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Tu Z, Pang L, Lai S, Zhu Y, Wu Y, Zhou Q, Qi H, Zhang Y, Dong Y, Gan Y, Wu J, Yu J, Tao W, Ma B, Wang H, Zhang A. The hidden threat: Comprehensive assessment of antibiotic and disinfectant resistance in commercial pig slaughterhouses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174222. [PMID: 38945230 DOI: 10.1016/j.scitotenv.2024.174222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 06/08/2024] [Accepted: 06/21/2024] [Indexed: 07/02/2024]
Abstract
The presence of antibiotic resistance genes (ARGs), disinfectant resistance genes (DRGs), and pathogens in animal food processing environments (FAPE) poses a significant risk to human health. However, knowledge of the contamination and risk profiles of a typical commercial pig slaughterhouse with periodic disinfectant applications is limited. By creating the overall metagenomics-based behavior and risk profiles of ARGs, DRGs, and microbiomes in a nine-section pig slaughterhouse, an important FAPE in China. A total of 454 ARGs and 84 DRGs were detected in the slaughterhouse with resistance genes for aminoglycosides and quaternary ammonium compounds, respectively. The entire slaughtering chain is a hotspot for pathogens, including 83 human pathogenic bacteria (HPB), with 47 core HPB. In addition, 68 high-risk ARGs were significantly correlated with 55 HPB, 30 of which were recognized as potential bacteria co-resistant to antibiotics and disinfectants, confirm a three-fold risk of ARGs, DRGs, and pathogens prevailing throughout the chain. Pre-slaughter pig house (PSPH) was the major risk source for ARGs, DRGs, and HPB. Moreover, 75 Escherichia coli and 47 Proteus mirabilis isolates showed sensitivity to potassium monopersulfate and sodium hypochlorite, suggesting that slaughterhouses should use such related disinfectants. By using whole genome multi-locus sequence typing and single nucleotide polymorphism analyses, genetically closely related bacteria were identified across distinct slaughter sections, suggesting bacterial transmission across the slaughter chain. Overall, this study underscores the critical role of the PSPH section as a major source of HPB, ARGs, and DRGs contamination in commercial pig slaughterhouses. Moreover, it highlights the importance of addressing clonal transmission and cross-contamination of antibiotic- and disinfectant-resistant bacteria within and between slaughter sections. These issues are primarily attributed to the microbial load carried by animals before slaughter, carcass handling, and content exposure during visceral treatment. Our findings provide valuable insights for One Health-oriented slaughterhouse management practices.
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Affiliation(s)
- Zunfang Tu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; Microbiological Testing and Research Department, Sichuan Institute for Drug Control (Sichuan Testing Center of Medical Devices), Chengdu 611731, China
| | - Lina Pang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Shanming Lai
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yixiao Zhu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yingting Wu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Quan Zhou
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haoxuan Qi
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yanhang Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yongyi Dong
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yumeng Gan
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jie Wu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jing Yu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Weilai Tao
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Bingcun Ma
- Microbiological Testing and Research Department, Sichuan Institute for Drug Control (Sichuan Testing Center of Medical Devices), Chengdu 611731, China
| | - Hongning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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Swinkels AF, Fischer EAJ, Korving L, Kusters NE, Wagenaar JA, Zomer AL. Selection for amoxicillin-, doxycycline-, and enrofloxacin-resistant Escherichia coli at concentrations lower than the ECOFF in broiler-derived cecal fermentations. Microbiol Spectr 2024:e0097024. [PMID: 39269186 DOI: 10.1128/spectrum.00970-24] [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: 04/22/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024] Open
Abstract
Antimicrobial resistance (AMR) is an emerging worldwide problem and a health threat for humans and animals. Antimicrobial usage in human and animal medicine or in agriculture results in selection for AMR. The selective concentration of antimicrobial compounds can be lower than the minimum inhibitory concentration and differs between environments, which can be a reason for bacterial resistance. Therefore, knowledge of the minimal selective concentration (MSC), under natural conditions, is essential to understand the selective window of bacteria when exposed to residual antimicrobials. In this study, we estimated the MSCs of three antimicrobials, amoxicillin, doxycycline, and enrofloxacin in a complex microbial community by conducting fermentation assays with cecal material derived from broilers. We examined the phenotypic resistance of Escherichia coli, resistome, and microbiome after 6 and 30 hours of fermenting in the presence of the antimicrobials of interest. The concentrations were estimated to be 10-100 times lower than the epidemiological cut-off values in E. coli for the respective antimicrobials as determined by EUCAST, resulting in an MSC between 0.08 and 0.8 mg/L for amoxicillin, 0.4 and 4 mg/L for doxycycline, and 0.0125 and 0.125 mg/L for enrofloxacin. Additionally, resistome analysis provided an MSC for doxycycline between 0.4 and 4 mg/L, but amoxicillin and enrofloxacin exposure did not induce a significant difference. Our findings indicate at which concentrations there is still selection for antimicrobial-resistant bacteria. This knowledge can be used to manage the risk of the emergence of antimicrobial-resistant bacteria.IMPORTANCEAntimicrobial resistance possibly affects human and animal health, as well as economic prosperity in the future. The rise of antimicrobial-resistant bacteria is a consequence of using antimicrobial compounds in humans and animals selecting for antimicrobial-resistant bacteria. Concentrations reached during treatment are known to be selective for resistant bacteria. However, at which concentrations residues are still selective is important, especially for antimicrobial compounds that remain in the environment at low concentrations. The data in this paper might inform decisions regarding guidelines and regulations for the use of specific antimicrobials. In this study, we are providing these minimal selective concentrations for amoxicillin, doxycycline, and enrofloxacin in complex environments.
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Affiliation(s)
- Aram F Swinkels
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Egil A J Fischer
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Lisa Korving
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Nina E Kusters
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jaap A Wagenaar
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- Wageningen Bioveterinary Research, Lelystad, the Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
| | - Aldert L Zomer
- Division of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
- WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, the Netherlands
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Liu J, Spencer N, Utter DR, Grossman AS, Lei L, Dos Santos NC, Shi W, Baker JL, Hasturk H, He X, Bor B. Persistent enrichment of multidrug-resistant Klebsiella in oral and nasal communities during long-term starvation. MICROBIOME 2024; 12:132. [PMID: 39030586 PMCID: PMC11264962 DOI: 10.1186/s40168-024-01854-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/03/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess clinically significant antibiotic resistance genes. Among these opportunistic pathogens, the Klebsiella genus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, the essential transmission factors influencing the spread of Klebsiella species among both healthy and diseased individuals remain unclear. RESULTS Here, we explored a possible explanation by investigating the ability of oral and nasal Klebsiella species to outcompete their native microbial community members under in vitro starvation conditions, which could be analogous to external hospital environments or the microenvironment of mechanical ventilators. When K. pneumoniae and K. aerogenes were present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became enriched in Klebsiella species. Furthermore, introducing K. pneumoniae exogenously into a native microbial community lacking K. pneumoniae, even at low inoculum, led to repeated enrichment under starvation. Precise monitoring of K. pneumoniae within these communities undergoing starvation indicated rapid initial growth and prolonged viability compared to other members of the microbiome. K. pneumoniae strains isolated from healthy individuals' oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence of Klebsiella species, other understudied opportunistic pathogens, such as Peptostreptococcus, increased in relative abundance under starvation conditions. CONCLUSIONS Our findings establish an environmental and microbiome community circumstance that allows for the enrichment of Klebsiella species and other opportunistic pathogens. Klebsiella's enrichment may hinge on its ability to quickly outgrow other members of the microbiome. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions could be an important factor that contributes to enhanced transmission in both commensal and pathogenic contexts. Video Abstract.
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Affiliation(s)
- Jett Liu
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Nell Spencer
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Daniel R Utter
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alex S Grossman
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Lei Lei
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases &, Department of Preventive Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Nídia Castro Dos Santos
- Dental Research Division, Guarulhos University, Guarulhos, São Paulo, Brazil
- Albert Einstein School of Dental Medicine, Albert Einstein Israelite Hospital, São Paulo, SP, Brazil
| | - Wenyuan Shi
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Jonathon L Baker
- Department of Oral Rehabilitation & Biosciences, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Hatice Hasturk
- Center for Clinical and Translational Research, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Xuesong He
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA
| | - Batbileg Bor
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA, 02142, USA.
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Voicu SN, Scărlătescu AI(A, Apetroaei MM, Nedea MI(I, Blejan IE, Udeanu DI, Velescu BȘ, Ghica M, Nedea OA, Cobelschi CP, Arsene AL. Evaluation of Neuro-Hormonal Dynamics after the Administration of Probiotic Microbial Strains in a Murine Model of Hyperthyroidism. Nutrients 2024; 16:1077. [PMID: 38613110 PMCID: PMC11013872 DOI: 10.3390/nu16071077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The microbiota-gut-brain axis has received increasing attention in recent years through its bidirectional communication system, governed by the ability of gut microorganisms to generate and regulate a wide range of neurotransmitters in the host body. In this research, we delve into the intricate area of microbial endocrinology by exploring the dynamic oscillations in neurotransmitter levels within plasma and brain samples. Our experimental model involved inducing hyperthyroidism in mice after a "probiotic load" timeframe using two strains of probiotics (Lactobacillus acidophilus, Saccharomyces boulardii, and their combination). These probiotic interventions continued throughout the experiment and were intended to uncover potential modulatory effects on neurotransmitter levels and discern if certain probiotic strains exhibit any protection from hyperthyroidism. Moreover, we aimed to outline the eventual connections between the gut microbiota and the hypothalamus-pituitary-thyroid axis. As our study reveals, there are significant fluctuations in crucial neurotransmitters within the hyperthyroidism model, related to the specific probiotic strain or combination. These findings could support future therapeutic approaches, help healthcare professionals choose between different probiotic therapies, and also allow us proceed with caution when administering such treatments, depending on the health status of hyperthyroid patients.
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Affiliation(s)
- Sorina Nicoleta Voicu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Splaiul Independenței 91–95, 050095 Bucharest, Romania;
| | - Anca Ioana (Amzăr) Scărlătescu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.I.S.); (M.I.N.); (D.I.U.); (B.Ș.V.); (M.G.); (A.L.A.)
| | - Miruna-Maria Apetroaei
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.I.S.); (M.I.N.); (D.I.U.); (B.Ș.V.); (M.G.); (A.L.A.)
| | - Marina Ionela (Ilie) Nedea
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.I.S.); (M.I.N.); (D.I.U.); (B.Ș.V.); (M.G.); (A.L.A.)
| | - Ionuț Emilian Blejan
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.I.S.); (M.I.N.); (D.I.U.); (B.Ș.V.); (M.G.); (A.L.A.)
| | - Denisa Ioana Udeanu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.I.S.); (M.I.N.); (D.I.U.); (B.Ș.V.); (M.G.); (A.L.A.)
| | - Bruno Ștefan Velescu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.I.S.); (M.I.N.); (D.I.U.); (B.Ș.V.); (M.G.); (A.L.A.)
| | - Manuela Ghica
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.I.S.); (M.I.N.); (D.I.U.); (B.Ș.V.); (M.G.); (A.L.A.)
| | - Octavian Alexandru Nedea
- Faculty of Biotechnical Systems Engineering, University Politehnica of Bucharest, Splaiul Independentei 313, 060042 Bucharest, Romania;
| | - Călin Pavel Cobelschi
- Faculty of Medicine, Transilvania University, Bulevardul Eroilor 29, 500036 Brașov, Romania
| | - Andreea Letiția Arsene
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, 6 Traian Vuia Street, 020956 Bucharest, Romania; (A.I.S.); (M.I.N.); (D.I.U.); (B.Ș.V.); (M.G.); (A.L.A.)
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Liu J, Spencer N, Utter DR, Grossman A, Santos NC, Shi W, Baker JL, Hasturk H, He X, Bor B. Persistent enrichment of multidrug resistant Klebsiella in oral and nasal communities during long-term starvation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572173. [PMID: 38187725 PMCID: PMC10769290 DOI: 10.1101/2023.12.18.572173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess a clinically-significant antibiotic-resistance genes. Among these opportunistic pathogens, the Klebsiella genus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, how Klebsiella transitions from an asymptomatic colonizer to a pathogen remains unclear. Here, we explored a possible explanation by investigating the ability of oral and nasal Klebsiella to outcompete their native microbial community members under in vitro starvation conditions, which could be analogous to external hospital environments. When Klebsiella was present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became dominated by Klebsiella. Furthermore, introducing K. pneumoniae exogenously into a native microbial community lacking K. pneumoniae, even at low inoculum, led to repeated dominance under starvation. K.pneumoniae strains isolated from healthy individuals' oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence of Klebsiella, other understudied opportunistic pathogens, such as Peptostreptococcus, dominate under starvation conditions. Our findings establish an environmental circumstance that allows for the outgrowth of Klebsiella and other opportunistic pathogens. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions may contribute to the colonization-to-infection transition of these opportunistic pathogens.
