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Dillon L, Dimonaco NJ, Creevey CJ. Accessory genes define species-specific routes to antibiotic resistance. Life Sci Alliance 2024; 7:e202302420. [PMID: 38228374 DOI: 10.26508/lsa.202302420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
A deeper understanding of the relationship between the antimicrobial resistance (AMR) gene carriage and phenotype is necessary to develop effective response strategies against this global burden. AMR phenotype is often a result of multi-gene interactions; therefore, we need approaches that go beyond current simple AMR gene identification tools. Machine-learning (ML) methods may meet this challenge and allow the development of rapid computational approaches for AMR phenotype classification. To examine this, we applied multiple ML techniques to 16,950 bacterial genomes across 28 genera, with corresponding MICs for 23 antibiotics with the aim of training models to accurately determine the AMR phenotype from sequenced genomes. This resulted in a >1.5-fold increase in AMR phenotype prediction accuracy over AMR gene identification alone. Furthermore, we revealed 528 unique (often species-specific) genomic routes to antibiotic resistance, including genes not previously linked to the AMR phenotype. Our study demonstrates the utility of ML in predicting AMR phenotypes across diverse clinically relevant organisms and antibiotics. This research proposes a rapid computational method to support laboratory-based identification of the AMR phenotype in pathogens.
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Affiliation(s)
- Lucy Dillon
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Nicholas J Dimonaco
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
- https://ror.org/02fa3aq29 Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- https://ror.org/02fa3aq29 Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
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2
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Yadav A, Ahlawat S, Sharma KK. Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study. J Appl Microbiol 2023; 134:lxad280. [PMID: 38006234 DOI: 10.1093/jambio/lxad280] [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: 08/08/2023] [Revised: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 11/26/2023]
Abstract
Metagenome sequencing techniques revolutionized the field of gut microbiome study. However, it is equipped with experimental and computational biases, which affect the downstream analysis results. Also, live microbial strains are needed for a better understanding of host-microbial crosstalks and for designing next-generation treatment therapies based on probiotic strains and postbiotic molecules. Conventional culturing methodologies are insufficient to get the dark gut matter on the plate; therefore, there is an urgent need to propose novel culturing methods that can fill the limitations of metagenomics. The current work aims to provide a consolidated evaluation of the available methods for host-microbe interaction with an emphasis on in vitro culturing of gut microbes using organoids, gut on a chip, and gut bioreactor. Further, the knowledge of microbial crosstalk in the gut helps us to identify core microbiota, and key metabolites that will aid in designing culturing media and co-culturing systems for gut microbiome study. After the deeper mining of the current culturing methods, we recommend that 3D-printed intestinal cells in a multistage continuous flow reactor equipped with an extended organoid system might be a good practical choice for gut microbiota-based studies.
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Affiliation(s)
- Asha Yadav
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Shruti Ahlawat
- Department of Microbiology, Faculty of Allied Health Sciences, SGT University, Gurugram 122505, Haryana, India
| | - Krishna K Sharma
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
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3
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Li S, Lian WH, Han JR, Ali M, Lin ZL, Liu YH, Li L, Zhang DY, Jiang XZ, Li WJ, Dong L. Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis. NPJ Biofilms Microbiomes 2023; 9:67. [PMID: 37736746 PMCID: PMC10516943 DOI: 10.1038/s41522-023-00439-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.
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Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
- School of Life Science, Jiaying University, Meizhou, 514015, China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Jia-Rui Han
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China
| | - Yong-Hong Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Dong-Ya Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Xian-Zhi Jiang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, 510700, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat‑sen University, Guangzhou, 510275, China.
