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Willems RPJ, van Dijk K, Dierikx CM, Twisk JWR, van der Klis FRM, de Greeff SC, Vandenbroucke-Grauls CMJE. Gastric acid suppression, lifestyle factors and intestinal carriage of ESBL and carbapenemase-producing Enterobacterales: a nationwide population-based study. J Antimicrob Chemother 2021; 77:237-245. [PMID: 34550358 PMCID: PMC8730682 DOI: 10.1093/jac/dkab345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/15/2021] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Gastric acid-suppressive therapy has been suggested to increase the risk for intestinal carriage of MDR Enterobacterales, but there is scarce community-based evidence substantiating this risk. OBJECTIVES To investigate if acid-suppressant use is associated with a risk of intestinal carriage of ESBL and carbapenemase-producing Enterobacterales (ESBL-E) in the open population, and to assess possible modifying factors. METHODS Within the framework of a nationwide seroprevalence study, we identified a population-based cross-sectional cohort comprising 2746 adults (≥18 years), who provided stool specimens between February 2016 and June 2017. Specimens were tested by phenotypic assays and confirmatory genotype analysis to detect carriage of ESBL-E. Covariate data were extracted from self-administered questionnaires. ORs and 95% CIs were estimated using multivariable multilevel logistic regression, controlling for confounders informed by directed acyclic graphs. RESULTS Among 2746 participants, 316 (11.5%) used acid suppressants; the prevalence of ESBL-E carriage was 7.4% (95% CI, 6.1%-8.6%). Current use of acid suppressants was not associated with ESBL-E carriage (adjusted OR [aOR], 1.05; 95% CI, 0.64-1.74); lifestyle and comorbidity did not modify this association. A higher BMI (≥25 kg/m2) (aOR, 1.42 [95% CI, 1.02-1.98]), non-Western ethnic origin (aOR, 1.96 [95% CI, 1.34-2.87]), travel to Eastern-Mediterranean, Western-Pacific or South-East Asia regions (aOR, 3.16 [95% CI, 1.71-5.83]) were associated with ESBL-E carriage. Sensitivity analyses confirmed these results; spline analysis supported a BMI-associated risk. CONCLUSIONS In this open population study, current use of acid suppressants was not associated with ESBL-E carriage. Travel to high-endemic regions and non-Western ethnicity were confirmed as risk factors, while a higher BMI emerged as a potential new risk for ESBL-E carriage.
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Affiliation(s)
- Roel P J Willems
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Karin van Dijk
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Cindy M Dierikx
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Jos W R Twisk
- Department of Clinical Epidemiology and Biostatistics, Amsterdam Public Health, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Fiona R M van der Klis
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Centre for Immunology of Infectious Diseases and Vaccines-Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sabine C de Greeff
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.,Centre for Epidemiology and Surveillance of Infectious Diseases-Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Christina M J E Vandenbroucke-Grauls
- Department of Medical Microbiology and Infection Prevention, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Amsterdam Medical Center, Amsterdam, The Netherlands
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102
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Perry MR, Lepper HC, McNally L, Wee BA, Munk P, Warr A, Moore B, Kalima P, Philip C, de Roda Husman AM, Aarestrup FM, Woolhouse MEJ, van Bunnik BAD. Secrets of the Hospital Underbelly: Patterns of Abundance of Antimicrobial Resistance Genes in Hospital Wastewater Vary by Specific Antimicrobial and Bacterial Family. Front Microbiol 2021; 12:703560. [PMID: 34566912 PMCID: PMC8461093 DOI: 10.3389/fmicb.2021.703560] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/10/2021] [Indexed: 01/05/2023] Open
Abstract
Background: Hospital wastewater is a major source of antimicrobial resistance (AMR) outflow into the environment. This study uses metagenomics to study how hospital clinical activity impacts antimicrobial resistance genes (ARGs) abundances in hospital wastewater. Methods: Sewage was collected over a 24-h period from multiple wastewater collection points (CPs) representing different specialties within a tertiary hospital site and simultaneously from community sewage works. High throughput shotgun sequencing was performed using Illumina HiSeq4000. ARG abundances were correlated to hospital antimicrobial usage (AMU), data on clinical activity and resistance prevalence in clinical isolates. Results: Microbiota and ARG composition varied between CPs and overall ARG abundance was higher in hospital wastewater than in community influent. ARG and microbiota compositions were correlated (Procrustes analysis, p=0.014). Total antimicrobial usage was not associated with higher ARG abundance in wastewater. However, there was a small positive association between resistance genes and antimicrobial usage matched to ARG phenotype (IRR 1.11, CI 1.06-1.16, p<0.001). Furthermore, analyzing carbapenem and vancomycin resistance separately indicated that counts of ARGs to these antimicrobials were positively associated with their increased usage [carbapenem rate ratio (RR) 1.91, 95% CI 1.01-3.72, p=0.07, and vancomycin RR 10.25, CI 2.32-49.10, p<0.01]. Overall, ARG abundance within hospital wastewater did not reflect resistance patterns in clinical isolates from concurrent hospital inpatients. However, for clinical isolates of the family Enterococcaceae and Staphylococcaceae, there was a positive relationship with wastewater ARG abundance [odds ratio (OR) 1.62, CI 1.33-2.00, p<0.001, and OR 1.65, CI 1.21-2.30, p=0.006 respectively]. Conclusion: We found that the relationship between hospital wastewater ARGs and antimicrobial usage or clinical isolate resistance varies by specific antimicrobial and bacterial family studied. One explanation, we consider is that relationships observed from multiple departments within a single hospital site will be detectable only for ARGs against parenteral antimicrobials uniquely used in the hospital setting. Our work highlights that using metagenomics to identify the full range of ARGs in hospital wastewater is a useful surveillance tool to monitor hospital ARG carriage and outflow and guide environmental policy on AMR.
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Affiliation(s)
- Meghan R. Perry
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
- NHS Lothian Infection Service, Edinburgh Clinical Infection Research Group, Edinburgh, United Kingdom
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Hannah C. Lepper
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Luke McNally
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Bryan A. Wee
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Amanda Warr
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Barbara Moore
- NHS Lothian Infection Service, Edinburgh Clinical Infection Research Group, Edinburgh, United Kingdom
| | - Pota Kalima
- NHS Lothian Infection Service, Edinburgh Clinical Infection Research Group, Edinburgh, United Kingdom
| | - Carol Philip
- NHS Lothian Infection Service, Edinburgh Clinical Infection Research Group, Edinburgh, United Kingdom
| | | | - Frank M. Aarestrup
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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Abstract
A central paradigm in microbiome data analysis, which we term the genome-centric paradigm, is that a linear (non-branching) DNA sequence is the ideal representation of a microbial genome. This representation is natural, as microbes indeed have non-branching genomes. Tremendous discoveries in microbiology were made under this paradigm, but is it always optimal for microbiome research? In this Commentary, we claim that the realization of this paradigm in metagenomic assembly, a fundamental step in the “metagenomics analysis pipeline,” suboptimally models the extensive genomic variability present in the microbiome. We outline our efforts to address these issues with a “genome-free” approach that eschews linear genomic representations in favor of a pan-metagenomic graph.
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104
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Sawicka-Durkalec A, Kursa O, Bednarz Ł, Tomczyk G. Occurrence of Mycoplasma spp. in wild birds: phylogenetic analysis and potential factors affecting distribution. Sci Rep 2021; 11:17065. [PMID: 34426624 PMCID: PMC8382738 DOI: 10.1038/s41598-021-96577-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
Different Mycoplasma species have been reported in avian hosts. However, the majority of studies focus on one particular species of Mycoplasma or one host. In our research, we screened a total of 1141 wild birds representing 55 species, 26 families, and 15 orders for the presence of mycoplasmas by conventional PCR based on the 16S rRNA gene. Selected PCR products were sequenced to perform the phylogenetic analysis. All mycoplasma-positive samples were tested for M. gallisepticum and M. synoviae, which are considered the major pathogens of commercial poultry. We also verified the influence of ecological characteristics of the tested bird species including feeding habits, habitat types, and movement patterns. The presence of Mycoplasma spp. was confirmed in 498 birds of 29 species, but none of the tested birds were positive for M. gallisepticum or M. synoviae. We found possible associations between the presence of Mycoplasma spp. and all investigated ecological factors. The phylogenetic analysis showed a high variability of Mycoplasma spp.; however, some clustering of sequences was observed regarding particular bird species. We found that wild migratory waterfowl, particularly the white-fronted goose (Anser albifrons) and mallard (Anas platyrhynchos) could be reservoirs and vectors of mycoplasmas pathogenic to commercial waterfowl.
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Affiliation(s)
- Anna Sawicka-Durkalec
- grid.419811.4Department of Poultry Diseases, National Veterinary Research Institute, Aleja Partyzantów 57, 24-100 Puławy, Poland
| | - Olimpia Kursa
- grid.419811.4Department of Poultry Diseases, National Veterinary Research Institute, Aleja Partyzantów 57, 24-100 Puławy, Poland
| | - Łukasz Bednarz
- Bird Horizons Foundation, Spółdzielcza 34, 24-220 Niedrzwica Duża, Poland
| | - Grzegorz Tomczyk
- grid.419811.4Department of Poultry Diseases, National Veterinary Research Institute, Aleja Partyzantów 57, 24-100 Puławy, Poland
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105
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Wu L, Xie X, Li Y, Liang T, Zhong H, Ma J, Yang L, Yang J, Li L, Xi Y, Li H, Zhang J, Chen X, Ding Y, Wu Q. Metagenomics-Based Analysis of the Age-Related Cumulative Effect of Antibiotic Resistance Genes in Gut Microbiota. Antibiotics (Basel) 2021; 10:1006. [PMID: 34439056 PMCID: PMC8388928 DOI: 10.3390/antibiotics10081006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/21/2022] Open
Abstract
Antibiotic resistance in bacteria has become a major global health problem. One of the main reservoirs of antibiotic resistance genes is the human gut microbiota. To characterise these genes, a metagenomic approach was used. In this study, a comprehensive antibiotic resistome catalog was established using fecal samples from 246 healthy individuals from world's longevity township in Jiaoling, China. In total, 606 antibiotic resistance genes were detected. Our results indicated that antibiotic resistance genes in the human gut microbiota accumulate and become more complex with age as older groups harbour the highest abundance of these genes. Tetracycline resistance gene type tetQ was the most abundant group of antibiotic resistance genes in gut microbiota, and the main carrier of antibiotic resistance genes was Bacteroides. Antibiotic efflux, inactivation, and target alteration were found to be the dominant antimicrobial resistance mechanisms. This research may help to establish a comprehensive antibiotic resistance catalog that includes extremely long-lived healthy people such as centenarians, and may provide potential recommendations for controlling the use of antibiotics.
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Affiliation(s)
- Lei Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (L.W.); (T.L.); (J.M.); (J.Y.); (X.C.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Xinqiang Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Ying Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Tingting Liang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (L.W.); (T.L.); (J.M.); (J.Y.); (X.C.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Haojie Zhong
- The First Affiliated Hospital, School of Clinical Medicine of Guangdong Pharmaceutical University, Guangzhou 510080, China;
| | - Jun Ma
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (L.W.); (T.L.); (J.M.); (J.Y.); (X.C.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Lingshuang Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Juan Yang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (L.W.); (T.L.); (J.M.); (J.Y.); (X.C.)
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Longyan Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Yu Xi
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Haixin Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
| | - Xuefeng Chen
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (L.W.); (T.L.); (J.M.); (J.Y.); (X.C.)
| | - Yu Ding
- Department of Food Science and Technology, Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China; (X.X.); (Y.L.); (L.Y.); (L.L.); (Y.X.); (H.L.); (J.Z.)
