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Cai S, Wang Z, Han X, Hu H, Quan J, Jiang Y, Du X, Zhou Z, Yu Y. The correlation between intestinal colonization and infection of carbapenem-resistant Klebsiella pneumoniae: A systematic review. J Glob Antimicrob Resist 2024; 38:187-193. [PMID: 38777180 DOI: 10.1016/j.jgar.2024.04.013] [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: 05/23/2023] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
As a widely spread Gram-negative bacteria, Klebsiella pneumoniae (KP) mainly causes acquired infections in hospitals, such as lung infections, urinary tract infections, and bloodstream infections. In recent years, the number of multidrug-resistant KP strains has increased dramatically, posing a great threat to human health. Carbapenem-resistant KP (CRKP) can be colonized in human body, especially in gastrointestinal tract, and some colonized patients can be infected during hospitalization, among which invasive operation, underlying disease, admission to intensive care unit, antibiotic use, severity of the primary disease, advanced age, operation, coma, and renal failure are common risk factors for secondary infection. Active screening and preventive measures can effectively prevent the occurrence of CRKP infection. Based on the epidemiological status, this study aims to discuss the correlation between colonization and secondary infection induced by CRKP and risk factors for their happening and provide some reference for nosocomial infection prevention and control.
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Affiliation(s)
- Shiqi Cai
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengan Wang
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinhong Han
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huangdu Hu
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingjing Quan
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoxing Du
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhihui Zhou
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Zheng L, Shen J, Chen R, Hu Y, Zhao W, Leung ELH, Dai L. Genome engineering of the human gut microbiome. J Genet Genomics 2024; 51:479-491. [PMID: 38218395 DOI: 10.1016/j.jgg.2024.01.002] [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: 10/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
The human gut microbiome, a complex ecosystem, significantly influences host health, impacting crucial aspects such as metabolism and immunity. To enhance our comprehension and control of the molecular mechanisms orchestrating the intricate interplay between gut commensal bacteria and human health, the exploration of genome engineering for gut microbes is a promising frontier. Nevertheless, the complexities and diversities inherent in the gut microbiome pose substantial challenges to the development of effective genome engineering tools for human gut microbes. In this comprehensive review, we provide an overview of the current progress and challenges in genome engineering of human gut commensal bacteria, whether executed in vitro or in situ. A specific focus is directed towards the advancements and prospects in cargo DNA delivery and high-throughput techniques. Additionally, we elucidate the immense potential of genome engineering methods to enhance our understanding of the human gut microbiome and engineer the microorganisms to enhance human health.
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Affiliation(s)
- Linggang Zheng
- Dr Neher's Biophysics Laboratory for Innovative Drug Discovery/State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau 999078, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Juntao Shen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ruiyue Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yucan Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Elaine Lai-Han Leung
- Cancer Center, Faculty of Health Science, University of Macau, Macau 999078, China; MOE Frontiers Science Center for Precision Oncology, University of Macau, Macau 999078, China.
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Singh H, Gibb B, Abdi R. Abundance and diversity of methicillin-resistant bacteria from bathroom surfaces at workplaces using CHROMagar media, 16S, and dnaJ gene sequence typing. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2024; 15:12-21. [PMID: 38736754 PMCID: PMC11087278 DOI: 10.62347/ejqk3362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/18/2024] [Indexed: 05/14/2024]
Abstract
University campus communities consist of dynamic and diverse human populations originated from different regions of the country or the world. Their national/global movement to and from campus may contribute to the spread and buildup of methicillin-resistant (MR) bacteria, including MR Staphylococci (MRS) on high-touch surfaces, sinks, and toilets. However, studies on MR bacteria contamination of surfaces, sinks, and toilets are scarce in workplaces outside of healthcare settings. Hence, little is known whether university communities contaminate campus bathrooms by MR bacteria. This study evaluated the abundance, identity, and phylogenetics of MR bacteria grown on CHROMagar MRSA media from bathrooms at workplaces. We collected 21 sink and 21 toilet swab samples from 10 buildings on campus and cultured them on CHROMagar MRSA media, extracted DNA from MR bacteria colonies, sequenced PCR products of 16S and dnaJ primers, determined the sequence identities by BLAST search, and constructed a phylogenetic tree. Of 42 samples, 57.1% (24/42) harbored MR bacteria. MR bacteria were more prevalent on the sink (61.9%) than in the toilet (52.2%) and in male bathrooms (54.2%) than in female bathrooms (41.7%). The colony count on the bathroom surfaces of 42 samples varied in that 42.9% (18/42), 33.3, 14.3, and 9.5% of samples harbored 0, 100, and > 1000 MR bacteria colonies, respectively. Of MR bacteria sequenced, BLAST search and phylogenetic analysis showed that Staphylococcus accounted for 60% of the MR bacteria and the rest were non-Staphylococci. Of Staphylococcus carrying MR (n = 15), 53.3% were S. hemolyticus followed by S. lugdunensis (26.7%), S. epidermidis (8%), and a newly discovered S. borealis in 2020 (4%). Of non-Staphylococci MR bacteria, 20% accounted for Sphingomonas koreensis. Campus bathrooms serve as a reservoir for diverse bacteria carrying MR, which pose a direct risk of infection and a potential source of horizontal gene transfer. To reduce the health risk posed by MR bacteria in high traffic areas such as bathrooms additional environmental monitoring and improved decontamination practices are needed.
