals to the river. Both PFASs and ARGs were observed consistently and ubiquitously, indicative of an anthropogenically-influenced system with no indications of any single point-source signature. While transboundary flux from the U.S. was an important source of pesticides to the Red River, especially for atrazine, observed concentrations of all measured contaminants suggest that known aquatic toxicological risk is minimal.

Effects of Subsurface Banding and Broadcast of Poultry Litter and Cover Crop on Soil Microbial Populations

Agronomic management is aimed at managing the crop environment to maximize crop yield, but soil biology is often ignored. This study aimed to compare the application of poultry litter via broadcast and subsurface banding versus standard inorganic fertilizer to cotton ( L.) and their effects on soil bacterial populations and fecal indicator bacteria. The study comprised a randomized complete block design, with fertilizer and time of application as treatment effects and cover crop as a main effect. Soil cores were collected and analyzed from 2008 to 2014. Fecal indicator bacteria were at detection limits for all treatments, where the integron 1 gene was significantly elevated in litter plots. There were few differences between litter application approaches, but both significantly increased key biogeochemical genes over control plots, whereas a cover crop only increased soil moisture and urease C. Data suggested a positive residual effect of litter application with 16S, phosphatase A, and urease C genes elevated over controls, but similar to standard fertilizer plots. High-throughput 16S ribosomal RNA analysis suggested increased diversity and enrichment indices in litter and standard fertilizer over untreated control plots. Litter and standard fertilizer effects persisted 4 and 2 yr after application, respectively, as evidenced by residual library community structures. This study demonstrated the positive effects of litter application on the soil bacterial community when compared with untreated control plots. Some differences between standard fertilization and litter practices were noted and suggest that there is a positive residual effect on soil microbial populations associated with both practices.

Development of a multiplex qPCR in real time for quantification and differential diagnosis of Salmonella Gallinarum and Salmonella Pullorum

Currently there are 2659 Salmonella serovars. The host-specific biovars Salmonella Pullorum and Salmonella Gallinarum cause systemic infections in food-producing and wild birds. Fast diagnosis is crucial to control the dissemination in avian environments. The present work describes the development of a multiplex qPCR in real time using a low-cost DNA dye (SYBr Green) to identify and quantify these biovars. Primers were chosen based on genomic regions of difference (RoD) and optimized to control dimers. Primers pSGP detect both host-specific biovars but not other serovars and pSG and pSP differentiate biovars. Three amplicons showed different melting temperatures (Tm), allowing differentiation. The pSGP amplicon (97 bp) showed Tm of 78°C for both biovars. The pSG amplicon (273 bp) showed a Tm of 86.2°C for S. Gallinarum and pSP amplicon (260 bp) dissociated at 84.8°C for S. Pullorum identification. The multiplex qPCR in real time showed high sensitivity and was capable of quantifying 10⁸-10¹ CFU of these biovars.

Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes

Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes. Virus-like particles were isolated from water samples collected across the Lambro River, from the spring to the high urbanized Milan area. The derived viromes were analyzed by shotgun metagenomic sequencing looking for the presence, relative abundance of bacterial genes with particular focus on those genes involved in antimicrobial resistance mechanisms. Antibiotic and heavy metal resistance genes have been identified in all virome samples together with a high abundance of reads assigned to cellular processes and signaling. Virome data compared to those identified in the microbiome isolated from the same sample revealed differences in terms of functional categories and their relative abundance. To verify the role of aquatic viral population in bacterial gene transfer, water-based mesocosms were perturbed or not perturbed with a low dose of tetracycline. The results obtained by qPCR assays revealed variation in abundance of tet genes in the virome and microbiome highlighting a relevant role of viral populations in microbial gene mobilization.

Assessment of food safety using a new real-time PCR assay for detection and quantification of virulence factors of enterococci in food samples

AIMS

Development of Taqman MGB real-time PCR (q-PCR) assays for the quantitative detection of virulence factor genes in pure culture and food samples with regard to food safety assessment.