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106
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Antibiotic Resistance Decreases the Efficacy of Endodontic Filling Pastes for Root Canal Treatment in Children's Teeth. CHILDREN-BASEL 2021; 8:children8080692. [PMID: 34438583 PMCID: PMC8391351 DOI: 10.3390/children8080692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/25/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
The antibacterial efficacy of antimicrobial filling pastes (AFP) used in the root canal treatment of primary teeth has been widely reported. However, antibiotic resistance as an emerging global problem could impact their current efficacy. This study aimed to evaluate the efficacy of two common AFP on susceptible or resistant bacteria isolated from primary necrotic molars. Microbiological samples were obtained and cultured from the root canals of 34 children. In total, 96 colony-forming units were obtained to determine their resistance to tetracycline, rifampicin, and chloramphenicol. They were identified as S. mutans or E. faecalis using polymerase chain reaction. The antimicrobial activity of CTZ paste (chloramphenicol, tetracycline, zinc oxide, and eugenol) and Guedes-Pinto modified (GPM) paste (rifampicin, prednisolone, iodoform, and camphorated paramonochlorophenol) were tested against the identified and selected microorganisms. Larger size inhibition zones were observed in both species when the tested strains were susceptible to the antibiotics in the AFP preparation. The efficacy of AFP containing antibiotics depends on the antibiotic resistance profile of the strain. Antibiotic resistance and its effect on the AFP were shown, which calls into question the use of simplified endodontic techniques that depend on antibiotics, since in these cases these techniques could not clinically eliminate resistant bacteria from the root canal.
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107
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Ottoni C, Borić D, Cheronet O, Sparacello V, Dori I, Coppa A, Antonović D, Vujević D, Price TD, Pinhasi R, Cristiani E. Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus. Proc Natl Acad Sci U S A 2021; 118:e2102116118. [PMID: 34312252 PMCID: PMC8364157 DOI: 10.1073/pnas.2102116118] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.
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Affiliation(s)
- Claudio Ottoni
- DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy;
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Vitale Sparacello
- Department of Environmental and Life Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Irene Dori
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le province di Verona, Rovigo e Vicenza, 37121 Verona, Italy
| | - Alfredo Coppa
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
- Department of Genetics, Harvard Medical School, Harvard University, Cambridge, MA 02138
| | | | - Dario Vujević
- Department of Archaeology, University of Zadar, 23000 Zadar, Croatia
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Emanuela Cristiani
- DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy;
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108
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Comparative Genomic Analysis of Extended-spectrum β-lactamase and mcr-1 Positive Escherichia coli from Gut Microbiota of Healthy Singaporeans. Appl Environ Microbiol 2021; 87:e0048821. [PMID: 34347523 DOI: 10.1128/aem.00488-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug resistant (MDR) Escherichia coli strains that carry extended-spectrum β-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we isolated and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the detection rates for ESBL-producing and mcr-positive Enterobacteriaceae are 25.7% (28/109) and 7.3% (8/109), respectively. Whole-genome sequencing analysis of the 37 E. coli isolates assigned them into 25 sequence types and six different phylogroups, suggesting that the MDR E. coli gut colonizers are highly diverse. We then analysed the genetic context of the resistance genes and found that composite transposons played important roles in the co-transfer of blaCTX-M-15/55 and qnrS1, as well as the acquisition of mcr-1. Furthermore, comparative genomic analysis showed that 12 of the 37 MDR E. coli isolates showed high similarity to ESBL-producing E. coli isolates from raw meat products in local markets. By analyzing the core genome SNPs shared by these isolates, we identified possible clonal transmission of a MDR E. coli clone between human and raw meat, as well as a group of highly similar IncI2 (Delta) plasmids that might be responsible for the dissemination of mcr-1 in a much wider geographic region. Together, these results suggest that antibiotic resistance may be transmitted between different environmental settings by the expansion of MDR E. coli clones, as well as by the dissemination of resistance plasmids. Importance The human gut can harbor both antibiotic resistant and virulent E. coli which may subsequently cause infections. In this study, we found that MDR E. coli isolates from the gut of healthy Singaporeans carry a diverse range of antibiotic resistance mechanisms and virulence factor genes, and are highly diverse to each other. By comparing their genomes with the ESBL-producing E. coli isolates from raw meat products that were sampled at a similar time from local markets, we detected a MDR E. coli clone that was possibly transmitted between humans and raw meat products. Furthermore, we also found that a group of resistance plasmids might be responsible for the dissemination of colistin resistance gene mcr-1 in Singapore, Malaysia and Europe. Our findings call for better countermeasures to block the transmission of antibiotic resistance.
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109
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Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms. mSystems 2021; 6:e0091320. [PMID: 34342537 PMCID: PMC8409726 DOI: 10.1128/msystems.00913-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antimicrobial resistance (AMR) is becoming one of the largest threats to public health worldwide, with the opportunistic pathogen Escherichia coli playing a major role in the AMR global health crisis. Unravelling the complex interplay between drug resistance and metabolic rewiring is key to understand the ability of bacteria to adapt to new treatments and to the development of new effective solutions to combat resistant infections. We developed a computational pipeline that combines machine learning with genome-scale metabolic models (GSMs) to elucidate the systemic relationships between genetic determinants of resistance and metabolism beyond annotated drug resistance genes. Our approach was used to identify genetic determinants of 12 AMR profiles for the opportunistic pathogenic bacterium E. coli. Then, to interpret the large number of identified genetic determinants, we applied a constraint-based approach using the GSM to predict the effects of genetic changes on growth, metabolite yields, and reaction fluxes. Our computational platform leads to multiple results. First, our approach corroborates 225 known AMR-conferring genes, 35 of which are known for the specific antibiotic. Second, integration with the GSM predicted 20 top-ranked genetic determinants (including accA, metK, fabD, fabG, murG, lptG, mraY, folP, and glmM) essential for growth, while a further 17 top-ranked genetic determinants linked AMR to auxotrophic behavior. Third, clusters of AMR-conferring genes affecting similar metabolic processes are revealed, which strongly suggested that metabolic adaptations in cell wall, energy, iron and nucleotide metabolism are associated with AMR. The computational solution can be used to study other human and animal pathogens. IMPORTANCEEscherichia coli is a major public health concern given its increasing level of antibiotic resistance worldwide and extraordinary capacity to acquire and spread resistance via horizontal gene transfer with surrounding species and via mutations in its existing genome. E. coli also exhibits a large amount of metabolic pathway redundancy, which promotes resistance via metabolic adaptability. In this study, we developed a computational approach that integrates machine learning with metabolic modeling to understand the correlation between AMR and metabolic adaptation mechanisms in this model bacterium. Using our approach, we identified AMR genetic determinants associated with cell wall modifications for increased permeability, virulence factor manipulation of host immunity, reduction of oxidative stress toxicity, and changes to energy metabolism. Unravelling the complex interplay between antibiotic resistance and metabolic rewiring may open new opportunities to understand the ability of E. coli, and potentially of other human and animal pathogens, to adapt to new treatments.
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Xue X, Wang L, Xing H, Zhao Y, Li X, Wang G, Wang Z. Characteristics of phytoplankton-zooplankton communities and the roles in the transmission of antibiotic resistance genes under the pressure of river contamination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146452. [PMID: 33770605 DOI: 10.1016/j.scitotenv.2021.146452] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Insight into the distribution of antibiotic resistance genes (ARGs) in phytoplankton-zooplankton communities (PZCs) is essential for the management and control of antibiotic resistance in aquatic ecosystems. This study characterized the profiles of PZCs and their carried ARGs in a typical urban river and ranked the factors (water physicochemical parameters, PZCs, bacterial abundance, and mobile genetic elements) influencing the dynamic of ARG profiles by the partial least squares path modeling. Results showed Cyanobacteria, Bacillariophyta and Chlorophyta were dominant phyla of phytoplankton, and Rotifera was with the highest abundance in zooplankton. River contamination markedly altered the structure of PZCs, increasing the abundance of phytoplankton and zooplankton, decreasing the diversity of phytoplankton while elevating in zooplankton. PZCs harbored large amounts of ARGs with average relative abundance of 2.35 × 10-2/copies nearly an order magnitude higher than the living water and most ARGs exhibited significant accumulation in PZCs with the aggravated environmental pollution. The partial least squares path modeling predicted the water parameters as the most important factor mainly playing indirect effects on ARGs via PZCs and bacterial communities, followed by mobile genetic elements as the most essential direct factor for ARGs profiles. Besides, PZCs were also important drivers for the carried ARGs via direct effects on the ARGs' composition and indirect effects on host bacterial communities of ARGs and their mobile genetic elements. The present study fills the gaps in knowledge about the distribution of ARGs in PZCs and provided a new perspective to decipher the key roles of PZCs in the maintenance and dissemination of ARGs in urban river ecosystems.
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Affiliation(s)
- Xue Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haoran Xing
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangju Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gaoxue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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111
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Wang Y, Lyu N, Liu F, Liu WJ, Bi Y, Zhang Z, Ma S, Cao J, Song X, Wang A, Zhang G, Hu Y, Zhu B, Gao GF. More diversified antibiotic resistance genes in chickens and workers of the live poultry markets. ENVIRONMENT INTERNATIONAL 2021; 153:106534. [PMID: 33799229 DOI: 10.1016/j.envint.2021.106534] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Poultry farms and LPMs are a reservoir of antimicrobial resistant bacteria and resistance genes from feces. The LPM is an important interface between humans, farm animals, and environments in a typical urban environment, and it is considered a reservoir for ARGs and viruses. However, the antibiotic resistomes shared between chicken farms and LPMs, and that of LPM workers and people who have no contact with the LPMs remains unknown. METHODS We characterized the resistome and bacterial microbiome of farm chickens and LPMs and LPM workers and control subjects. The mobile ARGs identified in chickens and the distribution of the mcr-family genes in publicly bacterial genomes and chicken gut metagenomes was analyzed, respectively. In addition, the prevalence of mcr-1 in LPMs following the ban on colistin-positive additives in China was explored. RESULTS By profiling the microbiomes and resistomes in chicken farms, LPMs, LPM workers, and LPM environments, we found that the bacterial community composition and resistomes were significantly different between the farms and the LPMs, and the LPM samples possessed more diversified ARGs (59 types) than the farms. Some mobile ARGs, such as mcr-1 and tet(X3), identified in chicken farms, LPMs, LPM workers, and LPM environments were also harbored by human clinical pathogens. Moreover, we found that the resistomes were significantly different between the LPM workers and those who have no contact with the LPMs, and more diversified ARGs (188 types) were observed in the LPM workers. It is also worth noting that mcr-10 was identified in both human (5.2%, 96/1,859) and chicken (1.5%, 14/910) gut microbiomes. Although mcr-1 prevalence decreased significantly in the LPMs across the eight provinces in China, from 190/333 (57.1%) samples in September 2016-March 2017 to 208/544 (38.2%) samples in August 2018-May 2019, it is widespread and continuous in the LPMs. CONCLUSION Live poultry trade has a significant effect on the diversity of ARGs in LPM workers, chickens, and environments in China, driven by human selection with the live poultry trade. Our findings highlight the live poultry trade as ARG disseminators into LPMs, which serve as an interface of LPM environments even LPM workers, and that could urge Government to have better control of LPMs in China. Further studies on the factors that promote antibiotic resistance exchange between LPM environments, human commensals, and pathogens, are warranted.