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Affiliation(s)
- Jett Liu
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
| | - Nell Spencer
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
| | - Daniel R. Utter
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alex Grossman
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
| | - Nídia C.D. Santos
- Dental Research Division, Guarulhos University, Guarulhos, SP, Brazil
- Albert Einstein School of Dental Medicine, Albert Einstein Israelite Hospital, São Paulo, SP, Brazil
| | - Wenyuan Shi
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
| | - Jonathon L. Baker
- Department of Oral Rehabilitation & Biosciences, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Hatice Hasturk
- Center for Clinical and Translational Research, ADA Forsyth Institute, Cambridge, MA 02138, USA
| | - Xuesong He
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Batbileg Bor
- Department of Microbiology, ADA Forsyth Institute, Cambridge, MA 02142, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
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Fu Y, Dou Q, Smalla K, Wang Y, Johnson TA, Brandt KK, Mei Z, Liao M, Hashsham SA, Schäffer A, Smidt H, Zhang T, Li H, Stedtfeld R, Sheng H, Chai B, Virta M, Jiang X, Wang F, Zhu Y, Tiedje JM. Gut microbiota research nexus: One Health relationship between human, animal, and environmental resistomes. MLIFE 2023; 2:350-364. [PMID: 38818274 PMCID: PMC10989101 DOI: 10.1002/mlf2.12101] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 06/01/2024]
Abstract
The emergence and rapid spread of antimicrobial resistance is of global public health concern. The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes (ARGs). In this review, we describe the reservoirs of gut ARGs and their dynamics in both animals and humans, use the One Health perspective to track the transmission of ARG-containing bacteria between humans, animals, and the environment, and assess the impact of antimicrobial resistance on human health and socioeconomic development. The gut resistome can evolve in an environment subject to various selective pressures, including antibiotic administration and environmental and lifestyle factors (e.g., diet, age, gender, and living conditions), and interventions through probiotics. Strategies to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic resistance. With the help of effective measures taken at the national, local, personal, and intestinal management, it will also result in preventing or minimizing the spread of infectious diseases. This review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.
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Affiliation(s)
- Yuhao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qingyuan Dou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) Federal Research Centre for Cultivated PlantsBraunschweigGermany
| | - Yu Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Kristian K. Brandt
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Sino‐Danish Center (SDC)BeijingChina
| | - Zhi Mei
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Maoyuan Liao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Syed A. Hashsham
- Department of Plant, Soil and Microbial Sciences, Center for Microbial EcologyMichigan State UniversityMichiganUSA
- Department of Civil and Environmental EngineeringMichigan State UniversityMichiganUSA
| | - Andreas Schäffer
- Institute for Environmental ResearchRWTH Aachen UniversityAachenGermany
| | - Hauke Smidt
- Laboratory of MicrobiologyWageningen University & ResearchWageningenThe Netherlands
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil EngineeringThe University of Hong KongPokfulamHong KongChina
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Center for Microbial EcologyMichigan State UniversityMichiganUSA
| | - Robert Stedtfeld
- Department of Civil and Environmental EngineeringMichigan State UniversityMichiganUSA
| | - Hongjie Sheng
- Institute of Agricultural Resources and EnvironmentJiangsu Academy of Agricultural SciencesNanjingChina
| | - Benli Chai
- Department of Plant, Soil and Microbial Sciences, Center for Microbial EcologyMichigan State UniversityMichiganUSA
| | - Marko Virta
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Xin Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fang Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yong‐Guan Zhu
- University of Chinese Academy of SciencesBeijingChina
- Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- State Key Laboratory of Urban and Regional EcologyChinese Academy of SciencesBeijingChina
| | - James M. Tiedje
- Department of Plant, Soil and Microbial Sciences, Center for Microbial EcologyMichigan State UniversityMichiganUSA
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Zenebe T, Eguale T, Desalegn Z, Beshah D, Gebre-Selassie S, Mihret A, Abebe T. Distribution of ß-Lactamase Genes Among Multidrug-Resistant and Extended-Spectrum ß-Lactamase-Producing Diarrheagenic Escherichia coli from Under-Five Children in Ethiopia. Infect Drug Resist 2023; 16:7041-7054. [PMID: 37954506 PMCID: PMC10637226 DOI: 10.2147/idr.s432743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023] Open
Abstract
Purpose Escherichia coli strains that produce extended-spectrum ß-lactamase (ESBL) and carbapenemase are among the major threats to global health. The objective of the present study was to determine the distribution of ß-lactamase genes among multidrug-resistant (MDR) and ESBL-producing Diarrheagenic E. coli (DEC) pathotypes isolated from under-five children in Ethiopia. Patients and Methods A cross-sectional study was conducted in Addis Ababa and Debre Berhan, Ethiopia. It was a health-facility-based study and conducted between December 2020 and August 2021. A total of 476 under-five children participated in the study. DEC pathotypes were detected by conventional Polymerase Chain Reaction (PCR) assay. After evaluating the antimicrobial susceptibility profile of the DEC strains by disk diffusion method, confirmation test was done for ESBL and carbapenemase production. ß-lactamase encoding genes were identified from phenotypically ESBLs and carbapenemase positive DEC strains using PCR assay. Results In total, 183 DEC pathotypes were isolated from the 476 under-five children. Seventy-nine (43%, 79/183) MDR-DEC pathotypes were identified. MDR was common among enteroaggregative E. coli (EAEC) (58%, 44/76), followed by enterotoxigenic E. coli (ETEC) (44%, 17/39)) and enteroinvasive E. coli (EIEC) (30%, 7/23). Phenotypically, a total of 30 MDR-DEC pathotypes (16.4%, 30/183) were tested positive for ESBLs. Few ETEC (5.1%, 2/39) and EAEC (2.6%, 2/76) were carbapenemase producers. The predominant β-lactamase genes identified was blaTEM (80%, 24/30) followed by blaCTX-M (73%, 22/30), blaSHV (60%, 18/30), blaNDM (13%, 4/30), and blaOXA-48 (13%, 4/30). Majority of the ß-lactamase encoding genes were detected in EAEC (50%) and ETEC (20%). Co-existence of different β-lactamase genes was found in the present study. Conclusion The blaTEM, blaCTX-M, blaSHV, blaNDM, and blaOXA-48, that are associated with serious and urgent threats globally, were detected in diarrheagenic E. coli isolates from under-five children in Ethiopia. This study also revealed the coexistence of the β-lactamase genes.
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Affiliation(s)
- Tizazu Zenebe
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Medical Laboratory Science, Debre Berhan University, Debre Berhan, Ethiopia
| | - Tadesse Eguale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Ohio State University, Global One Health LLC, Addis Ababa, Ethiopia
| | - Zelalem Desalegn
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Beshah
- Department of Medical Laboratory, Tikur Anbessa Specialized Hospital, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Gebre-Selassie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
- Bacterial and Viral Disease Research Directorate, Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - Tamrat Abebe
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
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8
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Din SRU, Saeed S, Khan SU, Arbi FM, Xuefang G, Zhong M. Bacteria-driven cancer therapy: Exploring advancements and challenges. Crit Rev Oncol Hematol 2023; 191:104141. [PMID: 37742883 DOI: 10.1016/j.critrevonc.2023.104141] [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: 08/08/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
Cancer, a serious fatal disease caused by the uncontrolled growth of cells, is the biggest challenge flagging around medicine and health fields. Conventionally, various treatments-based strategies such as radiotherapy, chemotherapy, and alternative cancer therapies possess drugs that cannot reach the cancerous tissues and make them toxic to noncancerous cells. Cancer immunotherapy has made outstanding achievements in reducing the chances of cancer. Our considerable attention towards cancer-directed immune responses and the mechanisms behind which immune cells kill cancer cells have progressively been helpful in the advancement of new therapies. Among them, bacteria-based cancer immunotherapy has achieved much more attention due to smart and robust mechanisms in activating the host anti-tumor response. Moreover, bacterial-based therapy can be utilized as a single monotherapy or in combination with multiple anticancer immunotherapies to accelerate productive clinical results. Herein, we comprehensively reviewed recent advancements, challenges, and future perspectives in developing bacterial-based cancer immunotherapies.
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Affiliation(s)
- Syed Riaz Ud Din
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Sumbul Saeed
- School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China; Women Medical and Dental College, Khyber Medical University, Peshawar, KPK 22020, Pakistan
| | - Fawad Mueen Arbi
- Quaid-e-Azam Medical College, Bahawalpur, Punjab 63100, Pakistan
| | - Guo Xuefang
- Department of Medical Microbiology, Dalian Medical University, Dalian 116044, China
| | - Mintao Zhong
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China.
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9
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Gupta U, Dey P. Rise of the guardians: Gut microbial maneuvers in bacterial infections. Life Sci 2023; 330:121993. [PMID: 37536616 DOI: 10.1016/j.lfs.2023.121993] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
AIMS Bacterial infections are one of the major causes of mortality globally. The gut microbiota, primarily comprised of the commensals, performs an important role in maintaining intestinal immunometabolic homeostasis. The current review aims to provide a comprehensive understanding of how modulation of the gut microbiota influences opportunistic bacterial infections. MATERIALS AND METHODS Primarily centered around mechanisms related to colonization resistance, nutrient, and metabolite-associated factors, mucosal immune response, and commensal-pathogen reciprocal interactions, we discuss how gut microbiota can promote or prevent bacterial infections. KEY FINDINGS Opportunistic infections can occur directly due to obligate pathogens or indirectly due to the overgrowth of opportunistic pathobionts. Gut microbiota-centered mechanisms of altered intestinal immunometabolic and metabolomic homeostasis play a significant role in infection promotion and prevention. Depletion in the population of commensals, increased abundance of pathobionts, and overall decrease in gut microbial diversity and richness caused due to prolonged antibiotic use are risk factors of opportunistic bacterial infections, including infections from multidrug-resistant spp. Gut commensals can limit opportunistic infections by mechanisms including the production of antimicrobials, short-chain fatty acids, bile acid metabolism, promoting mucin formation, and maintaining immunological balance at the mucosa. Gut microbiota-centered strategies, including the administration of probiotics and fecal microbiota transplantation, could help attenuate opportunistic bacterial infections. SIGNIFICANCE The current review discussed the gut microbial population and function-specific aspects contributing to bacterial infection susceptibility and prophylaxis. Collectively, this review provides a comprehensive understanding of the mechanisms related to the dual role of gut microbiota in bacterial infections.
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Affiliation(s)
- Upasana Gupta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Priyankar Dey
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India.
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10
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Zhang Y, Shen J, Cheng W, Roy B, Zhao R, Chai T, Sheng Y, Zhang Z, Chen X, Liang W, Hu W, Liao Q, Pan S, Zhuang W, Zhang Y, Chen R, Mei J, Wei H, Fang X. Microbiota-mediated shaping of mouse spleen structure and immune function characterized by scRNA-seq and Stereo-seq. J Genet Genomics 2023; 50:688-701. [PMID: 37156441 DOI: 10.1016/j.jgg.2023.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Gut microbes exhibit complex interactions with their hosts and shape an organism's immune system throughout its lifespan. As the largest secondary lymphoid organ, the spleen has a wide range of immunological functions. To explore the role of microbiota in regulating and shaping the spleen, we employ scRNA-seq and Stereo-seq technologies based on germ-free (GF) mice to detect differences in tissue size, anatomical structure, cell types, functions, and spatial molecular characteristics. We identify 18 cell types, 9 subtypes of T cells, and 7 subtypes of B cells. Gene differential expression analysis reveals that the absence of microorganisms results in alterations in erythropoiesis within the red pulp region and congenital immune deficiency in the white pulp region. Stereo-seq results demonstrate a clear hierarchy of immune cells in the spleen, including marginal zone (MZ) macrophages, MZ B cells, follicular B cells and T cells, distributed in a well-defined pattern from outside to inside. However, this hierarchical structure is disturbed in GF mice. Ccr7 and Cxcl13 chemokines are specifically expressed in the spatial locations of T cells and B cells, respectively. We speculate that the microbiota may mediate the structural composition or partitioning of spleen immune cells by modulating the expression levels of chemokines.