METHODS AND RESULTS

New Taqman primers and probes were designed for the ace, esp and gelE genes based on the determinants of virulence profiles of enterococcal strains from GenBank. The high specificity and accuracy of the Taqman probe assay was confirmed. The limit of detection for the different virulence genes was 10²  CFU ml^-1 or CFU g^-1 for pure culture and meat samples, and 10³  CFU g^-1 for cheese samples.

CONCLUSION

This method provides the specific and rapid detection and quantification of ace, esp and gelE genes compared to conventional PCR assays, thus allowing the rapid and direct safety assessment of Enterococcus genus in food samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study presents efficient methods that can be used directly on food products for the rapid quantification and tracing of virulence genes, regarding food safety assessment. Moreover, this is the first study to quantify these virulence factors using a specific Taqman q-PCR assay in food samples.

Combination of antibiotics suppressed the increase of a part of ARGs in fecal microorganism of weaned pigs

The presence of antibiotic resistance genes (ARGs) is one of the most important public health concerns. Six tetracycline resistance genes (TRGs-tetA, tetC, tetL, tetO, tetW, and tetX) were quantified using real-time quantitative polymerase chain reaction (qPCR) in the fecal microorganisms of weaned pigs. Two hundred 35-day-old weaned pigs were fed different dietary antibiotics for 28 days: (1) no antibiotic as the control treatment (CT); (2) chlortetracycline, bacitracin zinc and colistin sulfate (CBC); (3) bacitracin zinc and colistin sulfate (BC); and (4) chlortetracycline (CTC). The detection frequencies (DFs) of tetC, tetL, and tetW were 100 %; and the DFs of tetA, tetD, tetM, tetO, and tetX were 65 %. The relative abundances (tet/16S rRNA gene copy numbers) of six tet genes (tetA, tetC, tetL, tetO, tetW and tetX) were between 1.5 × 10(-4) and 2.0 × 10(-1). In the group CTC, the relative abundances of tetC (P < 0.01), tetL (P < 0.01), tetO (P < 0.05), tetW (P < 0.01), and tetX (P < 0.01) were greater than those of the group CT. Compared with the group CTC, the relative abundances of tetC (P < 0.01), tetL (P < 0.01), and tetW (P < 0.01) were decreased in the CBC and BC groups. These results indicate that a combination of different antibiotics suppressed the abundance increase of a part of tet genes, which suggests that a combination of antibiotics produces multiple selection pressures on fecal microorganism of pigs.

Cultivation and qPCR Detection of Pathogenic and Antibiotic-Resistant Bacterial Establishment in Naive Broiler Houses

Conventional commercial broiler production involves the rearing of more than 20,000 broilers in a single confined space for approximately 6.5 wk. This environment is known for harboring pathogens and antibiotic-resistant bacteria, but studies have focused on previously established houses with mature litter microbial populations. In the current study, a set of three naive houses were followed from inception through 11 broiler flocks and monitored for ambient climatic conditions, bacterial pathogens, and antibiotic resistance. Within the first 3 wk of the first flock cycle, 100% of litter samples were positive for and , whereas was cultivation negative but PCR positive. Antibiotic resistance genes were ubiquitously distributed throughout the litter within the first flock, approaching 10 to 10 genomic units g. Preflock litter levels were approximately 10 CFU g for heterotrophic plate count bacteria, whereas midflock levels were >10 colony forming units (CFU) g; other indicators demonstrated similar increases. The influence of intrahouse sample location was minor. In all likelihood, given that preflock levels were negative for pathogens and antibiotic resistance genes and 4 to 5 Log lower than flock levels for indicators, incoming birds most likely provided the colonizing microbiome, although other sources were not ruled out. Most bacterial groups experienced a cyclical pattern of litter contamination seen in other studies, whereas microbial stabilization required approximately four flocks. This study represents a first-of-its-kind view into the time required for bacterial pathogens and antibiotic resistance to colonize and establish in naive broiler houses.