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Affiliation(s)
- Harshul Singh
- Department of Biological and Chemical Sciences, Theobald Science Center, New York Institute of Technology (NYIT)Old Westbury, NY 11568, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Long Island University (LIU)Greenville, NY 11548, USA
| | - Bryan Gibb
- Department of Biological and Chemical Sciences, Theobald Science Center, New York Institute of Technology (NYIT)Old Westbury, NY 11568, USA
| | - Reta Abdi
- Department of Biomedical Sciences, College of Veterinary Medicine, Long Island University (LIU)Greenville, NY 11548, USA
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4
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Tiwari A, Krolicka A, Tran TT, Räisänen K, Ásmundsdóttir ÁM, Wikmark OG, Lood R, Pitkänen T. Antibiotic resistance monitoring in wastewater in the Nordic countries: A systematic review. ENVIRONMENTAL RESEARCH 2024; 246:118052. [PMID: 38163547 DOI: 10.1016/j.envres.2023.118052] [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: 10/20/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
The Nordic countries (Denmark, Finland, Iceland, Norway, and Sweden) have effectively kept lower antibiotic-resistant bacterial (ARB) pathogen rates than many other countries. However, in recent years, these five countries have encountered a rise in ARB cases and challenges in treating infections due to the growing prevalence of ARB pathogens. Wastewater-based surveillance (WBS) is a valuable supplement to clinical methods for ARB surveillance, but there is a lack of comprehensive understanding of WBS application for ARB in the Nordic countries. This review aims to compile the latest state-of-the-art developments in WBS for ARB monitoring in the Nordic countries and compare them with clinical surveillance practices. After reviewing 1480 papers from the primary search, 54 were found relevant, and 15 additional WBS-related papers were included. Among 69 studies analyzed, 42 dedicated clinical epidemiology, while 27 focused on wastewater monitoring. The PRISMA review of the literature revealed that Nordic countries focus on four major WBS objectives of ARB: assessing ARB in the human population, identifying ARB evading wastewater treatment, quantifying removal rates, and evaluating potential ARB evolution during the treatment process. In both clinical and wastewater contexts, the most studied targets were pathogens producing carbapenemase and extended-spectrum beta-lactamase (ESBL), primarily Escherichia coli and Klebsiella spp. However, vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have received more attention in clinical epidemiology than in wastewater studies, probably due to their lower detection rates in wastewater. Clinical surveillance has mostly used culturing, antibiotic susceptibility testing, and genotyping, but WBS employed PCR-based and metagenomics alongside culture-based techniques. Imported cases resulting from international travel and hospitalization abroad appear to have frequently contributed to the rise in ARB pathogen cases in these countries. The many similarities between the Nordic countries (e.g., knowledge exchange practices, antibiotic usage patterns, and the current ARB landscape) could facilitate collaborative efforts in developing and implementing WBS for ARB in population-level screening.
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Affiliation(s)
- Ananda Tiwari
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, 70701, Kuopio, Finland.
| | - Adriana Krolicka
- Norwegian Research Centre AS (NORCE), Nygårdstangen, 5838, Bergen, Norway
| | - Tam T Tran
- Norwegian Research Centre AS (NORCE), Nygårdstangen, 5838, Bergen, Norway
| | - Kati Räisänen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Odd-Gunnar Wikmark
- Norwegian Research Centre AS (NORCE), Nygårdstangen, 5838, Bergen, Norway; Unit for Environmental Science and Management, North West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Rolf Lood
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Tarja Pitkänen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, 70701, Kuopio, Finland; Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland.
