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Fu B, Xu J, Yin D, Sun C, Liu D, Zhai W, Bai R, Cao Y, Zhang Q, Ma S, Walsh TR, Hu F, Wang Y, Wu C, Shen J. Transmission of blaNDM in Enterobacteriaceae among animals, food and human. Emerg Microbes Infect 2024; 13:2337678. [PMID: 38629492 PMCID: PMC11034458 DOI: 10.1080/22221751.2024.2337678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/27/2024] [Indexed: 04/22/2024]
Abstract
Despite carbapenems not being used in animals, carbapenem-resistant Enterobacterales (CRE), particularly New Delhi metallo-β-lactamase-producing CRE (NDM-CRE), are prevalent in livestock. Concurrently, the incidence of human infections caused by NDM-CRE is rising, particularly in children. Although a positive association between livestock production and human NDM-CRE infections at the national level was identified, the evidence of direct transmission of NDM originating from livestock to humans remains largely unknown. Here, we conducted a cross-sectional study in Chengdu, Sichuan Province, to examine the prevalence of NDM-CRE in chickens and pigs along the breeding-slaughtering-retail chains, in pork in cafeterias of schools, and in colonizations and infections from children's hospital and examined the correlation of NDM-CRE among animals, foods and humans. Overall, the blaNDM increases gradually along the chicken and pig breeding (4.70%/2.0%) -slaughtering (7.60%/22.40%) -retail (65.56%/34.26%) chains. The slaughterhouse has become a hotspot for cross-contamination and amplifier of blaNDM. Notably, 63.11% of pork from the school cafeteria was positive for blaNDM. The prevalence of blaNDM in intestinal and infection samples from children's hospitals was 21.68% and 19.80%, respectively. whole genome sequencing (WGS) analysis revealed the sporadic, not large-scale, clonal spread of NDM-CRE along the chicken and pig breeding-slaughtering-retail chain, with further spreading via IncX3-blaNDM plasmid within each stage of whole chains. Clonal transmission of NDM-CRE is predominant in children's hospitals. The IncX3-blaNDM plasmid was highly prevalent among animals and humans and accounted for 57.7% of Escherichia coli and 91.3% of Klebsiella pneumoniae. Attention should be directed towards the IncX3 plasmid to control the transmission of blaNDM between animals and humans.
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Affiliation(s)
- Bo Fu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jian Xu
- Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People’s Republic of China
| | - Dandan Yin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics (MoH), Shanghai, People’s Republic of China
| | - Chengtao Sun
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Dejun Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Weishuai Zhai
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Rina Bai
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yue Cao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Qin Zhang
- Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People’s Republic of China
| | - Shizhen Ma
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Timothy R. Walsh
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
- Department of Zoology, Ineos-Oxford Institute of Antimicrobial Research, University of Oxford, Oxford, UK
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics (MoH), Shanghai, People’s Republic of China
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Congming Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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2
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Liu S, Yang X, Li R, Wang S, Han Z, Yang M, Zhang Y. IS6 family insertion sequences promote optrA dissemination between plasmids varying in transfer abilities. Appl Microbiol Biotechnol 2024; 108:132. [PMID: 38229329 DOI: 10.1007/s00253-023-12858-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/25/2023] [Accepted: 11/13/2023] [Indexed: 01/18/2024]
Abstract
Plasmids are the primary vectors for intercellular transfer of the oxazolidinone and phenicol cross-resistance gene optrA, while insertion sequences (ISs) are mobile genetic elements that can mobilize plasmid-borne optrA intracellularly. However, little is known about how the IS-mediated intracellular mobility facilitates the dissemination of the optrA gene between plasmid categories that vary in transfer abilities, including non-mobilizable, mobilizable, and conjugative plasmids. Here, we performed a holistic genomic study of 52 optrA-carrying plasmids obtained from searches guided by the Comprehensive Antibiotic Resistance Database. Among the 132 ISs identified within 10 kbp from the optrA gene in the plasmids, IS6 family genes were the most prevalent (86/132). Homologous gene arrays containing IS6 family genes were shared between different plasmids, especially between mobilizable and conjugative plasmids. All these indicated the central role of IS6 family genes in disseminating plasmid-borne optrA. Thirty-three of the 52 plasmids were harbored by Enterococcus faecalis found mainly in humans and animals. By Nanopore sequencing and inverse PCR, the potential of the enterococcal optrA to be transmitted from a mobilizable plasmid to a conjugative plasmid mediated by IS6 family genes was further confirmed in Enterococcus faecalis strains recovered from the effluents of anaerobic digestion systems for treating chicken manure. Our findings highlight the increased intercellular transfer abilities and dissemination risk of plasmid-borne optrA gene caused by IS-mediated intracellular mobility, and underscore the importance of routinely monitoring the dynamic genetic contexts of clinically important antibiotic resistance genes to effectively control this critical public health threat. KEY POINTS: • IS6 was prevalent in optrA-plasmids varying in intercellular transfer abilities. • Enterococcal optrA-plasmids were widespread among human, animal, and the environment. • IS6 elevated the dissemination risk of enterococcal optrA-plasmids.
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Affiliation(s)
- Shihai Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Shaolin Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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3
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Zhou CS, Cao GL, Liu BF, Liu W, Ma WL, Ren NQ. Deciphering the reduction of antibiotic resistance genes (ARGs) during medium-chain fatty acids production from waste activated sludge: Driven by inhibition of ARGs transmission and shift of microbial community. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134676. [PMID: 38788579 DOI: 10.1016/j.jhazmat.2024.134676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/18/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) by chain extension (CE) is a promising technology. However, the effects and mechanisms of CE process on the fate of antibiotic resistance genes (ARGs) remain unclear. In this study, the results showed that the removal efficiency of ARGs was 81.15 % in CE process, suggesting its efficacy in reducing environmental risks. Further, the observed decrease in mobile genetic elements (MGEs) indicated that CE process restricted the horizontal gene transfer (HGT). Complementing this, the increase in soluble organic matters and extracellular 16 S rDNA confirmed that MCFAs production caused bacterial damage. Decreased intracellular ARGs and increased extracellular ARGs further revealed that MCFAs production impaired ARGs hosts, thereby limiting the vertical gene transfer (VGT) of ARGs. Shift of microbial community combined with co-occurrence network analysis demonstrated that functional bacteria without host potential for ARGs were enriched, but potential ARGs and MGEs hosts decreased, showing the role of functional bacterial phylogeny and selection pressure of MCFAs in reducing ARGs. Finally, partial least squares path model was used to systematic verify the mechanism of ARGs removal in CE process, which was attributed to the inhibition of ARGs transmission (HGT and VGT) and shift of microbial community.
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Affiliation(s)
- Chun-Shuang Zhou
- National-Local Joint Engineering Research Center for Biomass Energy Development and Utilization, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guang-Li Cao
- National-Local Joint Engineering Research Center for Biomass Energy Development and Utilization, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Bing-Feng Liu
- National-Local Joint Engineering Research Center for Biomass Energy Development and Utilization, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wei Liu
- Heilongjiang Institute of Energy and Environment, Harbin 150007, China
| | - Wan-Li Ma
- National-Local Joint Engineering Research Center for Biomass Energy Development and Utilization, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nan-Qi Ren
- National-Local Joint Engineering Research Center for Biomass Energy Development and Utilization, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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Meng J, Ding J, Wang W, Gu B, Zhou F, Wu D, Fu X, Liu J. Reversal of gentamicin sulfate resistance in avian pathogenic Escherichia coli by matrine combined with berberine hydrochloride. Arch Microbiol 2024; 206:292. [PMID: 38849633 DOI: 10.1007/s00203-024-04021-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024]
Abstract
In recent years, the evolution of antibiotic resistance has led to the inefficacy of several antibiotics, and the reverse of resistance was a novel method to solve this problem. We previously demonstrated that matrine (Mat) and berberine hydrochloride (Ber) had a synergistic effect against multidrug-resistant Escherichia coli (MDREC). This study aimed to demonstrate the effect of Mat combined with Ber in reversing the resistance of MDREC. The MDREC was sequenced passaged in the presence of Mat, Ber, and a combination of Mat and Ber, which did not affect its growth. The reverse rate was up to 39.67% after MDREC exposed to Mat + Ber for 15 days. The strain that reversed resistance was named drug resistance reversed E. coli (DRREC) and its resistance to ampicillin, streptomycin, gentamicin, and tetracycline was reversed. The MIC of Gentamicin Sulfate (GS) against DRREC decreased 128-fold to 0.63 µg/mL, and it was stable within 20 generations. Furthermore, the susceptible phenotype of DRREC remained stable within 20 generations, as well. The LD50 of DRREC for chickens was 8.69 × 109 CFU/mL. qRT-PCR assays revealed that the transcript levels of antibiotic-resistant genes and virulence genes in the DRREC strain were significantly lower than that in the MDREC strain (P < 0.05). In addition, GS decreased the death, decreased the bacterial loading in organs, alleviated the injury of the spleen and liver, and decreased the cytokine levels in the chickens infected by the DRREC strain. In contrast, the therapeutic effect of GS in chickens infected with MDREC was not as evident. These findings suggest that the combination of Mat and Ber has potential for reversing resistance to MDREC.
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Affiliation(s)
- Jinwu Meng
- MOE Joint International Research Laboratory of Animal Health and Food Safety and Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, P R China
| | - Jinxue Ding
- MOE Joint International Research Laboratory of Animal Health and Food Safety and Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, P R China
| | - Weiran Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety and Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, P R China
| | - Bolin Gu
- MOE Joint International Research Laboratory of Animal Health and Food Safety and Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, P R China
| | - Fanting Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety and Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, P R China
| | - Desheng Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety and Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, P R China
| | - Xiang Fu
- MOE Joint International Research Laboratory of Animal Health and Food Safety and Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, P R China
| | - Jiaguo Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety and Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, P R China.
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He K, Lin J, Liang Y, Cui J, Chen Q, Dong Y, Ma X, He D, Yuan L. Coexistence of a nonresistance-conferring IncI1 plasmid favors persistence of the blaCTX-M-bearing IncFII plasmid in Escherichia coli. Microbiol Spectr 2024; 12:e0424023. [PMID: 38687059 DOI: 10.1128/spectrum.04240-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
The interaction between coexisting plasmids can affect plasmid-carried resistance gene persistence and spread. However, whether the persistence of the blaCTX-M gene in clinical Enterobacteriaceae is related to the interaction of coresident nonresistance-conferring plasmids has not been reported. This study was initiated to elucidate how a nonresistance-conferring IncI1 plasmid affected the blaCTX-M-bearing IncFII plasmid colocated on the same cell. Herein, we constructed three isogenic derivatives of E. coli C600, designated as C600FII, C600I1, and C600FII+I1, which harbored the blaCTX-M-IncFII plasmid and/or the nonresistance-IncI1 one. We discovered that strain C600FII+I1 conferred higher fitness advantages than strain C600FII; also, the stability of the blaCTX-M-IncFII plasmid was noticeably improved in an antibiotic-free environment when it coexisted with the IncI1 plasmid. To further explore why the IncI1 plasmid enhanced the persistence of the blaCTX-M-IncFII plasmid, we assessed the blaCTX-M-IncFII plasmid's copy numbers, conjugation frequencies, and rep gene expressions in strains C600FII and C600FII+I1. The results demonstrated that the rep expressions of the blaCTX-M-IncFII plasmid in strain C600FII+I1 was greatly decreased, along with the plasmid's copy numbers and mating efficiencies, compared to those in strain C600FII. Moreover, further study revealed that the intracellular ATP levels of strain C600FII+I1 were far lower than those of strain C600FII. Our findings confirmed that coexistence of the nonresistance-IncI1 plasmid can keep the blaCTX-M-IncFII plasmid more stable by increasing the fitness advantages of the host bacteria, which will pose a threat to preventing the long-term presence of the plasmid-carried blaCTX-M gene in clinical Enterobacteriaceae. IMPORTANCE So far, plasmid-carried blaCTX-M is still the most common extended-spectrum beta-lactamase (ESBL) genotype in clinical settings worldwide. Except for the widespread use of third-generation cephalosporins, the interaction between coexisting plasmids can also affect the long-term stable existence of the blaCTX-M gene; however, the study on that is still sparse. In the present study, we assess the interaction of coinhabitant plasmids blaCTX-M-IncFII and nonresistance-IncI1. Our results confirmed that the increased fitness advantages of strain C600FII+I1 were attributable to the cohabitant nonresistance-IncI1 plasmid, which largely reduced the intracellular ATP levels of host bacteria, thus decreasing the rep gene expression of the blaCTX-M-IncFII plasmid, its copy numbers, and mating efficiencies, while the higher fitness advantages of strain C600FII+I1 enhanced the persistence of the blaCTX-M-IncFII plasmid. The results indicate that the nonresistance-IncI1 plasmid contributes to the long-term existence of the blaCTX-M-IncFII plasmid, implying a potentially new strategy for controlling the spread of resistance plasmids in clinical settings by targeting nonresistance plasmids.