Assessment of Tetracyclines Residues and Tetracycline Resistant Bacteria in Conventional and Organic Baby Foods

Children are very vulnerable to bacterial infections and they are sometimes subject to antimicrobials for healing. The presence of resistance genes may counteract effects of antimicrobials. This work has thereby compared the amount of tetracycline resistance genes, tet(A) and tet(B), between conventional and organic meat-based or vegetable-based baby foods and used the quantification of these genes to assess the presence of tetracycline residues in these samples. Counts of bacteria harboring the tet(A) gene were higher than those containing tet(B), and there was no difference between the organic and the conventional samples. Samples with detectable amounts of tetracycline residues were also positive for the presence of tet genes, and when the presence of the genes was not detected, the samples were also negative for the presence of residues. The percentages of tetracycline residues were higher in organic samples than in conventional ones. It cannot be concluded that organic formulas are safer than conventional ones for the studied parameters.

Emergence of Extensively Drug-Resistant Proteus mirabilis Harboring a Conjugative NDM-1 Plasmid and a Novel Salmonella Genomic Island 1 Variant, SGI1-Z

Acquisition of blaNDM-1 in bacterial species, such as Proteus mirabilis that is intrinsically resistant to tetracycline, tigecycline and colistin, will make clinical treatment extremely difficult. Here, we characterized an NDM-1-producing clinical isolate of P. mirabilis (PM58) that displayed an extensively drug-resistant (XDR) phenotype, susceptible only to aztreonam. Molecular analysis revealed that PM58 harbored both a conjugative NDM-1 plasmid and a novel Salmonella genomic island 1 variant on chromosome.

Quantum dots and graphene oxide fluorescent switch based multivariate testing strategy for reliable detection of Listeria monocytogenes

Graphene oxide (GO) and quantum dots (QDs), as burgeoning types of nanomaterials, have gained tremendous interest in the biosensor field. In this work, we designed a novel multivariate testing strategy that depends on the fluorescence resonance energy transfer (FRET) effect between quantum dots (QDs) and graphene oxide (GO). It integrates the QD-GO FRET principle and QD probes with different emission peaks into a platform, aims at multiplex gene detection of a human infectious and highly pathogenic pathogen, Listeria monocytogenes (L. monocytogenes). With the development of a multiplex linear-after-the-exponential (LATE) polymerase chain reaction (PCR) system, the single-stranded DNA (ssDNA) products of hlyA genes and iap genes are obtained by simultaneous amplification of the target genes. Then with the hybridization of ssDNA products and QD probes, simultaneous homogeneous detection of two gene amplification products can be achieved by using GO as a fluorescence switch and monitoring the relevant emissions excited by a single light source. Distinguishable signals corresponding to target genes are obtained. With this developed approach, genomic DNA from L. monocytogenes can be detected as low as 100 fg/μL. Moreover, this platform has a good dynamic range from 10(2) to 10(6) fg/μL. It is indicated that this platform has potential to be a reliable complement for rapid gene detection technologies and is capable of reducing the false-negative and false-dismissal probabilities in routine tests.

Respiratory virus infections among children in South China

Acute respiratory tract infection is an important cause of morbidity and mortality with a worldwide disease burden. This study aimed to determine the prevalence and clinical characteristics of children with viral-induced acute respiratory tract infection, in Southern China. Nasopharyngeal aspirate samples from 1,980 pediatric patients with suspected acute respiratory tract infection, and 82 samples from healthy subject controls were collected for routine examination at the Second Affiliated Hospital of Shantou University Medical College, from October 2007 to August 2011. Specimens were tested by multiplex polymerase chain reaction (mPCR). At least one or more viruses were detected from 1,087 samples (54.9%). These included laboratory confirmations for 446 respiratory syncytial virus (RSV), 386 influenza virus A (FluA), 315 human rhinovirus (HRV), 135 human bocavirus (HBoV), 119 Parainfluenza virus 3 (PIV3), 82 Parainfluenza virus 1 (PIV1), 66 adenovirus (ADV), 53 WU polyomavirus (WUPyV), 52 human metapneumovirus (hMPV), and 29 influenza virus B (FluB) samples. Samples from healthy subjects were negative for any virus. Of the patients with positive specimens, 107 (9.8%) were admitted to pediatric intensive care unit (PICU). Co-infection with at least two of the viral pathogens under study was observed in 325 of the 1,980 patients (16.4% of the total number of cases). These findings may help in the diagnosis of viral infections of the respiratory tract in children, and help to consider current and potential therapeutic approaches for the treatment of acute respiratory tract infection, and further respiratory complications.

Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure wastewater as influenced by three swine management systems

The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to the microbial biota and ecological structure of both the pig and waste manure lagoon wastewater. While some of these changes may not be negative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater. The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created. Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries. Nearly all antibiotic resistance genes were detected in all farms. Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits on most farms, and decreased as the pigs aged. Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library. Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant. The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future "downstream" implications from both an environmental and public health perspective.

Impact of treatment strategies on cephalosporin and tetracycline resistance gene quantities in the bovine fecal metagenome

The study objective was to determine the effects of two treatment regimens on quantities of ceftiofur and tetracycline resistance genes in feedlot cattle. The two regimens were ceftiofur crystalline-free acid (CCFA) administered to either one or all steers within a pen and subsequent feeding/not feeding of therapeutic doses of chlortetracycline. A 26-day randomized controlled field trial was conducted on 176 steers. Real-time PCR was used to quantify bla_CMY-2, bla_CTX-M, tet(A), tet(B), and 16S rRNA gene copies/gram of feces from community DNA. A significant increase in ceftiofur resistance and a decrease in tetracycline resistance elements were observed among the treatment groups in which all steers received CCFA treatment, expressed as gene copies/gram of feces. Subsequent chlortetracycline administration led to rapid expansion of both ceftiofur and tetracycline resistance gene copies/gram of feces. Our data suggest that chlortetracycline is contraindicated when attempting to avoid expansion of resistance to critically important third-generation cephalosporins.

Characterization of multidrug-resistant Salmonella enterica serovars Indiana and Enteritidis from chickens in Eastern China

A total of 310 Salmonella isolates were isolated from 6 broiler farms in Eastern China, serotyped according to the Kauffmann-White classification. All isolates were examined for susceptibility to 17 commonly used antimicrobial agents, representative isolates were examined for resistance genes and class I integrons using PCR technology. Clonality was determined by pulsed-field gel electrophoresis (PFGE). There were two serotypes detected in the 310 Salmonella strains, which included 133 Salmonella enterica serovar Indiana isolates and 177 Salmonella enterica serovar Enteritidis isolates. Antimicrobial sensitivity results showed that the isolates were generally resistant to sulfamethoxazole, ampicillin, tetracycline, doxycycline and trimethoprim, and 95% of the isolates sensitive to amikacin and polymyxin. Among all Salmonella enterica serovar Indiana isolates, 108 (81.2%) possessed the blaTEM, floR, tetA, strA and aac (6')-Ib-cr resistance genes. The detected carriage rate of class 1 integrons was 66.5% (206/310), with 6 strains carrying gene integron cassette dfr17-aadA5. The increasing frequency of multidrug resistance rate in Salmonella was associated with increasing prevalence of int1 genes (rs = 0.938, P = 0.00039). The int1, blaTEM, floR, tetA, strA and aac (6')-Ib-cr positive Salmonella enterica serovar Indiana isolates showed five major patterns as determined by PFGE. Most isolates exhibited the common PFGE patterns found from the chicken farms, suggesting that many multidrug-resistant isolates of Salmonella enterica serovar Indiana prevailed in these sources. Some isolates with similar antimicrobial resistance patterns represented a variety of Salmonella enterica serovar Indiana genotypes, and were derived from a different clone.