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d'Humières C, Delavy M, Alla L, Ichou F, Gauliard E, Ghozlane A, Levenez F, Galleron N, Quinquis B, Pons N, Mullaert J, Bridier-Nahmias A, Condamine B, Touchon M, Rainteau D, Lamazière A, Lesnik P, Ponnaiah M, Lhomme M, Sertour N, Devente S, Docquier JD, Bougnoux ME, Tenaillon O, Magnan M, Ruppé E, Grall N, Duval X, Ehrlich D, Mentré F, Denamur E, Rocha EPC, Le Chatelier E, Burdet C. Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases. MICROBIOME 2024; 12:50. [PMID: 38468305 DOI: 10.1186/s40168-023-01746-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 12/20/2023] [Indexed: 03/13/2024]
Abstract
BACKGROUND Antibiotics notoriously perturb the gut microbiota. We treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days, and collected in each subject 12 faecal samples up to day 90. Using untargeted and targeted phenotypic and genotypic approaches, we studied the changes in the bacterial, phage and fungal components of the microbiota as well as the metabolome and the β-lactamase activity of the stools. This allowed assessing their degrees of perturbation and resilience. RESULTS While only two subjects had detectable concentrations of antibiotics in their faeces, suggesting important antibiotic degradation in the gut, the intravenous treatment perturbed very significantly the bacterial and phage microbiota, as well as the composition of the metabolome. In contrast, treatment impact was relatively low on the fungal microbiota. At the end of the surveillance period, we found evidence of resilience across the gut system since most components returned to a state like the initial one, even if the structure of the bacterial microbiota changed and the dynamics of the different components over time were rarely correlated. The observed richness of the antibiotic resistance genes repertoire was significantly reduced up to day 30, while a significant increase in the relative abundance of β-lactamase encoding genes was observed up to day 10, consistent with a concomitant increase in the β-lactamase activity of the microbiota. The level of β-lactamase activity at baseline was positively associated with the resilience of the metabolome content of the stools. CONCLUSIONS In healthy adults, antibiotics perturb many components of the microbiota, which return close to the baseline state within 30 days. These data suggest an important role of endogenous β-lactamase-producing anaerobes in protecting the functions of the microbiota by de-activating the antibiotics reaching the colon. Video Abstract.
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Affiliation(s)
- Camille d'Humières
- Université Paris Cité, IAME, INSERM, Paris, F-75018, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - Margot Delavy
- Institut Pasteur, Université Paris Cité, INRAE, USC2019, Unité Biologie Et Pathogénicité Fongiques, Paris, F-75015, France
| | - Laurie Alla
- Université Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, F-78350, France
| | - Farid Ichou
- ICANomics, Foundation of Innovation in Cardiometabolism and Nutrition (IHU ICAN), Paris, F-75013, France
| | - Emilie Gauliard
- Sorbonne Université, INSERM U938, Centre de Recherche Saint-Antoine, Paris, F-75012, France
| | - Amine Ghozlane
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, F-75015, France
| | - Florence Levenez
- Université Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, F-78350, France
| | - Nathalie Galleron
- Université Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, F-78350, France
| | - Benoit Quinquis
- Université Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, F-78350, France
| | - Nicolas Pons
- Université Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, F-78350, France
| | - Jimmy Mullaert
- Université Paris Cité, IAME, INSERM, Paris, F-75018, France
- AP-HP, Département d'Epidemiologie, Biostatistique and Recherche Clinique, Hôpital Bichat, Paris, F-75018, France
| | | | | | - Marie Touchon
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - Dominique Rainteau
- Sorbonne Université, INSERM U938, Centre de Recherche Saint-Antoine, Paris, F-75012, France
| | - Antonin Lamazière
- Sorbonne Université, INSERM U938, Centre de Recherche Saint-Antoine, Paris, F-75012, France
| | - Philippe Lesnik
- INSERM UMR-S 1166, Institute of Cardiometabolism and Nutrition, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, F-75013, France
