Progress 01/01/16 to 12/31/19
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Graduate and undergraduate students wereengaged in a research intensive environment and exposed to a broad range of research approaches and cultures. In addition, students reported their research progressperiodically in the forms of oral presentation and written reports. Undergraduate students have alsolearned how to make research notes, prepare project summary, and discuss research findings in a scientific manner.The team visited the collaborator's lab at Illinois Institute of Technology (IIT) in May 2017 to learn about DNA sequencing and metagenomics and interact with host students. Students also took the opportunity to discuss and integrate lab results that were collected separately. One undergraduate student received a 2017 award from the undergraduate research opportunity program (UROP) at WSU. Thisstudent was also elected asa member of Phi Beta Kappa, a highly selective national honor society. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Soil bacteria were recovered from urban agricultural soil in Detroit. The most prevalent antibiotic resistance phenotype demonstrated by Gram-negative bacteria was resistance to ampicillin (94.2%), followed by chloramphenicol (80.0%), cefoxitin (79.5%), gentamicin (78.4%) and ceftriaxone (71.1%). All Gram-positive bacteria were resistant to gentamicin, kanamycin and penicillin. Genes encoding resistance to quinolones, β-lactams and tetracyclines were the most prevalent and abundant in the soil. qepA and tetA, both encoding efflux pumps, predominated in the quinolone and tetracycline resistance genes tested, respectively. Positive correlation (P<0.05) was identified among groups of antibiotic resistance genes, and between antibiotic resistance genes and metal resistance genes. The data demonstrated a diverse population of antibiotic resistance in urban agricultural soils. Phenotypic determination together with soil metagenomics proved to be a valuable tool to study the nature and extent of antibiotic resistance in the environment.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Mafiz, A.I., L.N. Perera, Y. He, W. Zhang, S. Xiao, W. Hao, S. Sun, K. Zhou, and Y. Zhang. Case study on the soil antibiotic resistome in an urban community garden. International Journal of Antimicrobial Agents. 2018, 52: 241-250
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2018
Citation:
Zhang, Y. Soil microbiota as a reservoir of antibiotic resistance in urban agriculture and their potential of horizontal gene transfer. IAFP Annual Conference, Salt Lake City, UT, July 2018
Mafiz, A.I., Y. He, W. Zhang, and Y. Zhang. High prevalence of antibiotic resistance associated with urban agricultural environment with the potential of horizontal gene transfer. IAFP Annual Conference, Salt Lake City, UT, July 2018
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Zhang, Y. Understanding antibiotic resistance in the context of urban agriculture. American Chemical Society (ACS) Spring Conference, Orlando, FL, April 2019
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Progress 01/01/17 to 12/31/17
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Two undergraduate students were recruited to the project, together with two graduate students who were already on the team. Students worked together on urban agriculture practices, bacteria isolation, PCR, 16S rRNA sequence analysis, MIC determination, soil DNA extraction, data analysis, and technical presentation. The team visited the collaborator's lab at Illinois Institute of Technology (IIT) in May 2017 to learn about DNA sequencing and metagenomics and interact with host students. Students also took the opportunity to discuss and integrate lab results that were collected separately. One undergraduate student received a 2017 award from the undergraduate research opportunity program (UROP) at WSU. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