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Affiliation(s)
- Yin Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Juan Shen
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Wei Cheng
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bhaskar Roy
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Ruizhen Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Tailiang Chai
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yifei Sheng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Zhao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Xueting Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | | | - Weining Hu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Qijun Liao
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Shanshan Pan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Wen Zhuang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yangrui Zhang
- BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Rouxi Chen
- BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China
| | - Hong Wei
- Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
| | - Xiaodong Fang
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China; BGI-Sanya, BGI-Shenzhen, Sanya, Hainan 572025, China.
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11
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Ramay BM, Castillo C, Grajeda L, Santos LF, Romero JC, Lopez MR, Gomez A, Caudell M, Smith RM, Styczynski A, Herzig CTA, Bollinger S, Ning MF, Horton J, Omulo S, Palmer GH, Cordon-Rosales C, Call DR. Colonization With Antibiotic-Resistant Bacteria in a Hospital and Associated Communities in Guatemala: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study. Clin Infect Dis 2023; 77:S82-S88. [PMID: 37406049 PMCID: PMC10321699 DOI: 10.1093/cid/ciad222] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND We estimated the prevalence of colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) and carbapenem-resistant Enterobacterales (CRE) from a hospital and associated communities in western Guatemala. METHODS Randomly selected infants, children, and adults (<1, 1-17, and ≥18 years, respectively) were enrolled from the hospital (n = 641) during the coronavirus disease 2019 (COVID-19) pandemic, March to September 2021. Community participants were enrolled using a 3-stage cluster design between November 2019 and March 2020 (phase 1, n = 381) and between July 2020 and May 2021 (phase 2, with COVID-19 pandemic restrictions, n = 538). Stool samples were streaked onto selective chromogenic agar, and a Vitek 2 instrument was used to verify ESCrE or CRE classification. Prevalence estimates were weighted to account for sampling design. RESULTS The prevalence of colonization with ESCrE and CRE was higher among hospital patients compared to community participants (ESCrE: 67% vs 46%, P < .01; CRE: 37% vs 1%, P < .01). Hospital ESCrE colonization was higher for adults (72%) compared with children (65%) and infants (60%) (P < .05). Colonization was higher for adults (50%) than children (40%) in the community (P < .05). There was no difference in ESCrE colonization between phase 1 and 2 (45% and 47%, respectively, P > .05), although reported use of antibiotics among households declined (23% and 7%, respectively, P < .001). CONCLUSIONS While hospitals remain foci for ESCrE and CRE colonization, consistent with the need for infection control programs, community prevalence of ESCrE in this study was high, potentially adding to colonization pressure and transmission in healthcare settings. Better understanding of transmission dynamics and age-related factors is needed.
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Affiliation(s)
- Brooke M Ramay
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala Department, Republic of Guatemala
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Carmen Castillo
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala Department, Republic of Guatemala
| | - Laura Grajeda
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala Department, Republic of Guatemala
| | - Lucas F Santos
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala Department, Republic of Guatemala
| | - Juan Carlos Romero
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala Department, Republic of Guatemala
| | - Maria Renee Lopez
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala Department, Republic of Guatemala
| | - Andrea Gomez
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala Department, Republic of Guatemala
| | - Mark Caudell
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Rachel M Smith
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ashley Styczynski
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Carolyn T A Herzig
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Susan Bollinger
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mariangeli Freitas Ning
- Central America Regional Office, Centers for Disease Control and Prevention, Guatemala City, Guatemala Department, Republic of Guatemala
| | - Jennifer Horton
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Sylvia Omulo
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
- Washington State University Global Health–Kenya, Nairobi, Nairobi County, Kenya
| | - Guy H Palmer
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Celia Cordon-Rosales
- Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala Department, Republic of Guatemala
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
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12
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Nolan TM, Reynolds LJ, Sala-Comorera L, Martin NA, Stephens JH, O'Hare GMP, O'Sullivan JJ, Meijer WG. Land use as a critical determinant of faecal and antimicrobial resistance gene pollution in riverine systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162052. [PMID: 36758688 DOI: 10.1016/j.scitotenv.2023.162052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
The WHO recognises antimicrobial resistance (AMR) as a global health threat. The environment can act as a reservoir, facilitating the exchange and the physical movement of resistance. Aquatic environments are at particular risk of pollution, with large rivers subject to pollution from nearby human, industrial or agricultural activities. The land uses associated with these activities can influence the type of pollution. One type of pollution and a likely contributor to AMR pollution that lowers water quality is faecal pollution. Both pose an acute health risk and could have implications for resistance circulating in communities. The effects of land use are typically studied using physiochemical parameters or in isolation of one another. However, this study aimed to investigate the impact of different land uses on riverine systems. We explored whether differences in sources of faecal contamination are reflected in AMR gene concentrations across agricultural and urban areas. Water quality from three rivers impacted by different land uses was assessed over one year by quantifying faecal indicator bacteria (FIB), microbial source tracking markers (MST) and AMR genes. In addition, a multiparametric analysis of AMR gene pollution was carried out to understand whether agricultural and urban areas are similarly impacted. Faecal indicators varied greatly, with the highest levels of FIB and the human MST marker observed in urban regions. In addition, these faecal markers correlated with AMR genes. Similarly, significant correlations between the ruminant MST marker and AMR gene levels in agriculture areas were observed. Overall, applying multiparametric analyses to include AMR gene levels, separation and clustering of sites were seen based on land use characterisation. This study suggests that differences in prescription of antimicrobials used in animal and human healthcare may influence environmental resistomes across agricultural and urban areas. In addition, public health risks due to exposure to faecal contamination and AMR genes are highlighted.
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Affiliation(s)
- Tristan M Nolan
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Niamh A Martin
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Jayne H Stephens
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Gregory M P O'Hare
- School of Computer Science and Statistics, Trinity College Dublin, Dublin 2, Ireland
| | - John J O'Sullivan
- UCD School of Civil Engineering, UCD Dooge Centre for Water Resources Research and UCD Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
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13
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Neidhöfer C, Sib E, Neuenhoff M, Schwengers O, Dummin T, Buechler C, Klein N, Balks J, Axtmann K, Schwab K, Holderried TAW, Feldmann G, Brossart P, Engelhart S, Mutters NT, Bierbaum G, Parčina M. Hospital sanitary facilities on wards with high antibiotic exposure play an important role in maintaining a reservoir of resistant pathogens, even over many years. Antimicrob Resist Infect Control 2023; 12:33. [PMID: 37061726 PMCID: PMC10105422 DOI: 10.1186/s13756-023-01236-w] [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: 11/28/2022] [Accepted: 03/29/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Hospitals with their high antimicrobial selection pressure represent the presumably most important reservoir of multidrug-resistant human pathogens. Antibiotics administered in the course of treatment are excreted and discharged into the wastewater system. Not only in patients, but also in the sewers, antimicrobial substances exert selection pressure on existing bacteria and promote the emergence and dissemination of multidrug-resistant clones. In previous studies, two main clusters were identified in all sections of the hospital wastewater network that was investigated, one K. pneumoniae ST147 cluster encoding NDM- and OXA-48 carbapenemases and one VIM-encoding P. aeruginosa ST823 cluster. In the current study, we investigated if NDM- and OXA-48-encoding K. pneumoniae and VIM-encoding P. aeruginosa isolates recovered between 2014 and 2021 from oncological patients belonged to those same clusters. METHODS The 32 isolates were re-cultured, whole-genome sequenced, phenotypically tested for their antimicrobial susceptibility, and analyzed for clonality and resistance genes in silico. RESULTS Among these strains, 25 belonged to the two clusters that had been predominant in the wastewater, while two others belonged to a sequence-type less prominently detected in the drains of the patient rooms. CONCLUSION Patients constantly exposed to antibiotics can, in interaction with their persistently antibiotic-exposed sanitary facilities, form a niche that might be supportive for the emergence, the development, the dissemination, and the maintenance of certain nosocomial pathogen populations in the hospital, due to antibiotic-induced selection pressure. Technical and infection control solutions might help preventing transmission of microorganisms from the wastewater system to the patient and vice versa, particularly concerning the shower and toilet drainage. However, a major driving force might also be antibiotic induced selection pressure and parallel antimicrobial stewardship efforts could be essential.
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Affiliation(s)
- Claudio Neidhöfer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany.
| | - Esther Sib
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Marcel Neuenhoff
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Oliver Schwengers
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Tobias Dummin
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Christian Buechler
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Niklas Klein
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, Koblenz, Germany
| | - Julian Balks
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Katharina Axtmann
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Katjana Schwab
- Department of Oncology, Hematology, and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Tobias A W Holderried
- Department of Oncology, Hematology, and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Georg Feldmann
- Department of Oncology, Hematology, and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Peter Brossart
- Department of Oncology, Hematology, and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Steffen Engelhart
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Nico T Mutters
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
| | - Marijo Parčina
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg Campus 1, 53127, Bonn, Germany
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14
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Study on the interaction between grain polyphenols and intestinal microorganisms: A review. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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15
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Yusuf K, Sampath V, Umar S. Bacterial Infections and Cancer: Exploring This Association And Its Implications for Cancer Patients. Int J Mol Sci 2023; 24:3110. [PMID: 36834525 PMCID: PMC9958598 DOI: 10.3390/ijms24043110] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Bacterial infections are common in the etiology of human diseases owing to the ubiquity of bacteria. Such infections promote the development of periodontal disease, bacterial pneumonia, typhoid, acute gastroenteritis, and diarrhea in susceptible hosts. These diseases may be resolved using antibiotics/antimicrobial therapy in some hosts. However, other hosts may be unable to eliminate the bacteria, allowing them to persist for long durations and significantly increasing the carrier's risk of developing cancer over time. Indeed, infectious pathogens are modifiable cancer risk factors, and through this comprehensive review, we highlight the complex relationship between bacterial infections and the development of several cancer types. For this review, searches were performed on the PubMed, Embase, and Web of Science databases encompassing the entirety of 2022. Based on our investigation, we found several critical associations, of which some are causative: Porphyromonas gingivalis and Fusobacterium nucleatum are associated with periodontal disease, Salmonella spp., Clostridium perfringens, Escherichia coli, Campylobacter spp., and Shigella are associated with gastroenteritis. Helicobacter pylori infection is implicated in the etiology of gastric cancer, and persistent Chlamydia infections present a risk factor for the development of cervical carcinoma, especially in patients with the human papillomavirus (HPV) coinfection. Salmonella typhi infections are linked with gallbladder cancer, and Chlamydia pneumoniae infection is implicated in lung cancer, etc. This knowledge helps identify the adaptation strategies used by bacteria to evade antibiotic/antimicrobial therapy. The article also sheds light on the role of antibiotics in cancer treatment, the consequences of their use, and strategies for limiting antibiotic resistance. Finally, the dual role of bacteria in cancer development as well as in cancer therapy is briefly discussed, as this is an area that may help to facilitate the development of novel microbe-based therapeutics as a means of securing improved outcomes.
