Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer

Fifteen soil and 45 vegetable samples from Detroit community gardens were analyzed for potential antimicrobial resistance contamination. Soil bacteria were isolated and tested by antimicrobial susceptibility profiling, horizontal gene transfer, and whole-genome sequencing. High-throughput 16S rRNA s...

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Autores principales:	Abdullah Ibn Mafiz, Yingshu He, Wei Zhang, Yifan Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	antimicrobial resistance soil bacteria horizontal gene transfer urban agriculture whole genome sequencing Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7fd0b127a6e14f0eb216668b0479b68a
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spelling	oai:doaj.org-article:7fd0b127a6e14f0eb216668b0479b68a2021-11-30T13:49:33ZSoil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer1664-302X10.3389/fmicb.2021.771707https://doaj.org/article/7fd0b127a6e14f0eb216668b0479b68a2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmicb.2021.771707/fullhttps://doaj.org/toc/1664-302XFifteen soil and 45 vegetable samples from Detroit community gardens were analyzed for potential antimicrobial resistance contamination. Soil bacteria were isolated and tested by antimicrobial susceptibility profiling, horizontal gene transfer, and whole-genome sequencing. High-throughput 16S rRNA sequencing analysis was conducted on collected soil samples to determine the total bacterial composition. Of 226 bacterial isolates recovered, 54 were from soil and 172 from vegetables. A high minimal inhibitory concentration (MIC) was defined as the MIC greater than or equal to the resistance breakpoint of Escherichia coli for Gram-negative bacteria or Staphylococcus aureus for Gram-positive bacteria. The high MIC was observed in 63.4 and 69.8% of Gram-negative isolates from soil and vegetables, respectively, against amoxicillin/clavulanic acid, as well as 97.5 and 82.7% against ampicillin, 97.6 and 90.7% against ceftriaxone, 85.4 and 81.3% against cefoxitin, 65.8 and 70.5% against chloramphenicol, and 80.5 and 59.7% against ciprofloxacin. All Gram-positive bacteria showed a high MIC to gentamicin, kanamycin, and penicillin. Forty of 57 isolates carrying tetM (70.2%) successfully transferred tetracycline resistance to a susceptible recipient via conjugation. Whole-genome sequencing analysis identified a wide array of antimicrobial resistance genes (ARGs), including those encoding AdeIJK, Mex, and SmeDEF efflux pumps, suggesting a high potential of the isolates to become antimicrobial resistant, despite some inconsistency between the gene profile and the resistance phenotype. In conclusion, soil bacteria in urban community gardens can serve as a reservoir of antimicrobial resistance with the potential to transfer to clinically important pathogens, resulting in food safety and public health concerns.Abdullah Ibn MafizAbdullah Ibn MafizYingshu HeYingshu HeWei ZhangYifan ZhangFrontiers Media S.A.articleantimicrobial resistancesoil bacteriahorizontal gene transferurban agriculturewhole genome sequencingMicrobiologyQR1-502ENFrontiers in Microbiology, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	antimicrobial resistance soil bacteria horizontal gene transfer urban agriculture whole genome sequencing Microbiology QR1-502
spellingShingle	antimicrobial resistance soil bacteria horizontal gene transfer urban agriculture whole genome sequencing Microbiology QR1-502 Abdullah Ibn Mafiz Abdullah Ibn Mafiz Yingshu He Yingshu He Wei Zhang Yifan Zhang Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer
description	Fifteen soil and 45 vegetable samples from Detroit community gardens were analyzed for potential antimicrobial resistance contamination. Soil bacteria were isolated and tested by antimicrobial susceptibility profiling, horizontal gene transfer, and whole-genome sequencing. High-throughput 16S rRNA sequencing analysis was conducted on collected soil samples to determine the total bacterial composition. Of 226 bacterial isolates recovered, 54 were from soil and 172 from vegetables. A high minimal inhibitory concentration (MIC) was defined as the MIC greater than or equal to the resistance breakpoint of Escherichia coli for Gram-negative bacteria or Staphylococcus aureus for Gram-positive bacteria. The high MIC was observed in 63.4 and 69.8% of Gram-negative isolates from soil and vegetables, respectively, against amoxicillin/clavulanic acid, as well as 97.5 and 82.7% against ampicillin, 97.6 and 90.7% against ceftriaxone, 85.4 and 81.3% against cefoxitin, 65.8 and 70.5% against chloramphenicol, and 80.5 and 59.7% against ciprofloxacin. All Gram-positive bacteria showed a high MIC to gentamicin, kanamycin, and penicillin. Forty of 57 isolates carrying tetM (70.2%) successfully transferred tetracycline resistance to a susceptible recipient via conjugation. Whole-genome sequencing analysis identified a wide array of antimicrobial resistance genes (ARGs), including those encoding AdeIJK, Mex, and SmeDEF efflux pumps, suggesting a high potential of the isolates to become antimicrobial resistant, despite some inconsistency between the gene profile and the resistance phenotype. In conclusion, soil bacteria in urban community gardens can serve as a reservoir of antimicrobial resistance with the potential to transfer to clinically important pathogens, resulting in food safety and public health concerns.
format	article
author	Abdullah Ibn Mafiz Abdullah Ibn Mafiz Yingshu He Yingshu He Wei Zhang Yifan Zhang
author_facet	Abdullah Ibn Mafiz Abdullah Ibn Mafiz Yingshu He Yingshu He Wei Zhang Yifan Zhang
author_sort	Abdullah Ibn Mafiz
title	Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer
title_short	Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer
title_full	Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer
title_fullStr	Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer
title_full_unstemmed	Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer
title_sort	soil bacteria in urban community gardens have the potential to disseminate antimicrobial resistance through horizontal gene transfer
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/7fd0b127a6e14f0eb216668b0479b68a
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Soil Bacteria in Urban Community Gardens Have the Potential to Disseminate Antimicrobial Resistance Through Horizontal Gene Transfer

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