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4
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Campos-Madueno EI, Aldeia C, Perreten V, Sendi P, Moser AI, Endimiani A. Detection of blaCTX-M and blaDHA genes in stool samples of healthy people: comparison of culture- and shotgun metagenomic-based approaches. Front Microbiol 2023; 14:1236208. [PMID: 37720151 PMCID: PMC10501143 DOI: 10.3389/fmicb.2023.1236208] [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: 06/07/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023] Open
Abstract
We implemented culture- and shotgun metagenomic sequencing (SMS)-based methods to assess the gut colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESC-R-Ent) in 42 volunteers. Both methods were performed using native and pre-enriched (broth supplemented with cefuroxime) stools. Native culture screening on CHROMID® ESBL plates resulted in 17 positive samples, whereas the pre-enriched culture (gold-standard) identified 23 carriers. Overall, 26 ESC-R-Ent strains (24 Escherichia coli) were identified: 25 CTX-M and 3 DHA-1 producers (2 co-producing CTX-Ms). Using the SMS on native stool ("native SMS") with thresholds ≥60% for both identity and coverage, only 7 of the 23 pre-enriched culture-positive samples resulted positive for blaCTX-M/blaDHA genes (native SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 59.0%; specificity 100%). Moreover, an average of 31.5 and 24.6 antimicrobial resistance genes (ARGs) were detected in the 23 pre-enriched culture-positive and the 19 negative samples, respectively. When the pre-enriched SMS was implemented, more blaCTX-M/blaDHA genes were detected than in the native assay, including in stools that were pre-enriched culture-negative (pre-enriched SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 78.3%; specificity 75.0%). In addition, the pre-enriched SMS identified on average 38.6 ARGs/sample, whereas for the corresponding native SMS it was 29.4 ARGs/sample. Notably, stools resulting false-negative by using the native SMS had lower concentrations of ESC-R-Ent (average: ~105 vs. ~107 CFU/g) and E. coli classified reads (average: 193,959 vs. 1.45 million) than those of native SMS positive samples. Finally, the detection of blaCTX-M/blaDHA genes was compared with two well-established bioinformatic tools. In conclusion, only the pre-enriched SMS assured detection of most carriers of ESC-R-Ent. However, its performance was not comparable to the pre-enriched culture-based approach.
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Affiliation(s)
- Edgar I. Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Claudia Aldeia
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Parham Sendi
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Aline I. Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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5
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Inda-Webb ME, Jimenez M, Liu Q, Phan NV, Ahn J, Steiger C, Wentworth A, Riaz A, Zirtiloglu T, Wong K, Ishida K, Fabian N, Jenkins J, Kuosmanen J, Madani W, McNally R, Lai Y, Hayward A, Mimee M, Nadeau P, Chandrakasan AP, Traverso G, Yazicigil RT, Lu TK. Sub-1.4 cm 3 capsule for detecting labile inflammatory biomarkers in situ. Nature 2023; 620:386-392. [PMID: 37495692 DOI: 10.1038/s41586-023-06369-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/26/2023] [Indexed: 07/28/2023]
Abstract
Transient molecules in the gastrointestinal tract such as nitric oxide and hydrogen sulfide are key signals and mediators of inflammation. Owing to their highly reactive nature and extremely short lifetime in the body, these molecules are difficult to detect. Here we develop a miniaturized device that integrates genetically engineered probiotic biosensors with a custom-designed photodetector and readout chip to track these molecules in the gastrointestinal tract. Leveraging the molecular specificity of living sensors1, we genetically encoded bacteria to respond to inflammation-associated molecules by producing luminescence. Low-power electronic readout circuits2 integrated into the device convert the light emitted by the encapsulated bacteria to a wireless signal. We demonstrate in vivo biosensor monitoring in the gastrointestinal tract of small and large animal models and the integration of all components into a sub-1.4 cm3 form factor that is compatible with ingestion and capable of supporting wireless communication. With this device, diseases such as inflammatory bowel disease could be diagnosed earlier than is currently possible, and disease progression could be more accurately tracked. The wireless detection of short-lived, disease-associated molecules with our device could also support timely communication between patients and caregivers, as well as remote personalized care.