- ICANomics, Foundation of Innovation in Cardiometabolism and Nutrition (IHU ICAN), Paris, F-75013, France
| | - Maharajah Ponnaiah
- ICANomics, Foundation of Innovation in Cardiometabolism and Nutrition (IHU ICAN), Paris, F-75013, France
| | - Marie Lhomme
- ICANomics, Foundation of Innovation in Cardiometabolism and Nutrition (IHU ICAN), Paris, F-75013, France
| | - Natacha Sertour
- Institut Pasteur, Université Paris Cité, INRAE, USC2019, Unité Biologie Et Pathogénicité Fongiques, Paris, F-75015, France
| | - Savannah Devente
- Dipartimento di Biotecnologie Mediche, Università di Siena, Siena, I-53100, Italy
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università di Siena, Siena, I-53100, Italy
| | - Marie-Elisabeth Bougnoux
- Institut Pasteur, Université Paris Cité, INRAE, USC2019, Unité Biologie Et Pathogénicité Fongiques, Paris, F-75015, France
- AP-HP, Unité de Parasitologie-Mycologie, Service de Microbiologie Clinique, Hôpital Necker-Enfants-Malades, Paris, F-75015, France
| | | | - Mélanie Magnan
- Université Paris Cité, IAME, INSERM, Paris, F-75018, France
| | - Etienne Ruppé
- Université Paris Cité, IAME, INSERM, Paris, F-75018, France
- AP-HP, Laboratoire de Bactériologie, Hôpital Bichat, Paris, F-75018, France
| | - Nathalie Grall
- Université Paris Cité, IAME, INSERM, Paris, F-75018, France
- AP-HP, Laboratoire de Bactériologie, Hôpital Bichat, Paris, F-75018, France
| | - Xavier Duval
- Université Paris Cité, IAME, INSERM, Paris, F-75018, France
- AP-HP, Centre d'Investigation Clinique, INSERM CIC 1425, Hôpital Bichat, Paris, F-75018, France
| | - Dusko Ehrlich
- Université Paris-Saclay, INRAE, MetaGenoPolis, Jouy-en-Josas, F-78350, France
- University College London, Institute for Neurology, London, UK
| | - France Mentré
- Université Paris Cité, IAME, INSERM, Paris, F-75018, France
- AP-HP, Département d'Epidemiologie, Biostatistique and Recherche Clinique, Hôpital Bichat, Paris, F-75018, France
| | - Erick Denamur
- Université Paris Cité, IAME, INSERM, Paris, F-75018, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, F-75018, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | | | - Charles Burdet
- Université Paris Cité, IAME, INSERM, Paris, F-75018, France.
- AP-HP, Département d'Epidemiologie, Biostatistique and Recherche Clinique, Hôpital Bichat, Paris, F-75018, France.
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Nooij S, Vendrik KEW, Zwittink RD, Ducarmon QR, Keller JJ, Kuijper EJ, Terveer EM. Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection. Genome Med 2024; 16:37. [PMID: 38419010 PMCID: PMC10902993 DOI: 10.1186/s13073-024-01306-7] [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: 08/23/2023] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Multidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides difficile infections and can also be useful for other microbiota-related diseases. METHODS We study the effect of FMT in patients with multiple recurrent C. difficile infections on colonisation with MDR bacteria and antibiotic resistance genes (ARG) on the short (3 weeks) and long term (1-3 years), combining culture methods and faecal metagenomics. RESULTS Based on MDR culture (n = 87 patients), we notice a decrease of 11.5% in the colonisation rate of MDR bacteria after FMT (20/87 before FMT = 23%, 10/87 3 weeks after FMT). Metagenomic sequencing of patient stool samples (n = 63) shows a reduction in relative abundances of ARGs in faeces, while the number of different resistance genes in patients remained higher compared to stools of their corresponding healthy donors (n = 11). Furthermore, plasmid predictions in metagenomic data indicate that patients harboured increased levels of resistance plasmids, which appear unaffected by FMT. In the long term (n = 22 patients), the recipients' resistomes are still donor-like, suggesting the effect of FMT may last for years. CONCLUSIONS Taken together, we hypothesise that FMT restores the gut microbiota to a composition that is closer to the composition of healthy donors, and potential pathogens are either lost or decreased to very low abundances. This process, however, does not end in the days following FMT. It may take months for the gut microbiome to re-establish a balanced state. Even though a reservoir of resistance genes remains, a notable part of which on plasmids, FMT decreases the total load of resistance genes.