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Affiliation(s)
- Yanan Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Lyu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - William J Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Zewu Zhang
- Dongguan Municipal Center for Disease Control and Prevention, Dongguan 523129, China
| | - Sufang Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian Cao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Song
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Gaiping Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 450046, China; School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Key Laboratory of Antimicrobial Resistance and Pathogen Genomics, Beijing 100101, China; Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan 646000, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
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112
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Petitjean M, Condamine B, Burdet C, Denamur E, Ruppé E. Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes. Microb Genom 2021; 7:000489. [PMID: 34435947 PMCID: PMC8549366 DOI: 10.1099/mgen.0.000489] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 06/07/2021] [Indexed: 01/31/2023] Open
Abstract
Escherichia coli is a ubiquitous bacterium that has been widely exposed to antibiotics over the last 70 years. It has adapted by acquiring different antibiotic-resistance genes (ARGs), the census of which we aim to characterize here. To do so, we analysed 70 301 E. coli genomes obtained from the EnteroBase database and detected 1 027 651 ARGs using the AMRFinder, Mustard and ResfinderFG ARG databases. We observed a strong phylogroup and clonal lineage specific distribution of some ARGs, supporting the argument for epistasis between ARGs and the strain genetic background. However, each phylogroup had ARGs conferring a similar antibiotic class resistance pattern, indicating phenotypic adaptive convergence. The G+C content or the type of ARG was not associated with the frequency of the ARG in the database. In addition, we identified ARGs from anaerobic, non-Proteobacteria bacteria in four genomes of E. coli, supporting the hypothesis that the transfer between anaerobic bacteria and E. coli can spontaneously occur but remains exceptional. In conclusion, we showed that phylum barrier and intra-species phylogenetic history are major drivers of the acquisition of a resistome in E. coli.
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Affiliation(s)
| | | | - Charles Burdet
- IAME, INSERM, Université de Paris, F-75018 Paris, France
- Département d’Epidémiologie, Biostatistique et Recherche Clinique, Hôpital Bichat, APHP, F-75018 Paris, France
| | - Erick Denamur
- IAME, INSERM, Université de Paris, F-75018 Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, APHP, F-75018 Paris, France
| | - Etienne Ruppé
- IAME, INSERM, Université de Paris, F-75018 Paris, France
- Laboratoire de Bactériologie, Hôpital Bichat, APHP, F-75018 Paris, France
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113
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Diebold PJ, New FN, Hovan M, Satlin MJ, Brito IL. Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR. eLife 2021; 10:66834. [PMID: 34282723 PMCID: PMC8294855 DOI: 10.7554/elife.66834] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/30/2021] [Indexed: 12/17/2022] Open
Abstract
The horizonal transfer of plasmid-encoded genes allows bacteria to adapt to constantly shifting environmental pressures, bestowing functional advantages to their bacterial hosts such as antibiotic resistance, metal resistance, virulence factors, and polysaccharide utilization. However, common molecular methods such as short- and long-read sequencing of microbiomes cannot associate extrachromosomal plasmids with the genome of the host bacterium. Alternative methods to link plasmids to host bacteria are either laborious, expensive, or prone to contamination. Here we present the One-step Isolation and Lysis PCR (OIL-PCR) method, which molecularly links plasmid-encoded genes with the bacterial 16S rRNA gene via fusion PCR performed within an emulsion. After validating this method, we apply it to identify the bacterial hosts of three clinically relevant beta-lactamases within the gut microbiomes of neutropenic patients, as they are particularly vulnerable multidrug-resistant infections. We successfully detect the known association of a multi-drug resistant plasmid with Klebsiella pneumoniae, as well as the novel associations of two low-abundance genera, Romboutsia and Agathobacter. Further investigation with OIL-PCR confirmed that our detection of Romboutsia is due to its physical association with Klebsiella as opposed to directly harboring the beta-lactamase genes. Here we put forth a robust, accessible, and high-throughput platform for sensitively surveying the bacterial hosts of mobile genes, as well as detecting physical bacterial associations such as those occurring within biofilms and complex microbial communities.
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Affiliation(s)
- Peter J Diebold
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, United States
| | - Felicia N New
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, United States
| | - Michael Hovan
- Robert Wood Johnson Medical School, New Brunswick, United States
| | - Michael J Satlin
- Weill Cornell Medicine, Cornell University, New York, United States
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, United States
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114
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Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner. Nat Microbiol 2021; 6:1043-1054. [PMID: 34226711 PMCID: PMC8318886 DOI: 10.1038/s41564-021-00920-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 05/12/2021] [Indexed: 12/17/2022]
Abstract
Antimicrobial resistance poses a substantial threat to human health. The gut microbiome is considered a reservoir for potential spread of resistance genes from commensals to pathogens, termed the gut resistome. The impact of probiotics, commonly consumed by many in health or in conjunction with the administration of antibiotics, on the gut resistome is elusive. Reanalysis of gut metagenomes from healthy antibiotics-naïve humans supplemented with an 11-probiotic-strain preparation, allowing direct assessment of the gut resistome in situ along the gastrointestinal (GI) tract, demonstrated that probiotics reduce the number of antibiotic resistance genes exclusively in the gut of colonization-permissive individuals. In mice and in a separate cohort of humans, a course of antibiotics resulted in expansion of the lower GI tract resistome, which was mitigated by autologous faecal microbiome transplantation or during spontaneous recovery. In contrast, probiotics further exacerbated resistome expansion in the GI mucosa by supporting the bloom of strains carrying vancomycin resistance genes but not resistance genes encoded by the probiotic strains. Importantly, the aforementioned effects were not reflected in stool samples, highlighting the importance of direct sampling to analyse the effect of probiotics and antibiotics on the gut resistome. Analysing antibiotic resistance gene content in additional published clinical trials with probiotics further highlighted the importance of person-specific metagenomics-based profiling of the gut resistome using direct sampling. Collectively, these findings suggest opposing person-specific and antibiotic-dependent effects of probiotics on the resistome, whose contribution to the spread of antimicrobial resistance genes along the human GI tract merit further studies.
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115
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Sun HZ, Peng KL, Xue MY, Liu JX. Metagenomics analysis revealed the distinctive ruminal microbiome and resistive profiles in dairy buffaloes. Anim Microbiome 2021; 3:44. [PMID: 34210366 PMCID: PMC8247143 DOI: 10.1186/s42523-021-00103-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 05/31/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Antimicrobial resistance poses super challenges in both human health and livestock production. Rumen microbiota is a large reservoir of antibiotic resistance genes (ARGs), which show significant varations in different host species and lifestyles. To compare the microbiome and resistome between dairy cows and dairy buffaloes, the microbial composition, functions and harbored ARGs of rumen microbiota were explored between 16 dairy cows (3.93 ± 1.34 years old) and 15 dairy buffaloes (4.80 ± 3.49 years old) using metagenomics. RESULTS Dairy buffaloes showed significantly different bacterial species (LDA > 3.5 & P < 0.01), enriched KEGG pathways and CAZymes encoded genes (FDR < 0.01 & Fold Change > 2) in the rumen compared with dairy cows. Distinct resistive profiles were identified between dairy cows and dairy buffaloes. Among the total 505 ARGs discovered in the resistome of dairy cows and dairy buffaloes, 18 ARGs conferring resistance to 16 antibiotic classes were uniquely detected in dairy buffaloes. Gene tcmA (resistance to tetracenomycin C) presented high prevalence and age effect in dairy buffaloes, and was also highly positively correlated with 93 co-expressed ARGs in the rumen (R = 0.98 & P = 5E-11). In addition, 44 bacterial species under Lactobacillus genus were found to be associated with tcmA (R > 0.95 & P < 0.001). L. amylovorus and L. acidophilus showed greatest potential of harboring tcmA based on co-occurrence analysis and tcmA-containing contigs taxonomic alignment. CONCLUSIONS The current study revealed distinctive microbiome and unique ARGs in dairy buffaloes compared to dairy cattle. Our results provide novel understanding on the microbiome and resistome of dairy buffaloes, the unique ARGs and associated bacteria will help develop strategies to prevent the transmission of ARGs.
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Affiliation(s)
- Hui-Zeng Sun
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ke-Lan Peng
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ming-Yuan Xue
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jian-Xin Liu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
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116
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Crofts TS, McFarland AG, Hartmann EM. Mosaic Ends Tagmentation (METa) Assembly for Highly Efficient Construction of Functional Metagenomic Libraries. mSystems 2021; 6:e0052421. [PMID: 34184912 PMCID: PMC8269240 DOI: 10.1128/msystems.00524-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/07/2021] [Indexed: 11/20/2022] Open
Abstract
Functional metagenomic libraries, physical bacterial libraries which allow the high-throughput capture and expression of microbiome genes, have been instrumental in the sequence-naive and cultivation-independent exploration of metagenomes. However, preparation of these libraries is often limited by their high DNA input requirement and their low cloning efficiency. Here, we describe a new method, mosaic ends tagmentation (METa) assembly, for highly efficient functional metagenomic library preparation. We applied tagmentation to metagenomic DNA from soil and gut microbiomes to prepare DNA inserts for high-throughput cloning into functional metagenomic libraries. The presence of mosaic end sequences in the resulting DNA fragments synergized with homology-based assembly cloning to result in a 300-fold increase in cloning efficiency compared to traditional blunt-cloning-based protocols. We show that compared to published libraries prepared by state-of-the-art protocols, METa assembly is on average ca. 20- to 200-fold more efficient and can prepare gigabase-sized libraries with as little as 200 ng of input DNA. We show the usefulness of METa assembly first by using a normative 5-μg mass of soil metagenomic DNA to prepare a 700-Gb library that allowed us to discover novel nourseothricin resistance genes and a potentially new mode of resistance to this antibiotic and second by using only 300 ng of goose fecal metagenomic DNA to prepare a 27-Gb library that captured numerous tetracycline and colistin resistance genes. METa assembly provides a streamlined, flexible, and efficient method for preparing functional metagenomic libraries, enabling new avenues of genetic and biochemical research into low-biomass or scarce microbiomes. IMPORTANCE Medically and industrially important genes can be recovered from microbial communities by high-throughput sequencing, but precise annotation is often limited to characterized genes and their relatives. Cloning a metagenome en masse into an expression host to produce a functional metagenomic library, directly connecting genes to functions, is a sequence-naive and cultivation-independent method to discover novel genes. The process of preparing these libraries is DNA greedy and inefficient, however. Here, we describe a library preparation method that is an order of magnitude more efficient and less DNA greedy. This method is consistently efficient across libraries prepared from cultures, a soil microbiome, and a goose fecal microbiome and allowed us to discover new antibiotic resistance genes and mechanisms. This library preparation method will potentially allow the functional metagenomic exploration of microbiomes that were previously off limits due to their rarity or low microbial biomass, such as biomedical swabs or exotic samples.
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Affiliation(s)
- Terence S. Crofts
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Alexander G. McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
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117
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Nogueira T, Botelho A. Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures. Antibiotics (Basel) 2021; 10:787. [PMID: 34203511 PMCID: PMC8300701 DOI: 10.3390/antibiotics10070787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/20/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union's 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review.