Direct quantification and distribution of tetracycline-resistant genes in meat samples by real-time polymerase chain reaction

The evolution of antimicrobial-resistant bacteria has become a threat to food safety and methods to control them are necessary. Counts of tetracycline-resistant (TR) bacteria by microbiological methods were compared with those obtained by quantitative PCR (qPCR) in 80 meat samples. TR Enterobacteriaceae counts were similar between the count plate method and qPCR (P= 0.24), whereas TR aerobic mesophilic bacteria counts were significantly higher by the microbiological method (P < 0.001). The distribution of tetA and tetB genes was investigated in different types of meat. tetA was detected in chicken meat (40%), turkey meat (100%), pork (20%), and beef (40%) samples, whereas tetB was detected in chicken meat (45%), turkey meat (70%), pork (30%), and beef (35%) samples. The presence of tetracycline residues was also investigated by a receptor assay. This study offers an alternative and rapid method for monitoring the presence of TR bacteria in meat and furthers the understanding of the distribution of tetA and tetB genes.

Detection of aacA-aphD, qacEδ1, marA, floR, and tetA genes from multidrug-resistant bacteria: Comparative analysis of real-time multiplex PCR assays using EvaGreen(®) and SYBR(®) Green I dyes

We have developed multiplex real-time PCR assays that utilize DNA-intercalating dyes, SYBR Green I (SG) and EvaGreen (EG), with two primer sets (set 1=qacEδ1, tetA and aacA-aphD; set 2=tetA, marA, and floR) to simultaneously amplify the qacEδ1, tetA, aacA-aphD, marA, and floR genes. Validity of the multiplex PCR assays was confirmed by testing 83 bacterial isolates, including Staphylococcus aureus (28 isolates), Enterococcus spp. (17 isolates), Salmonella enterica serovar Typhimurium (8 isolates), Citrobacter spp. (9 isolates), Escherichia coli (14 isolates) and Aeromonas veronii (7 isolates), and performing sequence analysis of representative PCR products. Agarose gel analysis revealed the presence of correct size PCR products, and the differences in their thermal melting (T(m)) curves were used to distinguish various PCR products. Although T(m) peaks of different amplicons after EG-based singleplex and multiplex PCR assays were resolved nicely, only one or two peaks were seen for SG-bound amplicons. EG-based multiplex real-time PCR assays provided better peak resolution. There was a good correlation with a better linear relationship between the C(t) and log input DNA concentration for the set 1 and set 2 genes in EG-based assays (R(EG)(2)=0.9813and0.9803) than in SG-based assays (R(SG)(2)=0.5276and0.6255). The sensitivities of detection were 2.5-25fg and 25-250fg of template DNA in EG and SG-based singleplex and multiplex PCR assays, respectively. The assays, which could be completed in less than 45min, offer sensitive and rapid detection of qacEδ1, aacA-aphD, marA, floR, and tetA genes from a diverse group of multiple antibiotic-resistant bacterial strains.

Detection of Bacillus cereus with enteropathogenic potential by multiplex real-time PCR based on SYBR Green I

In order to meet the growing demand for fast and reliable detection of potentially toxinogenic Bacillus cereus, we developed a multiplex real-time PCR assay based on SYBR Green I with subsequent melting curve analysis. We designed and selected primers specific for genes of toxins responsible for diarrhoea (nheA, hblD and cytK1) and emesis (ces). A panel of 337 Bacillus strains was applied to the novel method on Light Cycler 2.0 with average melting temperature (T(m)) values of 73.85 degrees C (nheA), 87.01 degrees C (hblD), 78.66 degrees C (ces) and 82.19 degrees C (cytK1). An adapted version of the assay was also successfully run on Light Cycler 480 using one third (113 strains) of the total test panel. Verification of PCR results by conventional PCR as well as immunoassays and cytotoxicity tests gave an overall excellent correlation. Distinct melting peaks were only observed in B. cereus and B. cereus group strains but not in other Bacilli and Gram-positive or Gram-negative bacteria. Artificial contamination of three different food matrices with distinct bacterial counts revealed a detection limit of 10(1) CFU/g B. cereus cells after overnight enrichment. Thus, the novel multiplex real-time PCR turned out to be a reliable method for identification of B. cereus with enteropathogenic potential.