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Affiliation(s)
- Sam Nooij
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands.
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands.
| | - Karuna E W Vendrik
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
- Present address: Centre for Infectious Disease Control, Netherlands Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Romy D Zwittink
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
- Present address: Centre for Infectious Disease Control, Netherlands Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Quinten R Ducarmon
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
| | - Josbert J Keller
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Department of Gastroenterology, Haaglanden Medical Center, The Hague, Netherlands
| | - Ed J Kuijper
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
| | - Elisabeth M Terveer
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
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7
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Tadesse BT, Keddy KH, Rickett NY, Zhusupbekova A, Poudyal N, Lawley T, Osman M, Dougan G, Kim JH, Lee JS, Jeon HJ, Marks F. Vaccination to Reduce Antimicrobial Resistance Burden-Data Gaps and Future Research. Clin Infect Dis 2023; 77:S597-S607. [PMID: 38118013 PMCID: PMC10732565 DOI: 10.1093/cid/ciad562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023] Open
Abstract
Antimicrobial resistance (AMR) poses an immediate danger to global health. If unaddressed, the current upsurge in AMR threatens to reverse the achievements in reducing the infectious disease-associated mortality and morbidity associated with antimicrobial treatment. Consequently, there is an urgent need for strategies to prevent or slow the progress of AMR. Vaccines potentially contribute both directly and indirectly to combating AMR. Modeling studies have indicated significant gains from vaccination in reducing AMR burdens for specific pathogens, reducing mortality/morbidity, and economic loss. However, quantifying the real impact of vaccines in these reductions is challenging because many of the study designs used to evaluate the contribution of vaccination programs are affected by significant background confounding, and potential selection and information bias. Here, we discuss challenges in assessing vaccine impact to reduce AMR burdens and suggest potential approaches for vaccine impact evaluation nested in vaccine trials.
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Affiliation(s)
- Birkneh Tilahun Tadesse
- International Vaccine Institute, Seoul, Republic of Korea
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Center for Innovative Drug Development and Therapeutic Trials for Africa, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Nimesh Poudyal
- International Vaccine Institute, Seoul, Republic of Korea
| | - Trevor Lawley
- Wellcome Sanger Institute and Microbiotica, Cambridge, United Kingdom
| | - Majdi Osman
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Jerome H Kim
- International Vaccine Institute, Seoul, Republic of Korea
- Seoul National University, College of Natural Sciences, Seoul, Republic of Korea
| | - Jung-Seok Lee
- International Vaccine Institute, Seoul, Republic of Korea
| | - Hyon Jin Jeon
- International Vaccine Institute, Seoul, Republic of Korea
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
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8
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Clark JA, Curran MD, Gouliouris T, Conway Morris A, Bousfield R, Navapurkar V, Kean IRL, Daubney E, White D, Baker S, Pathan N. Rapid Detection of Antimicrobial Resistance Genes in Critically Ill Children Using a Custom TaqMan Array Card. Antibiotics (Basel) 2023; 12:1701. [PMID: 38136735 PMCID: PMC10740637 DOI: 10.3390/antibiotics12121701] [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: 11/01/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Bacteria are identified in only 22% of critically ill children with respiratory infections treated with antimicrobial therapy. Once an organism is isolated, antimicrobial susceptibility results (phenotypic testing) can take another day. A rapid diagnostic test identifying antimicrobial resistance (AMR) genes could help clinicians make earlier, informed antimicrobial decisions. Here we aimed to validate a custom AMR gene TaqMan Array Card (AMR-TAC) for the first time and assess its feasibility as a screening tool in critically ill children. An AMR-TAC was developed using a combination of commercial and bespoke targets capable of detecting 23 AMR genes. This was validated using isolates with known phenotypic resistance. The card was then tested on lower respiratory tract and faecal samples obtained from mechanically ventilated children in a single-centre observational study of respiratory infection. There were 82 children with samples available, with a median age of 1.2 years. Major comorbidity was present in 29 (35%) children. A bacterial respiratory pathogen was identified in 13/82 (16%) of children, of which 4/13 (31%) had phenotypic AMR. One AMR gene was detected in 49/82 (60%), and multiple AMR genes were detected in 14/82 (17%) children. Most AMR gene detections were not associated with the identification of phenotypic AMR. AMR genes are commonly detected in samples collected from mechanically ventilated children with suspected respiratory infections. AMR-TAC may have a role as an adjunct test in selected children in whom there is a high suspicion of antimicrobial treatment failure.