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Affiliation(s)
- Teresa Nogueira
- Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
- cE3c-Centre for Ecology, Evolution and Environmental Changes, Evolutionary Ecology of Microorganisms Group, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Ana Botelho
- Laboratory of Bacteriology and Mycology, INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal;
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118
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Ding Y, Saw WY, Tan LWL, Moong DKN, Nagarajan N, Teo YY, Seedorf H. Emergence of tigecycline- and eravacycline-resistant Tet(X4)-producing Enterobacteriaceae in the gut microbiota of healthy Singaporeans. J Antimicrob Chemother 2021; 75:3480-3484. [PMID: 32853333 DOI: 10.1093/jac/dkaa372] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/03/2020] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES The recently discovered tigecycline-inactivating enzyme Tet(X4) can confer high-level tigecycline resistance on its hosts, which makes it a public health concern. This study focused on isolation and screening of Tet(X4)-positive Enterobacteriaceae from the gut microbiota of a cohort of healthy individuals in Singapore. METHODS MinION and Illumina sequencing was performed to obtain the complete genome sequences of Escherichia coli 2EC1-1 and 94EC. Subsequently, 109 human faecal samples were screened retrospectively for eravacycline-resistant Enterobacteriaceae strains, which were further tested for tet(X4) by PCR. The taxonomy of the isolated strains was determined by 16S rRNA gene PCR and Sanger sequencing. RESULTS Comparative genomic analysis of E. coli 2EC1-1 and 94EC revealed that both carry tet(X4), which is encoded by IncI1-type plasmids p2EC1-1 and p94EC-2, respectively. Retrospective screening of faecal samples collected from 109 healthy individuals showed that the faecal carriage rate of Tet(X4)-producing Enterobacteriaceae is 10.1% (95% CI = 5.1%-17.3%), suggesting that tet(X4) is widely distributed in the gut microbiota of healthy individuals in Singapore. CONCLUSIONS To the best of our knowledge, this is the first report on the prevalence of tet(X4) in the gut microbiota of a healthy human cohort, as well as the first description of this resistance mechanism outside of China. Our findings suggest that surveillance of tet(X4) in community settings is vital to monitor the spread of this resistance mechanism.
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Affiliation(s)
- Yichen Ding
- Temasek Life Sciences Laboratory, 1 Research Link, 117604, Singapore
| | - Woei-Yuh Saw
- Baker Heart and Diabetes Institute, 75 Commercial Rd, Melbourne, 3004, Victoria, Australia
| | - Linda Wei Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, 117549, Singapore
| | - Don Kyin Nwe Moong
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, 117549, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, 138672, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 119077, Singapore
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, 117549, Singapore.,Genome Institute of Singapore, A*STAR, 138672, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 119077, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, 117546, Singapore.,Life Sciences Institute, National University of Singapore, 117456, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, 117604, Singapore.,Department of Biological Sciences, National University of Singapore, 117558, Singapore
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Kwon BR, Wei B, Cha SY, Shang K, Zhang JF, Jang HK, Kang M. Characterization of Extended-Spectrum Cephalosporin (ESC) Resistance in Salmonella Isolated from Chicken and Identification of High Frequency Transfer of blaCMY-2 Gene Harboring Plasmid In Vitro and In Vivo. Animals (Basel) 2021; 11:ani11061778. [PMID: 34198679 PMCID: PMC8232285 DOI: 10.3390/ani11061778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/03/2021] [Accepted: 06/10/2021] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The prevalence of extended-spectrum cephalosporin (ESC)-resistant Salmonella is of great concern, as these strains with the same β-lactamase (bla) genes were found in human and poultry. The objective is to characterize ESC-resistant Salmonella isolated from chicken and to determine the transferability of β-lactamase gene-harboring plasmid in vitro and in vivo. ESC resistance genes in Salmonella isolated from chickens and presented a comprehensive analysis of the highly frequent transfer of the blaCMY-2 gene in vitro and in vivo. In addition, this study has demonstrated the ease with which a blaCMY-2 gene-harboring plasmid can be rapidly transferred between Salmonella and pathogenic E. coli within the intestinal tracts of mice, even without antimicrobial selective pressure. Given the potential risk of the frequent transfer of the blaCMY-2 gene via the food chain to the human digestive tract, the molecular mechanism involved in the dissemination and maintenance of ESC resistance genes should be studied as further research in greater detail, and enhanced surveillance should be implemented to prevent the widespread of ESC resistant strains. Abstract A total of 136 Salmonella isolates from chicken feces and meat samples of the top 12 integrated chicken production companies throughout Korea were collected. Among the 17 ESC-resistant Salmonella; blaCTX-M-15 was the most prevalent gene and two strains carried blaTEM-1/blaCTX-M-15 and blaCMY-2, respectively. The transferable blaCTX-M-15 gene was carried by IncFII plasmid in three isolates and the blaCMY-2 gene carried by IncI1 plasmid in one isolate. blaCMY-2 gene-harboring strain was selected as the donor based on the high frequency of blaCMY-2 gene transfer in vitro and its transfer frequencies were determined at 10−3 transconjugants per recipient. The transfer of blaCMY-2 gene-harboring plasmid derived from chicken isolate into a human pathogen; enteroinvasive Escherichia coli (EIEC), presented in mouse intestine with about 10−1 transfer frequency without selective pressure. From the competition experiment; blaCMY-2 gene-harboring transconjugant showed variable fitness burden depends on the parent strains. Our study demonstrated direct evidence that the blaCMY-2 gene harboring Salmonella from chicken could frequently transfer its ESC-resistant gene to E. coli in a mouse intestine without antimicrobial pressure; resulting in the emergence of multidrug resistance in potentially virulent EIEC isolates of significance to human health; which can increase the risk of therapeutic inadequacy or failures.
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Affiliation(s)
- Bo-Ram Kwon
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan 54596, Korea; (B.-R.K.); (B.W.); (S.-Y.C.); (K.S.); (J.-F.Z.)
| | - Bai Wei
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan 54596, Korea; (B.-R.K.); (B.W.); (S.-Y.C.); (K.S.); (J.-F.Z.)
| | - Se-Yeoun Cha
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan 54596, Korea; (B.-R.K.); (B.W.); (S.-Y.C.); (K.S.); (J.-F.Z.)
| | - Ke Shang
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan 54596, Korea; (B.-R.K.); (B.W.); (S.-Y.C.); (K.S.); (J.-F.Z.)
| | - Jun-Feng Zhang
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan 54596, Korea; (B.-R.K.); (B.W.); (S.-Y.C.); (K.S.); (J.-F.Z.)
| | - Hyung-Kwan Jang
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan 54596, Korea; (B.-R.K.); (B.W.); (S.-Y.C.); (K.S.); (J.-F.Z.)
- Bio Disease Control (BIOD) Co., Ltd., Iksan 54596, Korea
- Correspondence: (H.-K.J.); (M.K.); Tel.: +82-63-850-0945 (H.-K.J.); Tel.: +82-63-850-0690 (M.K.); Fax: +82-63-858-9155 (H.-K.J.); Fax: +82-63-858-0686 (M.K.)
| | - Min Kang
- Department of Veterinary Infectious Diseases and Avian Diseases, College of Veterinary Medicine and Center for Poultry Diseases Control, Jeonbuk National University, Iksan 54596, Korea; (B.-R.K.); (B.W.); (S.-Y.C.); (K.S.); (J.-F.Z.)
- Bio Disease Control (BIOD) Co., Ltd., Iksan 54596, Korea
- Correspondence: (H.-K.J.); (M.K.); Tel.: +82-63-850-0945 (H.-K.J.); Tel.: +82-63-850-0690 (M.K.); Fax: +82-63-858-9155 (H.-K.J.); Fax: +82-63-858-0686 (M.K.)
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Colistin Selection of the Mcr-1 Gene in Broiler Chicken Intestinal Microbiota. Antibiotics (Basel) 2021; 10:antibiotics10060677. [PMID: 34198813 PMCID: PMC8228403 DOI: 10.3390/antibiotics10060677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 11/16/2022] Open
Abstract
Colistin has a long story of safe use in animals for the treatment and prevention of certain bacterial diseases. Nevertheless, the first description of the mcr-1 gene showed that colistin resistance can spread by horizontal gene transfer and changed the landscape. This study aimed to assess the effect of colistin administration on the dispersion of resistance in the microbiota of day-old broiler chicks and how the presence of mcr-1 genes influences the spread of colistin resistance determinants. In this study, 100 one-day-old chicks were divided into four groups of 25 animals (G1, G2, G3, and G4). Animals from G3/G4 were challenged with mcr-1-carrying Salmonella (day 7), while colistin (600 mg/L) was administered daily to G2/G4 animals through drinking water (from day 8 to day 15). Two quantitative PCR assays were performed to compare the amount of Salmonella and mcr-1 that were present in the caecal samples. We observed that levels of mcr-1 were higher in G3/G4 animals, especially G4, due to the spread of mcr-1-carrying Salmonella. On day 21, Salmonella levels decreased in G4, reaching similar values as those for G3, but mcr-1 levels remained significantly higher, suggesting that colistin may accelerate the spreading process when mcr-1-carrying bacteria reach the gut.
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Miguel-Arribas A, Val-Calvo J, Gago-Córdoba C, Izquierdo JM, Abia D, Wu LJ, Errington J, Meijer WJJ. A novel bipartite antitermination system widespread in conjugative elements of Gram-positive bacteria. Nucleic Acids Res 2021; 49:5553-5567. [PMID: 33999173 PMCID: PMC8191782 DOI: 10.1093/nar/gkab360] [Citation(s) in RCA: 3] [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: 02/22/2021] [Revised: 04/09/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulation allows adaptive and coordinated gene expression, and is essential for life. Processive antitermination systems alter the transcription elongation complex to allow the RNA polymerase to read through multiple terminators in an operon. Here, we describe the discovery of a novel bipartite antitermination system that is widespread among conjugative elements from Gram-positive bacteria, which we named conAn. This system is composed of a large RNA element that exerts antitermination, and a protein that functions as a processivity factor. Besides allowing coordinated expression of very long operons, we show that these systems allow differential expression of genes within an operon, and probably contribute to strict regulation of the conjugation genes by minimizing the effects of spurious transcription. Mechanistic features of the conAn system are likely to decisively influence its host range, with important implications for the spread of antibiotic resistance and virulence genes.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Córdoba
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - José M Izquierdo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular "Severo Ochoa", (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
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Antioxidant Molecules as a Source of Mitigation of Antibiotic Resistance Gene Dissemination. Antimicrob Agents Chemother 2021; 65:AAC.02658-20. [PMID: 33753335 DOI: 10.1128/aac.02658-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/16/2021] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli is the most commonly identified human pathogen and a prominent microorganism of the gut microbiota. Acquired resistance to antibiotics in this species is driven mainly by horizontal gene transfer and plasmid acquisition. Currently, the main concern is the acquisition of extended-spectrum β-lactamases of the CTX-M type in E. coli, a worldwide-observed phenomenon. Plasmids encoding CTX-M enzymes have different scaffolds and conjugate at different frequencies. Here, we show that the conjugation rates of several plasmid types encoding broad-spectrum β-lactamases are increased when the E. coli donor strain is exposed to subinhibitory concentrations of diverse orally given antibiotics, including fluoroquinolones, such as ciprofloxacin and levofloxacin, but also trimethoprim and nitrofurantoin. This study provides insights into underlying mechanisms leading to increased plasmid conjugation frequency in relation to DNA synthesis inhibitor-type antibiotics, involving reactive oxygen species (ROS) production and probably increased expression of genes involved in the SOS response. Furthermore, we show that some antioxidant molecules currently approved for unrelated clinical uses, such as edaravone, p-coumaric acid, and N-acetylcysteine, may antagonize the ability of antibiotics to increase plasmid conjugation rates. These results suggest that several antioxidative molecules might be used in combination with these "inducer" antibiotics to mitigate the unwanted increased resistance plasmid dissemination.
