A Glyphosate-Based Herbicide Cross-Selects for Antibiotic Resistance Genes in Bacterioplankton Communities

Abstract

Glyphosate-based herbicides (GBHs) such as Roundup formulations may have the unintended consequence of selecting for antibiotic resistance genes (ARGs), as demonstrated in previous experiments. However, the effects of GBHs on ARGs remain unknown in natural aquatic communities, which are often contaminated with pesticides from agricultural runoff.

Glyphosate resistance as a potential driver for the dissemination of multidrug-resistant clinical strains

“…Most glyphosate-resistant strains found in the environment were phylogenetically related to MDR clinical strains. As previously suggested by da Barbosa Costa et al (2022) and confirmed by our study, this could be due to cross-selection via efflux pumps. Our genomic comparison of environmental and clinical strains ( Figure 6 ) supports that hypothesis, as it generally showed a higher number of efflux pumps in those isolates that were more resistant to the herbicide.…”

“…Strains with class I EPSPS were generally more resistant to glyphosate than those with class II EPSPS. The three previously described glyphosate resistance mechanisms were analyzed: (1) target site modification (EPSPS classes II, III, and IV aroA genes), (2) inactivating enzymes ( phn genes), and (3) efflux pumps, such as yhhS ( Staub et al, 2012 ), mexAB ( da Barbosa Costa et al, 2022 ), and acrAB ( Singh et al, 2022 ). Figure 6 shows a correlation analysis between MIC GBH and AMR determinants, including EPSPS classes and the number of phn and efflux pump genes.…”

“…The phnJ gene was detected in approximately half of the analyzed genomes. We identified efflux pump genes from the RND, SMR, MFS, MATE, and ABC families, with the RND-type systems MexAB and AcrAB being particularly noteworthy due to their documented links to GBH stress ( Pöppe et al, 2020 ; da Barbosa Costa et al, 2022 ; Singh et al, 2022 ). MexAB system genes increase under GBH stress ( da Barbosa Costa et al, 2022 ) and were ubiquitous in Pantoea , Klebsiella , and Stenotrophomonas isolates.…”

“…We identified efflux pump genes from the RND, SMR, MFS, MATE, and ABC families, with the RND-type systems MexAB and AcrAB being particularly noteworthy due to their documented links to GBH stress ( Pöppe et al, 2020 ; da Barbosa Costa et al, 2022 ; Singh et al, 2022 ). MexAB system genes increase under GBH stress ( da Barbosa Costa et al, 2022 ) and were ubiquitous in Pantoea , Klebsiella , and Stenotrophomonas isolates. They were variably present in Enterobacter , Acinetobacter , Serratia , Escherichia , and Pseudomonas isolates and absent in Scandinavium , Rossellomorea , and Staphylococcus isolates.…”

Glyphosate resistance as a potential driver for the dissemination of multidrug-resistant clinical strains

“…Most glyphosate-resistant strains found in the environment were phylogenetically related to MDR clinical strains. As previously suggested by da Barbosa Costa et al (2022) and confirmed by our study, this could be due to cross-selection via efflux pumps. Our genomic comparison of environmental and clinical strains ( Figure 6 ) supports that hypothesis, as it generally showed a higher number of efflux pumps in those isolates that were more resistant to the herbicide.…”

“…Strains with class I EPSPS were generally more resistant to glyphosate than those with class II EPSPS. The three previously described glyphosate resistance mechanisms were analyzed: (1) target site modification (EPSPS classes II, III, and IV aroA genes), (2) inactivating enzymes ( phn genes), and (3) efflux pumps, such as yhhS ( Staub et al, 2012 ), mexAB ( da Barbosa Costa et al, 2022 ), and acrAB ( Singh et al, 2022 ). Figure 6 shows a correlation analysis between MIC GBH and AMR determinants, including EPSPS classes and the number of phn and efflux pump genes.…”

“…The phnJ gene was detected in approximately half of the analyzed genomes. We identified efflux pump genes from the RND, SMR, MFS, MATE, and ABC families, with the RND-type systems MexAB and AcrAB being particularly noteworthy due to their documented links to GBH stress ( Pöppe et al, 2020 ; da Barbosa Costa et al, 2022 ; Singh et al, 2022 ). MexAB system genes increase under GBH stress ( da Barbosa Costa et al, 2022 ) and were ubiquitous in Pantoea , Klebsiella , and Stenotrophomonas isolates.…”

“…We identified efflux pump genes from the RND, SMR, MFS, MATE, and ABC families, with the RND-type systems MexAB and AcrAB being particularly noteworthy due to their documented links to GBH stress ( Pöppe et al, 2020 ; da Barbosa Costa et al, 2022 ; Singh et al, 2022 ). MexAB system genes increase under GBH stress ( da Barbosa Costa et al, 2022 ) and were ubiquitous in Pantoea , Klebsiella , and Stenotrophomonas isolates. They were variably present in Enterobacter , Acinetobacter , Serratia , Escherichia , and Pseudomonas isolates and absent in Scandinavium , Rossellomorea , and Staphylococcus isolates.…”

A glyphosate-based herbicide selects for genetic changes while retaining within-species diversity in a freshwater bacterioplankton community

“…As evidence for this, we found that GBH selected for a decreased copy number of transcription and translation genes in GBH-sensitive MAGs, but not in GBH-resistant MAGs. Together with previous findings that GBH selects for multidrug efflux pumps in bacterioplankton communities (36), our results highlight that targets of selection can be diverse in natural communities, not always centered on canonical resistance mutations.…”