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Affiliation(s)
- Kun He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Jiayu Lin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yulei Liang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Junling Cui
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Qiuru Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yanbin Dong
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xiaoyuan Ma
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Dandan He
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Li Yuan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
- Key Laboratory of Quality and Safety Control of Poultry Products (Zhengzhou), Ministry of Agriculture and Rural Affairs, Zhengzhou, China
- Zhengzhou Key Laboratory of Research and Evaluation of Traditional Chinese Veterinary Medicine, Zhengzhou, China
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6
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Ha Y, Ma HR, Wu F, Weiss A, Duncker K, Xu HZ, Lu J, Golovsky M, Reker D, You L. Data-driven learning of structure augments quantitative prediction of biological responses. PLoS Comput Biol 2024; 20:e1012185. [PMID: 38829926 DOI: 10.1371/journal.pcbi.1012185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
Multi-factor screenings are commonly used in diverse applications in medicine and bioengineering, including optimizing combination drug treatments and microbiome engineering. Despite the advances in high-throughput technologies, large-scale experiments typically remain prohibitively expensive. Here we introduce a machine learning platform, structure-augmented regression (SAR), that exploits the intrinsic structure of each biological system to learn a high-accuracy model with minimal data requirement. Under different environmental perturbations, each biological system exhibits a unique, structured phenotypic response. This structure can be learned based on limited data and once learned, can constrain subsequent quantitative predictions. We demonstrate that SAR requires significantly fewer data comparing to other existing machine-learning methods to achieve a high prediction accuracy, first on simulated data, then on experimental data of various systems and input dimensions. We then show how a learned structure can guide effective design of new experiments. Our approach has implications for predictive control of biological systems and an integration of machine learning prediction and experimental design.
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Affiliation(s)
- Yuanchi Ha
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina, United States of America
| | - Helena R Ma
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina, United States of America
| | - Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Katherine Duncker
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina, United States of America
| | - Helen Z Xu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Jia Lu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina, United States of America
| | - Max Golovsky
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
| | - Daniel Reker
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina, United States of America
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
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7
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Zongo PD, Cabanel N, Royer G, Depardieu F, Hartmann A, Naas T, Glaser P, Rosinski-Chupin I. An antiplasmid system drives antibiotic resistance gene integration in carbapenemase-producing Escherichia coli lineages. Nat Commun 2024; 15:4093. [PMID: 38750030 PMCID: PMC11096173 DOI: 10.1038/s41467-024-48219-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024] Open
Abstract
Plasmids carrying antibiotic resistance genes (ARG) are the main mechanism of resistance dissemination in Enterobacterales. However, the fitness-resistance trade-off may result in their elimination. Chromosomal integration of ARGs preserves resistance advantage while relieving the selective pressure for keeping costly plasmids. In some bacterial lineages, such as carbapenemase producing sequence type ST38 Escherichia coli, most ARGs are chromosomally integrated. Here we reproduce by experimental evolution the mobilisation of the carbapenemase blaOXA-48 gene from the pOXA-48 plasmid into the chromosome. We demonstrate that this integration depends on a plasmid-induced fitness cost, a mobile genetic structure embedding the ARG and a novel antiplasmid system ApsAB actively involved in pOXA-48 destabilization. We show that ApsAB targets high and low-copy number plasmids. ApsAB combines a nuclease/helicase protein and a novel type of Argonaute-like protein. It belongs to a family of defense systems broadly distributed among bacteria, which might have a strong ecological impact on plasmid diffusion.
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Affiliation(s)
- Pengdbamba Dieudonné Zongo
- Ecology and Evolution of Antibiotic Resistance Unit, Institut Pasteur, Paris, France
- Sorbonne Université, Paris, France
- Université Paris Cité, Paris, France
| | - Nicolas Cabanel
- Ecology and Evolution of Antibiotic Resistance Unit, Institut Pasteur, Paris, France
- Université Paris Cité, Paris, France
| | - Guilhem Royer
- Ecology and Evolution of Antibiotic Resistance Unit, Institut Pasteur, Paris, France
- Université Paris Cité, Paris, France
| | - Florence Depardieu
- Université Paris Cité, Paris, France
- Synthetic Biology Unit, Institut Pasteur, Paris, France
| | - Alain Hartmann
- UMR AgroEcologie 1347, INRAe, Université Bourgogne Franche-Comté, Dijon, France
| | - Thierry Naas
- Team ReSIST, INSERM UMR 1184, Paris-Saclay University, Le Kremlin-Bicêtre, France
- Department of Bacteriology-Hygiene, Bicêtre Hospital, APHP, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance Unit, Institut Pasteur, Paris, France
- Université Paris Cité, Paris, France
| | - Isabelle Rosinski-Chupin
- Ecology and Evolution of Antibiotic Resistance Unit, Institut Pasteur, Paris, France.
- Université Paris Cité, Paris, France.
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8
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Dos Santos LA, Cayô R, Valiatti TB, Gales AC, de Araújo LFB, Rodrigues FM, de Carvalho TS, Vaz MAB, Campanharo M. Biodiversity of carbapenem-resistant bacteria in clinical samples from the Southwest Amazon region (Rondônia/Brazil). Sci Rep 2024; 14:9383. [PMID: 38654061 DOI: 10.1038/s41598-024-59733-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
Brazil is recognized for its biodiversity and the genetic variability of its organisms. This genetic variability becomes even more valuable when it is properly documented and accessible. Understanding bacterial diversity through molecular characterization is necessary as it can improve patient treatment, reduce the length of hospital stays and the selection of resistant bacteria, and generate data for health and epidemiological surveillance. In this sense, in this study, we aimed to understand the biodiversity and molecular epidemiology of carbapenem-resistant bacteria in clinical samples recovered in the state of Rondônia, located in the Southwest Amazon region. Retrospective data from the Central Public Health Laboratories (LACEN/RO) between 2018 and 2021 were analysed using the Laboratory Environment Manager Platform (GAL). Seventy-two species with carbapenem resistance profiles were identified, of which 25 species carried at least one gene encoding carbapenemases of classes A (blaKPC-like), B (blaNDM-like, blaSPM-like or blaVIM-like) and D (blaOXA-23-like, blaOXA-24-like, blaOXA-48-like, blaOXA-58-like or blaOXA-143-like), among which we will highlight Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Serratia marcescens, and Providencia spp. With these results, we hope to contribute to the field by providing epidemiological molecular data for state surveillance on bacterial resistance and assisting in public policy decision-making.
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Affiliation(s)
- Levy Assis Dos Santos
- Federal University of Rondônia Foundation (UNIR), Postgraduate Program in Conservation and Use of Natural Resources (PPGReN), Porto Velho, RO, Brazil.
- Central Public Health Laboratory of Rondônia (LACEN/RO), Medical Biology Center, Porto Velho, RO, Brazil.
| | - Rodrigo Cayô
- Laboratory ALERTA, Department of Medicine, Paulista School of Medicine (EPM), Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
- Laboratory of Bacteriology and Immunology (LIB), Department of Biological Sciences (DCB), Institute of Environmental, Chemical and Pharmaceutical Sciences (ICAQF), Federal University of São Paulo (UNIFESP), Diadema, SP, Brazil
| | - Tiago Barcelos Valiatti
- Laboratory ALERTA, Department of Medicine, Paulista School of Medicine (EPM), Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Ana Cristina Gales
- Laboratory ALERTA, Department of Medicine, Paulista School of Medicine (EPM), Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Larissa Fatarelli Bento de Araújo
- Federal University of Rondônia Foundation (UNIR), Postgraduate Program in Conservation and Use of Natural Resources (PPGReN), Porto Velho, RO, Brazil
| | - Fernando Marques Rodrigues
- Central Public Health Laboratory of Rondônia (LACEN/RO), Medical Biology Center, Porto Velho, RO, Brazil
| | - Tatiane Silva de Carvalho
- Central Public Health Laboratory of Rondônia (LACEN/RO), Medical Biology Center, Porto Velho, RO, Brazil
| | - Marcos André Braz Vaz
- Department of Informatics and Statistics, Federal University of Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Marcela Campanharo
- Federal University of Rondônia Foundation (UNIR), Postgraduate Program in Conservation and Use of Natural Resources (PPGReN), Porto Velho, RO, Brazil
- Department of Agricultural and Biological Sciences (DCAB), Federal University of Espirito Santo, São Mateus, ES, Brazil
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9
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Hamrick GS, Maddamsetti R, Son HI, Wilson ML, Davis HM, You L. Programming Dynamic Division of Labor Using Horizontal Gene Transfer. ACS Synth Biol 2024; 13:1142-1151. [PMID: 38568420 DOI: 10.1021/acssynbio.3c00615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The metabolic engineering of microbes has broad applications, including biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multistep pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is the division of labor (DOL) in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted interstrain population dynamics. Through modeling, we show that dynamic division of labor (DDOL), which we define as the DOL between indiscrete populations capable of dynamic and reversible interchange, can overcome these limitations and enable the robust maintenance of burdensome, multistep pathways. We propose that DDOL can be mediated by horizontal gene transfer (HGT) and use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.
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Affiliation(s)
- Grayson S Hamrick
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Rohan Maddamsetti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
| | - Hye-In Son
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
| | - Maggie L Wilson
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
| | - Harris M Davis
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Center for Quantitative Biodesign, Duke University, Durham, North Carolina 27708, United States
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27708, United States
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10
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Kogay R, Wolf YI, Koonin EV. Defence systems and horizontal gene transfer in bacteria. Environ Microbiol 2024; 26:e16630. [PMID: 38643972 PMCID: PMC11034907 DOI: 10.1111/1462-2920.16630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/05/2024] [Indexed: 04/23/2024]
Abstract
Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.
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Affiliation(s)
- Roman Kogay
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
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11
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Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore RM, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Ruscheweyh HJ, Sunagawa S, Mclellan SL, Willis AD, Comstock LE, Eren AM. A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell 2024; 187:1206-1222.e16. [PMID: 38428395 DOI: 10.1016/j.cell.2024.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 10/03/2023] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.