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Affiliation(s)
- Kafayat Yusuf
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Venkatesh Sampath
- Department of Pediatrics and Gastroenterology, Children’s Mercy Hospital, Kansas City, KS 66160, USA
| | - Shahid Umar
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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16
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Tiwari A, Kurittu P, Al-Mustapha AI, Heljanko V, Johansson V, Thakali O, Mishra SK, Lehto KM, Lipponen A, Oikarinen S, Pitkänen T, Heikinheimo A. Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review. Front Microbiol 2022; 13:977106. [PMID: 36590429 PMCID: PMC9798455 DOI: 10.3389/fmicb.2022.977106] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Infectious diseases caused by antibiotic-resistant bacterial (ARB) pathogens are a serious threat to human and animal health. The active surveillance of ARB using an integrated one-health approach can help to reduce the emergence and spread of ARB, reduce the associated economic impact, and guide antimicrobial stewardship programs. Wastewater surveillance (WWS) of ARB provides composite samples for a total population, with easy access to the mixed community microbiome. This concept is emerging rapidly, but the clinical utility, sensitivity, and uniformity of WWS of ARB remain poorly understood especially in relation to clinical evidence in sewershed communities. Here, we systematically searched the literature to identify studies that have compared findings from WWS of ARB and antibiotic resistance genes (ARG) with clinical evidence in parallel, thereby evaluating how likely WWS of ARB and ARG can relate to the clinical cases in communities. Initially, 2,235 articles were obtained using the primary search keywords, and 1,219 articles remained after de-duplication. Among these, 35 articles fulfilled the search criteria, and an additional 13 relevant articles were included by searching references in the primary literature. Among the 48 included papers, 34 studies used a culture-based method, followed by 11 metagenomics, and three PCR-based methods. A total of 28 out of 48 included studies were conducted at the single sewershed level, eight studies involved several countries, seven studies were conducted at national or regional scales, and five at hospital levels. Our review revealed that the performance of WWS of ARB pathogens has been evaluated more frequently for Escherichia coli, Enterococcus spp., and other members of the family Enterobacteriaceae, but has not been uniformly tested for all ARB pathogens. Many wastewater-based ARB studies comparing the findings with clinical evidence were conducted to evaluate the public health risk but not to relate with clinical evidence and to evaluate the performance of WWS of ARB. Indeed, relating WWS of ARB with clinical evidence in a sewershed is not straightforward, as the source of ARB in wastewater cannot be only from symptomatic human individuals but can also be from asymptomatic carriers as well as from animal sources. Further, the varying fates of each bacterial species and ARG within the sewerage make the aim of connecting WWS of ARB with clinical evidence more complicated. Therefore, future studies evaluating the performance of many AMR pathogens and their genes for WWS one by one can make the process simpler and the interpretation of results easier.
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Affiliation(s)
- Ananda Tiwari
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland,*Correspondence: Ananda Tiwari,
| | - Paula Kurittu
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ahmad I. Al-Mustapha
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland,Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria,Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Development, Ilorin, Nigeria
| | - Viivi Heljanko
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Venla Johansson
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ocean Thakali
- Department of Civil Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Shyam Kumar Mishra
- School of Optometry and Vision Science, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Kirsi-Maarit Lehto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anssi Lipponen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Tarja Pitkänen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland,Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland,Finnish Food Authority, Seinäjoki, Finland
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17
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Gan B, Sun N, Lai J, Wan Z, Li L, Wang Y, Zeng Y, Zeng D, Pan K, Fang J, Shu G, Wang H, Xin J, Ni X. Dynamic Monitoring of Changes in Fecal Flora of Giant Pandas in Mice: Co-Occurrence Network Reconstruction. Microbiol Spectr 2022; 11:e0199122. [PMID: 36472469 PMCID: PMC10100740 DOI: 10.1128/spectrum.01991-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Giant pandas are uniquely vulnerable mammals in western China. It is important to develop an animal model to explore the intestinal flora of giant pandas to understand the relationship between digestive diseases and flora. Existing animal models of intestinal flora focus on human flora-associated animals, such as mice, and there is a very limited amount of knowledge regarding giant panda flora-associated animals. To fill this gap, fecal microorganisms from giant pandas were transplanted into pseudosterile and germfree mice using single and multiple gavages. Fecal samples were collected from mice at four time points after transplantation for microbial community analysis. We determined that compared to pseudosterile mice, the characteristics of intestinal flora in pandas were better reproduced in germfree mice. There was no significant difference in microbial diversity between germfree mice and giant panda gut microbes from day 3 to day 21. Germfree mice at the phylum level possessed large amounts of Firmicutes and Proteobacteria, and at the genus level, Escherichia-Shigella, Clostridium sensu stricto 1, and Streptococcus dominated the intestinal flora structure. The microbial community co-occurrence network based on indicator species indicated that germfree mice transplanted with fecal bacteria tended to form a microbial community co-occurrence network similar to that of giant pandas, while pseudosterile mice tended to restore the microbial community co-occurrence network originally present in these mice. Our data are helpful for the study of giant panda flora-associated animals and provide new insights for the in vitro study of giant panda intestinal flora. IMPORTANCE The giant panda is a unique vulnerable mammal in western China, and its main cause of death is digestive system diseases regardless of whether these animals are in the wild or in captivity. The relationship between the intestinal flora and the host exerts a significant impact on the nutrition and health of the giant pandas. However, the protected status of the giant panda has made in vivo, repeatable, and large-sample sampling studies of their intestinal flora difficult. This greatly hinders the research depth of the giant panda intestinal flora from the source. The development and utilization of specific animal models to simulate the structure and characteristics of the intestinal flora provide another means to deal with these research limitations. However, current research examining giant panda flora-associated animals is limited. This study is the first to reveal dynamic changes in the fecal flora of giant pandas in mice after transplantation.
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Affiliation(s)
- Baoxing Gan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ning Sun
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Lai
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhiqiang Wan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lianxin Li
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanyan Wang
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Fang
- Department of Basic Veterinary, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Gang Shu
- Department of Pharmacy, College of Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hesong Wang
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jinge Xin
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
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18
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Aghamohammad S, Rohani M. Antibiotic resistance and the alternatives to conventional antibiotics: The role of probiotics and microbiota in combating antimicrobial resistance. Microbiol Res 2022; 267:127275. [PMID: 36493661 DOI: 10.1016/j.micres.2022.127275] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
From the introduction of the first antibiotic to the present day, the emergence of antibiotic resistance has been a difficult problem for medicine. Regardless of the type of antibiotic resistance, the presence of resistant isolates in clinical and even asymptomatic fecal carriers becomes a difficult public health problem. Therefore, the use of new antimicrobial combination therapies or alternative agents with antimicrobial activity that have the least side effects, including plant-, metal-, and nanoparticle-based agents, could be crucial and useful. Recently, the use of probiotics as a hypothetical candidate to combat infectious disease control and antimicrobial resistance has received notable attention. Considering the alteration of the microbiota in fecal carriers and also in patients with resistant bacterial isolates, the use of probiotics could have an appropriate effect on the balance of the microbial population. In this review, we have attempted to discuss the history of antimicrobial resistance and provide an overview of microbiota change and the use of probiotics as new agents with antimicrobial activity associated with the emergence of resistant isolates.
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Affiliation(s)
| | - Mahdi Rohani
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran.
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19
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Herrera G, Arboleda JC, Pérez-Jaramillo JE, Patarroyo MA, Ramírez JD, Muñoz M. Microbial Interdomain Interactions Delineate the Disruptive Intestinal Homeostasis in Clostridioides difficile Infection. Microbiol Spectr 2022; 10:e0050222. [PMID: 36154277 PMCID: PMC9602525 DOI: 10.1128/spectrum.00502-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile infection (CDI) creates an imbalance in the intestinal microbiota due to the interaction of the components making up this ecosystem, but little is known about the impact of this disease on other microbial members. This work has thus been aimed at evaluating the taxonomic composition, potential gene-associated functions, virulence factors, and antimicrobial resistance profiles of gut microbiomes. A total of 48 DNA samples obtained from patients with health care facility-acquired (HCFO) and community-onset (CO) diarrhea were distributed in the following four groups according to CDI status: HCFO/+ (n = 13), HCFO/- (n = 8), CO/+ (n = 13), and CO/- (n = 14). These samples were subjected to shotgun metagenomics sequencing. Although the CDI groups' microbiota had microbiome alterations, the greatest imbalance was observed in the in the HCFO+/- groups, with an increase in common pathogens and phage populations, as well as a decrease in beneficial microorganisms that leads to a negative impact on some intestinal homeostasis-related metabolic processes. A reduction in the relative abundance of butyrate metabolism-associated genes was also detected in the HCFO groups (P < 0.01), with an increase in some virulence factors and antibiotic-resistance markers. A set of 51 differentially abundant species in the groups with potential association to CDI enabled its characterization, leading to their spatial separation by onset. Strong correlations between phages and some archaeal and bacterial phyla were identified. This highlighted the need to study the microbiota's various components since their imbalance is multifactorial, with some pathogens contributing to a greater or lesser extent because of their interaction with the ecosystem they inhabit. IMPORTANCE Clostridioides difficile infection represents a serious public health problem in different countries due to its high morbi-mortality and the high costs it represents for health care systems. Studies have shown the impact of this infection on intestinal microbiome homeostasis, mainly on bacterial populations. Our research provides evidence of the impact of CDI at both the compositional (bacteria, archaea, and viruses), and functional levels, allowing us to understand that the alterations of the microbiota occur systemically and are caused by multiple perturbations generated by different members of the microbiota as well as by some pathogens that take advantage of the imbalance to proliferate. Likewise, the 51 differentially abundant species in the study groups with potential association to CDI found in this study could help us envisage future treatments against this and other inflammatory diseases, improving future therapeutic options for patients.
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Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan Camilo Arboleda
- Unidad de Bioprospección and Estudio de Microbiomas, Programa de Estudio y Control de Enfermedades Tropicales (PECET), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia
- Semillero de Investigación en Bioinformática-GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Juan E. Pérez-Jaramillo
- Semillero de Investigación en Bioinformática-GenomeSeq, Seccional Oriente, Universidad de Antioquia, Medellín, Colombia
- Grupo de Fundamentos y Enseñanza de la Física y los Sistemas Dinámicos, Instituto de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- Health Sciences Division, Universidad Santo Tomás, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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20
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Pan X, Zhou Z, Liu B, Wu Z. A novel therapeutic concern: Antibiotic resistance genes in common chronic diseases. Front Microbiol 2022; 13:1037389. [DOI: 10.3389/fmicb.2022.1037389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Infections caused by multidrug-resistant bacteria carrying antibiotic resistance genes pose a severe threat to global public health and human health. In clinical practice, it has been found that human gut microbiota act as a “reservoir” of antibiotic resistance genes (ARGs) since gut microbiota contain a wide variety of ARGs, and that the structure of the gut microbiome is influenced by the profile of the drug resistance genes present. In addition, ARGs can spread within and between species of the gut microbiome in multiple ways. To better understand gut microbiota ARGs and their effects on patients with chronic diseases, this article reviews the generation of ARGs, common vectors that transmit ARGs, the characteristics of gut microbiota ARGs in common chronic diseases, their impact on prognosis, the current state of treatment for ARGs, and what should be addressed in future research.
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21
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Appel TM, Vehreschild MJ. [Role of the gut microbiome in the development and transfer of antibiotic resistances]. INNERE MEDIZIN (HEIDELBERG, GERMANY) 2022; 63:1043-1050. [PMID: 36048186 DOI: 10.1007/s00108-022-01400-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Antimicrobial resistance (AR) is a natural phenomenon resulting from the exposure of bacteria to antibacterial substances. The intestinal microbiome plays a central role in the development and transmission of AR. In its physiological state, the intestinal microbiome has several mechanisms that contribute to what is referred to as colonization resistance against potentially pathogenic and often multiresistant bacteria. Exposure to broad-spectrum antibiotics can disrupt those mechanisms, facilitating colonization with these pathogens. The persistence of antibiotic selection pressure favors growth of multiresistant bacteria and their dominance within the intestinal microbiota. Under these circumstances, the risk of the development of invasive infections increases. Antibiotic stewardship programs, the use of narrow-spectrum antibiotics, and the administration of substances that protect the intestinal microbiome from antibiotic exposure can prevent these processes. Several interventions such as the administration of probiotics, oral antibiotics, and fecal microbiome transfers are potential strategies for decolonizing patients with multidrug resistant bacteria; to date, however, no intervention has been proven to be consistently effective.
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Affiliation(s)
- Tobias M Appel
- Zentrum für Innere Medizin, Medizinische Klinik 2, Infektiologie, Universitätsklinikum Frankfurt, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Deutschland
| | - Maria J Vehreschild
- Zentrum für Innere Medizin, Medizinische Klinik 2, Infektiologie, Universitätsklinikum Frankfurt, Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Deutschland.