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Affiliation(s)
- John A. Clark
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
| | - Martin D. Curran
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Theodore Gouliouris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Andrew Conway Morris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge CB2 2QQ, UK
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Rachel Bousfield
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge CB2 0QQ, UK;
| | - Vilas Navapurkar
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
| | - Iain R. L. Kean
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Esther Daubney
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Deborah White
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK;
| | - Nazima Pathan
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; (I.R.L.K.); (E.D.); (D.W.); (N.P.)
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK; (T.G.); (A.C.M.); (R.B.); (V.N.)
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9
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Sharma K, Tak V, Nag VL, Bhatia PK, Kothari N. An observational study on carbapenem-resistant Enterobacterales (CRE) colonisation and subsequent risk of infection in an adult intensive care unit (ICU) at a tertiary care hospital in India. Infect Prev Pract 2023; 5:100312. [PMID: 37868258 PMCID: PMC10585280 DOI: 10.1016/j.infpip.2023.100312] [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: 07/25/2022] [Accepted: 02/26/2023] [Indexed: 10/24/2023] Open
Abstract
Background Carbapenem-resistant Enterobacterales (CRE) are a global health problem with a growing prevalence. India has a high prevalence of CRE. CRE infections are difficult to treat, and are associated with significant morbidity and mortality. Colonisation is generally a prerequisite for infection and the prevention of CRE colonisation is key to the prevention of CRE infection. Objectives To determine the prevalence of CRE colonisation and subsequent infections in an adult intensive care unit (ICU) in India. Methods We conducted a prospective observational study in which perirectal swabs were obtained along with relevant clinical details of consenting adult patients upon ICU admission between January 2019 and August 2020. Rectal screening was performed using MacConkey agar plates with ertapenem disks and further identification was performed using conventional microbiological techniques. Ertapenem minimum inhibitory concentration (MIC) was determined using an epsillometer (E) test. The modified carbapenem inactivation (mCIM) test and EDTA carbapenem inactivation test (eCIM) were performed to confirm carbapenem resistance using the Clinical Laboratory Standards Institute (CLSI) 2020 guidelines. Results 192 ICU patients were screened for CRE. 37 patients were found to be colonised with CRE. Klebsiella pneumoniae (N=25; 67.6%) was the most frequent CRE isolate, followed by Escherichia coli (N=11; 29.7%) and one Enterobacter species (N=1; 2.7%). 89.2% (33/37) patients developed CRE infection. Pneumonia was the most common CRE infection identified in 12/33 (36.4%) patients.during the hospital stay. The median duration of hospital stay was longer (17 days) for CRE colonised compared to CRE non-colonised patients (9 days) (P<0.001). Death occurred in 27 % (N=10/37) of CRE-colonised patients during the hospital admission. Conclusion CRE colonisation is associated with high risk of subsequent CRE infection and longer ICU and hospital admission.
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Affiliation(s)
- Kirtika Sharma
- All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India
| | - Vibhor Tak
- All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India
| | - Vijaya Lakshmi Nag
- All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India
| | | | - Nikhil Kothari
- All India Institute of Medical Sciences, Jodhpur, Rajasthan, 342005, India
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10
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Literacka E, Konior M, Izdebski R, Żabicka D, Herda M, Gniadkowski M, Korzeniewski K. High risk of intestinal colonization with ESBL-producing Escherichia coli among soldiers of military contingents in specific geographic regions. Eur J Clin Microbiol Infect Dis 2023; 42:1523-1530. [PMID: 37857920 PMCID: PMC10651695 DOI: 10.1007/s10096-023-04684-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023]
Abstract
One-hundred Polish soldiers of a contingent in Afghanistan in 2019 were screened for Enterobacterales resistant to newer-generation β-lactams at their departure and return. Seventeen percent were colonized in the gut at the departure, whereas 70% acquired carriage in Afghanistan. The commonest organisms were extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec; 96.6%). All isolates were sequenced and were clonally diverse overall, even within the same sequence type, indicating that independent acquisitions mainly. ESBL-Ec were often multi-drug-resistant. Soldiers stationing in certain regions are at high risk of acquiring resistant bacteria that may cause endogenous infection, be transmitted to vulnerable individuals, and spread resistance genes.