Tetracycline resistance genes and tetracycline resistant lactose-fermenting Enterobacteriaceae in activated sludge of sewage treatment plants

Activated sludges were sampled from five sewage treatment plants (STPs) distributed in three geographically isolated areas, i.e., Hong Kong (Shatin, Stanley), Shanghai (Minhang) in China, and the bay area in California (Palo Alto and San Jose) of the United States. Among the tested 14 tetracycline resistance (tet) genes, nine genes encompassing efflux pumps (tetA, tetC, tetE, and tetG), ribosomal protection proteins (tetM, tetO, tetQ, and tetS), and enzymatic modification (tetX) were commonly detected in the STP sludge samples, whereas five genes encompassing efflux pumps [tetB, tetD, tetL, tetK, and tetA(P)] were not detected in any sludge sample. Additionally, 109 lactose-fermenting Enterobacteriaceae (LFE) strains were isolated from the activated sludge of the Shatin STP. Tetracycline-resistant (TR) LFE accounted for 32% of the total 109 LFE strains. The occurrence frequencies of tet genes among all TR-LEF strains varied from 0 to 91%, i.e., tetC (91%), tetA (46%), tetE (9%), tetG (6%), and tetD (6%). Finally, quantitative real-time polymerase chain reaction was used to quantify the change of tetC and tetA genes as the indicator of TR-LEF in the Shatin and Stanley STPs. The results showed that the concentrations of tetC and tetA genes in STP effluent ranged from 10(4) to 10(5) copies/mL, significantly lower than those in the influent by 3 orders of magnitude.

The tetracycline resistance gene tet39 is present in both Gram-negative and Gram-positive bacteria from a polluted river, Southwestern Nigeria

AIM

Previous analysis of tet39 suggests it may be present in other bacterial species. Hence, we investigated the host range of tet39 among bacterial from a poultry waste polluted river in Southwestern Nigeria.

METHODS AND RESULTS

Thirteen resistant bacterial isolated from the water and sediment of the polluted river was investigated for the presence of tetracycline resistance genes tetA, tetB, tetC, tet39 and the transposon integrase gene of the Tn916/1545 family by PCR. While tetA, tetB, tetC and integrase genes cannot be detected in any of the organisms, tet39 was detected in eight of the tested organisms including three Gram-positive species. Sequence analysis showed the genes have high sequence identities (> or =99%) with tet39 of Acinetobacter sp. LUH5605, the first and only bacterial genus from which the gene has been reported to date. This is a novel observation.

CONCLUSIONS

This study shows that apart from Acinetobacter, tet39 is present in other bacterial species tested in this study.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study adds to available information on the occurrence and distribution of tet39 among environmental bacteria and suggests that the gene has a broader host range than previously reported.

Rapid detection of genetically modified organisms on a continuous-flow polymerase chain reaction microfluidics

The ability to perform DNA amplification on a microfluidic device is very appealing. In this study, a compact continuous-flow polymerase chain reaction (PCR) microfluidics was developed for rapid analysis of genetically modified organisms (GMOs) in genetically modified soybeans. The device consists of three pieces of copper and a transparent polytetrafluoroethylene capillary tube embedded in the spiral channel fabricated on the copper. On this device, the P35S and Tnos sequences were successfully amplified within 9min, and the limit of detection of the DNA sample was estimated to be 0.005 ng microl(-1). Furthermore, a duplex continuous-flow PCR was also reported for the detection of the P35S and Tnos sequences in GMOs simultaneously. This method was coupled with the intercalating dye SYBR Green I and the melting curve analysis of the amplified products. Using this method, temperature differences were identified by the specific melting temperature values of two sequences, and the limit of detection of the DNA sample was assessed to be 0.01 ng microl(-1). Therefore, our results demonstrated that the continuous-flow PCR assay could discriminate the GMOs in a cost-saving and less time-consuming way.