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123
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Sheikh SW, Ali A, Ahsan A, Shakoor S, Shang F, Xue T. Insights into Emergence of Antibiotic Resistance in Acid-Adapted Enterohaemorrhagic Escherichia coli. Antibiotics (Basel) 2021; 10:522. [PMID: 34063307 PMCID: PMC8147483 DOI: 10.3390/antibiotics10050522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of multidrug-resistant pathogens presents a global challenge for treating and preventing disease spread through zoonotic transmission. The water and foodborne Enterohaemorrhagic Escherichia coli (EHEC) are capable of causing intestinal and systemic diseases. The root cause of the emergence of these strains is their metabolic adaptation to environmental stressors, especially acidic pH. Acid treatment is desired to kill pathogens, but the protective mechanisms employed by EHECs cross-protect against antimicrobial peptides and thus facilitate opportunities for survival and pathogenesis. In this review, we have discussed the correlation between acid tolerance and antibiotic resistance, highlighting the identification of novel targets for potential production of antimicrobial therapeutics. We have also summarized the molecular mechanisms used by acid-adapted EHECs, such as the two-component response systems mediating structural modifications, competitive inhibition, and efflux activation that facilitate cross-protection against antimicrobial compounds. Moving beyond the descriptive studies, this review highlights low pH stress as an emerging player in the development of cross-protection against antimicrobial agents. We have also described potential gene targets for innovative therapeutic approaches to overcome the risk of multidrug-resistant diseases in healthcare and industry.
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Affiliation(s)
- Salma Waheed Sheikh
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| | - Ahmad Ali
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China;
| | - Asma Ahsan
- Faculty of Life Sciences, University of Central Punjab, Lahore 54000, Punjab, Pakistan;
| | - Sidra Shakoor
- Station de Neucfchateau, CIRAD, 97130 Sainte-Marie, Capesterre Belle Eau, Guadeloupe, France;
| | - Fei Shang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
| | - Ting Xue
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China;
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Khare A. Experimental systems biology approaches reveal interaction mechanisms in model multispecies communities. Trends Microbiol 2021; 29:1083-1094. [PMID: 33865676 DOI: 10.1016/j.tim.2021.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/29/2022]
Abstract
Interactions between microorganisms in multispecies communities are thought to have substantial consequences for the community. Identifying the molecules and genetic pathways that contribute to such interplay is thus crucial to understand as well as modulate community dynamics. Here I focus on recent studies that utilize experimental systems biology techniques to study these phenomena in simplified model microbial communities. These unbiased biochemical and genomic approaches have identified novel interactions and described the underlying genetic and molecular mechanisms. I discuss the insights provided by these studies, describe innovative strategies used to investigate less tractable organisms and environments, and highlight the utility of integrating these and more targeted methods to comprehensively characterize interactions between species in microbial communities.
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Affiliation(s)
- Anupama Khare
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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125
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Fecal Microbiome and Resistome Profiling of Healthy and Diseased Pakistani Individuals Using Next-Generation Sequencing. Microorganisms 2021; 9:microorganisms9030616. [PMID: 33802711 PMCID: PMC8002588 DOI: 10.3390/microorganisms9030616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
In this paper, we aimed to characterize the fecal microbiome and its resistomes of healthy and diseased subjects infected with multidrug-resistant Escherichia coli using next-generation sequencing (NGS). After initial screening, 26 stools samples belonging to healthy (n = 13) and diseased subjects (n = 13) were selected and subjected to NGS. A total of 23 and 42 antibiotic-resistant genes (ARGs) conferring resistance to 6 and 9 classes of antibiotics were identified in the resistomes of healthy and diseased subjects, respectively. Bacteroidetes were found to be the major phylum in both healthy and diseased subjects; however, Proteobacteria was predominantly present in the diseased subjects only. Microbial dysbiosis and predominance of various ARGs in the resistome of diseased subjects reflect the excessive usage of antibiotics in Pakistan and warrants immediate attention to regulate the use of various antimicrobials.
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126
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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: 144] [Impact Index Per Article: 36.0] [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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127
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Liang C, Wei D, Zhang S, Ren Q, Shi J, Liu L. Removal of antibiotic resistance genes from swine wastewater by membrane filtration treatment. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 210:111885. [PMID: 33421714 DOI: 10.1016/j.ecoenv.2020.111885] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/12/2020] [Accepted: 12/22/2020] [Indexed: 05/09/2023]
Abstract
Antibiotic resistance genes (ARGs) have attracted extensive attention as an emerging environmental contaminant potentially threatening humans. One of the main emission sources of ARGs is swine wastewater. In this study, integrated membrane filtration including ultrafiltration and two-stage reverse osmosis was conducted for swine wastewater treatment. The abundances of 16 target ARGs, which accounted for 72.64% of the total ARGs in swine wastewater according to metagenomic sequencing, were quantified by quantitative real-time PCR (qPCR) during each stage of the membrane filtration process. The results showed that integrated membrane filtration could reduce more than 99.0% of conventional pollutants and 99.79% of ARGs (from 3.02 × 108 copy numbers/mL to 6.45 × 105 copy numbers/mL). Principal component analysis (PCA) indicated that the removal efficiency of ARGs subtype by membrane filtration did not depend on ARGs type. However, strong correlations were found between ARGs and the wastewater quality indicators TP, SS and EC according to Cooccurrence patterns, indicating that ARG removal was closely associated with insoluble solid particles and soluble ions in swine wastewater. These results showed that membrane filtration could not only remove conventional pollutants such as nitrogen and phosphorus but also reduce the emerging pollutant of ARGs and decrease the risk of ARGs flowing into natural water.
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Affiliation(s)
- Chengyu Liang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Wei
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai 200241, China
| | - Siying Zhang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuhui Ren
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai 200241, China.
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Sehgal K, Khanna S. Gut microbiome and Clostridioides difficile infection: a closer look at the microscopic interface. Therap Adv Gastroenterol 2021; 14:1756284821994736. [PMID: 33747125 PMCID: PMC7905718 DOI: 10.1177/1756284821994736] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
The pathogenesis of Clostridioides difficile infection (CDI) was recognized with its link to the use of antimicrobials. Antimicrobials significantly alter gut microbiota structure and composition, which led to the discovery of the association of this gut perturbation with the development of CDI. A number of factors implicated in its pathogenesis, such as advancing age, proton-pump inhibitors, and gastrointestinal diseases, are linked to gut microbiota perturbations. In an effort to better understand CDI, a multitude of studies have tried to ascertain protective and predictive microbial footprints linked with CDI. It has further been realized that CDI in itself can alter the gut microbiome. Its spore-forming capability poses as an impediment in the management of the infection and contributes to its recurrence. Antibiotic therapies used for its management have also been linked to gut microbiota changes, making its treatment a little more challenging. In an effort to exploit and utilize this association, gut microbial restoration therapies, particularly in the form of fecal microbial transplant, are increasingly being put to use and are proving to be beneficial. In this review, we summarize the association of the gut microbiome and microbial perturbation with initial and recurrent CDI.
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Affiliation(s)
- Kanika Sehgal
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
| | - Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
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de Nies L, Lopes S, Busi SB, Galata V, Heintz-Buschart A, Laczny CC, May P, Wilmes P. PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. MICROBIOME 2021; 9:49. [PMID: 33597026 PMCID: PMC7890817 DOI: 10.1186/s40168-020-00993-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/29/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is essential to identify virulence factors and antimicrobial resistance genes in situ. At present, there is a clear lack of computational approaches to simultaneously identify these factors in metagenomic datasets. RESULTS Here, we present PathoFact, a tool for the contextualized prediction of virulence factors, bacterial toxins, and antimicrobial resistance genes with high accuracy (0.921, 0.832 and 0.979, respectively) and specificity (0.957, 0.989 and 0.994). We evaluate the performance of PathoFact on simulated metagenomic datasets and perform a comparison to two other general workflows for the analysis of metagenomic data. PathoFact outperforms all existing workflows in predicting virulence factors and toxin genes. It performs comparably to one pipeline regarding the prediction of antimicrobial resistance while outperforming the others. We further demonstrate the performance of PathoFact on three publicly available case-control metagenomic datasets representing an actual infection as well as chronic diseases in which either pathogenic potential or bacterial toxins are hypothesized to play a role. In each case, we identify virulence factors and AMR genes which differentiated between the case and control groups, thereby revealing novel gene associations with the studied diseases. CONCLUSION PathoFact is an easy-to-use, modular, and reproducible pipeline for the identification of virulence factors, bacterial toxins, and antimicrobial resistance genes in metagenomic data. Additionally, our tool combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, PathoFact's modules for virulence factors, toxins, and antimicrobial resistance genes can be applied independently, thereby making it a flexible and versatile tool. PathoFact, its models, and databases are freely available at https://pathofact.lcsb.uni.lu . Video abstract.
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Affiliation(s)
- Laura de Nies
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg
| | - Sara Lopes
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg
| | - Valentina Galata
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg
| | - Anna Heintz-Buschart
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg
- Metagenomics Support Unit, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH-UFZ, Halle (Saale), Germany
| | - Cedric Christian Laczny
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Systems Ecology Research Group, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg.
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Li Z, Xia J, Jiang L, Tan Y, An Y, Zhu X, Ruan J, Chen Z, Zhen H, Ma Y, Jie Z, Xiao L, Yang H, Wang J, Kristiansen K, Xu X, Jin L, Nie C, Krutmann J, Liu X, Wang J. Characterization of the human skin resistome and identification of two microbiota cutotypes. MICROBIOME 2021; 9:47. [PMID: 33597039 PMCID: PMC7890624 DOI: 10.1186/s40168-020-00995-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/29/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity. RESULTS In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. Of note, the abundance of ARGs was significantly higher in Chinese than Americans, while multidrug-resistant bacteria ("superbugs") existed on the skin of both Americans and Chinese. A detailed analysis of microbial signatures identified Moraxella osloensis as a species specific for Chinese skin. Importantly, Moraxella osloensis proved to be a signature species for one of two robust patterns of microbial networks present on Chinese skin, with Cutibacterium acnes indicating the second one. Each of such "cutotypes" was associated with distinct patterns of data-driven marker genes, functional modules, and host skin properties. The two cutotypes markedly differed in functional modules related to their metabolic characteristics, indicating that host-dependent trophic chains might underlie their development. CONCLUSIONS The development of the iHSMGC will facilitate further studies on the human skin microbiome. In the present study, it was used to further characterize the human skin resistome. It also allowed to discover the existence of two cutotypes on the human skin. The latter finding will contribute to a better understanding of the interpersonal complexity of the skin microbiome. Video abstract.