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22
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Postek W, Pacocha N, Garstecki P. Microfluidics for antibiotic susceptibility testing. LAB ON A CHIP 2022; 22:3637-3662. [PMID: 36069631 DOI: 10.1039/d2lc00394e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
- Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA 02142, USA.
| | - Natalia Pacocha
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
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23
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Pérez-Nadales E, M. Natera A, Recio-Rufián M, Guzmán-Puche J, Marín-Sanz JA, Martín-Pérez C, Cano Á, Castón JJ, Elías-López C, Machuca I, Gutiérrez-Gutiérrez B, Martínez-Martínez L, Torre-Cisneros J. Prognostic Significance of the Relative Load of KPC-Producing Klebsiella pneumoniae within the Intestinal Microbiota in a Prospective Cohort of Colonized Patients. Microbiol Spectr 2022; 10:e0272821. [PMID: 35766500 PMCID: PMC9431423 DOI: 10.1128/spectrum.02728-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/20/2022] [Indexed: 12/03/2022] Open
Abstract
Increased relative bacterial load of KPC-producing Klebsiella pneumoniae (KPC-KP) within the intestinal microbiota has been associated with KPC-KP bacteremia. Prospective observational study of KPC-KP adult carriers with a hospital admission at recruitment or within the three prior months (January 2018 to February 2019). A qPCR-based assay was developed to measure the relative load of KPC-KP in rectal swabs (RLKPC, proportion of blaKPC relative to 16S rRNA gene copy number). We generated Fine-Gray competing risk and Cox regression models for survival analysis of all-site KPC-KP infection and all-cause mortality, respectively, at 90 and 30 days. The median RLKPC at baseline among 80 KPC-KP adult carriers was 0.28% (range 0.001% to 2.70%). Giannella Risk Score (GRS) was independently associated with 90-day and 30-day all-site infection (adjusted subdistribution hazard ratio [aHR] 1.23, 95% CI = 1.15 to 1.32, P < 0.001). RLKPC (adjusted hazard ratio [aHR] 1.04, 95% CI = 1.01 to 1.07, P = 0.008) and age (aHR 1.05, 95% CI = 1.01 to 1.10, P = 0.008) were independent predictors of 90-day all-cause mortality in a Cox model stratified by length of hospital stay (LOHS) ≥20 days. An adjusted Cox model for 30-day all-cause mortality, stratified by LOHS ≥14 days, included RLKPC (aHR 1.03, 95% CI = 1.00 to 1.06, P = 0.027), age (aHR 1.10, 95% CI = 1.03 to 1.18, P = 0.004), and severe KPC-KP infection (INCREMENT-CPE score >7, aHR 2.96, 95% CI = 0.97 to 9.07, P = 0.057). KPC-KP relative intestinal load was independently associated with all-cause mortality in our clinical setting, after adjusting for age and severe KPC-KP infection. Our study confirms the utility of GRS to predict infection risk in patients colonized by KPC-KP. IMPORTANCE The rapid dissemination of carbapenemase-producing Enterobacterales represents a global public health threat. Increased relative load of KPC-producing Klebsiella pneumoniae (KPC-KP) within the intestinal microbiota has been associated with an increased risk of bloodstream infection by KPC-KP. We developed a qPCR assay for quantification of the relative KPC-KP intestinal load (RLKPC) in 80 colonized patients and examined its association with subsequent all-site KPC-KP infection and all-cause mortality within 90 days. Giannella Risk Score, which predicts infection risk in colonized patients, was independently associated with the development of all-site KPC-KP infection. RLKPC was not associated with all-site KPC-KP infection, possibly reflecting the large heterogeneity in patient clinical conditions and infection types. RLKPC was an independent predictor of all-cause mortality within 90 and 30 days in our clinical setting. We hypothesize that KPC-KP load may behave as a surrogate marker for the severity of the patient's clinical condition.
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Affiliation(s)
- Elena Pérez-Nadales
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
- Department of Agricultural Chemistry, Edaphology and Microbiology and Department of Medical and Surgical Sciences, University of Cordoba, Cordoba, Spain
| | - Alejandra M. Natera
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
| | - Manuel Recio-Rufián
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
- Clinical Units of Infectious Diseases and Microbiology, Reina Sofía University Hospital, Cordoba, Spain
| | - Julia Guzmán-Puche
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
- Clinical Units of Infectious Diseases and Microbiology, Reina Sofía University Hospital, Cordoba, Spain
| | - Juan Antonio Marín-Sanz
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
| | - Carlos Martín-Pérez
- Doctor in Medicine, specialist in Family and Community Medicine in the Andalusian Health Service, Granada, Spain
| | - Ángela Cano
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
- Clinical Units of Infectious Diseases and Microbiology, Reina Sofía University Hospital, Cordoba, Spain
| | - Juan José Castón
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
- Department of Agricultural Chemistry, Edaphology and Microbiology and Department of Medical and Surgical Sciences, University of Cordoba, Cordoba, Spain
- Clinical Units of Infectious Diseases and Microbiology, Reina Sofía University Hospital, Cordoba, Spain
| | - Cristina Elías-López
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
| | - Isabel Machuca
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
- Clinical Units of Infectious Diseases and Microbiology, Reina Sofía University Hospital, Cordoba, Spain
| | - Belén Gutiérrez-Gutiérrez
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen Macarena, Institute of Biomedicine of Seville (IBiS), Seville, Spain
| | - Luis Martínez-Martínez
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
- Department of Agricultural Chemistry, Edaphology and Microbiology and Department of Medical and Surgical Sciences, University of Cordoba, Cordoba, Spain
- Clinical Units of Infectious Diseases and Microbiology, Reina Sofía University Hospital, Cordoba, Spain
| | - Julián Torre-Cisneros
- Spanish Network for Research in Infectious Diseases (REIPI), Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases (GC-03) and Clinical and Molecular Microbiology (GC-24) Groups, Maimonides Biomedical Research Institute of Cordoba, Reina Sofía University Hospital, University of Cordoba (IMIBIC/HURS/UCO), Cordoba, Spain
- Department of Agricultural Chemistry, Edaphology and Microbiology and Department of Medical and Surgical Sciences, University of Cordoba, Cordoba, Spain
- Clinical Units of Infectious Diseases and Microbiology, Reina Sofía University Hospital, Cordoba, Spain
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24
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Buta-Hubeny M, Korzeniewska E, Hubeny J, Zieliński W, Rolbiecki D, Harnisz M, Paukszto Ł. Structure of the manure resistome and the associated mobilome for assessing the risk of antimicrobial resistance transmission to crops. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152144. [PMID: 34864022 DOI: 10.1016/j.scitotenv.2021.152144] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 05/23/2023]
Abstract
In this study, the impact of bovine and poultry manure on the quantitative and qualitative composition of antibiotic resistance genes (ARGs) and the environmental mobilome associated with antimicrobial resistance in soil and crops was determined with the use of next generation sequencing methods. The aim of the study was to perform a metagenomic analysis of manure to estimate the risk of the transmission of ARGs and bacterial drug resistance carriers to fertilized soil and crops. The total copy number of ARGs was nearly four times higher in poultry manure (555 ppm) than in bovine manure (140 ppm), and this relationship was also noted in fertilized soil. Poultry manure induced a much greater increase in the concentrations of ARGs in the soil environment (196.4 ppm) than bovine manure (137.8 ppm) immediately after supplementation. The application of poultry manure led to the highest increase in the abundance of genes encoding resistance to tetracyclines (9%), aminoglycosides (3.5%), sulfonamides (3%), bacitracin (2%), chloramphenicol (2%), and macrolide-lincosamide-streptogramin antibiotics (1%). Heavy metals were stronger promoters of antibiotic resistance in the environment than antibiotics. Antibiotics exerted a greater influence on maintaining the diversity of ARGs than on increasing their abundance in soil. Large quantities of insertion sequences (IS), including those associated with the mobility of ARGs in the population of ESKAPEE pathogens, are introduced to soil with manure. These IS remain stable for up to several months, which indicates that manure, in particular poultry manure, significantly increases the risk of rapid ARG transfer to the environment. Manure also largely contributes to an increase in the diversity of the resistome and mobilome in the metagenome of bacteria isolated from crops. Bacteria of the phylum Proteobacteria appear to play a major role in the transmission of multiple ARGs in crops grown for human and animal consumption.
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Affiliation(s)
- Martyna Buta-Hubeny
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland.
| | - Jakub Hubeny
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
| | - Wiktor Zieliński
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
| | - Damian Rolbiecki
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
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25
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Liu C, Li Z, Ding J, Zhen H, Fang M, Nie C. Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer. Front Microbiol 2022; 12:765291. [PMID: 34975790 PMCID: PMC8715872 DOI: 10.3389/fmicb.2021.765291] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/11/2021] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer deaths and continuously increases new cancer cases globally. Accumulating evidence links risks of CRC to antibiotic use. Long-term use and abuse of antibiotics increase the resistance of the gut microbiota; however, whether CRC is associated with antibiotic resistance in gut microbiota is still unclear. In this study, we performed a de novo assembly to metagenomic sequences in 382 CRC patients and 387 healthy controls to obtain representative species-level genome bins (rSGBs) and plasmids and analyzed the abundance variation of species and antibiotic resistance genes (ARGs). Twenty-five species and 65 ARGs were significantly enriched in the CRC patients, and among these ARGs, 12 were multidrug-resistant genes (MRGs), which mainly included acrB, TolC, marA, H-NS, Escherichia coli acrR mutation, and AcrS. These MRGs could confer resistance to fluoroquinolones, tetracyclines, cephalosporins, and rifamycin antibiotics by antibiotic efflux and inactivation. A classification model was built using the abundance of species and ARGs and achieved areas under the curve of 0.831 and 0.715, respectively. Our investigation has identified the antibiotic resistance types of ARGs and suggested that E. coli is the primary antibiotic resistance reservoir of ARGs in CRC patients, providing valuable evidence for selecting appropriate antibiotics in the CRC treatment.
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Affiliation(s)
- Chuanfa Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Zhiming Li
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jiahong Ding
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Hefu Zhen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Mingyan Fang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Chao Nie
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
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26
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Changes in the gut microbiota and risk of colonization by multidrug-resistant bacteria, infection and death in critical care patients. Clin Microbiol Infect 2022; 28:975-982. [DOI: 10.1016/j.cmi.2022.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 11/22/2022]
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27
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de Souza-Silva TG, Oliveira IA, da Silva GG, Giusti FCV, Novaes RD, de Almeida Paula HA. Impact of microplastics on the intestinal microbiota: A systematic review of preclinical evidence. Life Sci 2022; 294:120366. [DOI: 10.1016/j.lfs.2022.120366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 12/14/2022]
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28
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Alcedo K, Ruiz J, Ochoa TJ, Riveros M. High Prevalence of blaCTX-M in Fecal Commensal Escherichia coli from Healthy Children. Infect Chemother 2022; 54:59-69. [PMID: 35132833 PMCID: PMC8987167 DOI: 10.3947/ic.2021.0102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/17/2021] [Indexed: 01/01/2023] Open
Abstract
Background Antibiotic-resistant Escherichia coli can colonize the intestinal tract of healthy children, causing concern when antibiotic resistance is related to the presence of transferable mechanisms, such as extended-spectrum β-lactamases (ESBLs). Materials and Methods Fecal samples from 41 healthy children from two villages of rural Peru were cultured on ceftriaxone-disks. ESBL production was confirmed with double disk synergy. In all ESBL-produced isolates, antibiotic susceptibility to 12 antibacterial agents was established by disk diffusion, while clonal relationships were determined by repetitive extragenic palindromic-polymerase chain reaction (REP-PCR). Presence of ST131 was determined using PCR. Results Ceftriaxone-resistant microorganisms were recovered from 39 samples belonging to 22 out of 41 children (53.7%). Of these, 80 ceftriaxone-resistant and two ceftriaxone-intermediate E. coli from inside ceftriaxone-halos were confirmed as ESBL-producers. All isolates were multidrug-resistant. In 79/80 (98.8%) ceftriaxone-resistant isolates, the presence of blaCTX-M was detected alone (58 isolates, or together with other β-lactamase (blaTEM, 17 isolates; blaOXA-1-like, 3 isolates; blaTEM + blaOXA-1-like, 1 isolate), while in one isolate no such ESBL was identified. The two ceftriaxone-intermediate isolates recovered from the same sample, carried a blaTEM and blaSHV respectively. Thirty-four different clones were identified, with 4 clones being recovered from different samples from the same child. Twelve clones were disseminated among different children, including 5 clones disseminated between both villages. Two clones, accounting for 3 isolates and both recovered from the same children, belonged to E. coli ST131. Conclusion This study demonstrates high prevalence of ESBL-carriers among healthy children living in a rural area of Peru, stressing the need for continuous surveillance and search for public health control measures.