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Affiliation(s)
- Emily C Fogarty
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Matthew S Schechter
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Madeline L Sheahan
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Iva Veseli
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Moody
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Phoebe A Rice
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry, University of Chicago, Chicago, IL 60637, USA
| | - Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Mark Mimee
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Sandra L Mclellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53204, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Laurie E Comstock
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany; Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany; Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany.
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12
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Maddamsetti R, Yao Y, Wang T, Gao J, Huang VT, Hamrick GS, Son HI, You L. Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria. Nat Commun 2024; 15:1449. [PMID: 38365845 PMCID: PMC10873360 DOI: 10.1038/s41467-024-45638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024] Open
Abstract
Horizontal gene transfer (HGT) and gene duplication are often considered as separate mechanisms driving the evolution of new functions. However, the mobile genetic elements (MGEs) implicated in HGT can copy themselves, so positive selection on MGEs could drive gene duplications. Here, we use a combination of modeling and experimental evolution to examine this hypothesis and use long-read genome sequences of tens of thousands of bacterial isolates to examine its generality in nature. Modeling and experiments show that antibiotic selection can drive the evolution of duplicated antibiotic resistance genes (ARGs) through MGE transposition. A key implication is that duplicated ARGs should be enriched in environments associated with antibiotic use. To test this, we examined the distribution of duplicated ARGs in 18,938 complete bacterial genomes with ecological metadata. Duplicated ARGs are highly enriched in bacteria isolated from humans and livestock. Duplicated ARGs are further enriched in an independent set of 321 antibiotic-resistant clinical isolates. Our findings indicate that duplicated genes often encode functions undergoing positive selection and horizontal gene transfer in microbial communities.
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Affiliation(s)
- Rohan Maddamsetti
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Yi Yao
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Teng Wang
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Junheng Gao
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Vincent T Huang
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Grayson S Hamrick
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, NC, USA
| | - Hye-In Son
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Lingchong You
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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13
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Yan Y, Li X, Yu K, Wu Z, Sun Y, Cheng Z, Zhao B, Nie C, Xia Y. Systematic evaluation of the impact of standard storage conditions on plasmid conjugation behavior in wastewater samples. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 343:123283. [PMID: 38176637 DOI: 10.1016/j.envpol.2023.123283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/29/2023] [Accepted: 12/30/2023] [Indexed: 01/06/2024]
Abstract
Filter mating experiment is widely used to study the conjugation behavior of plasmids and associated antibiotic resistance in environmental settings, however, the influence and biases brought by sample storage conditions (temperature and duration) were not yet systematically elaborated. This study systematically investigated the influence of standard storage conditions (4 °C, -20 °C, -80 °C) on plasmid conjugation behavior in influent (Inf) and activated sludge (AS) samples from sewage treatment plants (STP). The findings revealed a significant reduction in conjugation efficiency under all the tested storage conditions except for 1-week storage at 4 °C. Notably, storing at -80 °C maintained conjugation activities in activated sludge more effectively compared to -20 °C. However, the preservation performance was less effective for influent samples, which consist mainly of anaerobe-dominant communities. Systematic loss of IncH-type plasmids was observed in influent samples stored at 4 °C and -20 °C. Correspondingly, the plasmid-carrying resistome genotypes detected in the influent samples showed a clear downward trend with the increase in storage duration when stored at 4 °C and -20 °C. A relatively uniform composition in terms of incompatibility type and resistome profile was observed across activated sludge samples, regardless of the varied storage conditions. This study highlights the critical impact of storage conditions on plasmid conjugation behavior and resistome composition, offering valuable insights for optimal sample handling in resistome research.
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Affiliation(s)
- Yuxi Yan
- School of Environment, Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiang Li
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Kaiqiang Yu
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziqi Wu
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuhong Sun
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhanwen Cheng
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Cailong Nie
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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14
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Kogay R, Wolf YI, Koonin EV. Defense systems and horizontal gene transfer in bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579689. [PMID: 38410456 PMCID: PMC10896350 DOI: 10.1101/2024.02.09.579689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages that generally impose fitness costs on their hosts. However, a substantial fraction of bacterial genes is involved in defense mechanisms that limit the propagation of MGEs, raising the possibility that they can actively restrict HGT. Here we examine whether defense systems curb HGT by exploring the connections between HGT rate and the presence of 73 defense systems in 12 bacterial species. We found that only 6 defense systems, 3 of which are different CRISPR-Cas subtypes, are associated with the reduced gene gain rate on the scale of species evolution. The hosts of such defense systems tend to have a smaller pangenome size and harbor fewer phage-related genes compared to genomes lacking these systems, suggesting that these defense mechanisms inhibit HGT by limiting the integration of prophages. We hypothesize that restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and fitness effect of HGT in bacterial populations.
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Affiliation(s)
- Roman Kogay
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine. National Institutes of Health, Bethesda, MD 20894, USA
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15
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Paganini JA, Kerkvliet JJ, Vader L, Plantinga NL, Meneses R, Corander J, Willems RJL, Arredondo-Alonso S, Schürch AC. PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli. Microb Genom 2024; 10:001193. [PMID: 38376388 PMCID: PMC10926690 DOI: 10.1099/mgen.0.001193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
Accurate reconstruction of Escherichia coli antibiotic resistance gene (ARG) plasmids from Illumina sequencing data has proven to be a challenge with current bioinformatic tools. In this work, we present an improved method to reconstruct E. coli plasmids using short reads. We developed plasmidEC, an ensemble classifier that identifies plasmid-derived contigs by combining the output of three different binary classification tools. We showed that plasmidEC is especially suited to classify contigs derived from ARG plasmids with a high recall of 0.941. Additionally, we optimized gplas, a graph-based tool that bins plasmid-predicted contigs into distinct plasmid predictions. Gplas2 is more effective at recovering plasmids with large sequencing coverage variations and can be combined with the output of any binary classifier. The combination of plasmidEC with gplas2 showed a high completeness (median=0.818) and F1-Score (median=0.812) when reconstructing ARG plasmids and exceeded the binning capacity of the reference-based method MOB-suite. In the absence of long-read data, our method offers an excellent alternative to reconstruct ARG plasmids in E. coli.
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Affiliation(s)
- Julian A. Paganini
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jesse J. Kerkvliet
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lisa Vader
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nienke L. Plantinga
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rodrigo Meneses
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Rob J. L. Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Anita C. Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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16
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Zhu S, Hong J, Wang T. Horizontal gene transfer is predicted to overcome the diversity limit of competing microbial species. Nat Commun 2024; 15:800. [PMID: 38280843 PMCID: PMC10821886 DOI: 10.1038/s41467-024-45154-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024] Open
Abstract
Natural microbial ecosystems harbor substantial diversity of competing species. Explaining such diversity is challenging, because in classic theories it is extremely infeasible for a large community of competing species to stably coexist in homogeneous environments. One important aspect mostly overlooked in these theories, however, is that microbes commonly share genetic materials with their neighbors through horizontal gene transfer (HGT), which enables the dynamic change of species growth rates due to the fitness effects of the mobile genetic elements (MGEs). Here, we establish a framework of species competition by accounting for the dynamic gene flow among competing microbes. Combining theoretical derivation and numerical simulations, we show that in many conditions HGT can surprisingly overcome the biodiversity limit predicted by the classic model and allow the coexistence of many competitors, by enabling dynamic neutrality of competing species. In contrast with the static neutrality proposed by previous theories, the diversity maintained by HGT is highly stable against random perturbations of microbial fitness. Our work highlights the importance of considering gene flow when addressing fundamental ecological questions in the world of microbes and has broad implications for the design and engineering of complex microbial consortia.
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Affiliation(s)
- Shiben Zhu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Juken Hong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Teng Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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17
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Azman AA, Leow ATC, Noor NDM, Noor SAM, Latip W, Ali MSM. Worldwide trend discovery of structural and functional relationship of metallo-β-lactamase for structure-based drug design: A bibliometric evaluation and patent analysis. Int J Biol Macromol 2024; 256:128230. [PMID: 38013072 DOI: 10.1016/j.ijbiomac.2023.128230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/11/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Metallo-β-lactamase (MBL) is an enzyme produced by clinically important bacteria that can inactivate many commonly used antibiotics, making them a significant concern in treating bacterial infections and the risk of having high antibiotic resistance issues among the community. This review presents a bibliometric and patent analysis of MBL worldwide research trend based on the Scopus and World Intellectual Property Organization databases in 2013-2022. Based on the keywords related to MBL in the article title, abstract, and keywords, 592 research articles were retrieved for further analysis using various tools such as Microsoft Excel to determine the frequency analysis, VOSviewer for bibliometric networks visualization, and Harzing's Publish or Perish for citation metrics analysis. Standard bibliometric parameters were analysed to evaluate the field's research trend, such as the growth of publications, topographical distribution, top subject area, most relevant journal, top cited documents, most relevant authors, and keyword trend analysis. Within 10 years, MBL discovery has shown a steady and continuous growth of interest among the community of researchers. United States of America, China, and the United Kingdom are the top 3 countries contribute high productivity to the field. The patent analysis also shows several impactful filed patents, indicating the significance of development research on the structural and functional relationship of MBL for an effective structure-based drug design (SBDD). Developing new MBL inhibitors using SBDD could help address the research gap and provide new successful therapeutic options for treating MBL-producing bacterial infections.
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Affiliation(s)
- Ameera Aisyah Azman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Siti Aminah Mohd Noor
- Center for Defence Foundation Studies, National Defence University of Malaysia, Kem Perdana Sungai Besi, Kuala Lumpur 57000, Malaysia
| | - Wahhida Latip
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
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18
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Yang QE, Ma X, Zeng L, Wang Q, Li M, Teng L, He M, Liu C, Zhao M, Wang M, Hui D, Madsen JS, Liao H, Walsh TR, Zhou S. Interphylum dissemination of NDM-5-positive plasmids in hospital wastewater from Fuzhou, China: a single-centre, culture-independent, plasmid transmission study. THE LANCET. MICROBE 2024; 5:e13-e23. [PMID: 38006896 DOI: 10.1016/s2666-5247(23)00227-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 07/05/2023] [Accepted: 07/20/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND The global spread of plasmid-borne carbapenem resistance is an ongoing public health challenge; however, the nature of such horizontal gene transfer events among complex bacterial communities remains poorly understood. We examined the in-situ transfer of the globally dominant New Delhi metallo-β-lactamase (NDM)-5-positive IncX3 plasmid (denoted pX3_NDM-5) in hospital wastewater to simulate a real-world, One Health antimicrobial resistance context. METHODS For this transmission study, we tagged pX3_NDM-5 with the green fluorescent protein gene, gfp, using a CRISPR-based method and transferred the plasmid to a donor Escherichia coli strain. Bacteria were extracted from a hospital wastewater treatment plant (Fujian Provincial Maternity and Children's Hospital, Fuzhou, China) as the bacterial recipient community. We mixed this recipient community with the E coli donor strain carrying the gfp-tagged plasmid, both with and without sodium hypochlorite (NaClO) as an environmental stressor, and conducted several culture-based and culture-independent conjugation assays. The conjugation events were observed microscopically and quantified by fluorescence-activated cell sorting. We analysed the taxonomic composition of the sorted transconjugal pool by 16S rRNA gene amplicon sequencing and assessed the stability of the plasmid in the isolated transconjugants and its ability to transfer back to E coli. FINDINGS We show that the plasmid pX3_NDM-5 has a broad host range and can transfer across various bacterial phyla, including between Gram-negative and Gram-positive bacteria. Although environmental stress with NaClO did not affect the overall plasmid transfer frequency, it reduced the breadth of the transconjugant pool. The taxonomic composition of the transconjugal pool was distinct from that of the recipient communities, and environmental stress modulated the permissiveness of some operational taxonomic units towards the acquisition of pX3_NDM-5. Notably, pX3_NDM-5 transconjugants included the Gram-positive pathogen Enterococcus faecalis, and the plasmid could subsequently be reconjugated back to E coli. These findings suggest that E faecalis could act as a natural shuttle vector for the wide dissemination of pX3_NDM-5 plasmids. INTERPRETATION Our culture-independent conjugation model simulates natural environmental conditions and challenges the established theory that Gram-negative and Gram-positive bacteria rarely exchange clinically important plasmids. The data show that plasmids disseminate more widely across genera and phyla than previously thought. These findings have substantial implications when considering the spread of antimicrobial resistance across One Health sectors. FUNDING The Laboratory of Lingnan Modern Agriculture Project, the National Natural Science Foundation of China, the Natural Science Foundation of Fujian Province of China, and the Outstanding Young Research Talents Program of Fujian Agriculture and Forestry University.
