Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens

Stedtfeld, Robert D.; Williams, Maggie R.; Fakher, Umama; Johnson, Timothy A.; Stedtfeld, Tiffany M.; Wang, Fang; Khalife, Walid; Hughes, Mary J.; Etchebarne, Brett; Tiedje, James M.; Hashsham, Syed A.

doi:10.1093/femsec/fiw020

Cited by 33 publications

(22 citation statements)

References 35 publications

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“…The cphA gene (β‐lactam resistance) has been found to be intrinsic in environmental isolates of A. jandaei and Aeromonas hydrophila (Balsalobre et al ., ). The mexF and oprD multidrug resistance genes were proposed to naturally occur in water (Stedtfeld et al ., ). The vanC gene can encode resistance to vancomycin, which is considered as one of the last‐resort defence against organisms like Streptococcus pneumonia and Enterococcus (Gilmore and Hoch, ), and this gene is ancient in natural environments (D'Costa et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes

Wang

Singh

et al. 2018

Environmental Microbiology

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Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance.

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Section: Discussionmentioning

confidence: 97%

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes

Wang

Singh

et al. 2018

Environmental Microbiology

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“…Sample and primers were dispensed into the SmartChip™ using a Multi-sample Nano-dispenser (Wafergen Biosystems, Fremont, CA). PCR cycling conditions and initial data processing were performed as previously described (Wang et al 2014; Stedtfeld et al 2016). Amplification reactions on the SmartChip™ consisted of 1×LightCycler 480 SYBR® Green I Master Mix (Roche Inc., USA), nuclease-free PCR-grade water, 10 ng/μl cDNA template per sample in the qPCR reaction (0.5 ng per reaction well), and 0.5 μM of each forward and reverse primer.…”

Section: Methodsmentioning

confidence: 99%

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

Stedtfeld¹,

Sallach

Crawford

et al. 2017

Appl Microbiol Biotechnol

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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.

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“…Another study quantified the intI1 gene abundance in different land use, with higher abundance observed in agricultural, industrial, and urban settings compared to national parks (Borruso et al, 2016). We previously observed a high correlation (R 2 = 0.76) between total ARGs and intI1 gene measured using qPCR in water samples collected from 30 fresh surface water and influent lines from three waste water treatment plants (WWTPs) in Michigan (Stedtfeld et al, 2016b). Selective reduction of ARGs using anaerobic digestion also correlated with reduced counts of the intI1 gene (Burch et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

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

Stedtfeld¹,

Stedtfeld²,

Waseem³

et al. 2017

Journal of Environmental Management

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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.

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Antimicrobial resistance dashboard application for mapping environmental occurrence and resistant pathogens

Cited by 33 publications

References 35 publications

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes

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

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

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