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Affiliation(s)
- Katherine Alcedo
- Laboratorio de Infectología Pediátrica, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joaquim Ruiz
- Laboratorio de Microbiología Molecular y Genómica Bacteriana, Universidad Científica del Sur, Lima, Peru
| | - Theresa J. Ochoa
- Laboratorio de Infectología Pediátrica, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Pediatrics University of Texas School of Public Health, Houston, Texas, USA
| | - Maribel Riveros
- Laboratorio de Infectología Pediátrica, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Ciencias Naturales y Matemática, Universidad Nacional Federico Villarreal, Lima, Peru
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29
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Bhargava K, Nath G, Bhargava A, Aseri GK, Jain N. Phage therapeutics: from promises to practices and prospectives. Appl Microbiol Biotechnol 2021; 105:9047-9067. [PMID: 34821965 PMCID: PMC8852341 DOI: 10.1007/s00253-021-11695-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 01/09/2023]
Abstract
The rise in multi-drug resistant bacteria and the inability to develop novel antibacterial agents limits our arsenal against infectious diseases. Antibiotic resistance is a global issue requiring an immediate solution, including the development of new antibiotic molecules and other alternative modes of therapy. This article highlights the mechanism of bacteriophage treatment that makes it a real solution for multidrug-resistant infectious diseases. Several case reports identified phage therapy as a potential solution to the emerging challenge of multi-drug resistance. Bacteriophages, unlike antibiotics, have special features, such as host specificity and do not impact other commensals. A new outlook has also arisen with recent advancements in the understanding of phage immunobiology, where phages are repurposed against both bacterial and viral infections. Thus, the potential possibility of phages in COVID-19 patients with secondary bacterial infections has been briefly elucidated. However, significant obstacles that need to be addressed are to design better clinical studies that may contribute to the widespread use of bacteriophage therapy against multi-drug resistant pathogens. In conclusion, antibacterial agents can be used with bacteriophages, i.e. bacteriophage-antibiotic combination therapy, or they can be administered alone in cases when antibiotics are ineffective.Key points• AMR, a consequence of antibiotic generated menace globally, has led to the resurgence of phage therapy as an effective and sustainable solution without any side effects and high specificity against refractory MDR bacterial infections.• Bacteriophages have fewer adverse reactions and can thus be used as monotherapy as well as in conjunction with antibiotics.• In the context of the COVID-19 pandemic, phage therapy may be a viable option.
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Affiliation(s)
- Kanika Bhargava
- Amity Institute of Microbial Technology, Amity University Rajasthan, Jaipur, 303 002 India
- Department of Microbiology, IMS, Banaras Hindu University, Varanasi, 221005 India
| | - Gopal Nath
- Department of Microbiology, IMS, Banaras Hindu University, Varanasi, 221005 India
| | - Amit Bhargava
- Department of Medicine, Hayes Memorial Hospital, SHUATS, Allahabad, 211007 India
| | - G. K. Aseri
- Amity Institute of Microbial Technology, Amity University Rajasthan, Jaipur, 303 002 India
| | - Neelam Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 303 002 India
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30
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Niegowska M, Sanseverino I, Navarro A, Lettieri T. Knowledge gaps in the assessment of antimicrobial resistance in surface waters. FEMS Microbiol Ecol 2021; 97:fiab140. [PMID: 34625810 PMCID: PMC8528692 DOI: 10.1093/femsec/fiab140] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022] Open
Abstract
The spread of antibiotic resistance in the water environment has been widely described. However, still many knowledge gaps exist regarding the selection pressure from antibiotics, heavy metals and other substances present in surface waters as a result of anthropogenic activities, as well as the extent and impact of this phenomenon on aquatic organisms and humans. In particular, the relationship between environmental concentrations of antibiotics and the acquisition of ARGs by antibiotic-sensitive bacteria as well as the impact of heavy metals and other selective agents on antimicrobial resistance (AMR) need to be defined. Currently, established safety values are based on the effects of antibiotic toxicity neglecting the question of AMR spread. In turn, risk assessment of antibiotics in waterbodies remains a complex question implicating multiple variables and unknowns reinforced by the lack of harmonized protocols and official guidelines. In the present review, we discussed current state-of-the-art and the knowledge gaps related to pressure exerted by antibiotics and heavy metals on aquatic environments and their relationship to the spread of AMR. Along with this latter, we reflected on (i) the risk assessment in surface waters, (ii) selective pressures contributing to its transfer and propagation and (iii) the advantages of metagenomics in investigating AMR. Furthermore, the role of microplastics in co-selection for metal and antibiotic resistance, together with the need for more studies in freshwater are highlighted.
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Affiliation(s)
- Magdalena Niegowska
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Isabella Sanseverino
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Anna Navarro
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Teresa Lettieri
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi 2749, 21027 Ispra, Italy
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31
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Mujawdiya PK, Kapur S. Modulation of Gut Microbiota through Dietary Phytochemicals as a Novel Anti-infective Strategy. Curr Drug Discov Technol 2021; 17:498-506. [PMID: 31702513 DOI: 10.2174/1570163816666191107124214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/08/2019] [Accepted: 09/08/2019] [Indexed: 02/07/2023]
Abstract
Quorum Sensing (QS) is a phenomenon in which bacterial cells communicate with each other with the help of several low molecular weight compounds. QS is largely dependent on population density, and it triggers when the concentration of quorum sensing molecules accumulate in the environment and crosses a particular threshold. Once a certain population density is achieved and the concentration of molecules crosses a threshold, the bacterial cells show a collective behavior in response to various chemical stimuli referred to as "auto-inducers". The QS signaling is crucial for several phenotypic characteristics responsible for bacterial survival such as motility, virulence, and biofilm formation. Biofilm formation is also responsible for making bacterial cells resistant to antibiotics. The human gut is home to trillions of bacterial cells collectively called "gut microbiota" or "gut microbes". Gut microbes are a consortium of more than 15,000 bacterial species and play a very crucial role in several body functions such as metabolism, development and maturation of the immune system, and the synthesis of several essential vitamins. Due to its critical role in shaping human survival and its modulating impact on body metabolisms, the gut microbial community has been referred to as "the forgotten organ" by O`Hara et al. (2006) [1]. Several studies have demonstrated that chemical interaction between the members of bacterial cells in the gut is responsible for shaping the overall microbial community. Recent advances in phytochemical research have generated a lot of interest in finding new, effective, and safer alternatives to modern chemical-based medicines. In the context of antimicrobial research various plant extracts have been identified with Quorum Sensing Inhibitory (QSI) activities among bacterial cells. This review focuses on the mechanism of quorum sensing and quorum sensing inhibitors isolated from natural sources.
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Affiliation(s)
- Pavan K Mujawdiya
- Department of Biological Sciences, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad- 500078, India
| | - Suman Kapur
- Department of Biological Sciences, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Hyderabad- 500078, India
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32
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Mejía-Pitta A, Broset E, de la Fuente-Nunez C. Probiotic engineering strategies for the heterologous production of antimicrobial peptides. Adv Drug Deliv Rev 2021; 176:113863. [PMID: 34273423 PMCID: PMC8440409 DOI: 10.1016/j.addr.2021.113863] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 06/10/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022]
Abstract
Engineered probiotic bacteria represent an innovative approach for treating and detecting a wide range of diseases including those caused by infectious agents. Antimicrobial peptides (AMPs) are promising alternatives to conventional antibiotics for combating antibiotic-resistant infections. These molecules can be delivered orally to the gut by using engineered probiotics, which confer protection against AMP degradation, thus enabling numerous applications including treating drug-resistant enteric pathogens and remodeling the microbiota in real time. Here, we provide an update on the current state of the art on AMP-producing probiotics, discuss methods to enhance gut colonization, and end by outlining future perspectives.
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Affiliation(s)
- Adriana Mejía-Pitta
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Esther Broset
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America.
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33
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Vallé Q, Roques BB, Bousquet-Mélou A, Dahlhaus D, Ramon-Portugal F, Dupouy V, Bibbal D, Ferran AA. Prediction of Minocycline Activity in the Gut From a Pig Preclinical Model Using a Pharmacokinetic -Pharmacodynamic Approach. Front Microbiol 2021; 12:671376. [PMID: 34305836 PMCID: PMC8299485 DOI: 10.3389/fmicb.2021.671376] [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: 02/23/2021] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
The increase of multidrug-resistant (MDR) bacteria has renewed interest in old antibiotics, such as minocycline, that can be active against various MDR Gram-negative pathogens. The elimination of minocycline by both kidneys and liver makes it suitable for impaired renal function patients. However, the drawback is the possible elimination of a high amount of drug in the intestines, with potential impact on the digestive microbiota during treatment. This study aimed to predict the potential activity of minocycline against Enterobacterales in the gut after parenteral administration, by combining in vivo and in vitro studies. Total minocycline concentrations were determined by UPLC-UV in the plasma and intestinal content of piglets following intravenous administration. In parallel, the in vitro activity of minocycline was assessed against two Escherichia coli strains in sterilized intestinal contents, and compared to activity in a standard broth. We found that minocycline concentrations were 6–39 times higher in intestinal contents than plasma. Furthermore, minocycline was 5- to 245-fold less active in large intestine content than in a standard broth. Using this PK-PD approach, we propose a preclinical pig model describing the link between systemic and gut exposure to minocycline, and exploring its activity against intestinal Enterobacterales by taking into account the impact of intestinal contents.
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Affiliation(s)
- Quentin Vallé
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France.,Virbac, Carros, France
| | | | | | - David Dahlhaus
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | | | - Delphine Bibbal
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Aude A Ferran
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
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34
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Shah T, Baloch Z, Shah Z, Cui X, Xia X. The Intestinal Microbiota: Impacts of Antibiotics Therapy, Colonization Resistance, and Diseases. Int J Mol Sci 2021; 22:ijms22126597. [PMID: 34202945 PMCID: PMC8235228 DOI: 10.3390/ijms22126597] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
Trillions of microbes exist in the human body, particularly the gastrointestinal tract, coevolved with the host in a mutually beneficial relationship. The main role of the intestinal microbiome is the fermentation of non-digestible substrates and increased growth of beneficial microbes that produce key antimicrobial metabolites such as short-chain fatty acids, etc., to inhibit the growth of pathogenic microbes besides other functions. Intestinal microbiota can prevent pathogen colonization through the mechanism of colonization resistance. A wide range of resistomes are present in both beneficial and pathogenic microbes. Giving antibiotic exposure to the intestinal microbiome (both beneficial and hostile) can trigger a resistome response, affecting colonization resistance. The following review provides a mechanistic overview of the intestinal microbiome and the impacts of antibiotic therapy on pathogen colonization and diseases. Further, we also discuss the epidemiology of immunocompromised patients who are at high risk for nosocomial infections, colonization and decolonization of multi-drug resistant organisms in the intestine, and the direct and indirect mechanisms that govern colonization resistance to the pathogens.
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Affiliation(s)
- Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Yunnan Key Laboratory of Sustainable Utilization of Panax Notoginseng, Kunming 650500, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Correspondence: (Z.B.); (X.C.); (X.X.)
| | - Zahir Shah
- Faculty of Animal Husbandry and Veterinary Sciences, College of Veterinary Sciences, The University of Agriculture Peshawar, Peshawar 25120, Pakistan;
| | - Xiuming Cui
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Yunnan Key Laboratory of Sustainable Utilization of Panax Notoginseng, Kunming 650500, China
- Correspondence: (Z.B.); (X.C.); (X.X.)
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Correspondence: (Z.B.); (X.C.); (X.X.)
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35
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Neil K, Allard N, Rodrigue S. Molecular Mechanisms Influencing Bacterial Conjugation in the Intestinal Microbiota. Front Microbiol 2021; 12:673260. [PMID: 34149661 PMCID: PMC8213034 DOI: 10.3389/fmicb.2021.673260] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/10/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial conjugation is a widespread and particularly efficient strategy to horizontally disseminate genes in microbial populations. With a rich and dense population of microorganisms, the intestinal microbiota is often considered a fertile environment for conjugative transfer and a major reservoir of antibiotic resistance genes. In this mini-review, we summarize recent findings suggesting that few conjugative plasmid families present in Enterobacteriaceae transfer at high rates in the gut microbiota. We discuss the importance of mating pair stabilization as well as additional factors influencing DNA transfer efficiency and conjugative host range in this environment. Finally, we examine the potential repurposing of bacterial conjugation for microbiome editing.