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Affiliation(s)
- Qiu E Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaodan Ma
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingshuang Zeng
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinqin Wang
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Minchun Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Teng
- Department of Veterinary Medicine, College of Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Mingzhen He
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chen Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengshi Zhao
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengzhu Wang
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deng Hui
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jonas Stenløkke Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Hanpeng Liao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Timothy R Walsh
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK.
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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19
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Castañeda-Barba S, Top EM, Stalder T. Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era. Nat Rev Microbiol 2024; 22:18-32. [PMID: 37430173 DOI: 10.1038/s41579-023-00926-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 07/12/2023]
Abstract
Antimicrobial resistance (AMR) poses a substantial threat to human health. The widespread prevalence of AMR is, in part, due to the horizontal transfer of antibiotic resistance genes (ARGs), typically mediated by plasmids. Many of the plasmid-mediated resistance genes in pathogens originate from environmental, animal or human habitats. Despite evidence that plasmids mobilize ARGs between these habitats, we have a limited understanding of the ecological and evolutionary trajectories that facilitate the emergence of multidrug resistance (MDR) plasmids in clinical pathogens. One Health, a holistic framework, enables exploration of these knowledge gaps. In this Review, we provide an overview of how plasmids drive local and global AMR spread and link different habitats. We explore some of the emerging studies integrating an eco-evolutionary perspective, opening up a discussion about the factors that affect the ecology and evolution of plasmids in complex microbial communities. Specifically, we discuss how the emergence and persistence of MDR plasmids can be affected by varying selective conditions, spatial structure, environmental heterogeneity, temporal variation and coexistence with other members of the microbiome. These factors, along with others yet to be investigated, collectively determine the emergence and transfer of plasmid-mediated AMR within and between habitats at the local and global scale.
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Affiliation(s)
- Salvador Castañeda-Barba
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA.
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20
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Li X, Brejnrod A, Thorsen J, Zachariasen T, Trivedi U, Russel J, Vestergaard GA, Stokholm J, Rasmussen MA, Sørensen SJ. Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults. Nat Commun 2023; 14:8526. [PMID: 38135681 PMCID: PMC10746713 DOI: 10.1038/s41467-023-44289-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Despite their crucial importance for human health, there is still relatively limited knowledge on how the gut resistome changes or responds to antibiotic treatment across ages, especially in the latter case. Here, we use fecal metagenomic data from 662 Danish infants and 217 young adults to fill this gap. The gut resistomes are characterized by a bimodal distribution driven by E. coli composition. The typical profile of the gut resistome differs significantly between adults and infants, with the latter distinguished by higher gene and plasmid abundances. However, the predominant antibiotic resistance genes (ARGs) are the same. Antibiotic treatment reduces bacterial diversity and increased ARG and plasmid abundances in both cohorts, especially core ARGs. The effects of antibiotic treatments on the gut microbiome last longer in adults than in infants, and different antibiotics are associated with distinct impacts. Overall, this study broadens our current understanding of gut resistome dynamics and the impact of antibiotic treatment across age groups.
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Affiliation(s)
- Xuanji Li
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Asker Brejnrod
- Department of Health Technology, Technical University of Denmark, Section of Bioinformatics, 2800 Kgs, Lyngby, Denmark
| | - Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Trine Zachariasen
- Department of Health Technology, Technical University of Denmark, Section of Bioinformatics, 2800 Kgs, Lyngby, Denmark
| | - Urvish Trivedi
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jakob Russel
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Gisle Alberg Vestergaard
- Department of Health Technology, Technical University of Denmark, Section of Bioinformatics, 2800 Kgs, Lyngby, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Food Science, Section of Microbiology and Fermentation, University of Copenhagen, 1958, Frederiksberg C, Denmark
| | - Morten Arendt Rasmussen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
- Department of Food Science, Section of Microbiology and Fermentation, University of Copenhagen, 1958, Frederiksberg C, Denmark.
| | - Søren Johannes Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100, Copenhagen, Denmark.
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21
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Alonso-del Valle A, Toribio-Celestino L, Quirant A, Pi CT, DelaFuente J, Canton R, Rocha EPC, Ubeda C, Peña-Miller R, San Millan A. Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria. Proc Natl Acad Sci U S A 2023; 120:e2314135120. [PMID: 38096417 PMCID: PMC10741383 DOI: 10.1073/pnas.2314135120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Conjugative plasmids play a key role in the dissemination of antimicrobial resistance (AMR) genes across bacterial pathogens. AMR plasmids are widespread in clinical settings, but their distribution is not random, and certain associations between plasmids and bacterial clones are particularly successful. For example, the globally spread carbapenem resistance plasmid pOXA-48 can use a wide range of enterobacterial species as hosts, but it is usually associated with a small number of specific Klebsiella pneumoniae clones. These successful associations represent an important threat for hospitalized patients. However, knowledge remains limited about the factors determining AMR plasmid distribution in clinically relevant bacteria. Here, we combined in vitro and in vivo experimental approaches to analyze pOXA-48-associated AMR levels and conjugation dynamics in a collection of wild-type enterobacterial strains isolated from hospitalized patients. Our results revealed significant variability in these traits across different bacterial hosts, with Klebsiella spp. strains showing higher pOXA-48-mediated AMR and conjugation frequencies than Escherichia coli strains. Using experimentally determined parameters, we developed a simple mathematical model to interrogate the contribution of AMR levels and conjugation permissiveness to plasmid distribution in bacterial communities. The simulations revealed that a small subset of clones, combining high AMR levels and conjugation permissiveness, play a critical role in stabilizing the plasmid in different polyclonal microbial communities. These results help to explain the preferential association of plasmid pOXA-48 with K. pneumoniae clones in clinical settings. More generally, our study reveals that species- and strain-specific variability in plasmid-associated phenotypes shape AMR evolution in clinically relevant bacterial communities.
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Affiliation(s)
- Aida Alonso-del Valle
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Anna Quirant
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia46020, Spain
| | - Carles Tardio Pi
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca62209, México
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Unidad Académica Yucatán, Universidad Nacional Autónoma de México, Yucatán04510, México
| | - Javier DelaFuente
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramon y Cajal de Investigacion Sanitaria, Madrid28034, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid28029, Spain
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université de Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris75015, France
| | - Carles Ubeda
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana, Valencia46020, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid28029, Spain
| | - Rafael Peña-Miller
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca62209, México
| | - Alvaro San Millan
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, Madrid28049, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid28029, Spain
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22
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Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, Ahmed S, Kulkarni V, Deshpande P, Alexander M, Thi Hoa N, Christakis NA, Iqbal NT, Ali SA, Mathad JS, Brito IL. Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. Nat Commun 2023; 14:7366. [PMID: 37963868 PMCID: PMC10645880 DOI: 10.1038/s41467-023-42998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.
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Affiliation(s)
- Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Matthew W Rhee
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Qiaojuan Shi
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Nguyen Vinh Trung
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
| | | | | | - Vandana Kulkarni
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Prasad Deshpande
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Mallika Alexander
- Johns Hopkins University Clinical Trials Unit, Byramjee Jeejeebhoy Government Medical College, Pune, Maharashtra, India
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Ho Chi Minh city, Viet Nam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Microbiology Department and Center for Tropical Medicine Research, Ngoc Thach University of Medicine, Ho Chi Minh city, Vietnam
| | | | | | | | | | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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23
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Ogunlana L, Kaur D, Shaw LP, Jangir P, Walsh T, Uphoff S, MacLean RC. Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings. THE ISME JOURNAL 2023; 17:2058-2069. [PMID: 37723338 PMCID: PMC10579358 DOI: 10.1038/s41396-023-01509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023]
Abstract
Antibiotic resistance tends to carry fitness costs, making it difficult to understand how resistance can be maintained in the absence of continual antibiotic exposure. Here we investigate this problem in the context of mcr-1, a globally disseminated gene that confers resistance to colistin, an agricultural antibiotic that is used as a last resort for the treatment of multi-drug resistant infections. Here we show that regulatory evolution has fine-tuned the expression of mcr-1, allowing E. coli to reduce the fitness cost of mcr-1 while simultaneously increasing colistin resistance. Conjugative plasmids have transferred low-cost/high-resistance mcr-1 alleles across an incredible diversity of E. coli strains, further stabilising mcr-1 at the species level. Regulatory mutations were associated with increased mcr-1 stability in pig farms following a ban on the use of colistin as a growth promoter that decreased colistin consumption by 90%. Our study shows how regulatory evolution and plasmid transfer can combine to stabilise resistance and limit the impact of reducing antibiotic consumption.
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Affiliation(s)
- Lois Ogunlana
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Divjot Kaur
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Liam P Shaw
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Pramod Jangir
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Timothy Walsh
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - R C MacLean
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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24
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Weiss A, Wang T, You L. Promotion of plasmid maintenance by heterogeneous partitioning of microbial communities. Cell Syst 2023; 14:895-905.e5. [PMID: 37820728 PMCID: PMC10591896 DOI: 10.1016/j.cels.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/09/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023]
Abstract
Transferable plasmids play a critical role in shaping the functions of microbial communities. Previous studies suggested multiple mechanisms underlying plasmid persistence and abundance. Here, we focus on the interplay between heterogeneous community partitioning and plasmid fates. Natural microbiomes often experience partitioning that creates heterogeneous local communities with reduced population sizes and biodiversity. Little is known about how population partitioning affects the plasmid fate through the modulation of community structure. By modeling and experiments, we show that heterogeneous community partitioning can paradoxically promote the persistence of a plasmid that would otherwise not persist in a global community. Among the local communities created by partitioning, a minority will primarily consist of members able to transfer the plasmid fast enough to support its maintenance by serving as a local plasmid haven. Our results provide insights into plasmid maintenance and suggest a generalizable approach to modulate plasmid persistence for engineering and medical applications.
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Affiliation(s)
- Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Teng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Quantitative Biodesign, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA.