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Affiliation(s)
- M E Inda-Webb
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - M Jimenez
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Q Liu
- Electrical and Computer Engineering Department, Boston University, Boston, MA, USA
| | - N V Phan
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J Ahn
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Steiger
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - A Wentworth
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - A Riaz
- Electrical and Computer Engineering Department, Boston University, Boston, MA, USA
| | - T Zirtiloglu
- Electrical and Computer Engineering Department, Boston University, Boston, MA, USA
| | - K Wong
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - K Ishida
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N Fabian
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Comparative Medicine, MIT, Cambridge, MA, USA
| | - J Jenkins
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J Kuosmanen
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - W Madani
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - R McNally
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Y Lai
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - A Hayward
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Comparative Medicine, MIT, Cambridge, MA, USA
| | - M Mimee
- Department of Microbiology, Biological Sciences Division and Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | | | - A P Chandrakasan
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - G Traverso
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - R T Yazicigil
- Electrical and Computer Engineering Department, Boston University, Boston, MA, USA.
| | - T K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Senti Biosciences, South San Francisco, CA, USA.
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6
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Zhang Z, Zhang G, Ju F. Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of the Clinically Important Fraction of the β-Lactam Resistome. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11429-11439. [PMID: 35930686 DOI: 10.1021/acs.est.2c03627] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High bacterial community diversity and complexity greatly challenge the cost-efficient monitoring of clinically prevalent antibiotic-resistant bacteria, which are usually present as rare and important populations involved in the environmental dissemination of clinical resistance. Here, we introduce culture-enriched phenotypic metagenomics that integrates culture enrichment, phenotypic screening, and metagenomic analyses as an emerging standardized methodology for targeted resistome monitoring and apply it to decipher the extended-spectrum β-lactam resistome in a municipal wastewater treatment plant (WWTP) and its receiving river. The results showed that clinically prevalent carbapenemase genes (e.g., the NDM and KPC families) and extended-spectrum β-lactamase genes (e.g., the CTX-M, TEM, and OXA families) were prevalent in the WWTP and showed prominent potential in horizontal dissemination. Strikingly, carbapenem and polymyxin resistance genes co-occurred in the highly virulent nosocomial pathogens Enterobacter kobei and Citrobacter freundii. Overall, this study exemplifies phenotypic metagenomics for high-throughput surveillance of a targeted clinically important fraction of antibiotic resistomes and substantially expands current knowledge on extended-spectrum β-lactam resistance in WWTPs.
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Affiliation(s)
- Zhiguo Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Guoqing Zhang
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou 310030, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang, China
- The Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China
- Research Center for Industries of the Future (RCIF), School of Engineering, Westlake University, Hangzhou 310030, Zhejiang, China
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7
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George PBL, Rossi F, St-Germain MW, Amato P, Badard T, Bergeron MG, Boissinot M, Charette SJ, Coleman BL, Corbeil J, Culley AI, Gaucher ML, Girard M, Godbout S, Kirychuk SP, Marette A, McGeer A, O’Shaughnessy PT, Parmley EJ, Simard S, Reid-Smith RJ, Topp E, Trudel L, Yao M, Brassard P, Delort AM, Larios AD, Létourneau V, Paquet VE, Pedneau MH, Pic É, Thompson B, Veillette M, Thaler M, Scapino I, Lebeuf M, Baghdadi M, Castillo Toro A, Cayouette AB, Dubois MJ, Durocher AF, Girard SB, Diaz AKC, Khalloufi A, Leclerc S, Lemieux J, Maldonado MP, Pilon G, Murphy CP, Notling CA, Ofori-Darko D, Provencher J, Richer-Fortin A, Turgeon N, Duchaine C. Antimicrobial Resistance in the Environment: Towards Elucidating the Roles of Bioaerosols in Transmission and Detection of Antibacterial Resistance Genes. Antibiotics (Basel) 2022; 11:antibiotics11070974. [PMID: 35884228 PMCID: PMC9312183 DOI: 10.3390/antibiotics11070974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/15/2022] [Indexed: 02/01/2023] Open
Abstract
Antimicrobial resistance (AMR) is continuing to grow across the world. Though often thought of as a mostly public health issue, AMR is also a major agricultural and environmental problem. As such, many researchers refer to it as the preeminent One Health issue. Aerial transport of antimicrobial-resistant bacteria via bioaerosols is still poorly understood. Recent work has highlighted the presence of antibiotic resistance genes in bioaerosols. Emissions of AMR bacteria and genes have been detected from various sources, including wastewater treatment plants, hospitals, and agricultural practices; however, their impacts on the broader environment are poorly understood. Contextualizing the roles of bioaerosols in the dissemination of AMR necessitates a multidisciplinary approach. Environmental factors, industrial and medical practices, as well as ecological principles influence the aerial dissemination of resistant bacteria. This article introduces an ongoing project assessing the presence and fate of AMR in bioaerosols across Canada. Its various sub-studies include the assessment of the emissions of antibiotic resistance genes from many agricultural practices, their long-distance transport, new integrative methods of assessment, and the creation of dissemination models over short and long distances. Results from sub-studies are beginning to be published. Consequently, this paper explains the background behind the development of the various sub-studies and highlight their shared aspects.