Glyphosate resistance as a potential driver for the dissemination of multidrug-resistant clinical strains

“…Most glyphosate-resistant strains found in the environment were phylogenetically related to MDR clinical strains. As previously suggested by da Barbosa Costa et al (2022) and confirmed by our study, this could be due to cross-selection via efflux pumps. Our genomic comparison of environmental and clinical strains ( Figure 6 ) supports that hypothesis, as it generally showed a higher number of efflux pumps in those isolates that were more resistant to the herbicide.…”

“…Strains with class I EPSPS were generally more resistant to glyphosate than those with class II EPSPS. The three previously described glyphosate resistance mechanisms were analyzed: (1) target site modification (EPSPS classes II, III, and IV aroA genes), (2) inactivating enzymes ( phn genes), and (3) efflux pumps, such as yhhS ( Staub et al, 2012 ), mexAB ( da Barbosa Costa et al, 2022 ), and acrAB ( Singh et al, 2022 ). Figure 6 shows a correlation analysis between MIC GBH and AMR determinants, including EPSPS classes and the number of phn and efflux pump genes.…”

“…The phnJ gene was detected in approximately half of the analyzed genomes. We identified efflux pump genes from the RND, SMR, MFS, MATE, and ABC families, with the RND-type systems MexAB and AcrAB being particularly noteworthy due to their documented links to GBH stress ( Pöppe et al, 2020 ; da Barbosa Costa et al, 2022 ; Singh et al, 2022 ). MexAB system genes increase under GBH stress ( da Barbosa Costa et al, 2022 ) and were ubiquitous in Pantoea , Klebsiella , and Stenotrophomonas isolates.…”

“…We identified efflux pump genes from the RND, SMR, MFS, MATE, and ABC families, with the RND-type systems MexAB and AcrAB being particularly noteworthy due to their documented links to GBH stress ( Pöppe et al, 2020 ; da Barbosa Costa et al, 2022 ; Singh et al, 2022 ). MexAB system genes increase under GBH stress ( da Barbosa Costa et al, 2022 ) and were ubiquitous in Pantoea , Klebsiella , and Stenotrophomonas isolates. They were variably present in Enterobacter , Acinetobacter , Serratia , Escherichia , and Pseudomonas isolates and absent in Scandinavium , Rossellomorea , and Staphylococcus isolates.…”

A glyphosate-based herbicide selects for genetic changes while retaining within-species diversity in a freshwater bacterioplankton community

“…As evidence for this, we found that GBH selected for a decreased copy number of transcription and translation genes in GBH-sensitive MAGs, but not in GBH-resistant MAGs. Together with previous findings that GBH selects for multidrug efflux pumps in bacterioplankton communities (36), our results highlight that targets of selection can be diverse in natural communities, not always centered on canonical resistance mutations.…”

Glyphosate resistance as a potential driver for the dissemination of multidrug-resistant clinical strains

“…Most glyphosate-resistant strains found in the environment were phylogenetically related to MDR clinical strains. As previously suggested by da Barbosa Costa et al (2022) and confirmed by our study, this could be due to cross-selection via efflux pumps. Our genomic comparison of environmental and clinical strains ( Figure 6 ) supports that hypothesis, as it generally showed a higher number of efflux pumps in those isolates that were more resistant to the herbicide.…”

“…Strains with class I EPSPS were generally more resistant to glyphosate than those with class II EPSPS. The three previously described glyphosate resistance mechanisms were analyzed: (1) target site modification (EPSPS classes II, III, and IV aroA genes), (2) inactivating enzymes ( phn genes), and (3) efflux pumps, such as yhhS ( Staub et al, 2012 ), mexAB ( da Barbosa Costa et al, 2022 ), and acrAB ( Singh et al, 2022 ). Figure 6 shows a correlation analysis between MIC GBH and AMR determinants, including EPSPS classes and the number of phn and efflux pump genes.…”

“…The phnJ gene was detected in approximately half of the analyzed genomes. We identified efflux pump genes from the RND, SMR, MFS, MATE, and ABC families, with the RND-type systems MexAB and AcrAB being particularly noteworthy due to their documented links to GBH stress ( Pöppe et al, 2020 ; da Barbosa Costa et al, 2022 ; Singh et al, 2022 ). MexAB system genes increase under GBH stress ( da Barbosa Costa et al, 2022 ) and were ubiquitous in Pantoea , Klebsiella , and Stenotrophomonas isolates.…”

“…We identified efflux pump genes from the RND, SMR, MFS, MATE, and ABC families, with the RND-type systems MexAB and AcrAB being particularly noteworthy due to their documented links to GBH stress ( Pöppe et al, 2020 ; da Barbosa Costa et al, 2022 ; Singh et al, 2022 ). MexAB system genes increase under GBH stress ( da Barbosa Costa et al, 2022 ) and were ubiquitous in Pantoea , Klebsiella , and Stenotrophomonas isolates. They were variably present in Enterobacter , Acinetobacter , Serratia , Escherichia , and Pseudomonas isolates and absent in Scandinavium , Rossellomorea , and Staphylococcus isolates.…”

A glyphosate-based herbicide selects for genetic changes while retaining within-species diversity in a freshwater bacterioplankton community

“…As evidence for this, we found that GBH selected for a decreased copy number of transcription and translation genes in GBH-sensitive MAGs, but not in GBH-resistant MAGs. Together with previous findings that GBH selects for multidrug efflux pumps in bacterioplankton communities (36), our results highlight that targets of selection can be diverse in natural communities, not always centered on canonical resistance mutations.…”