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25
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Hamrick GS, Maddamsetti R, Son HI, Wilson ML, Davis HM, You L. Programming dynamic division of labor using horizontal gene transfer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560696. [PMID: 37873187 PMCID: PMC10592921 DOI: 10.1101/2023.10.03.560696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The metabolic engineering of microbes has broad applications, including in biomanufacturing, bioprocessing, and environmental remediation. The introduction of a complex, multi-step pathway often imposes a substantial metabolic burden on the host cell, restraining the accumulation of productive biomass and limiting pathway efficiency. One strategy to alleviate metabolic burden is division of labor (DOL), in which different subpopulations carry out different parts of the pathway and work together to convert a substrate into a final product. However, the maintenance of different engineered subpopulations is challenging due to competition and convoluted inter-strain population dynamics. Through modeling, we show that dynamic division of labor (DDOL) mediated by horizontal gene transfer (HGT) can overcome these limitations and enable the robust maintenance of burdensome, multi-step pathways. We also use plasmid genomics to uncover evidence that DDOL is a strategy utilized by natural microbial communities. Our work suggests that bioengineers can harness HGT to stabilize synthetic metabolic pathways in microbial communities, enabling the development of robust engineered systems for deployment in a variety of contexts.
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26
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Gionchetta G, Snead D, Semerad S, Beck K, Pruden A, Bürgmann H. Dynamics of antibiotic resistance markers and Escherichia coli invasion in riverine heterotrophic biofilms facing increasing heat and flow stagnation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 893:164658. [PMID: 37321511 DOI: 10.1016/j.scitotenv.2023.164658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023]
Abstract
As motivation to address environmental dissemination of antimicrobial resistance (AMR) is mounting, there is a need to characterize mechanisms by which AMR can propagate under environmental conditions. Here we investigated the effect of temperature and stagnation on the persistence of wastewater-associated antibiotic resistance markers in riverine biofilms and the invasion success of genetically-tagged Escherichia coli. Biofilms grown on glass slides incubated in-situ downstream of a wastewater treatment plant effluent discharge point were transferred to laboratory-scale flumes fed with filtered river water under potentially stressful temperature and flow conditions: recirculation flow at 20 °C, stagnation at 20 °C, and stagnation at 30 °C. After 14 days, quantitative PCR and amplicon sequencing were used to quantify bacteria, biofilms diversity, resistance markers (sul1, sul2, ermB, tetW, tetM, tetB, blaCTX-M-1, intI1) and E. coli. Resistance markers significantly decreased over time regardless of the treatment applied. Although invading E. coli were initially able to colonize the biofilms, its abundance subsequently declined. Stagnation was associated with a shift in biofilm taxonomic composition, but there was no apparent effect of flow conditions or the simulated river-pool warming (30 °C) on AMR persistence or invasion success of E. coli. Results however indicated that antibiotic resistance markers in the riverine biofilms decreased under the experimental conditions in the absence of exposure to external inputs of antibiotics and AMR.
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Affiliation(s)
- G Gionchetta
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - D Snead
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, MI, USA; Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - S Semerad
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - K Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland
| | - A Pruden
- Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - H Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Surface Waters - Research and Management, 6047 Kastanienbaum, Switzerland.
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27
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Sünderhauf D, Klümper U, Gaze WH, Westra ER, van Houte S. Interspecific competition can drive plasmid loss from a focal species in a microbial community. THE ISME JOURNAL 2023; 17:1765-1773. [PMID: 37558861 PMCID: PMC10504238 DOI: 10.1038/s41396-023-01487-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
Plasmids are key disseminators of antimicrobial resistance genes and virulence factors, and it is therefore critical to predict and reduce plasmid spread within microbial communities. The cost of plasmid carriage is a key metric that can be used to predict plasmids' ecological fate, and it is unclear whether plasmid costs are affected by growth partners in a microbial community. We carried out competition experiments and tracked plasmid maintenance using a model system consisting of a synthetic and stable five-species community and a broad host-range plasmid, engineered to carry different payloads. We report that both the cost of plasmid carriage and its long-term maintenance in a focal strain depended on the presence of competitors, and that these interactions were species specific. Addition of growth partners increased the cost of a high-payload plasmid to a focal strain, and accordingly, plasmid loss from the focal species occurred over a shorter time frame. We propose that the destabilising effect of interspecific competition on plasmid maintenance may be leveraged in clinical and natural environments to cure plasmids from focal strains.
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Affiliation(s)
- David Sünderhauf
- Centre for Ecology and Conservation, University of Exeter, Environment and Sustainability Institute, Penryn, TR10 9FE, UK.
| | - Uli Klümper
- Department Hydrosciences, Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn, TR10 9FE, UK
| | - Edze R Westra
- Centre for Ecology and Conservation, University of Exeter, Environment and Sustainability Institute, Penryn, TR10 9FE, UK
| | - Stineke van Houte
- Centre for Ecology and Conservation, University of Exeter, Environment and Sustainability Institute, Penryn, TR10 9FE, UK.
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28
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Hall JPJ. Microbial Musings: Spring 2023. Microbiology (Reading) 2023; 169. [PMID: 37561018 DOI: 10.1099/mic.0.001379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023] Open
Affiliation(s)
- James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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29
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Dewan I, Uecker H. A mathematician's guide to plasmids: an introduction to plasmid biology for modellers. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001362. [PMID: 37505810 PMCID: PMC10433428 DOI: 10.1099/mic.0.001362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023]
Abstract
Plasmids, extrachromosomal DNA molecules commonly found in bacterial and archaeal cells, play an important role in bacterial genetics and evolution. Our understanding of plasmid biology has been furthered greatly by the development of mathematical models, and there are many questions about plasmids that models would be useful in answering. In this review, we present an introductory, yet comprehensive, overview of the biology of plasmids suitable for modellers unfamiliar with plasmids who want to get up to speed and to begin working on plasmid-related models. In addition to reviewing the diversity of plasmids and the genes they carry, their key physiological functions, and interactions between plasmid and host, we also highlight selected plasmid topics that may be of particular interest to modellers and areas where there is a particular need for theoretical development. The world of plasmids holds a great variety of subjects that will interest mathematical biologists, and introducing new modellers to the subject will help to expand the existing body of plasmid theory.
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Affiliation(s)
- Ian Dewan
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
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30
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Guidotti-Takeuchi M, Melo RTD, Ribeiro LNDM, Dumont CF, Ribeiro RAC, Brum BDA, de Amorim Junior TLIF, Rossi DA. Interference with Bacterial Conjugation and Natural Alternatives to Antibiotics: Bridging a Gap. Antibiotics (Basel) 2023; 12:1127. [PMID: 37508224 PMCID: PMC10376302 DOI: 10.3390/antibiotics12071127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Horizontal gene transfer (HGT) in food matrices has been investigated under conditions that favor gene exchange. However, the major challenge lies in determining the specific conditions pertaining to the adapted microbial pairs associated with the food matrix. HGT is primarily responsible for enhancing the microbial repertoire for the evolution and spread of antimicrobial resistance and is a major target for controlling pathogens of public health concern in food ecosystems. In this study, we investigated Salmonella Heidelberg (SH) and Escherichia coli (EC) regarding gene exchange under conditions mimicking the industrial environment, with the coproducts whey (SL) and chicken juice (CJ). The S. Heidelberg strain was characterized by antibiotic susceptibility standards and PCR to detect the blaTEM gene. A concentration of 0.39 mg/mL was determined to evaluate the anti-conjugation activity of nanostructured lipid nanocarriers (NLCs) of essential oils to mitigate β-lactam resistance gene transfer. The results showed that the addition of these coproducts promoted an increase of more than 3.5 (whey) and 2.5 (chicken juice) orders of magnitude in the conjugation process (p < 0.01), and NLCs of sage essential oil significantly reduced the conjugation frequency (CF) by 74.90, 90.6, and 124.4 times when compared to the transfers in the absence of coproducts and the presence of SL and CJ, respectively. For NLCs from olibanum essential oil, the decrease was 4.46-fold for conjugations without inhibitors and 3.12- and 11.3-fold in the presence of SL and CJ. NLCs associated with sage and olibanum essential oils effectively control the transfer of antibiotic resistance genes and are a promising alternative for use at industrial levels.
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Affiliation(s)
- Micaela Guidotti-Takeuchi
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | - Roberta Torres de Melo
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | | | - Carolyne Ferreira Dumont
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | | | - Bárbara de Araújo Brum
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
| | | | - Daise Aparecida Rossi
- Laboratory of Molecular Epidemiology, Federal University of Uberlândia, Uberlândia 38402-018, MG, Brazil
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31
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Zhu S, Yang B, Wang Z, Liu Y. Augmented dissemination of antibiotic resistance elicited by non-antibiotic factors. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115124. [PMID: 37327521 DOI: 10.1016/j.ecoenv.2023.115124] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/24/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023]
Abstract
The emergence and rapid spread of antibiotic resistance seriously compromise the clinical efficacy of current antibiotic therapies, representing a serious public health threat worldwide. Generally, drug-susceptible bacteria can acquire antibiotic resistance through genetic mutation or gene transfer, among which horizontal gene transfer (HGT) plays a dominant role. It is widely acknowledged that the sub-inhibitory concentrations of antibiotics are the key drivers in promoting the transmission of antibiotic resistance. However, accumulating evidence in recent years has shown that in addition to antibiotics, non-antibiotics can also accelerate the horizontal transfer of antibiotic resistance genes (ARGs). Nevertheless, the roles and potential mechanisms of non-antibiotic factors in the transmission of ARGs remain largely underestimated. In this review, we depict the four pathways of HGT and their differences, including conjugation, transformation, transduction and vesiduction. We summarize non-antibiotic factors accounting for the enhanced horizontal transfer of ARGs and their underlying molecular mechanisms. Finally, we discuss the limitations and implications of current studies.
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Affiliation(s)
- Shuyao Zhu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Bingqing Yang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhiqiang Wang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Yuan Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China.
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32
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Ma Y, Ramoneda J, Johnson DR. Timing of antibiotic administration determines the spread of plasmid-encoded antibiotic resistance during microbial range expansion. Nat Commun 2023; 14:3530. [PMID: 37316482 DOI: 10.1038/s41467-023-39354-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023] Open
Abstract
Plasmids are the main vector by which antibiotic resistance is transferred between bacterial cells within surface-associated communities. In this study, we ask whether there is an optimal time to administer antibiotics to minimize plasmid spread in new bacterial genotypes during community expansion across surfaces. We address this question using consortia of Pseudomonas stutzeri strains, where one is an antibiotic resistance-encoding plasmid donor and the other a potential recipient. We allowed the strains to co-expand across a surface and administered antibiotics at different times. We find that plasmid transfer and transconjugant proliferation have unimodal relationships with the timing of antibiotic administration, where they reach maxima at intermediate times. These unimodal relationships result from the interplay between the probabilities of plasmid transfer and loss. Our study provides mechanistic insights into the transfer and proliferation of antibiotic resistance-encoding plasmids within microbial communities and identifies the timing of antibiotic administration as an important determinant.
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Affiliation(s)
- Yinyin Ma
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland.
- Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH), 8092, Zürich, Switzerland.
| | - Josep Ramoneda
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland
- Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado, Boulder, CO, 80309, USA
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600, Dübendorf, Switzerland.
- Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland.