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Affiliation(s)
| | | | - Sébastien Rodrigue
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada
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36
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Cuscó A, Pérez D, Viñes J, Fàbregas N, Francino O. Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces. BMC Genomics 2021; 22:330. [PMID: 33957869 PMCID: PMC8103633 DOI: 10.1186/s12864-021-07607-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
Background Long-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample. Results We used nanopore long-read metagenomics and frameshift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were > 90% complete with < 5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs that are potential HQ MAGs. These HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Catenibacterium, Blautia, and Enterococcus genera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific –Succinivibrio, Prevotellamassilia, Phascolarctobacterium, Blautia_A sp900541345–, whereas others are more broadly distributed among animal and human microbiomes –Sutterella, Catenibacterium, Enterococcus, and Blautia sp003287895. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Moreover, we show that long reads are essential to detect mobilome functions, usually missed in short-read MAGs. Conclusions We recovered eight single-contig HQ MAGs from canine feces of a healthy dog with nanopore long-reads. We also retrieved relevant biological insights from these specific bacterial species previously missed in public databases, such as complete ribosomal operons and mobilome functions. The high-molecular-weight DNA extraction improved the assembly’s contiguity, whereas the high-accuracy basecalling, the raw read error correction, the assembly polishing, and the frameshift correction reduced the insertion and deletion errors. Both experimental and analytical steps ensured the retrieval of complete bacterial genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07607-0.
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Affiliation(s)
- Anna Cuscó
- Vetgenomics, Ed Eureka, Parc de Recerca UAB, Barcelona, Spain.
| | - Daniel Pérez
- Molecular Genetics Veterinary Service (SVGM), Veterinary School, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joaquim Viñes
- Vetgenomics, Ed Eureka, Parc de Recerca UAB, Barcelona, Spain.,Molecular Genetics Veterinary Service (SVGM), Veterinary School, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Norma Fàbregas
- Vetgenomics, Ed Eureka, Parc de Recerca UAB, Barcelona, Spain
| | - Olga Francino
- Molecular Genetics Veterinary Service (SVGM), Veterinary School, Universitat Autònoma de Barcelona, Barcelona, Spain
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Abstract
Animals live in symbiosis with numerous microbe species. While some can protect hosts from infection and benefit host health, components of the microbiota or changes to the microbial landscape have the potential to facilitate infections and worsen disease severity. Pathogens and pathobionts can exploit microbiota metabolites, or can take advantage of a depletion in host defences and changing conditions within a host, to cause opportunistic infection. The microbiota might also favour a more virulent evolutionary trajectory for invading pathogens. In this review, we consider the ways in which a host microbiota contributes to infectious disease throughout the host's life and potentially across evolutionary time. We further discuss the implications of these negative outcomes for microbiota manipulation and engineering in disease management.
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Affiliation(s)
- Emily J. Stevens
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kieran A. Bates
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kayla C. King
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Lauxen AI, Kobauri P, Wegener M, Hansen MJ, Galenkamp NS, Maglia G, Szymanski W, Feringa BL, Kuipers OP. Mechanism of Resistance Development in E. coli against TCAT, a Trimethoprim-Based Photoswitchable Antibiotic. Pharmaceuticals (Basel) 2021; 14:ph14050392. [PMID: 33919397 PMCID: PMC8143356 DOI: 10.3390/ph14050392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 11/16/2022] Open
Abstract
During the last decades, a continuous rise of multi-drug resistant pathogens has threatened antibiotic efficacy. To tackle this key challenge, novel antimicrobial therapies are needed with increased specificity for the site of infection. Photopharmacology could enable such specificity by allowing for the control of antibiotic activity with light, as exemplified by trans/cis-tetra-ortho-chloroazobenzene-trimethoprim (TCAT) conjugates. Resistance development against the on (irradiated, TCATa) and off (thermally adapted, TCATd) states of TCAT were compared to that of trimethoprim (TMP) in Escherichia coli mutant strain CS1562. Genomics and transcriptomics were used to explore the acquired resistance. Although TCAT shows TMP-like dihydrofolate reductase (DHFR) inhibition in vitro, transcriptome analyses show different responses in acquired resistance. Resistance against TCATa (on) relies on the production of exopolysaccharides and overexpression of TolC. While resistance against TCATd (off) follows a slightly different gene expression profile, both indicate hampering the entrance of the molecule into the cell. Conversely, resistance against TMP is based on alterations in cell metabolism towards a more persister-like phenotype, as well as alteration of expression levels of enzymes involved in the folate biosynthesis. This study provides a deeper understanding of the development of new therapeutic strategies and the consequences on resistance development against photopharmacological drugs.
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Affiliation(s)
- Anna I. Lauxen
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands;
| | - Piermichele Kobauri
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
| | - Michael Wegener
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
| | - Mickel J. Hansen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
| | - Nicole S. Galenkamp
- Groningen Biomolecular Science & Biotechnology Institute, University of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands; (N.S.G.); (G.M.)
| | - Giovanni Maglia
- Groningen Biomolecular Science & Biotechnology Institute, University of Groningen, Nijenborg 4, 9747 AG Groningen, The Netherlands; (N.S.G.); (G.M.)
| | - Wiktor Szymanski
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
- Medical Imaging Center, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
- Correspondence: (W.S.); (B.L.F.); (O.P.K.)
| | - Ben L. Feringa
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands; (P.K.); (M.W.); (M.J.H.)
- Correspondence: (W.S.); (B.L.F.); (O.P.K.)
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands;
- Correspondence: (W.S.); (B.L.F.); (O.P.K.)
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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: 1.3] [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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Rochegüe T, Haenni M, Cazeau G, Metayer V, Madec JY, Ferry T, Lupo A. An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes. Diagn Microbiol Infect Dis 2021; 100:115328. [PMID: 33819858 DOI: 10.1016/j.diagmicrobio.2021.115328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 01/28/2023]
Abstract
Early antibiotic resistance determinants (ARDs) detection in humans or animals is crucial to counteract their propagation. The ARDs quantification is fundamental to understand the perturbation caused by disruptors, such as antibiotics, during therapies. Forty-three qPCRs on the most diffused ARDs and integrons among human and animal Enterobacterales, and one on the 16S rDNA for bacteria quantification, were developed. The qPCRs, using hydrolysis probes, operated with a unique amplification condition and were tested analytically and diagnostically performing 435 reactions on five positive and negative controls for each qPCR. Diagnostic sensitivity and specificity were confirmed by PCR and genome sequencing of control isolates, demonstrating 100% performance for all qPCRs. An easy and rapid discrimination method for the epidemiologically relevant blaCTX-Ms is provided. This large, noncommercial qPCRs inventory could serve for precise quantification of ARDs, but also as a rapid screening tool for surveillance purposes, providing the basis for further high-throughput developments.
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Affiliation(s)
- Tony Rochegüe
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Géraldine Cazeau
- ANSES - Université de Lyon, Unité Epidémiologie et Appui à la Surveillance (EAS), Lyon, France
| | - Véronique Metayer
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Tristan Ferry
- Service des maladies infectieuses et tropicales, CHU de Lyon, Hôpital de la Croix-Rousse, Lyon, France; Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Agnese Lupo
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France.
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M D, Vijaya Kumar D, Ballamoole KK, Shetty A V, Chakraborty A, Karunasagar I. Occurrence of antibiotic resistance among Gram negative bacteria isolated from effluents of fish processing plants in and around Mangalore. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2020; 30:653-660. [PMID: 31112036 DOI: 10.1080/09603123.2019.1618799] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/10/2019] [Indexed: 06/09/2023]
Abstract
The presence of antibiotic-resistant bacteria in seafood not only poses a serious health risk for the consumers but also contributes to the spread of these antibiotic-resistant bacteria in the natural environments through the effluents discharged from the fish processing plants. The aims of this study were to isolate Gram-negative bacteria from the effluents of fish processing plants in and around Mangalore, India and to profile their antibiotic resistance pattern. Maximum resistance was seen for ampicillin (40.78%) followed by tetracycline (40.22%) and nitrofurantoin (29.05%). Further, the detection of genes that contribute to antibiotic resistance revealed the presence of sulfonamide resistance genes (sul1 and sul2) and extended spectrum β-lactamase genes (bla CTX-M, bla TEM) in a few isolates. The presence of such bacteria in fish processing effluents is a matter of great concern because they can contribute significantly to the antibiotic resistance in the natural environment. It is imperative that seafood processing plants follow the safe disposal of effluents in order to reduce or eliminate the antibiotic resistance menace.
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Affiliation(s)
- Divyashree M
- UNESCO MIRCEN for Medical and Marine Biotechnology, Nitte University Center for Science Education and Research, Nitte (Deemed to be Universuty) , Mangaluru, Karnataka, India
| | - Deekshit Vijaya Kumar
- UNESCO MIRCEN for Medical and Marine Biotechnology, Nitte University Center for Science Education and Research, Nitte (Deemed to be Universuty) , Mangaluru, Karnataka, India
| | - Krishna Kumar Ballamoole
- UNESCO MIRCEN for Medical and Marine Biotechnology, Nitte University Center for Science Education and Research, Nitte (Deemed to be Universuty) , Mangaluru, Karnataka, India
| | - Veena Shetty A
- Department of Microbiology, K.S.Hegde Medical Academy, Nitte (Deemed to be University) , Mangaluru, Karnataka, India
| | - Anirban Chakraborty
- UNESCO MIRCEN for Medical and Marine Biotechnology, Nitte University Center for Science Education and Research, Nitte (Deemed to be Universuty) , Mangaluru, Karnataka, India
| | - Indrani Karunasagar
- UNESCO MIRCEN for Medical and Marine Biotechnology, Nitte University Center for Science Education and Research, Nitte (Deemed to be Universuty) , Mangaluru, Karnataka, India
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Acquired Genetic Elements that Contribute to Antimicrobial Resistance in Frequent Gram-Negative Causative Agents of Healthcare-Associated Infections. Am J Med Sci 2020; 360:631-640. [PMID: 32747008 DOI: 10.1016/j.amjms.2020.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/26/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance (AMR) is a worldwide public health problem that reduces therapeutic options and increases the risk of death. The causative agents of healthcare-associated infections (HAIs) are drug-resistant microorganisms of the nosocomial environment, which have developed different mechanisms of AMR. The hospital-associated microbiota has been proposed to be a reservoir of genes associated with AMR and an environment where the transfer of genetic material among organisms may occur. The ESKAPE group (Enterococcus faecalis and Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter aerogenes and Escherichia coli) is a frequent causative agents of HAIs. In this review, we address the issue of acquired genetic elements that contribute to AMR in the most frequent Gram-negative of ESKAPE, with a focus on last resort antimicrobial agents and the role of transference of genetic elements for the development of AMR.
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Sanchez JJ, Alam MA, Stride CB, Haque MA, Das S, Mahfuz M, Roth DE, Sly PD, Long KZ, Ahmed T. Campylobacter infection and household factors are associated with childhood growth in urban Bangladesh: An analysis of the MAL-ED study. PLoS Negl Trop Dis 2020; 14:e0008328. [PMID: 32407313 PMCID: PMC7252635 DOI: 10.1371/journal.pntd.0008328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 05/27/2020] [Accepted: 04/27/2020] [Indexed: 01/24/2023] Open
Abstract
The dual burden of enteric infection and childhood malnutrition continues to be a global health concern and a leading cause of morbidity and death among children. Campylobacter infection, in particular, is highly prevalent in low- and middle-income countries, including Bangladesh. We examined longitudinal data to evaluate the trajectories of change in child growth, and to identify associations with Campylobacter infection and household factors. The study analyzed data from 265 children participating in the MAL-ED Study in Mirpur, Bangladesh. We applied latent growth curve modelling to evaluate the trajectories of change in children's height, as measured by length-for-age z-score (LAZ), from age 0-24 months. Asymptomatic and symptomatic Campylobacter infections were included as 3- and 6-month lagged time-varying covariates, while household risk factors were included as time-invariant covariates. Maternal height and birth order were positively associated with LAZ at birth. An inverse association was found between increasing age and LAZ. Campylobacter infection prevalence increased with age, with over 70% of children 18-24 months of age testing positive for infection. In the final model, Campylobacter infection in the preceding 3-month interval was negatively associated with LAZ at 12, 15, and 18 months of age; similarly, infection in the preceding 6-month interval was negatively associated with LAZ at 15, 18, and 21 months of age. Duration of antibiotic use and access to treated drinking water were negatively associated with Campylobacter infection, with the strength of the latter effect increasing with children's age. Campylobacter infection had a significant negative effect on child's growth and this effect was most powerful between 12 and 21 months. The treatment of drinking water and increased antibiotic use have a positive indirect effect on linear child growth trajectory, acting via their association with Campylobacter infection.