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Affiliation(s)
- Paul B. L. George
- Département de Médecine Moléculaire, Université Laval, Quebec City, QC G1V 0A6, Canada; (P.B.L.G.); (J.C.); (I.S.)
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
| | - Florent Rossi
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont-Auvergne, 63178 Clermont-Ferrand, France; (P.A.); (A.-M.D.)
| | - Magali-Wen St-Germain
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont-Auvergne, 63178 Clermont-Ferrand, France; (P.A.); (A.-M.D.)
| | - Thierry Badard
- Centre de Recherche en Données et Intelligence Géospatiales (CRDIG), Quebec City, QC G1V 0A6, Canada;
| | - Michel G. Bergeron
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec-Université Laval, Axe Maladies Infectieuses et Immunitaires, Quebec City, QC G1V 4G2, Canada; (M.G.B.); (M.B.); (É.P.)
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec-Université Laval, Axe Maladies Infectieuses et Immunitaires, Quebec City, QC G1V 4G2, Canada; (M.G.B.); (M.B.); (É.P.)
| | - Steve J. Charette
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Brenda L. Coleman
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; (B.L.C.); (A.M.)
| | - Jacques Corbeil
- Département de Médecine Moléculaire, Université Laval, Quebec City, QC G1V 0A6, Canada; (P.B.L.G.); (J.C.); (I.S.)
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec-Université Laval, Axe Maladies Infectieuses et Immunitaires, Quebec City, QC G1V 4G2, Canada; (M.G.B.); (M.B.); (É.P.)
| | - Alexander I. Culley
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Marie-Lou Gaucher
- Research Chair in Meat Safety, Département de Pathologie et Microbiologie, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | | | - Stéphane Godbout
- Institut de Recherche et de Développement en Agroenvironnement (IRDA), Quebec City, QC G1P 3W8, Canada; (S.G.); (A.D.L.); (A.K.C.D.)
- Département des Sols et de Génie Agroalimentaire, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Shelley P. Kirychuk
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada; (S.P.K.); (B.T.); (A.C.T.); (C.A.N.)
| | - André Marette
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Institut sur la Nutrition et les Aliments Fonctionnels, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Allison McGeer
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada; (B.L.C.); (A.M.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Patrick T. O’Shaughnessy
- Department of Occupational and Environmental Health, The University of Iowa, Iowa City, IA 52246, USA;
| | - E. Jane Parmley
- Canadian Wildlife Health Cooperative, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.J.R.-S.); (M.P.M.)
| | - Serge Simard
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Richard J. Reid-Smith
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.J.R.-S.); (M.P.M.)