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33
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Chen Z, Shen J, Xu X, Feng H, Wang M. Adsorption of antibiotic, heavy metal and antibiotic plasmid by a wet-state silicon-rich biochar/ferrihydrite composite to inhibit antibiotic resistance gene proliferation/transformation. CHEMOSPHERE 2023; 324:138356. [PMID: 36898437 DOI: 10.1016/j.chemosphere.2023.138356] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/15/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Decreasing bioaccessible antibiotics, heavy metals, and antibiotic resistance genes (ARGs) in soil by adsorption is an attractive, but unrealized, approach for ARG risk reduction. This approach has the potential to reduce the (co)selection pressure from antibiotics and heavy metals on bacteria and ARG horizontal gene transformation to pathogens. Here, a wet-state silicon-rich biochar/ferrihydrite composite (SiC-Fe(W)) synthesized by loading ferrihydrite onto rice straw-derived biochar was examined for i) adsorption of oxytetracycline and Cu2+ to reduce (co)selection pressure and ii) adsorption of extracellular antibiotic resistance plasmid pBR322 (containing tetA and blaTEM-1) to inhibit ARG transformation. SiC-Fe(W) gained the adsorption priority of biochar (for Cu2+) and wet-state ferrihydrite (for oxytetracycline and pBR322) and showed adsorptive enhancement (for Cu2+ and oxytetracycline) from a more wrinkled and exposed surface from biochar silica-dispersed ferrihydrite and a more negatively charged biochar, and the adsorption capacity for SiC-Fe(W) was 17-135 times that of soil. Correspondingly, 10 g/kg SiC-Fe(W) amendment increased the soil adsorption coefficient Kd by 31%-1417% and reduced the selection pressure from dissolved oxytetracycline, co-selection pressure from dissolved Cu2+, and transformation frequency of pBR322 (assessed with Escherichia coli). The development of Fe-O-Si bonds on silicon-rich biochar in alkaline enhanced ferrihydrite stability and adsorption capacity (for oxytetracycline), presenting a new potential strategy of biochar/ferrihydrite composite synthesis for adsorptive inhibition of ARG proliferation and transformation in ARG pollution control.
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Affiliation(s)
- Zaiming Chen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Jiahao Shen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Xiaoqin Xu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Huajun Feng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou, 310012, China.
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34
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Ahmad M, Prensky H, Balestrieri J, ElNaggar S, Gomez-Simmonds A, Uhlemann AC, Traxler B, Singh A, Lopatkin AJ. Tradeoff between lag time and growth rate drives the plasmid acquisition cost. Nat Commun 2023; 14:2343. [PMID: 37095096 PMCID: PMC10126158 DOI: 10.1038/s41467-023-38022-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Conjugative plasmids drive genetic diversity and evolution in microbial populations. Despite their prevalence, plasmids can impose long-term fitness costs on their hosts, altering population structure, growth dynamics, and evolutionary outcomes. In addition to long-term fitness costs, acquiring a new plasmid introduces an immediate, short-term perturbation to the cell. However, due to the transient nature of this plasmid acquisition cost, a quantitative understanding of its physiological manifestations, overall magnitudes, and population-level implications, remains unclear. To address this, here we track growth of single colonies immediately following plasmid acquisition. We find that plasmid acquisition costs are primarily driven by changes in lag time, rather than growth rate, for nearly 60 conditions covering diverse plasmids, selection environments, and clinical strains/species. Surprisingly, for a costly plasmid, clones exhibiting longer lag times also achieve faster recovery growth rates, suggesting an evolutionary tradeoff. Modeling and experiments demonstrate that this tradeoff leads to counterintuitive ecological dynamics, whereby intermediate-cost plasmids outcompete both their low and high-cost counterparts. These results suggest that, unlike fitness costs, plasmid acquisition dynamics are not uniformly driven by minimizing growth disadvantages. Moreover, a lag/growth tradeoff has clear implications in predicting the ecological outcomes and intervention strategies of bacteria undergoing conjugation.
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Affiliation(s)
- Mehrose Ahmad
- Department of Biology, Barnard College, New York, NY, 10027, USA
| | - Hannah Prensky
- Department of Biology, Barnard College, New York, NY, 10027, USA
| | | | - Shahd ElNaggar
- Department of Biology, Barnard College, New York, NY, 10027, USA
| | - Angela Gomez-Simmonds
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, NY, 10032, USA
| | - Anne-Catrin Uhlemann
- Department of Medicine, Division of Infectious Diseases, Columbia University Medical Center, New York, NY, 10032, USA
| | - Beth Traxler
- Department Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, 19717, USA
| | - Allison J Lopatkin
- Department of Biology, Barnard College, New York, NY, 10027, USA.
- Department Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, 10027, USA.
- Data Science Institute, Columbia University, New York, NY, 10027, USA.
- Department of Chemical Engineering, University of Rochester, Rochester, NY, 14627, USA.
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14627, USA.
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35
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Marken JP, Murray RM. Addressable and adaptable intercellular communication via DNA messaging. Nat Commun 2023; 14:2358. [PMID: 37095088 PMCID: PMC10126159 DOI: 10.1038/s41467-023-37788-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/31/2023] [Indexed: 04/26/2023] Open
Abstract
Engineered consortia are a major research focus for synthetic biologists because they can implement sophisticated behaviors inaccessible to single-strain systems. However, this functional capacity is constrained by their constituent strains' ability to engage in complex communication. DNA messaging, by enabling information-rich channel-decoupled communication, is a promising candidate architecture for implementing complex communication. But its major advantage, its messages' dynamic mutability, is still unexplored. We develop a framework for addressable and adaptable DNA messaging that leverages all three of these advantages and implement it using plasmid conjugation in E. coli. Our system can bias the transfer of messages to targeted receiver strains by 100- to 1000-fold, and their recipient lists can be dynamically updated in situ to control the flow of information through the population. This work lays the foundation for future developments that further utilize the unique advantages of DNA messaging to engineer previously-inaccessible levels of complexity into biological systems.
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Affiliation(s)
- John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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36
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Moura de Sousa J, Lourenço M, Gordo I. Horizontal gene transfer among host-associated microbes. Cell Host Microbe 2023; 31:513-527. [PMID: 37054673 DOI: 10.1016/j.chom.2023.03.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Horizontal gene transfer is an important evolutionary force, facilitating bacterial diversity. It is thought to be pervasive in host-associated microbiomes, where bacterial densities are high and mobile elements are frequent. These genetic exchanges are also key for the rapid dissemination of antibiotic resistance. Here, we review recent studies that have greatly extended our knowledge of the mechanisms underlying horizontal gene transfer, the ecological complexities of a network of interactions involving bacteria and their mobile elements, and the effect of host physiology on the rates of genetic exchanges. Furthermore, we discuss other, fundamental challenges in detecting and quantifying genetic exchanges in vivo, and how studies have contributed to start overcoming these challenges. We highlight the importance of integrating novel computational approaches and theoretical models with experimental methods where multiple strains and transfer elements are studied, both in vivo and in controlled conditions that mimic the intricacies of host-associated environments.
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Affiliation(s)
- Jorge Moura de Sousa
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, 75015 Paris, France
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, F-75015 Paris, France
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande,6, Oeiras, Portugal.
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37
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Tiwari SK, van der Putten BCL, Fuchs TM, Vinh TN, Bootsma M, Oldenkamp R, La Ragione R, Matamoros S, Hoa NT, Berens C, Leng J, Álvarez J, Ferrandis-Vila M, Ritchie JM, Fruth A, Schwarz S, Domínguez L, Ugarte-Ruiz M, Bethe A, Huber C, Johanns V, Stamm I, Wieler LH, Ewers C, Fivian-Hughes A, Schmidt H, Menge C, Semmler T, Schultsz C. Genome-wide association reveals host-specific genomic traits in Escherichia coli. BMC Biol 2023; 21:76. [PMID: 37038177 PMCID: PMC10088187 DOI: 10.1186/s12915-023-01562-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/10/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Escherichia coli is an opportunistic pathogen which colonizes various host species. However, to what extent genetic lineages of E. coli are adapted or restricted to specific hosts and the genomic determinants of such adaptation or restriction is poorly understood. RESULTS We randomly sampled E. coli isolates from four countries (Germany, UK, Spain, and Vietnam), obtained from five host species (human, pig, cattle, chicken, and wild boar) over 16 years, from both healthy and diseased hosts, to construct a collection of 1198 whole-genome sequenced E. coli isolates. We identified associations between specific E. coli lineages and the host from which they were isolated. A genome-wide association study (GWAS) identified several E. coli genes that were associated with human, cattle, or chicken hosts, whereas no genes associated with the pig host could be found. In silico characterization of nine contiguous genes (collectively designated as nan-9) associated with the human host indicated that these genes are involved in the metabolism of sialic acids (Sia). In contrast, the previously described sialic acid regulon known as sialoregulon (i.e. nanRATEK-yhcH, nanXY, and nanCMS) was not associated with any host species. In vitro growth experiments with a Δnan-9 E. coli mutant strain, using the sialic acids 5-N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) as sole carbon source, showed impaired growth behaviour compared to the wild-type. CONCLUSIONS This study provides an extensive analysis of genetic determinants which may contribute to host specificity in E. coli. Our findings should inform risk analysis and epidemiological monitoring of (antimicrobial resistant) E. coli.
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Affiliation(s)
- Sumeet K Tiwari
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Program, Norwich Research Park, Norwich, UK
| | - Boas C L van der Putten
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Thilo M Fuchs
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Trung N Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Veterinary Medicine, College of Agriculture, Can Tho University, Can Tho, Vietnam
| | | | - Rik Oldenkamp
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Life and Environment, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Roberto La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Sebastien Matamoros
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ngo T Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Tropical medicine and global health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Microbiology- Parasitology Unit, Biomedical Research Center and Microbiology Department, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Christian Berens
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Joy Leng
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Julio Álvarez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | | | - Jenny M Ritchie
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Angelika Fruth
- Robert Koch Institute, Enteropathogenic Bacteria and Legionella, Wernigerode, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Lucas Domínguez
- Tropical medicine and global health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Microbiology- Parasitology Unit, Biomedical Research Center and Microbiology Department, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Charlotte Huber
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Vanessa Johanns
- Robert Koch Institute, Advanced Light and Electron Microscopy, Berlin, Germany
| | - Ivonne Stamm
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Kornwestheim, Germany
| | | | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Giessen, Germany
| | - Amanda Fivian-Hughes
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Herbert Schmidt
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, University of Hohenheim, Stuttgart, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Torsten Semmler
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany.
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
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38
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Dai Y, Farag M, Lee D, Zeng X, Kim K, Son HI, Guo X, Su J, Peterson N, Mohammed J, Ney M, Shapiro DM, Pappu RV, Chilkoti A, You L. Programmable synthetic biomolecular condensates for cellular control. Nat Chem Biol 2023; 19:518-528. [PMID: 36747054 PMCID: PMC10786170 DOI: 10.1038/s41589-022-01252-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 12/21/2022] [Indexed: 02/08/2023]
Abstract
The formation of biomolecular condensates mediated by a coupling of associative and segregative phase transitions plays a critical role in controlling diverse cellular functions in nature. This has inspired the use of phase transitions to design synthetic systems. While design rules of phase transitions have been established for many synthetic intrinsically disordered proteins, most efforts have focused on investigating their phase behaviors in a test tube. Here, we present a rational engineering approach to program the formation and physical properties of synthetic condensates to achieve intended cellular functions. We demonstrate this approach through targeted plasmid sequestration and transcription regulation in bacteria and modulation of a protein circuit in mammalian cells. Our approach lays the foundation for engineering designer condensates for synthetic biology applications.
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Affiliation(s)
- Yifan Dai
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
- Duke Center for Quantitative Biodesign, Duke University, Durham, NC, USA
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Dongheon Lee
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Xiangze Zeng
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Kyeri Kim
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Hye-In Son
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Xiao Guo
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Jonathan Su
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Nikhil Peterson
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Javid Mohammed
- Department of Immunology, Duke University, Durham, NC, USA
| | - Max Ney
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Daniel Mark Shapiro
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA.