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Affiliation(s)
- Zhiming Li
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
| | - Jingjing Xia
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
- IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Liuyiqi Jiang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yimei Tan
- Human Phenome Institute, Fudan University, Shanghai, China
- Department of Skin & Cosmetic Research, Shanghai Skin Disease Hospital, Shanghai, China
| | - Yitai An
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
| | - Xingyu Zhu
- Human Phenome Institute, Fudan University, Shanghai, China
- Institute for Six-sector Economy, Fudan University, Shanghai, China
| | - Jie Ruan
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
| | - Zhihua Chen
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
| | - Hefu Zhen
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
| | - Yanyun Ma
- Human Phenome Institute, Fudan University, Shanghai, China
- Institute for Six-sector Economy, Fudan University, Shanghai, China
| | - Zhuye Jie
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Li Jin
- Human Phenome Institute, Fudan University, Shanghai, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
| | - Chao Nie
- BGI-Shenzhen, Shenzhen, China
- China National Genebank, Shenzhen, China
| | - Jean Krutmann
- Human Phenome Institute, Fudan University, Shanghai, China
- IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
- Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
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Li Y, Xu Z, Han W, Cao H, Umarov R, Yan A, Fan M, Chen H, Duarte CM, Li L, Ho PL, Gao X. HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes. MICROBIOME 2021; 9:40. [PMID: 33557954 PMCID: PMC7871585 DOI: 10.1186/s40168-021-01002-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/08/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND The spread of antibiotic resistance has become one of the most urgent threats to global health, which is estimated to cause 700,000 deaths each year globally. Its surrogates, antibiotic resistance genes (ARGs), are highly transmittable between food, water, animal, and human to mitigate the efficacy of antibiotics. Accurately identifying ARGs is thus an indispensable step to understanding the ecology, and transmission of ARGs between environmental and human-associated reservoirs. Unfortunately, the previous computational methods for identifying ARGs are mostly based on sequence alignment, which cannot identify novel ARGs, and their applications are limited by currently incomplete knowledge about ARGs. RESULTS Here, we propose an end-to-end Hierarchical Multi-task Deep learning framework for ARG annotation (HMD-ARG). Taking raw sequence encoding as input, HMD-ARG can identify, without querying against existing sequence databases, multiple ARG properties simultaneously, including if the input protein sequence is an ARG, and if so, what antibiotic family it is resistant to, what resistant mechanism the ARG takes, and if the ARG is an intrinsic one or acquired one. In addition, if the predicted antibiotic family is beta-lactamase, HMD-ARG further predicts the subclass of beta-lactamase that the ARG is resistant to. Comprehensive experiments, including cross-fold validation, third-party dataset validation in human gut microbiota, wet-experimental functional validation, and structural investigation of predicted conserved sites, demonstrate not only the superior performance of our method over the state-of-art methods, but also the effectiveness and robustness of the proposed method. CONCLUSIONS We propose a hierarchical multi-task method, HMD-ARG, which is based on deep learning and can provide detailed annotations of ARGs from three important aspects: resistant antibiotic class, resistant mechanism, and gene mobility. We believe that HMD-ARG can serve as a powerful tool to identify antibiotic resistance genes and, therefore mitigate their global threat. Our method and the constructed database are available at http://www.cbrc.kaust.edu.sa/HMDARG/ . Video abstract (MP4 50984 kb).
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Affiliation(s)
- Yu Li
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
- Department of Computer Science and Engineering (CSE), The Chinese University of Hong Kong (CUHK), Hong Kong, People's Republic of China
| | - Zeling Xu
- School of Biological Sciences, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Wenkai Han
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Huiluo Cao
- Carol Yu Center for Infection and Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Ramzan Umarov
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Ming Fan
- Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Huan Chen
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, People's Republic of China
| | - Carlos M Duarte
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia
| | - Lihua Li
- Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Pak-Leung Ho
- Carol Yu Center for Infection and Department of Microbiology, The University of Hong Kong, Hong Kong, People's Republic of China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955, Saudi Arabia.
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132
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Tyagi N, Kumar A. Evaluation of recreational risks due to exposure of antibiotic-resistance bacteria from environmental water: A proposed framework. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 279:111626. [PMID: 33243622 DOI: 10.1016/j.jenvman.2020.111626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
This research provides a framework for the human health risk assessment due to exposure of AR (antibiotic resistance) E. coli from recreational water (swimming activity). Literature-based epidemiological studies were used for f-value formulation (i.e., AR E. coli/total number of E. coli isolates) and the theoretical calculation of AR and non-AR E. coli concentrations. Risk was estimated using calculated values by considering four different dose-response (D-R) scenarios with known characteristics due to current lack of availability of D-R for AR bacteria. f-values ranged between 0.14 and 0.59 and the order of calculated theoretical values of maximum AR E. coli are as follows: ampicillin or amoxicillin (38 CFU/dip) > co-trimoxazole (19 CFU/dip) ~ tetracycline (18 CFU/dip) > ceftriaxone or cefotaxime or ceftazidime (10 CFU/dip) ~ ciprofloxacin or ofloxacin (9 CFU/dip). The risk of infection was considerably high for theoretical calculated concentration values regardless of the chosen D-R model (annual risk of infection (95th percentile) = 1, Spearman's rank correlation coefficient = -0.06 to 0.94), under the conditions studied. Further, AR levels of human gastrointestinal-tract were determined using literature-reported data in stool samples and indicated that the resistance level was very high in healthy human (range: 3.7 × 107-8.4 × 107 CFU/g of wet lumen content). The maximum allowable concentration values for AR E. coli and non-ARB (0.0075 CFU/dip and 2.56 CFU/dip) were found to be smaller than the USEPA recreational water quality guidelines (≤126 CFU/100 mL), which can help the USEPA and other regulatory bodies in revisiting the current guidelines. So based on the noted results, we can conclude that the maintenance of inventory of actual measured concentration of ARB in the recreational water sites is needed to prevent unwanted complication related to the treatment of infectious sustained by resistant microbes.
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Affiliation(s)
- Neha Tyagi
- Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India.
| | - Arun Kumar
- Department of Civil Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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133
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McGivern BB, McDonell RK, Morris SK, LaPara TM, Donato JJ. Novel class 1 integron harboring antibiotic resistance genes in wastewater-derived bacteria as revealed by functional metagenomics. Plasmid 2021; 114:102563. [PMID: 33515651 DOI: 10.1016/j.plasmid.2021.102563] [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: 10/21/2020] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 11/15/2022]
Abstract
Combatting antibiotic resistance is critical to our ability to treat infectious diseases. Here, we identified and characterized diverse antimicrobial resistance genes, including potentially mobile elements, from synthetic wastewater treatment microcosms exposed to the antibacterial agent triclosan. After seven weeks of exposure, the microcosms were subjected to functional metagenomic selection across 13 antimicrobials. This was achieved by cloning the combined genetic material from the microcosms, introducing this genetic library into E. coli, and selecting for clones that grew on media supplemented with one of the 13 antimicrobials. We recovered resistant clones capable of growth on media supplemented with a single antimicrobial, yielding 13 clones conferring resistance to at least one antimicrobial agent. Antibiotic susceptibility analysis revealed resistance ranging from 4 to >50 fold more resistant, while one clone showed resistance to multiple antibiotics. Using both Sanger and SMRT sequencing, we identified the predicted active gene(s) on each clone. One clone that conferred resistance to tetracycline contained a gene encoding a novel tetA-type efflux pump that was named TetA(62). Three clones contained predicted active genes on class 1 integrons. One integron had a previously unreported genetic arrangement and was named In1875. This study demonstrated the diversity and potential for spread of resistance genes present in human-impacted environments.
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Affiliation(s)
- Bridget B McGivern
- Chemistry Department, University of St. Thomas, St. Paul, MN 55105, United States of America
| | - Rylie K McDonell
- Chemistry Department, University of St. Thomas, St. Paul, MN 55105, United States of America
| | - Sydney K Morris
- Chemistry Department, University of St. Thomas, St. Paul, MN 55105, United States of America
| | - Timothy M LaPara
- Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, MN 55455, United States of America
| | - Justin J Donato
- Chemistry Department, University of St. Thomas, St. Paul, MN 55105, United States of America.
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134
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Kumar M, Sarma DK, Shubham S, Kumawat M, Verma V, Nina PB, JP D, Kumar S, Singh B, Tiwari RR. Futuristic Non-antibiotic Therapies to Combat Antibiotic Resistance: A Review. Front Microbiol 2021; 12:609459. [PMID: 33574807 PMCID: PMC7870489 DOI: 10.3389/fmicb.2021.609459] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/04/2021] [Indexed: 12/26/2022] Open
Abstract
The looming problem of resistance to antibiotics in microorganisms is a global health concern. The drug-resistant microorganisms originating from anthropogenic sources and commercial livestock farming have posed serious environmental and health challenges. Antibiotic-resistant genes constituting the environmental "resistome" get transferred to human and veterinary pathogens. Hence, deciphering the origin, mechanism and extreme of transfer of these genetic factors into pathogens is extremely important to develop not only the therapeutic interventions to curtail the infections, but also the strategies to avert the menace of microbial drug-resistance. Clinicians, researchers and policymakers should jointly come up to develop the strategies to prevent superfluous exposure of pathogens to antibiotics in non-clinical settings. This article highlights the present scenario of increasing antimicrobial-resistance in pathogenic bacteria and the clinical importance of unconventional or non-antibiotic therapies to thwart the infectious pathogenic microorganisms.
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Affiliation(s)
- Manoj Kumar
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | | | - Swasti Shubham
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Manoj Kumawat
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Vinod Verma
- Stem Cell Research Centre, Department of Hematology, SGPGIMS, Lucknow, India
| | | | - Devraj JP
- ICMR- National Institute of Nutrition, Hyderabad, India
| | - Santosh Kumar
- ICMR- National Institute of Nutrition, Hyderabad, India
| | - Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
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135
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Nikoloudaki O, Lemos Junior WJF, Campanaro S, Di Cagno R, Gobbetti M. Role prediction of Gram-negative species in the resistome of raw cow's milk. Int J Food Microbiol 2021; 340:109045. [PMID: 33465548 DOI: 10.1016/j.ijfoodmicro.2021.109045] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 12/24/2022]
Abstract
Extended use of antibiotics in dairy farming for therapeutic and prophylactic reasons, but also the higher prevalence of antibiotic resistant bacteria (ARB) in the farm environment raised the concern of consuming raw cow's milk and its derived products. The aim of this study was to predict by shotgun metagenomic analyses the presence of antibiotic resistance genes (ARGs) mainly correlated with Gram-negative bacteria in antibiotic residue free raw cow's milk derived exclusively from healthy animal from South Tyrol (Northern Italy), chosen as a model system. Assessment of shotgun metagenomic data of reconstructed scaffolds, revealed the existence of Pseudomonas spp. as the most abundant Gram-negative species in the raw cow's milk samples bearing ARGs. Besides, ARGs also linked to lactic acid bacteria such as Lactococcus sp. and Lactobacillus sp. ARGs correlated to microbiome found in milk samples conferred resistance towards aminoglycoside-streptothricin, beta-lactamase, macrolide, tetracycline, carbapenem, cephalosporin, penam, peptide, penem, fluoroquinolone, chloramphenicol and elfamycin antibiotics. Further bioinformatic processing included de-novo reassembly of all metagenomic sequences from all milk samples in one, to reconstruct metagenome assembled genomes (MAGs), which were further used to investigate mobile genetic elements (MGE). Analyses of the reconstructed MAGs showed that, MAG 9 (Pseudomonas sp1.) contained the oriT gene (origin of transfer gene) needed for transferring virulent factors. Although the presence of Pseudomonas is common in raw cow's milk, pasteurization treatment reduces their survivability. Nevertheless, attention should be paid on Pseudomonas spp. due to their intrinsic resistance to antibiotics and their capability of transferring virulent factors to other bacteria.
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Affiliation(s)
- Olga Nikoloudaki
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
| | - Wilson J F Lemos Junior
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padova, Via 8 Febbraio 1848, 2, 35122 Padova, Italy.