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada; (C.P.M.); (D.O.-D.)
| | - Edward Topp
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3, Canada;
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Luc Trudel
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
| | - Maosheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China;
| | - Patrick Brassard
- Département des Sols et de Génie Agroalimentaire, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Anne-Marie Delort
- Institut de Chimie de Clermont-Ferrand, SIGMA Clermont, CNRS, Université Clermont-Auvergne, 63178 Clermont-Ferrand, France; (P.A.); (A.-M.D.)
| | - Araceli D. Larios
- Institut de Recherche et de Développement en Agroenvironnement (IRDA), Quebec City, QC G1P 3W8, Canada; (S.G.); (A.D.L.); (A.K.C.D.)
- Tecnológico Nacional de México/ITS de Perote, Perote 91270, Mexico
| | - Valérie Létourneau
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Valérie E. Paquet
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Marie-Hélène Pedneau
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Émilie Pic
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec-Université Laval, Axe Maladies Infectieuses et Immunitaires, Quebec City, QC G1V 4G2, Canada; (M.G.B.); (M.B.); (É.P.)
| | - Brooke Thompson
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada; (S.P.K.); (B.T.); (A.C.T.); (C.A.N.)
| | - Marc Veillette
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Mary Thaler
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Ilaria Scapino
- Département de Médecine Moléculaire, Université Laval, Quebec City, QC G1V 0A6, Canada; (P.B.L.G.); (J.C.); (I.S.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Maria Lebeuf
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Mahsa Baghdadi
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Alejandra Castillo Toro
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada; (S.P.K.); (B.T.); (A.C.T.); (C.A.N.)
| | - Amélia Bélanger Cayouette
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Marie-Julie Dubois
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Institut sur la Nutrition et les Aliments Fonctionnels, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Alicia F. Durocher
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Sarah B. Girard
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Andrea Katherín Carranza Diaz
- Institut de Recherche et de Développement en Agroenvironnement (IRDA), Quebec City, QC G1P 3W8, Canada; (S.G.); (A.D.L.); (A.K.C.D.)
- Département des Sols et de Génie Agroalimentaire, Université Laval, Quebec City, QC G1V 0A6, Canada;
| | - Asmaâ Khalloufi
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Research Chair in Meat Safety, Département de Pathologie et Microbiologie, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Samantha Leclerc
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Joanie Lemieux
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Centre de Recherche en Infectiologie, Centre de Recherche du CHU de Québec-Université Laval, Axe Maladies Infectieuses et Immunitaires, Quebec City, QC G1V 4G2, Canada; (M.G.B.); (M.B.); (É.P.)
| | - Manuel Pérez Maldonado
- Department of Population Medicine, University of Guelph, Guelph, ON N1G 2W1, Canada; (R.J.R.-S.); (M.P.M.)
| | - Geneviève Pilon
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Colleen P. Murphy
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada; (C.P.M.); (D.O.-D.)
| | - Charly A. Notling
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada; (S.P.K.); (B.T.); (A.C.T.); (C.A.N.)
| | - Daniel Ofori-Darko
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1G 3W4, Canada; (C.P.M.); (D.O.-D.)
| | - Juliette Provencher
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Annabelle Richer-Fortin
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Nathalie Turgeon
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
| | - Caroline Duchaine
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Quebec City, QC G1V 0A6, Canada; (F.R.); (M.-W.S.-G.); (S.J.C.); (A.I.C.); (L.T.); (V.E.P.); (M.T.); (M.B.); (A.B.C.); (A.F.D.); (S.B.G.); (A.K.); (S.L.); (J.L.); (J.P.); (A.R.-F.)
- Centre de Recherche de L’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec City, QC G1V 4G5, Canada; (A.M.); (S.S.); (V.L.); (M.-H.P.); (M.V.); (M.L.); (M.-J.D.); (G.P.); (N.T.)