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Affiliation(s)
- J. Johanna Sanchez
- Children’s Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Md. Ashraful Alam
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Christopher B. Stride
- The Institute of Work Psychology, University of Sheffield, Sheffield, United Kingdom
| | - Md. Ahshanul Haque
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Subhasish Das
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Mustafa Mahfuz
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh
| | - Daniel E. Roth
- Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Peter D. Sly
- Children’s Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Kurt Z. Long
- Children’s Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh
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van Staa TP, Palin V, Li Y, Welfare W, Felton TW, Dark P, Ashcroft DM. The effectiveness of frequent antibiotic use in reducing the risk of infection-related hospital admissions: results from two large population-based cohorts. BMC Med 2020; 18:40. [PMID: 32114981 PMCID: PMC7050123 DOI: 10.1186/s12916-020-1504-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/27/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Previous research reported that individuals prescribed antibiotics frequently develop antimicrobial resistance. The objective of this study was to evaluate whether frequent antibiotic use is associated with reduced hospital admissions for infection-related complications. METHODS Population-based cohort study analysing electronic health records from primary care linked to hospital admission records. The study population included patients prescribed a systemic antibiotic, recent record of selected infections and no history of chronic obstructive pulmonary disease. Propensity-matched cohorts were identified based on quintiles of prior antibiotic use in 3 years before. RESULTS A total of 1.8 million patients were included. Repeated antibiotic use was frequent. The highest rates of hospital admissions for infection-related complications were observed shortly after antibiotic start in all prior exposure quintiles. For patients with limited prior antibiotic use, rates then dropped quickly and substantially. In contrast, reductions over time were substantially less in patients with frequent prior antibiotic use, with rates remaining elevated over the following 6 months. In patients without comorbidity comparing the highest to lowest prior exposure quintiles in the Clinical Practice Research Databank, the IRRs were 1.18 [95% CI 0.90-1.55] in the first 3 days after prescription, 1.44 [95% CI 1.14-1.81] in the days 4-30 after and 3.22 [95% CI 2.29-4.53] in the 3-6 months after. CONCLUSIONS Repeated courses of antibiotics, although common practice, may have limited benefit and indicator of adverse outcomes. A potential mechanism is that antibiotics may cause dysbiosis (perturbations of intestinal microbiota), contributing to colonization with resistant bacteria. Antibiotics should be used judiciously and only periodically unless indicated. Antimicrobial stewardship should include activities focusing on the substantive number of patients who repeatedly but intermittently get antibiotics.
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Affiliation(s)
- Tjeerd Pieter van Staa
- Centre for Health Informatics, Division of Informatics, Imaging and Data Science, Faculty of Biology, Medicine and Health, School of Health Sciences, The University of Manchester, Manchester Academic Health Science Centre, Vaughan House, Manchester, M13 9PL, UK. .,Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, the Netherlands.
| | - Victoria Palin
- Centre for Health Informatics, Division of Informatics, Imaging and Data Science, Faculty of Biology, Medicine and Health, School of Health Sciences, The University of Manchester, Manchester Academic Health Science Centre, Vaughan House, Manchester, M13 9PL, UK
| | - Yan Li
- Centre for Health Informatics, Division of Informatics, Imaging and Data Science, Faculty of Biology, Medicine and Health, School of Health Sciences, The University of Manchester, Manchester Academic Health Science Centre, Vaughan House, Manchester, M13 9PL, UK
| | - William Welfare
- Public Health England North West, 3 Piccadilly Place, London Road, Manchester, M1 3BN, UK
| | - Timothy W Felton
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Intensive Care Unit, Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
| | - Paul Dark
- Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Darren M Ashcroft
- Centre for Pharmacoepidemiology and Drug Safety, NIHR Greater Manchester Patient Safety Translational Research Centre, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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Rubin J, Mussio K, Xu Y, Suh J, Riley LW. Prevalence of Antimicrobial Resistance Genes and Integrons in Commensal Gram-Negative Bacteria in a College Community. Microb Drug Resist 2020; 26:1227-1235. [PMID: 31985343 DOI: 10.1089/mdr.2019.0279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although the human intestinal microbiome has been shown to harbor antimicrobial drug resistance genes (ARGs), the prevalence of such genes in a healthy population and their impact on extraintestinal infections that occur in that community are not well established. This study sought to identify ARG prevalence and their mobile elements in the intestines of a healthy community population at a California University, and compared these genes to those previously identified among uropathogenic Escherichia coli isolated from patients with urinary tract infection from the same community. We isolated Gram-negative bacteria (GNB) from fecal samples of healthy volunteers and screened them by polymerase chain reaction for class 1 integron cassette sequences and ARGs encoding resistance against ampicillin, trimethoprim-sulfamethoxazole, gentamicin, and colistin. We found antimicrobial-resistant GNB from 83 (81%) of 102 nonredundant rectal swab samples. Seventy-four (72%) of these samples contained β-lactamase genes (blaTEM, blaSHV, blaCTX-M, blaOXA, and blaOXY), dihydrofolate reductase (DHFR) genes (dhfr-A17, dhfr-A12, dhfr-A7, dhfr-A5, dhfr-A21, dhfr-A1, dhfr-A13, and dhfr-7), and aminoglycoside resistance genes (aadA5, aadA2, aadA1, and aadB). Integron sequences were found in 37 (36%) fecal samples. These genes were found in 11 different GNB species. The high prevalence of clinically common ARGs and integrons harbored by GNB in the intestine of a healthy population suggest that human intestines may serve as a major reservoir of these mobile ARGs that appear in E. coli strains causing extraintestinal infections in the same community.
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Affiliation(s)
- Julia Rubin
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Kaitlyn Mussio
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Yuqi Xu
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing, China
| | - Joy Suh
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
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Aira A, Fehér C, Rubio E, Soriano A. The Intestinal Microbiota as a Reservoir and a Therapeutic Target to Fight Multi-Drug-Resistant Bacteria: A Narrative Review of the Literature. Infect Dis Ther 2019; 8:469-482. [PMID: 31654298 PMCID: PMC6856238 DOI: 10.1007/s40121-019-00272-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Indexed: 12/12/2022] Open
Abstract
The appearance and dissemination of antibiotic-resistant bacteria, particularly in specific closed environments such as intensive care units of acute care hospitals, have become a major health concern. The intestinal microbiota has various functions including host protection from overgrowth or colonization by unwanted bacteria. The exposure to antibiotics significantly reduces the bacterial density of intestinal microbiota leaving an ecologic void that can be occupied by potentially pathogenic and/or resistant bacteria frequently present in hospital settings. Consequently, the intestinal microbiota of inpatients acts as a major reservoir and plays a critical role in perpetuating the spread of resistant bacteria. There are novel innovative methods to protect the host microbiota during antibiotic treatment, but they do not offer a solution for already established colonization by resistant microorganisms. Fecal microbiota transfer (FMT) is a promising intervention to achieve this goal; however, controlled trials report lower success rates than initial retrospective studies, especially in case of gram negatives. The aim of the present article is to highlight the importance of the intestinal microbiota in the global spread of multi-drug-resistant (MDR) microorganisms and to review the recent advances to protect the human microbiota from the action of antibiotics as well as a critical discussion about the evidence of decolonization of MDR microorganisms by FMT.
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Affiliation(s)
- Andrea Aira
- Department of Infectious Diseases, Hospital Clínic, IDIBAPS, Catalonia, Barcelona, Spain
| | - Csaba Fehér
- Department of Infectious Diseases, Hospital Clínic, IDIBAPS, Catalonia, Barcelona, Spain
| | - Elisa Rubio
- Department of Clinical Microbiology, Hospital Clínic, Catalonia, Barcelona, Spain
| | - Alex Soriano
- Department of Infectious Diseases, Hospital Clínic, IDIBAPS, Catalonia, Barcelona, Spain.
- University of Barcelona, IDIBAPS, Catalonia, Barcelona, Spain.
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Yoon YK, Suh JW, Kang EJ, Kim JY. Efficacy and safety of fecal microbiota transplantation for decolonization of intestinal multidrug-resistant microorganism carriage: beyond Clostridioides difficile infection. Ann Med 2019; 51:379-389. [PMID: 31468999 PMCID: PMC7877873 DOI: 10.1080/07853890.2019.1662477] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Persistent reservoirs of multidrug-resistant microorganisms (MDRO) that are prevalent in hospital settings and communities can lead to the spread of MDRO. Currently, there are no effective decolonization strategies, especially non-pharmacological strategies without antibiotic regimens. Our aim was to evaluate the efficacy and safety of fecal microbiota transplantation (FMT) for the eradication of MDRO. A systematic literature search was performed to identify studies on the use of FMT for the decolonization of MDRO. PubMed, EMBASE, Web of Science, and Cochrane Library were searched from inception through January 2019. Of the 1395 articles identified, 20 studies met the inclusion and exclusion criteria. Overall, the efficacy of FMT for the eradication of each MDRO was 70.3% (102/146) in 121 patients from the 20 articles. The efficacy rates were 68.2% (30/44) for gram-positive bacteria and 70.6% (72/102) for gram-negative bacteria. Minor adverse events, including vomiting, diarrhea, abdominal pain, and ileus, were reported in patients who received FMT. FMT could be a promising strategy to eradicate MDRO in patients. Further studies are needed to confirm these findings and establish a comprehensive FMT protocol for standardized treatment.Key messagesThe development of new antibiotics lags behind the emergence of multidrug-resistant microorganisms (MDRO). New strategies are needed.Theoretically, fecal microbiota transplantation (FMT) might recover the diversity and function of commensal microbiota from dysbiosis in MDRO carriers and help restore colonization resistance to pathogens.A literature review indicated that FMT could be a promising strategy to eradicate MDRO in patients.
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Affiliation(s)
- Young Kyung Yoon
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Jin Woong Suh
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Eun-Ji Kang
- Korea University Medical Library, Seoul, Korea
| | - Jeong Yeon Kim
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
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Das L, Virmani R, Sharma V, Rawat D, Singh Y. Human Milk Microbiota: Transferring the Antibiotic Resistome to Infants. Indian J Microbiol 2019; 59:410-416. [PMID: 31762502 DOI: 10.1007/s12088-019-00824-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Commensal bacterial population is believed to be a reservoir for antibiotic resistance genes (ARGs). The infant gut microbiota has relatively higher abundance of ARGs than the adults. These genes can get transferred from commensals to pathogens by horizontal gene transfer, which magnifies the spectrum of antibiotic resistance in the environment. The presence of ARGs in neo-nates and infants, with no prior antibiotic exposure, questions their origin in the naïve commensal population. Breast milk microbiota that is responsible for the initial seeding of infant gut microbiota has also been found to harbour a vast array of ARGs. This review discusses the recent findings that indicate the potential of breast milk microbiota to act as a vehicle for transmission of ARGs to infants.
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Affiliation(s)
- Lahari Das
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Richa Virmani
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vishal Sharma
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Deepti Rawat
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
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Gargiullo L, Del Chierico F, D’Argenio P, Putignani L. Gut Microbiota Modulation for Multidrug-Resistant Organism Decolonization: Present and Future Perspectives. Front Microbiol 2019; 10:1704. [PMID: 31402904 PMCID: PMC6671974 DOI: 10.3389/fmicb.2019.01704] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/10/2019] [Indexed: 01/10/2023] Open
Abstract
The emergence of antimicrobial resistance (AMR) is of great concern to global public health. Treatment of multi-drug resistant (MDR) infections is a major clinical challenge: the increase in antibiotic resistance leads to a greater risk of therapeutic failure, relapses, longer hospitalizations, and worse clinical outcomes. Currently, there are no validated treatments for many MDR or pandrug-resistant (PDR) infections, and preventing the spread of these pathogens through hospital infection control procedures and antimicrobial stewardship programs is often the only tool available to healthcare providers. Therefore, new solutions to control the colonization of MDR pathogens are urgently needed. In this narrative review, we discuss current knowledge of microbiota-mediated mechanisms of AMR and strategies for MDR colonization control. We focus particularly on fecal microbiota transplantation for MDR intestinal decolonization and report updated literature on its current clinical use.
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Affiliation(s)
- Livia Gargiullo
- Division of Immunology and Infectious Diseases, University-Hospital Pediatric Department, Bambino Gesù Children’s Hospital, IRCSS, Rome, Italy
| | | | - Patrizia D’Argenio
- Division of Immunology and Infectious Diseases, University-Hospital Pediatric Department, Bambino Gesù Children’s Hospital, IRCSS, Rome, Italy
| | - Lorenza Putignani
- Human Microbiome Unit and Parasitology Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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