- Duke Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
| | - Lingchong You
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA.
- Duke Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
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Orlek A, Anjum MF, Mather AE, Stoesser N, Walker AS. Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis. Sci Rep 2023; 13:2500. [PMID: 36781908 PMCID: PMC9925765 DOI: 10.1038/s41598-023-29530-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
Plasmids are major vectors of bacterial antibiotic resistance, but understanding of factors associated with plasmid antibiotic resistance gene (ARG) carriage is limited. We curated > 14,000 publicly available plasmid genomes and associated metadata. Duplicate and replicate plasmids were excluded; where possible, sample metadata was validated externally (BacDive database). Using Generalised Additive Models (GAMs) we assessed the influence of 12 biotic/abiotic factors (e.g. plasmid genetic factors, isolation source, collection date) on ARG carriage, modelled as a binary outcome. Separate GAMs were built for 10 major ARG types. Multivariable analysis indicated that plasmid ARG carriage patterns across time (collection years), isolation sources (human/livestock) and host bacterial taxa were consistent with antibiotic selection pressure as a driver of plasmid-mediated antibiotic resistance. Only 0.42% livestock plasmids carried carbapenem resistance (compared with 12% human plasmids); conversely, tetracycline resistance was enriched in livestock vs human plasmids, reflecting known prescribing practices. Interpreting results using a timeline of ARG type acquisition (determined by literature review) yielded additional novel insights. More recently acquired ARG types (e.g. colistin and carbapenem) showed increases in plasmid carriage during the date range analysed (1994-2019), potentially reflecting recent onset of selection pressure; they also co-occurred less commonly with ARGs of other types, and virulence genes. Overall, this suggests that following acquisition, plasmid ARGs tend to accumulate under antibiotic selection pressure and co-associate with other adaptive genes (other ARG types, virulence genes), potentially re-enforcing plasmid ARG carriage through co-selection.
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Affiliation(s)
- Alex Orlek
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK.
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, Addlestone, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich, UK
- University of East Anglia, Norwich, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre (BRC), University of Oxford, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre (BRC), University of Oxford, Oxford, UK
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Conjugative RP4 Plasmid-Mediated Transfer of Antibiotic Resistance Genes to Commensal and Multidrug-Resistant Enteric Bacteria In Vitro. Microorganisms 2023; 11:microorganisms11010193. [PMID: 36677486 PMCID: PMC9860721 DOI: 10.3390/microorganisms11010193] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023] Open
Abstract
Many antibiotic-resistant bacteria carry resistance genes on conjugative plasmids that are transferable to commensals and pathogens. We determined the ability of multiple enteric bacteria to acquire and retransfer a broad-host-range plasmid RP4. We used human-derived commensal Escherichia coli LM715-1 carrying a chromosomal red fluorescent protein gene and green fluorescent protein (GFP)-labeled broad-host-range RP4 plasmid with ampR, tetR, and kanR in in vitro matings to rifampicin-resistant recipients, including Escherichia coli MG1655, Dec5α, Vibrio cholerae, Pseudomonas putida, Pseudomonas aeruginosa, Klebsiella pneumoniae, Citrobacter rodentium, and Salmonella Typhimurium. Transconjugants were quantified on selective media and confirmed using fluorescence microscopy and PCR for the GFP gene. The plasmid was transferred from E. coli LM715-1 to all tested recipients except P. aeruginosa. Transfer frequencies differed between specific donor-recipient pairings (10-2 to 10-8). Secondary retransfer of plasmid from transconjugants to E. coli LM715-1 occurred at frequencies from 10-2 to 10-7. A serial passage plasmid persistence assay showed plasmid loss over time in the absence of antibiotics, indicating that the plasmid imposed a fitness cost to its host, although some plasmid-bearing cells persisted for at least ten transfers. Thus, the RP4 plasmid can transfer to multiple clinically relevant bacterial species without antibiotic selection pressure.
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41
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Tang T, Chen Y, Du Y, Yao B, Liu M. Effects of functional modules and bacterial clusters response on transmission performance of antibiotic resistance genes under antibiotic stress during anaerobic digestion of livestock wastewater. JOURNAL OF HAZARDOUS MATERIALS 2023; 441:129870. [PMID: 36063716 DOI: 10.1016/j.jhazmat.2022.129870] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/06/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
The formation and transmission of antibiotic resistance genes (ARGs) have attracted increasing attention. It is unclear whether the internal mechanisms by which antibiotics affect horizontal gene transfer (HGT) of ARGs during anaerobic digestion (AD) were influenced by dose and type. We investigated the effects of two major antibiotics (oxytetracycline, OTC, and sulfamethoxazole, SMX) on ARGs during AD according to antibiotic concentration in livestock wastewater influent. The low-dose antibiotic (0.5 mg/L) increased ROS and SOS responses, promoting the formation of ARGs. Meanwhile, low-dose antibiotics could also promote the spread of ARGs by promoting pili, communication responses, and the type IV secretion system (T4SS). However, different types and doses of antibiotics would lead to changes in the above functional modules and then affect the enrichment of ARGs. With the increasing dose of SMX, the advantages of pili and communication responses would gradually change. In the OTC system, low-dose has the strongest promoting ability in both pili and communication responses. Similarly, an increase in the dose of SMX would change T4SS from facilitation to inhibition, while OTC completely inhibits T4SS. Microbial and network analysis also revealed that low-dose antibiotics were more favorable for the growth of host bacteria.
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Affiliation(s)
- Taotao Tang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ying Chen
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Ye Du
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Bing Yao
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China
| | - Min Liu
- College of Architecture and Environment, Sichuan University, Chengdu 610065, PR China.
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Yu Z, Henderson IR, Guo J. Non-caloric artificial sweeteners modulate conjugative transfer of multi-drug resistance plasmid in the gut microbiota. Gut Microbes 2023; 15:2157698. [PMID: 36524841 PMCID: PMC9762752 DOI: 10.1080/19490976.2022.2157698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Non-caloric artificial sweeteners have been widely permitted as table sugar substitutes with high intensities of sweetness. They can pass through the intestinal tract without significant metabolization and frequently encounter the gut microbiome, which is composed of diverse bacterial species and is a pool of antibiotic resistance genes (ARGs). However, little is known about whether these sweeteners could accelerate the spread of ARGs in the gut microbiome. Here, we established an in vitro conjugation model by using Escherichia coli that carries chromosome-inserted Tn7 lacIq-pLpp-mCherry and plasmid-encoded gfpmut3b gene as the donor and murine fecal bacteria as the recipient. We found that four commonly used artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) can increase reactive oxygen species (ROS) production and promote plasmid-mediated conjugative transfer to the gut microbiome. Cell sorting and 16S rRNA gene amplicon sequencing analysis of fecal samples reveal that the tested sweeteners can promote the broad-host-range plasmid permissiveness to both Gram-negative and Gram-positive gut bacteria. The increased plasmid permissiveness was also validated with a human pathogen Klebsiella pneumoniae. Collectively, our study demonstrates that non-caloric artificial sweeteners can induce oxidative stress and boost the plasmid-mediated conjugative transfer of ARGs among the gut microbiota and a human pathogen. Considering the soaring consumption of these sweeteners and the abundance of mobile ARGs in the human gut, our results highlight the necessity of performing a thorough risk assessment of antibiotic resistance associated with the usage of artificial sweeteners as food additives.
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Affiliation(s)
- Zhigang Yu
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Australia
| | - Ian R Henderson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Australia
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Feng X, Hua R, Zhang W, Liu Y, Luo C, Li T, Chen X, Zhu H, Wang Y, Lu Y. Comparison of the gut microbiome and resistome in captive African and Asian elephants on the same diet. Front Vet Sci 2023; 10:986382. [PMID: 36875997 PMCID: PMC9978182 DOI: 10.3389/fvets.2023.986382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
Elephants are endangered species and threatened with extinction. They are monogastric herbivorous, hindgut fermenters and their digestive strategy requires them to consume large amounts of low quality forage. The gut microbiome is important to their metabolism, immune regulation, and ecological adaptation. Our study investigated the structure and function of the gut microbiota as well as the antibiotic resistance genes (ARGs) in captive African and Asian elephants on the same diet. Results showed that captive African and Asian elephants had distinct gut bacterial composition. MetaStats analysis showed that the relative abundance of Spirochaetes (FDR = 0.00) and Verrucomicrobia (FDR = 0.01) at the phylum level as well as Spirochaetaceae (FDR = 0.01) and Akkermansiaceae (FDR = 0.02) at the family level varied between captive African and Asian elephants. Among the top ten functional subcategories at level 2 (57 seed pathway) of Kyoto Encyclopedia of Genes and Genomes (KEGG) database, the relative gene abundance of cellular community-prokaryotes, membrane transport, and carbohydrate metabolism in African elephants were significantly lower than those in Asian elephants (0.98 vs. 1.03%, FDR = 0.04; 1.25 vs. 1.43%, FDR = 0.03; 3.39 vs. 3.63%; FDR = 0.02). Among the top ten functional subcategories at level 2 (CAZy family) of CAZy database, MetaStats analysis showed that African elephants had higher relative gene abundance of Glycoside Hydrolases family 28 (GH 28) compared to Asian elephants (0.10 vs. 0.08%, FDR = 0.03). Regarding the antibiotic resistance genes carried by gut microbes, MetaStats analysis showed that African elephants had significantly higher relative abundance of vanO (FDR = 0.00), tetQ (FDR = 0.04), and efrA (FDR = 0.04) than Asian elephants encoding resistance for glycopeptide, tetracycline, and macrolide/rifamycin/fluoroquinolone antibiotic, respectively. In conclusion, captive African and Asian elephants on the same diet have distinct gut microbial communities. Our findings established the ground work for future research on improving gut health of captive elephants.
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Affiliation(s)
- Xin Feng
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Rong Hua
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
| | - Wanying Zhang
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Yuhang Liu
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Caiyu Luo
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Tonghao Li
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Xiaolin Chen
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Hui Zhu
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Youcong Wang
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Yan Lu
- Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing, China
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Palomino A, Gewurz D, DeVine L, Zajmi U, Moralez J, Abu-Rumman F, Smith RP, Lopatkin AJ. Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment. THE ISME JOURNAL 2023; 17:151-162. [PMID: 36261510 PMCID: PMC9750983 DOI: 10.1038/s41396-022-01329-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 09/21/2022] [Accepted: 09/28/2022] [Indexed: 12/15/2022]
Abstract
Conjugative plasmids often encode antibiotic resistance genes that provide selective advantages to their bacterial hosts during antibiotic treatment. Previous studies have predominantly considered these established genes as the primary benefit of antibiotic-mediated plasmid dissemination. However, many genes involved in cellular metabolic processes may also protect against antibiotic treatment and provide selective advantages. Despite the diversity of such metabolic genes and their potential ecological impact, their plasmid-borne prevalence, co-occurrence with canonical antibiotic resistance genes, and phenotypic effects remain widely understudied. To address this gap, we focused on Escherichia coli, which can often act as a pathogen, and is known to spread antibiotic resistance genes via conjugation. We characterized the presence of metabolic genes on 1,775 transferrable plasmids and compared their distribution to that of known antibiotic resistance genes. We found high abundance of genes involved in cellular metabolism and stress response. Several of these genes demonstrated statistically significant associations or disassociations with known antibiotic resistance genes at the strain level, indicating that each gene type may impact the spread of the other across hosts. Indeed, in vitro characterization of 13 statistically relevant metabolic genes confirmed that their phenotypic impact on antibiotic susceptibility was largely consistent with in situ relationships. These results emphasize the ecological importance of metabolic genes on conjugal plasmids, and that selection dynamics of E. coli pathogens arises as a complex consequence of both canonical mechanisms and their interactions with metabolic pathways.