- Correspondence:
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8
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Kumari R, Yadav Y, Misra R, Das U, Das Adhikari U, Malakar P, Dubey GP. Emerging frontiers of antibiotics use and their impacts on the human gut microbiome. Microbiol Res 2022; 263:127127. [PMID: 35914416 DOI: 10.1016/j.micres.2022.127127] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/17/2022] [Accepted: 07/11/2022] [Indexed: 02/07/2023]
Abstract
Antibiotics, the primary drugs used to cure bacterial diseases, are increasingly becoming ineffective due to the emergence of multiple drug resistance (MDR) leading to recurrence of previously sensitive pathogens. Human gut microbiome (GM), known to play an important role in various physiological processes, consists of pool of diverse microbes. Indiscriminate use of antibiotics during the life span of an individual may lead to development of resistant microbes e.g. Vibrio, Acinetobacter, Escherichia, Klebsiella, Clostridia, etc. in the human GM. Transmission of antibiotic resistant genes (ARGs) between pathogenic and commensal bacteria occurs more frequently in microbiome communities wherein bacteria communicate and exchange cellular constituents both among themselves and with the host. Additionally, co-factors like 'early vs. late' exposure, type of antibiotics and duration of treatment modulate the adverse effects of antibiotics on GM maturation. Furthermore, factors like mode of birth, ethnicity, malnutrition, demography, diet, lifestyle, etc., which influence GM composition, can also indirectly alter the host response to antibiotics. Currently, advanced 'omics' and culturomics approaches are revealing novel avenues to study the interplay between antibiotics and the microbiome and to identify resistant genes in these bacterial communities. Here, we discuss the recent developments that have given insights into the effects of antibiotics on the homeostatic balance of the gut microbiome and thus on human health.
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Affiliation(s)
- Rekha Kumari
- Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India.
| | - Yasha Yadav
- Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India
| | - Richa Misra
- Department of Zoology, Sri Venkateswara College, University of Delhi, Delhi 1100021, India
| | - Utpal Das
- Department of Neurosciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Upasana Das Adhikari
- The Ragon Institute of MGH, MIT and Harvard, 400 Technology Square Cambridge, MA 02139, USA
| | - Pushkar Malakar
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gyanendra P Dubey
- Molecular Microbial Pathogenesis Unit, Institut Pasteur, 28 rue du Docteur Roux, 75724 Cedex 15 Paris, France.
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9
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Ferrocino I, Rantsiou K, Cocolin L. Microbiome and -omics application in food industry. Int J Food Microbiol 2022; 377:109781. [DOI: 10.1016/j.ijfoodmicro.2022.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022]
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10
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Smith-Page K, Kugadas A, Lin T, Delaney M, Bry L, Gadjeva M. Conjunctival Commensal Isolation and Identification in Mice. J Vis Exp 2021:10.3791/61672. [PMID: 33999020 PMCID: PMC8258654 DOI: 10.3791/61672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The ocular surface was once considered immune privileged and abiotic, but recently it appears that there is a small, but persistent commensal presence. Identification and monitoring of bacterial species at the ocular mucosa have been challenging due to their low abundance and limited availability of appropriate methodology for commensal growth and identification. There are two standard approaches: culture based or DNA sequencing methods. The first method is problematic due to the limited recoverable bacteria and the second approach identifies both live and dead bacteria leading to an aberrant representation of the ocular space. We developed a robust and sensitive method for bacterial isolation by building upon standard microbiological culturing techniques. This is a swab-based technique, utilizing an "in-lab" made thin swab that targets the lower conjunctiva, followed by an amplification step for aerobic and facultative anaerobic genera. This protocol has allowed us to isolate and identify conjunctival species such as Corynebacterium spp., Coagulase Negative Staphylococcus spp., Streptococcus spp., etc. The approach is suitable to define commensal diversity in mice under different disease conditions.