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Affiliation(s)
- E Literacka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland.
| | - M Konior
- Department of Epidemiology and Tropical Medicine, Military Institute of Medicine - National Research Institute, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - M Herda
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - K Korzeniewski
- Department of Epidemiology and Tropical Medicine, Military Institute of Medicine - National Research Institute, Warsaw, Poland
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11
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Katkowska M, Garbacz K, Kwapisz E, Suligowska K, Kusiak A, Cichońska D, Świetlik D. High oral carriage of multidrug resistant Gram-negative bacilli in adolescents: the SOPKARD-Junior study. Front Cell Infect Microbiol 2023; 13:1265777. [PMID: 38035342 PMCID: PMC10687414 DOI: 10.3389/fcimb.2023.1265777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction The colonization of the oral cavity by potentially pathogenic antimicrobial-resistant bacteria in adolescents and its consequences is very poorly understood. The present study focused on the occurrence of oral colonization by Gram-negative bacilli (GNB) and their multidrug resistance, including the production of extended-spectrum β-lactamases (ESBLs) and carbapenemases, among healthy adolescents and risk factors associated with GNB colonization. Materials and methods This study was conducted as part of "A program for the early detection of risk factors for lifestyle diseases SOPKARD-Junior" (SOPKARD-Junior). Oral samples were collected from 182 adolescents from four public elementary schools in Sopot, Poland, aged 13-14 years. Bacterial strains were identified by the MALDI-TOF MS method. Screening of antimicrobial resistance was performed using a disk diffusion method. The NG-Test® CARBA-5 was used to detect and differentiate the five most widely distributed carbapenemases. Demographic and clinical data were collected and statistical analysis of risk factors was performed. Results A total of 68 out of 182 (37.4%) healthy adolescents was documented oral colonization with Gram-negative bacilli, including 50/182 (27.5%) multidrug resistant (MDR-GNB) strains. Over 60% of oral carriage concerned three main genera Enterobacter spp., Pseudomonas spp., and Serratia spp., which were detected in 22.1%, 19.1%, and 19.1% of participants, respectively. Citrobacter spp., Escherichia coli, Klebsiella spp., Hafnia spp., Aeromonas spp., Acinetobacter spp., and Stenotrophomonas spp. were also isolated. The antimicrobial resistance to ampicillin (100%), ceftazidime (69.1%), meropenem (60.3%), gentamycin (60.3%), piperacillin/tazobactam (52.9%), and piperacillin (45.6%) were the most common. Among 73.5% GNB strains multidrug resistance was observed, including all Pseudomonas spp. strains. Among MDR-GNB, 30.4% were resistant to four groups of antibiotics, half of the MDR Pseudomonas spp. strains were resistant to 10 groups of antibiotics. Extended-spectrum β-lactamases were produced by Enterobacter cloacae, Klebsiella spp., and Serratia spp. (7.4%). Colonization by ESBLs-positive GNB strains was significantly associated with recurrent respiratory infections, nasal congestion, and bronchitis (p<0.05). Conclusion Our study revealed high oral carriage of multi-drug resistant Gram-negative bacilli in healthy adolescents and the association of ESBL-producing strains with respiratory infections. Further studies on oral colonization with GNB are necessary due to the possibility of distinct infections and the acquisition of antibiotic resistance by resident microbiota.