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
| | - Marco Gobbetti
- Faculty of Science and Technology, Libera Università di Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
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136
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Yuan Y, Chen Y, Yao F, Zeng M, Xie Q, Shafiq M, Noman SM, Jiao X. Microbiomes and Resistomes in Biopsy Tissue and Intestinal Lavage Fluid of Colorectal Cancer. Front Cell Dev Biol 2021; 9:736994. [PMID: 34604238 PMCID: PMC8484797 DOI: 10.3389/fcell.2021.736994] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/19/2021] [Indexed: 02/05/2023] Open
Abstract
Aim: The gut microbiome plays a crucial role in colorectal cancer (CRC) tumorigenesis, but compositions of microorganisms have been inconsistent in previous studies due to the different types of specimens. We investigated the microbiomes and resistomes of CRC patients with colonic biopsy tissue and intestinal lavage fluid (IVF). Methods: Paired samples (biopsy tissue and IVF) were collected from 20 patients with CRC, and their gut microbiomes and resistomes were measured by shotgun metagenomics. Clinical and laboratory data were recorded. Bioinformatics (KneadData, Kraken2, and FMAP) and statistical analysis were done using the R (v4.0.2) software. Results: Bacterial diversity in IVF was higher than in tissue samples, and bacterial operational taxonomic units (OTUs) were 2,757 in IVF vs. 197 in tissue. β-diversity showed distinct clusters in paired samples. The predominant bacteria in IVF were phylum Proteobacteria, while the predominant bacteria of tissue were phylum Actinobacteria. Twenty-seven representative bacteria were selected to form six bacterial clusters, which showed only Firmicutes Cluster 1, and the Bacteroidetes Cluster 1 were significantly more abundant in the IVF group than those in the tissue group (p < 0.05). The Firmicutes Cluster 2, Bacteroidetes Cluster 2, Pathogen Cluster, and Prevotella Cluster were not significantly different between IVF and tissue (p > 0.05). Correlation analysis revealed that some bacteria could have effects on metabolic and inflammatory parameters of CRC patients. A total of 1,295 antibiotic resistance genes (ARGs) were detected in the gut microbiomes, which conferred multidrug resistance, as well as resistance to tetracycline, aminoglycoside, and more. Co-occurrence patterns revealed by the network showed mainly ARG-carrying bacteria to be similar between IVF and tissue, but leading bacteria located in the hub differed between IVF and tissue. Conclusion: Heterogeneity of microbiota is particularly evident when studied with IVF and tissue samples, but bacterial clusters that have close relationships with CRC carcinogenesis are not significantly different, using IVF as an alternative to tissue for gut microbiome, and resistome assessment may be a feasible method.
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Affiliation(s)
- Yumeng Yuan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, China
| | - Yihuan Chen
- The Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Fen Yao
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, China
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Mi Zeng
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, China
| | - Qingdong Xie
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, China
| | - Muhammad Shafiq
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, China
| | - Sohail Muhammad Noman
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, China
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, China
- *Correspondence: Xiaoyang Jiao,
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137
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Tansirichaiya S, Reynolds LJ, Roberts AP. Functional Metagenomic Screening for Antimicrobial Resistance in the Oral Microbiome. Methods Mol Biol 2021; 2327:31-50. [PMID: 34410638 DOI: 10.1007/978-1-0716-1518-8_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A large proportion of bacteria, from a multitude of environments, are not yet able to be grown in the laboratory, and therefore microbiological and molecular biological investigations of these bacteria are challenging. A way to circumvent this challenge is to analyze the metagenome, the entire collection of DNA molecules that can be isolated from a particular environment or sample. This collection of DNA molecules can be sequenced and assembled to determine what is present and infer functional potential, or used as a PCR template to detect known target DNA and potentially unknown regions of DNA nearby those targets; however assigning functions to new or conserved hypothetical, functionally cryptic, genes is difficult. Functional metagenomics allows researchers to determine which genes are responsible for selectable phenotypes, such as resistance to antimicrobials and metabolic capabilities, without the prerequisite needs to grow the bacteria containing those genes or to already know which genes are of interest. It is estimated that a third of the resident species of the human oral cavity is not yet cultivable and, together with the ease of sample acquisition, makes this metagenome particularly suited to functional metagenomic studies. Here we describe the methodology related to the collection of saliva samples, extraction of metagenomic DNA, construction of metagenomic libraries, as well as the description of functional assays that have previously led to the identification of new genes conferring antimicrobial resistance.
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Affiliation(s)
- Supathep Tansirichaiya
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway.
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
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138
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Hu T, Dai Q, Chen H, Zhang Z, Dai Q, Gu X, Yang X, Yang Z, Zhu L. Geographic pattern of antibiotic resistance genes in the metagenomes of the giant panda. Microb Biotechnol 2021; 14:186-197. [PMID: 32812361 PMCID: PMC7888472 DOI: 10.1111/1751-7915.13655] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/01/2020] [Indexed: 12/17/2022] Open
Abstract
The rise in infections by antibiotic-resistant bacteria poses a serious public health problem worldwide. The gut microbiome of animals is a reservoir for antibiotic resistance genes (ARGs). However, the correlation between the gut microbiome of wild animals and ARGs remains controversial. Here, based on the metagenomes of giant pandas (including three wild populations from the Qinling, Qionglai and Xiaoxiangling Mountains, and two major captive populations from Yaan and Chengdu), we investigated the potential correlation between the constitution of the gut microbiome and the composition of ARGs across the different geographic locations and living environments. We found that the types of ARGs were correlated with gut microbiome composition. The NMDS cluster analysis using Jaccard distance of the ARGs composition of the gut microbiome of wild giant pandas displayed a difference based on geographic location. Captivity also had an effect on the differences in ARGs composition. Furthermore, we found that the Qinling population exhibited profound dissimilarities of both gut microbiome composition and ARGs (the highest proportion of Clostridium and vancomycin resistance genes) when compared to the other wild and captive populations studies, which was supported by previous giant panda whole-genome sequencing analysis. In this study, we provide an example of a potential consensus pattern regarding host population genetics, symbiotic gut microbiome and ARGs. We revealed that habitat isolation impacts the ARG structure in the gut microbiome of mammals. Therefore, the difference in ARG composition between giant panda populations will provide some basic information for their conservation and management, especially for captive populations.
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Affiliation(s)
- Ting Hu
- College of Life SciencesNanjing Normal UniversityNanjing210046China
| | - Qinlong Dai
- Sichan Liziping National Nature ReserveShimianChina
- Shimian Research Center of Giant Panda Small Population Conservation and RejuvenationShimianChina
| | - Hua Chen
- Mingke Biotechnology Co., Ltd.HangzhouChina
| | - Zheng Zhang
- College of Life SciencesNanjing Normal UniversityNanjing210046China
| | - Qiang Dai
- Chengdu Institute of BiologyChinese Academy of SciencesChengduChina
| | - Xiaodong Gu
- Sichuan Station of Wildlife Survey and ManagementChengdu610082China
| | - Xuyu Yang
- Sichuan Station of Wildlife Survey and ManagementChengdu610082China
| | - Zhisong Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education)China West Normal UniversityNanchong637002China
| | - Lifeng Zhu
- College of Life SciencesNanjing Normal UniversityNanjing210046China
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139
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Targeting the gut microbiome: An emerging trend in hematopoietic stem cell transplantation. Blood Rev 2020; 48:100790. [PMID: 33573867 DOI: 10.1016/j.blre.2020.100790] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/09/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022]
Abstract
Mounting evidence has demonstrated the critical role of the gut microbiome in different cancer treatment modalities showing intensive crosstalk between microbiota and the host immune system. In cancer patients receiving hematopoietic stem cell transplantation (HSCT), conditioning regimens including chemotherapy, radiotherapy, and immunosuppressive therapy, as well as antimicrobial prophylaxis, result in intestinal barrier disruption and massive changes in microbiota composition. According to clinical studies, a drastic loss of microbial diversity during HSCT is associated with enhanced pro-inflammatory immune response and an increased risk of transplant-related complications such as graft-versus-host disease (GvHD) and mortality. In this review, we outline the current understanding of the role of microbiota diversity in the patient response to cancer therapies and highlight the impact of changes in the gut microbiome on clinical outcomes in post-HSCT patients. Moreover, the therapeutic implications of microbiota modulation by probiotics, prebiotics, and fecal microbiota transplantation (FMT) in hematologic cancer patients receiving HSCT are discussed.
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140
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Andersson DI, Balaban NQ, Baquero F, Courvalin P, Glaser P, Gophna U, Kishony R, Molin S, Tønjum T. Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiol Rev 2020; 44:171-188. [PMID: 31981358 DOI: 10.1093/femsre/fuaa001] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
Antibiotic resistance is one of the major challenges facing modern medicine worldwide. The past few decades have witnessed rapid progress in our understanding of the multiple factors that affect the emergence and spread of antibiotic resistance at the population level and the level of the individual patient. However, the process of translating this progress into health policy and clinical practice has been slow. Here, we attempt to consolidate current knowledge about the evolution and ecology of antibiotic resistance into a roadmap for future research as well as clinical and environmental control of antibiotic resistance. At the population level, we examine emergence, transmission and dissemination of antibiotic resistance, and at the patient level, we examine adaptation involving bacterial physiology and host resilience. Finally, we describe new approaches and technologies for improving diagnosis and treatment and minimizing the spread of resistance.
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Affiliation(s)
- Dan I Andersson
- Department of Medical Biochemistry and Microbiology, University of Uppsala, BMC, Husargatan 3, 75237, Uppsala, Sweden
| | - Nathalie Q Balaban
- The Racah Institute of Physics, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Jerusalem, Israel
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal Health Research Institute, Ctra. Colmenar Viejo Km 9,100 28034 - Madrid, Madrid, Spain
| | - Patrice Courvalin
- French National Reference Center for Antibiotics, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, Paris, France
| | - Uri Gophna
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, 121 Jack Green building, Tel-Aviv University, Ramat-Aviv, 6997801, Tel Aviv, Israel
| | - Roy Kishony
- Faculty of Biology, The Technion, Technion City, Haifa 3200003, Haifa, Israel
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220 2800 Kgs.Lyngby, Lyngby, Denmark
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, OUS HF Rikshospitalet Postboks 4950 Nydalen 0424 Oslo, Oslo, Norway.,Oslo University Hospital, P. O. Box 4950 Nydalen N-0424 Oslo, Oslo, Norway
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141
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Integron gene cassettes harboring novel variants of D-alanine-D-alanine ligase confer high-level resistance to D-cycloserine. Sci Rep 2020; 10:20709. [PMID: 33244063 PMCID: PMC7691350 DOI: 10.1038/s41598-020-77377-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/10/2020] [Indexed: 11/08/2022] Open
Abstract
Antibiotic resistance poses an increasing threat to global health. To tackle this problem, the identification of principal reservoirs of antibiotic resistance genes (ARGs) plus an understanding of drivers for their evolutionary selection are important. During a PCR-based screen of ARGs associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding a d-alanine-d-alanine ligase (ddl6 and ddl7) located within gene cassettes in the first position of a reverse integron were identified. Treponema denticola was identified as the likely host of the ddl cassettes. Both ddl6 and ddl7 conferred high level resistance to d-cycloserine when expressed in Escherichia coli with ddl7 conferring four-fold higher resistance to D-cycloserine compared to ddl6. A SNP was found to be responsible for this difference in resistance phenotype between the two ddl variants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection of ddl containing integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP and d-cycloserine binding pockets of Ddl.