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Affiliation(s)
- Kirsten Smith-Page
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School
| | - Abirami Kugadas
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School
| | - Tiffany Lin
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School
| | - Mary Delaney
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School; Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School; Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School
| | - Mihaela Gadjeva
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School;
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11
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Kim DW, Cha CJ. Antibiotic resistome from the One-Health perspective: understanding and controlling antimicrobial resistance transmission. Exp Mol Med 2021; 53:301-309. [PMID: 33642573 PMCID: PMC8080597 DOI: 10.1038/s12276-021-00569-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/31/2023] Open
Abstract
The concept of the antibiotic resistome was introduced just over a decade ago, and since then, active resistome studies have been conducted. In the present study, we describe the previously established concept of the resistome, which encompasses all types of antibiotic resistance genes (ARGs), and the important findings from each One-Health sector considering this concept, thereby emphasizing the significance of the One-Health approach in understanding ARG transmission. Cutting-edge research methodologies are essential for deciphering the complex resistome structure in the microbiomes of humans, animals, and the environment. Based on the recent achievements of resistome studies in multiple One-Health sectors, future directions for resistome research have been suggested to improve the understanding and control of ARG transmission: (1) ranking the critical ARGs and their hosts; (2) understanding ARG transmission at the interfaces of One-Health sectors; (3) identifying selective pressures affecting the emergence, transmission, and evolution of ARGs; and (4) elucidating the mechanisms that allow an organism to overcome taxonomic barriers in ARG transmission.
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Affiliation(s)
- Dae-Wi Kim
- grid.411545.00000 0004 0470 4320Division of Life Sciences, Jeonbuk National University, Jeonju, 54896 Republic of Korea
| | - Chang-Jun Cha
- grid.254224.70000 0001 0789 9563Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546 Republic of Korea
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12
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Ho J, Yeoh YK, Barua N, Chen Z, Lui G, Wong SH, Yang X, Chan MCW, Chan PKS, Hawkey PM, Ip M. Systematic review of human gut resistome studies revealed variable definitions and approaches. Gut Microbes 2020; 12:1700755. [PMID: 31942825 PMCID: PMC7524153 DOI: 10.1080/19490976.2019.1700755] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
In this review, we highlight the variations of gut resistome studies, which may preclude comparisons and translational interpretations. Of 22 included studies, a range of 12 to 2000 antibiotic resistance (AR) genes were profiled. Overall, studies defined a healthy gut resistome as subjects who had not taken antibiotics in the last three to 12 months prior to sampling. In studies with de novo assembly, AR genes were identified based on variable nucleotide or amino acid sequence similarities. Different marker genes were used for defining resistance to a given antibiotic class. Validation of phenotypic resistance in the laboratory is frequently lacking. Cryptic resistance, collateral sensitivity and the interaction with repressors or promotors were not investigated. International consensus is needed for selecting marker genes to define resistance to a given antibiotic class in addition to uniformity in phenotypic validation and bioinformatics pipelines.
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Affiliation(s)
- Jeffery Ho
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yun Kit Yeoh
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Nilakshi Barua
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Grace Lui
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,Department of Medicine & Therapeutics, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H Wong
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,Department of Medicine & Therapeutics, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiao Yang
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Martin CW Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul KS Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peter M Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Margaret Ip
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China,Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China,Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China,CONTACT Margaret Ip Department of Microbiology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
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13
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Munck C, Sheth RU, Cuaresma E, Weidler J, Stump SL, Zachariah P, Chong DH, Uhlemann AC, Abrams JA, Wang HH, Freedberg DE. The effect of short-course antibiotics on the resistance profile of colonizing gut bacteria in the ICU: a prospective cohort study. Crit Care 2020; 24:404. [PMID: 32646458 PMCID: PMC7350675 DOI: 10.1186/s13054-020-03061-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/04/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The need for early antibiotics in the intensive care unit (ICU) is often balanced against the goal of antibiotic stewardship. Long-course antibiotics increase the burden of antimicrobial resistance within colonizing gut bacteria, but the dynamics of this process are not fully understood. We sought to determine how short-course antibiotics affect the antimicrobial resistance phenotype and genotype of colonizing gut bacteria in the ICU by performing a prospective cohort study with assessments of resistance at ICU admission and exactly 72 h later. METHODS Deep rectal swabs were performed on 48 adults at the time of ICU admission and exactly 72 h later, including patients who did and did not receive antibiotics. To determine resistance phenotype, rectal swabs were cultured for methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). In addition, Gram-negative bacterial isolates were cultured against relevant antibiotics. To determine resistance genotype, quantitative PCR (qPCR) was performed from rectal swabs for 87 established resistance genes. Within-individual changes in antimicrobial resistance were calculated based on culture and qPCR results and correlated with exposure to relevant antibiotics (e.g., did β-lactam antibiotic exposure associate with a detectable change in β-lactam resistance over this 72-h period?). RESULTS Of 48 ICU patients, 41 (85%) received antibiotics. Overall, there was no increase in the antimicrobial resistance profile of colonizing gut bacteria during the 72-h study period. There was also no increase in antimicrobial resistance after stratification by receipt of antibiotics (i.e., no detectable increase in β-lactam, vancomycin, or macrolide resistance regardless of whether patients received those same antibiotics). This was true for both culture and PCR. Antimicrobial resistance pattern at ICU admission strongly predicted resistance pattern after 72 h. CONCLUSIONS Short-course ICU antibiotics made little detectable difference in the antimicrobial resistance pattern of colonizing gut bacteria over 72 h in the ICU. This provides an improved understanding of the dynamics of antimicrobial resistance in the ICU and some reassurance that short-course antibiotics may not adversely impact the stewardship goal of reducing antimicrobial resistance.