A total of 207 soil bacteria recovered from 41 soil samples collected from an urban agricultural garden were further characterized. Bacteria belonged to four phyla, including Bacteroidetes (53.10%), Proteobacteria (38.65%), Firmicutes (6.76%), and Actinobacteria (1.45%) as identified by 16S rRNA gene sequencing. Metagenomics revealed Proteobacteria (37.32%), Actinobacteria (19.45%), Firmicutes (12.28%), and Bacteroidetes (9.76%) from soil DNA. Gram-negative bacteria demonstrated the highest antibiotic resistance to ampicillin (94.2%), followed by chloramphenicol (80.0%), cefoxitin (79.5%), gentamicin (78.4%), and ceftriaxone (71.1%). Gram-positive bacteria were all resistant to gentamicin, kanamycin, and penicillin. Resistance genes to quinolone, β-lactam, and tetracycline were the most prevalent and abundant genes identified in the soil. qepA and tetA, both encoding efflux pumps, predominated in quinolone and tetracycline resistance genes, respectively. Positive correlation (p < 0.05) was identified among groups of antibiotic resistance genes and between antibiotic resistance genes and metal resistance genes. The data demonstrated a diverse population of antibiotic resistance in urban agricultural soils. Phenotypic determination together with soil metagenomics proved to be a valuable tool to study the nature and extent of antibiotic resistance in the environment. A manuscript has been submitted and is currently under review.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2017
Citation:
Mafiz, A., L.N. Perera, S. Xiao, W. Hao, and Y. Zhang. Antibiotic Resistance in Detroit Urban Agricultural Soils. The 4th International Symposium on the Environmental Dimension of Antibiotic Resistance (EDAR-4). East Lansing, MI, August, 2017
Mafiz, A., L.N. Perera, S. Xiao, W. Hao, and Y. Zhang. Antibiotic Resistance Reservoir in Urban Agricultural Soils. International Association of Food Protection (IAFP) Annual Conference. Tampa, FL, July 2017
- Type:
Journal Articles
Status:
Under Review
Year Published:
2017
Citation:
Prevalence of antibiotic resistance phenotypes and genotypes in urban agricultural soils
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Progress 01/01/16 to 12/31/16
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Two graduate students (one PhD student and one Master student) have been trained on sample preparation, bacteria isolation, PCR, 16S rRNA sequence analysis, MIC determination, soil DNA extraction, data analysis, and technical presentation. We have also recruited two highly-motivated undergraduate students to participate in this research. They are learning the scientific principles, technology, operational procedures of food safety microbiology, and laboratory equipment associated with the project. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Sample description: Soil and vegetable samples have been collected from three urban gardens (GJG, OU, and EUF) in metro Detroit. The sampling plot was 20 meter X 20 meter from each garden. We started with the analysis of 15 soil samples, 5 per garden, including one from each corner of the plot and one in the center. A total of 45 vegetables, including leafy greens and root vegetables, were 5 from GJG, 19 from OU, and 21 from EUF. In addition, 36 more soils were included from the same plot at EUF to provide a more accurate picture of the spatial distribution of soil bacteria in association with their antimicrobial resistance. Soil bacteria were isolated from the samples using R2A agar, supplemented with ampicillin, streptomycin, and tetracycline, individually. Bacteria were identified by 16S rRNA gene sequencing. We were able to isolate common soil bacteria from soil and vegetables associated with urban agriculture. A total of 289 soil bacteria, including 71 and 218, respectively, were isolated from 15 soil samples and 45 vegetables. The diversity of the bacteria was evidenced by the identification of 38 genera. The most prevalent bacteria were Stenotrophomonas, Pseudomonas, and Chryseobacterium. Garden wise, the predominant bacteria were Pseudomonas at GJG, Pseudomonas at OU, and Stenotrophomonas at EUF. There was no clear distinction between soil and vegetables in terms of the diversity of the bacteria. When including more soil samples from the same garden, we were able to isolate and characterize 207 soil bacteria from a total of 41 samples at EUF. The bacteria belonged to four phyla: Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria. The predominant genera identified wereChryseobacterium,Stenotrophomonas, andSphingobacterium. Although the prevalence of individual soil bacterium was different from what was obtained based on 5 samples, common genera and phyla were identified in both situations. The 207 bacteria were then analyzed by MIC determination using Sensititre plates and interpreted according to the resistance breakpoints recommended by CLSI for E. coli and S. aureus. High prevalence of resistance and high MIC were observed, especially to β-lactam (ampicillin, amoxicillin, cefoxitin, ceftriaxone, penicillin) and aminoglycoside (gentamicin, kanamycin, streptomycin) antibiotics.
Publications
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