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Affiliation(s)
- Alana Palomino
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Danya Gewurz
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Lela DeVine
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Ujana Zajmi
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Jenifer Moralez
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA
| | - Fatima Abu-Rumman
- grid.261241.20000 0001 2168 8324Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314 USA
| | - Robert P. Smith
- grid.261241.20000 0001 2168 8324Department of Biological Sciences, Halmos College of Arts and Science, Nova Southeastern University, Fort Lauderdale, FL 33314 USA ,grid.261241.20000 0001 2168 8324Cell Therapy Institute, Kiran Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314 USA
| | - Allison J. Lopatkin
- grid.470930.90000 0001 2182 2351Department of Biology, Barnard College, New York, NY 10027 USA ,grid.21729.3f0000000419368729Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10027 USA ,grid.21729.3f0000000419368729Data Science Institute, Columbia University, New York, NY 10027 USA ,grid.21729.3f0000000419368729Department of Systems Biology, Columbia University, New York, NY 10027 USA ,grid.16416.340000 0004 1936 9174Department of Chemical Engineering, University of Rochester, Rochester, NY 14627 USA
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45
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Bethke JH, Ma HR, Tsoi R, Cheng L, Xiao M, You L. Vertical and horizontal gene transfer tradeoffs direct plasmid fitness. Mol Syst Biol 2022; 19:e11300. [PMID: 36573357 PMCID: PMC9912019 DOI: 10.15252/msb.202211300] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022] Open
Abstract
Plasmid fitness is directed by two orthogonal processes-vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.
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Affiliation(s)
- Jonathan H Bethke
- Department of Molecular Genetics and MicrobiologyDuke UniversityNCDurhamUSA
| | - Helena R Ma
- Department of Biomedical EngineeringDuke UniversityNCDurhamUSA,Center for Quantitative BiodesignDuke UniversityNCDurhamUSA
| | - Ryan Tsoi
- Department of Biomedical EngineeringDuke UniversityNCDurhamUSA
| | - Li Cheng
- BGI‐ShenzhenShenzhenChina,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI‐ShenzhenShenzhenChina,School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouChina
| | - Minfeng Xiao
- BGI‐ShenzhenShenzhenChina,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI‐ShenzhenShenzhenChina
| | - Lingchong You
- Department of Molecular Genetics and MicrobiologyDuke UniversityNCDurhamUSA,Department of Biomedical EngineeringDuke UniversityNCDurhamUSA,Center for Quantitative BiodesignDuke UniversityNCDurhamUSA,School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouChina
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Choudhary MI, Römling U, Nadeem F, Bilal HM, Zafar M, Jahan H, ur-Rahman A. Innovative Strategies to Overcome Antimicrobial Resistance and Tolerance. Microorganisms 2022; 11:microorganisms11010016. [PMID: 36677308 PMCID: PMC9863313 DOI: 10.3390/microorganisms11010016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial resistance and tolerance are natural phenomena that arose due to evolutionary adaptation of microorganisms against various xenobiotic agents. These adaptation mechanisms make the current treatment options challenging as it is increasingly difficult to treat a broad range of infections, associated biofilm formation, intracellular and host adapted microbes, as well as persister cells and microbes in protected niches. Therefore, novel strategies are needed to identify the most promising drug targets to overcome the existing hurdles in the treatment of infectious diseases. Furthermore, discovery of novel drug candidates is also much needed, as few novel antimicrobial drugs have been introduced in the last two decades. In this review, we focus on the strategies that may help in the development of innovative small molecules which can interfere with microbial resistance mechanisms. We also highlight the recent advances in optimization of growth media which mimic host conditions and genome scale molecular analyses of microbial response against antimicrobial agents. Furthermore, we discuss the identification of antibiofilm molecules and their mechanisms of action in the light of the distinct physiology and metabolism of biofilm cells. This review thus provides the most recent advances in host mimicking growth media for effective drug discovery and development of antimicrobial and antibiofilm agents.
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Affiliation(s)
- M. Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Correspondence: (U.R.); (H.J.); Tel.: +46-8-5248-7319 (U.R.); +92-21-111-232-292 (ext. 301) (H.J.)
| | - Faiza Nadeem
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Hafiz Muhammad Bilal
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Munirah Zafar
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Humera Jahan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- Correspondence: (U.R.); (H.J.); Tel.: +46-8-5248-7319 (U.R.); +92-21-111-232-292 (ext. 301) (H.J.)
| | - Atta ur-Rahman
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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Xu X, Fu H, Wan G, Huang J, Zhou Z, Rao Y, Liu L, Wen C. Prevalence and genetic diversity of Aeromonas veronii isolated from aquaculture systems in the Poyang Lake area, China. Front Microbiol 2022; 13:1042007. [PMID: 36578578 PMCID: PMC9791064 DOI: 10.3389/fmicb.2022.1042007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
The area around Poyang Lake is the main aquaculture area in Jiangxi Province, China, and an important base for the supply of freshwater aquatic products. Aquaculture in the Poyang Lake area is severely threatened by diseases caused by bacterial pathogens, and Aeromonas veronii has been the main pathogen in recent years. In this paper, ERIC-PCR genotyping, virulence gene and antimicrobial resistance gene detection, and drug susceptibility tests were carried out on 46 A. veronii isolates obtained from aquaculture systems in the Poyang Lake area from 2016 to 2020. The results showed that the A. veronii strains in the Poyang Lake area had high genetic diversity, and 46 strains produced 36 ERIC genotypes. There were no geographical and temporal differences in the cluster analysis results and no dominant clones. All 13 virulence genes tested were detected, and all isolates had harbored 2 or more virulence genes, with a maximum of 12 virulence genes detected. Among the 22 antimicrobial resistance genes selected, 15 were detected; 97.8% of the isolates contained 2 or more antimicrobial resistance genes, with a maximum of 9 antimicrobial resistance genes. Drug susceptibility tests showed that some strains were resistant to a variety of traditionally effective drugs for Aeromomas, such as enrofloxacin and florfenicol. This study provides a reference for exploring the impact of aquaculture in the Poyang Lake area on public health.
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Affiliation(s)
- Xiandong Xu
- College of Life Science, Education Ministry Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China,Fisheries Research Institute of Jiangxi Province, Nanchang, China
| | - Huiyun Fu
- Fisheries Research Institute of Jiangxi Province, Nanchang, China
| | - Guoyuan Wan
- Fisheries Research Institute of Jiangxi Province, Nanchang, China
| | - Jiangfeng Huang
- Fisheries Research Institute of Jiangxi Province, Nanchang, China
| | - Zhiyong Zhou
- Fisheries Research Institute of Jiangxi Province, Nanchang, China
| | - Yi Rao
- Fisheries Research Institute of Jiangxi Province, Nanchang, China
| | - Lihui Liu
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Chungen Wen
- College of Life Science, Education Ministry Key Laboratory of Poyang Lake Environment and Resource Utilization, Nanchang University, Nanchang, China,*Correspondence: Chungen Wen,
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48
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Biofilms preserve the transmissibility of a multi-drug resistance plasmid. NPJ Biofilms Microbiomes 2022; 8:95. [PMID: 36481746 PMCID: PMC9732292 DOI: 10.1038/s41522-022-00357-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
Self-transmissible multidrug resistance (MDR) plasmids are a major health concern because they can spread antibiotic resistance to pathogens. Even though most pathogens form biofilms, little is known about how MDR plasmids persist and evolve in biofilms. We hypothesize that (i) biofilms act as refugia of MDR plasmids by retaining them in the absence of antibiotics longer than well-mixed planktonic populations and that (ii) the evolutionary trajectories that account for the improvement of plasmid persistence over time differ between biofilms and planktonic populations. In this study, we evolved Acinetobacter baumannii with an MDR plasmid in biofilm and planktonic populations with and without antibiotic selection. In the absence of selection, biofilm populations were better able to maintain the MDR plasmid than planktonic populations. In planktonic populations, plasmid persistence improved rapidly but was accompanied by a loss of genes required for the horizontal transfer of plasmids. In contrast, in biofilms, most plasmids retained their transfer genes, but on average, plasmid, persistence improved less over time. Our results showed that biofilms can act as refugia of MDR plasmids and favor the horizontal mode of plasmid transfer, which has important implications for the spread of MDR.
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Bacterial Resistance to β-Lactam Antibiotics in Municipal Wastewater: Insights from a Full-Scale Treatment Plant in Poland. Microorganisms 2022; 10:microorganisms10122323. [PMID: 36557576 PMCID: PMC9783957 DOI: 10.3390/microorganisms10122323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
This study investigated enzymatic and genetic determinants of bacterial resistance to β-lactam antibiotics in the biocenosis involved in the process of biological treatment of wastewater by activated sludge. The frequency of bacteria resistant to selected antibiotics and the activity of enzymes responsible for resistance to β-lactam antibiotics were estimated. The phenomenon of selection and spread of a number of genes determining antibiotic resistance was traced using PCR and gene sequencing. An increase in the percentage of bacteria showing resistance to β-lactam antibiotics in the microflora of wastewater during the treatment process was found. The highest number of resistant microorganisms, including multi-resistant strains, was recorded in the aeration chamber. Significant amounts of these bacteria were also present in treated wastewater, where the percentage of penicillin-resistant bacteria exceeded 50%, while those resistant to the new generation β-lactam antibiotics meropenem and imipenem were found at 8.8% and 6.4%, respectively. Antibiotic resistance was repeatedly accompanied by the activity of enzymes such as carbapenemases, metallo-β-lactamases, cephalosporinases and β-lactamases with an extended substrate spectrum. The activity of carbapenemases was shown in up to 97% of the multi-resistant bacteria. Studies using molecular biology techniques showed a high frequency of genes determining resistance to β-lactam antibiotics, especially the blaTEM1 gene. The analysis of the nucleotide sequences of blaTEM1 gene variants present in bacteria at different stages of wastewater treatment showed 50-100% mutual similarity of.
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Wang T, Weiss A, Aqeel A, Wu F, Lopatkin AJ, David LA, You L. Horizontal gene transfer enables programmable gene stability in synthetic microbiota. Nat Chem Biol 2022; 18:1245-1252. [PMID: 36050493 PMCID: PMC10018779 DOI: 10.1038/s41589-022-01114-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/15/2022] [Indexed: 11/09/2022]
Abstract
The functions of many microbial communities exhibit remarkable stability despite fluctuations in the compositions of these communities. To date, a mechanistic understanding of this function-composition decoupling is lacking. Statistical mechanisms have been commonly hypothesized to explain such decoupling. Here, we proposed that dynamic mechanisms, mediated by horizontal gene transfer (HGT), also enable the independence of functions from the compositions of microbial communities. We combined theoretical analysis with numerical simulations to illustrate that HGT rates can determine the stability of gene abundance in microbial communities. We further validated these predictions using engineered microbial consortia of different complexities transferring one or more than a dozen clinically isolated plasmids, as well as through the reanalysis of data from the literature. Our results demonstrate a generalizable strategy to program the gene stability of microbial communities.
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Affiliation(s)
- Teng Wang
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Ammara Aqeel
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Allison J Lopatkin
- Department of Chemical Engineering, University of Rochester, Rochester, NY, USA
| | - Lawrence A David
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.
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