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Affiliation(s)
- Christian Munck
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA.
| | - Ravi U Sheth
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA
| | - Edward Cuaresma
- Department of Medicine, Columbia University Irving Medical Center, New York, USA
| | - Jessica Weidler
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Stephania L Stump
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Philip Zachariah
- Division of Pediatric Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - David H Chong
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Irving Medical Center, New York, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, USA
| | - Julian A Abrams
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, 630 West 168th Street, P&S 3-401, New York, NY, 10032, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Irving Medical Center, 3960 Broadway, New York, NY, 10032, USA
| | - Daniel E Freedberg
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Center, 630 West 168th Street, P&S 3-401, New York, NY, 10032, USA.
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14
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Peto L, Fawcett NJ, Crook DW, Peto TEA, Llewelyn MJ, Walker AS. Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae. PLoS One 2019; 14:e0222831. [PMID: 31703058 PMCID: PMC6839868 DOI: 10.1371/journal.pone.0222831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 09/07/2019] [Indexed: 01/02/2023] Open
Abstract
Metagenomic sequencing of fecal DNA can usefully characterise an individual's intestinal resistome but is limited by its inability to detect important pathogens that may be present at low abundance, such as carbapenemase or extended-spectrum beta-lactamase producing Enterobacteriaceae. Here we aimed to develop a hybrid protocol to improve detection of resistance genes in Enterobacteriaceae by using a short period of culture enrichment prior to sequencing of DNA extracted directly from the enriched sample. Volunteer feces were spiked with carbapenemase-producing Enterobacteriaceae and incubated in selective broth culture for 6 hours before sequencing. Different DNA extraction methods were compared, including a plasmid extraction protocol to increase the detection of plasmid-associated resistance genes. Although enrichment prior to sequencing increased the detection of carbapenemase genes, the differing growth characteristics of the spike organisms precluded accurate quantification of their concentration prior to culture. Plasmid extraction increased detection of resistance genes present on plasmids, but the effects were heterogeneous and dependent on plasmid size. Our results demonstrate methods of improving the limit of detection of selected resistance mechanisms in a fecal resistome assay, but they also highlight the difficulties in using these techniques for accurate quantification and should inform future efforts to achieve this goal.
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Affiliation(s)
- Leon Peto
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
- * E-mail:
| | - Nicola J. Fawcett
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
| | - Derrick W. Crook
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
- National Infection Service, Public Health England, Colindale, London, England, United Kingdom
| | - Tim E. A. Peto
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
| | - Martin J. Llewelyn
- Department of Global Health and Infection, Brighton and Sussex Medical School, Falmer, Sussex, England, United Kingdom
- Department of Microbiology and Infection, Brighton and Sussex University Hospitals NHS Trust, Brighton, England, United Kingdom
| | - A. Sarah Walker
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, England, United Kingdom
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