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142
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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: 2.2] [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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143
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Chen YM, Holmes EC, Chen X, Tian JH, Lin XD, Qin XC, Gao WH, Liu J, Wu ZD, Zhang YZ. Diverse and abundant resistome in terrestrial and aquatic vertebrates revealed by transcriptional analysis. Sci Rep 2020; 10:18870. [PMID: 33139761 PMCID: PMC7608656 DOI: 10.1038/s41598-020-75904-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
Despite increasing evidence that antibiotic resistant pathogens are shared among humans and animals, the diversity, abundance and patterns of spread of antibiotic resistance genes (ARGs) in wildlife remains unclear. We identified 194 ARGs associated with phenotypic resistance to 13 types of antibiotic in meta-transcriptomic data generated from a broad range of lower vertebrates residing in both terrestrial and aquatic habitats. These ARGs, confirmed by PCR, included those that shared high sequence similarity to clinical isolates of public health concern. Notably, the lower vertebrate resistome varied by ecological niche of the host sampled. The resistomes in marine fish shared high similarity and were characterized by very high abundance, distinct from that observed in other habitats. An assessment of ARG mobility found that ARGs in marine fish were frequently co-localized with mobile elements, indicating that they were likely spread by horizontal gene transfer. Together, these data reveal the remarkable diversity and transcriptional levels of ARGs in lower vertebrates, and suggest that these wildlife species might play an important role in the global spread of ARGs.
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Affiliation(s)
- Yan-Mei Chen
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jun-Hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang, China
| | - Xin-Cheng Qin
- Department of Zoonosis, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping Beijing, China
| | - Wen-Hua Gao
- Department of Zoonosis, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping Beijing, China
| | - Jing Liu
- Department of Zoonosis, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping Beijing, China
| | - Zhong-Dao Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Yong-Zhen Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
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144
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Coman V, Vodnar DC. Gut microbiota and old age: Modulating factors and interventions for healthy longevity. Exp Gerontol 2020; 141:111095. [PMID: 32979504 PMCID: PMC7510636 DOI: 10.1016/j.exger.2020.111095] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023]
Abstract
Our gut microbiota is a complex and dynamic ecosystem with a paramount role in shaping our metabolic and immunological functions. Recent research suggests that aging may negatively affect the composition, diversity, and function of our microbiota mainly due to alterations in diet and immunologic reactivity (i.e. immunosenescence), and increased incidence of certain diseases and, therefore, increased exposure to certain medication (e.g. antibiotics, proton pump inhibitors). In turn, this aging-related gut dysbiosis may contribute to the initiation and/or progress of other metabolic diseases, and consequently, to a decrease in healthy longevity. On the positive side, promising therapeutic interventions, such as diet supplementation with prebiotics, probiotics and synbiotics, or fecal microbiota transplantation, aimed to counteract these aging-related deleterious consequences, could improve our health, and extend our healthy lifespan. In this context, the current review aims to assess the latest progress in identifying the key elements affecting the gut microbiota of the older adults and their mechanism of action, and the effectiveness of the therapeutic interventions aimed at restoring the diversity and healthy functions of the gut microbiota in older individuals.
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Affiliation(s)
- Vasile Coman
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Mănăştur 3-5, 400372 Cluj-Napoca, Romania.
| | - Dan Cristian Vodnar
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Mănăştur 3-5, 400372 Cluj-Napoca, Romania; Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Mănăștur 3-5, 400372 Cluj-Napoca, Romania.
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145
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Is the term "anti-anaerobic" still relevant? Int J Infect Dis 2020; 102:178-180. [PMID: 33127500 DOI: 10.1016/j.ijid.2020.10.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 12/22/2022] Open
Abstract
For decades, the term "anti-anaerobic" has been commonly used to refer to antibiotics exhibiting activity against anaerobic bacteria, also designated as anaerobes. This term is used in various situations ranging from infections associated with well-identified pathogens like Clostridioides difficile, or Fusobacterium necrophorum in Lemierre's syndrome, that require specific antibiotic treatments to polymicrobial infections generally resulting from the decreased permeability of anatomical barriers (e.g., intestinal translocation and stercoral peritonitis) or infectious secondary localizations (e.g., brain abscess and infectious pleurisy). In these cases, the causal bacteria generally remain unidentified and the antimicrobial treatment is empirical. However, major progress in the knowledge of human bacterial microbiotas in the last 10 years has shown how diverse are the species involved in these communities. Here, we sought to reappraise the concept of anti-anaerobic spectrum in the light of recent advances in the microbiota field. We first highlight that the term anaerobic itself does not represent the tremendous diversity of the bacteria it spans, and then we stress that the antibiotic susceptibility profiles for most anaerobic bacteria remain unaddressed. Furthermore, we provide examples challenging the relevance of the "anti-anaerobic" spectrum from a clinical and ecological perspective.
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146
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Kumar SB, Arnipalli SR, Ziouzenkova O. Antibiotics in Food Chain: The Consequences for Antibiotic Resistance. Antibiotics (Basel) 2020; 9:antibiotics9100688. [PMID: 33066005 PMCID: PMC7600537 DOI: 10.3390/antibiotics9100688] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/28/2020] [Accepted: 10/08/2020] [Indexed: 12/14/2022] Open
Abstract
Antibiotics have been used as essential therapeutics for nearly 100 years and, increasingly, as a preventive agent in the agricultural and animal industry. Continuous use and misuse of antibiotics have provoked the development of antibiotic resistant bacteria that progressively increased mortality from multidrug-resistant bacterial infections, thereby posing a tremendous threat to public health. The goal of our review is to advance the understanding of mechanisms of dissemination and the development of antibiotic resistance genes in the context of nutrition and related clinical, agricultural, veterinary, and environmental settings. We conclude with an overview of alternative strategies, including probiotics, essential oils, vaccines, and antibodies, as primary or adjunct preventive antimicrobial measures or therapies against multidrug-resistant bacterial infections. The solution for antibiotic resistance will require comprehensive and incessant efforts of policymakers in agriculture along with the development of alternative therapeutics by experts in diverse fields of microbiology, biochemistry, clinical research, genetic, and computational engineering.
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147
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Lin H, Wang Q, Yuan M, Liu L, Chen Z, Zhao Y, Das R, Duan Y, Xu X, Xue Y, Luo Y, Mao D. The prolonged disruption of a single-course amoxicillin on mice gut microbiota and resistome, and recovery by inulin, Bifidobacterium longum and fecal microbiota transplantation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:114651. [PMID: 32474336 DOI: 10.1016/j.envpol.2020.114651] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/08/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
The usages of antibiotics in treating the pathogenic infections could alter the gut microbiome and associated resistome, causing long term adverse impact on human health. In this study, mice were treated with human-simulated regimen 25.0 mg kg-1 of amoxicillin for seven days, and their gut microbiota and resistome were characterized using the 16S rRNA amplicons sequencing and the high-throughput qPCR, respectively. Meanwhile, the flora restorations after individual applications of inulin, Bifidobacterium longum (B. longum), and fecal microbiota transplantation (FMT) were analyzed for up to 35 days. The results revealed the prolonged negative impact of single course AMX exposure on mice gut microbiota and resistome. To be specific, pathobionts of Klebsiella and Escherichia-Shigella were significantly enriched, while prebiotics of Bifidobacterium and Lactobacillus were dramatically depleted. Furthermore, β-lactam resistance genes and efflux resistance genes were obviously enriched after amoxicillin exposure. Compared to B. longum, FMT and inulin were demonstrated to preferably restore the gut microbiota via reconstituting microbial community and stimulating specific prebiotic respectively. Such variation of microbiome caused their distinct alleviations on resistome alteration. Inulin earned the greatest elimination on AMX induced ARG abundance and diversity enrichment. FMT and B. longum caused remove of particular ARGs such as ndm-1, blaPER. Network analysis revealed that most of the ARGs were prone to be harbored by Firmicutes and Proteobacteria. In general, gut resistome shift was partly associated with the changing bacterial community structures and transposase and integron. Taken together, these results demonstrated the profound disruption of gut microbiota and resistome after single-course amoxicillin treatment and different restoration by inulin, B. longum and FMT.
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Affiliation(s)
- Huai Lin
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300350, China
| | - Qing Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300350, China; Hebei Key Laboratory of Air Pollution Cause and Impact (preparatory), College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Meng Yuan
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Lei Liu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300350, China
| | - Zeyou Chen
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300350, China
| | - Yanhui Zhao
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300350, China
| | - Ranjit Das
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300350, China
| | - Yujing Duan
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300350, China
| | - Ximing Xu
- School of Statistics and Data Science, Nankai University, Tianjin, 300071, China
| | - Yingang Xue
- Key Laboratory of Environmental Protection of Water Environment Biological Monitoring, Changzhou Environmental Monitoring Center, Changzhou, 213002, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin, 300350, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin, 300071, China.
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148
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Galindo-Méndez M. Antimicrobial Resistance in Escherichia coli. E. COLI INFECTIONS - IMPORTANCE OF EARLY DIAGNOSIS AND EFFICIENT TREATMENT 2020. [DOI: 10.5772/intechopen.93115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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149
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Watkins RR, Bonomo RA. Overview: The Ongoing Threat of Antimicrobial Resistance. Infect Dis Clin North Am 2020; 34:649-658. [PMID: 33011053 DOI: 10.1016/j.idc.2020.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The effectiveness of antibiotics continues to erode because of the relentless spread of antimicrobial resistance (AMR). Public and private foundations, professional organizations, and international health agencies recognize the threat posed by AMR and have issued calls for action. One of the main drivers of AMR is overprescription of antibiotics, both in human and in veterinary medicine. The One Health concept is a response from a broad group of stakeholders to counter the global health threat posed by AMR. In this article, we discuss current trends in AMR and suggest strategies to mitigate its ongoing dissemination.
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Affiliation(s)
- Richard R Watkins
- Division of Infectious Diseases, Cleveland Clinic Akron General, Akron, OH, USA; Department of Medicine, Northeast Ohio Medical University, Rootstown, OH, USA.
| | - Robert A Bonomo
- Medical Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA; Case VA Center for Antimicrobial Resistance and Epidemiology (Case VA-CARES), Case Western Reserve University, Cleveland, OH, USA
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150
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Schwartz DJ, Langdon AE, Dantas G. Understanding the impact of antibiotic perturbation on the human microbiome. Genome Med 2020; 12:82. [PMID: 32988391 PMCID: PMC7523053 DOI: 10.1186/s13073-020-00782-x] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/11/2020] [Indexed: 02/08/2023] Open
Abstract
The human gut microbiome is a dynamic collection of bacteria, archaea, fungi, and viruses that performs essential functions for immune development, pathogen colonization resistance, and food metabolism. Perturbation of the gut microbiome's ecological balance, commonly by antibiotics, can cause and exacerbate diseases. To predict and successfully rescue such perturbations, first, we must understand the underlying taxonomic and functional dynamics of the microbiome as it changes throughout infancy, childhood, and adulthood. We offer an overview of the healthy gut bacterial architecture over these life stages and comment on vulnerability to short and long courses of antibiotics. Second, the resilience of the microbiome after antibiotic perturbation depends on key characteristics, such as the nature, timing, duration, and spectrum of a course of antibiotics, as well as microbiome modulatory factors such as age, travel, underlying illness, antibiotic resistance pattern, and diet. In this review, we discuss acute and chronic antibiotic perturbations to the microbiome and resistome in the context of microbiome stability and dynamics. We specifically discuss key taxonomic and resistance gene changes that accompany antibiotic treatment of neonates, children, and adults. Restoration of a healthy gut microbial ecosystem after routine antibiotics will require rationally managed exposure to specific antibiotics and microbes. To that end, we review the use of fecal microbiota transplantation and probiotics to direct recolonization of the gut ecosystem. We conclude with our perspectives on how best to assess, predict, and aid recovery of the microbiome after antibiotic perturbation.
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Affiliation(s)
- D. J. Schwartz
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - A. E. Langdon
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - G. Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
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