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Affiliation(s)
- Marta Katkowska
- Department of Oral Microbiology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Katarzyna Garbacz
- Department of Oral Microbiology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Kwapisz
- Department of Oral Microbiology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Klaudia Suligowska
- Department of Dental Techniques and Masticatory System Dysfunctions, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
- Department of Preventive Medicine and Education, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Aida Kusiak
- Department of Periodontology and Oral Mucosa Diseases, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Dominika Cichońska
- Department of Periodontology and Oral Mucosa Diseases, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Świetlik
- Division of Biostatistics and Neural Networks, Medical University of Gdansk, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
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12
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Zheng Y, Han F, Ho A, Xue Y, Wu Z, Chen X, Sandberg JK, Ma S, Leeansyah E. Role of MAIT cells in gastrointestinal tract bacterial infections in humans: More than a gut feeling. Mucosal Immunol 2023; 16:740-752. [PMID: 37353006 DOI: 10.1016/j.mucimm.2023.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023]
Abstract
Mucosa-associated invariant T (MAIT) cells are the largest population of unconventional T cells in humans. These antimicrobial T cells are poised with rapid effector responses following recognition of the cognate riboflavin (vitamin B2)-like metabolite antigens derived from microbial riboflavin biosynthetic pathway. Presentation of this unique class of small molecule metabolite antigens is mediated by the highly evolutionarily conserved major histocompatibility complex class I-related protein. In humans, MAIT cells are widely found along the upper and lower gastrointestinal tracts owing to their high expression of chemokine receptors and homing molecules directing them to these tissue sites. In this review, we discuss recent findings regarding the roles MAIT cells play in various gastrointestinal bacterial infections, and how their roles appear to differ depending on the etiological agents and the anatomical location. We further discuss the potential mechanisms by which MAIT cells contribute to pathogen control, orchestrate adaptive immunity, as well as their potential contribution to inflammation and tissue damage during gastrointestinal bacterial infections, and the ensuing tissue repair following resolution. Finally, we propose and discuss the use of the emerging three-dimensional organoid technology to test different hypotheses regarding the role of MAIT cells in gastrointestinal bacterial infections, inflammation, and immunity.
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Affiliation(s)
- Yichao Zheng
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Precision Medicine and Healthcare Research Centre, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Fei Han
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Amanda Ho
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Precision Medicine and Healthcare Research Centre, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Yiting Xue
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Precision Medicine and Healthcare Research Centre, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Zhengyu Wu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xingchi Chen
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Shaohua Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China; Precision Medicine and Healthcare Research Centre, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Edwin Leeansyah
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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13
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Au SX, Mohd Padzil A, Muhd Noor ND, Matsumura H, Raja Abdul Rahman RNZ, Normi YM. Probing the substrate binding modes and catalytic mechanisms of BLEG-1, a promiscuous B3 metallo-β-lactamase with glyoxalase II properties. PLoS One 2023; 18:e0291012. [PMID: 37672512 PMCID: PMC10482274 DOI: 10.1371/journal.pone.0291012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/19/2023] [Indexed: 09/08/2023] Open
Abstract
BLEG-1 from Bacillus lehensis G1 is an evolutionary divergent B3 metallo-β-lactamase (MBL) that exhibited both β-lactamase and glyoxalase II (GLXII) activities. Sequence, phylogeny, biochemical and structural relatedness of BLEG-1 to B3 MBL and GLXII suggested BLEG-1 might be an intermediate in the evolutionary path of B3 MBL from GLXII. The unique active site cavity of BLEG-1 that recognizes both β-lactam antibiotics and S-D-lactoylglutathione (SLG) had been postulated as the key factor for its dual activity. In this study, dynamic ensembles of BLEG-1 and its substrate complexes divulged conformational plasticity and binding modes of structurally distinct substrates to the enzyme, providing better insights into its structure-to-function relationship and enzymatic promiscuity. Our results highlight the flexible nature of the active site pocket of BLEG-1, which is governed by concerted loop motions involving loop7+α3+loop8 and loop12 around the catalytic core, thereby moulding the binding pocket and facilitate interactions of BLEG-1 with both ampicillin and SLG. The distribution of (i) predominantly hydrophobic amino acids in the N-terminal domain, and (ii) flexible amino acids with polar and/or charged side chains in both N- and C-termini provide additional advantages to BLEG-1 in confining the aromatic group of ampicillin, and polar groups of SLG, respectively. The importance of these residues for substrates binding was further confirmed by the reduction in MBL and GLXII activities upon alanine substitutions of Ile-10, Phe-57, Arg-94, Leu-95, and Arg-159. Based on molecular dynamics simulation, mutational, and biochemical data presented herein, the catalytic mechanisms of BLEG-1 toward the hydrolysis of β-lactams and SLG were proposed.
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Affiliation(s)
- Shaw Xian Au
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Azyyati Mohd Padzil
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Hiroyoshi Matsumura
- College of Life Sciences, Ritsumeikan University, Noji-Higashi, Kusatsu, Japan
| | - Raja Noor Zaliha Raja Abdul Rahman
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yahaya M. Normi
- Enzyme and Microbial Technology (EMTech) Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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14
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Zasowski EJ, Ali M, Anugo A, Ibragimova N, Dotson KM, Endres BT, Begum K, Alam MJ, Garey KW. Comparison of Risk Stratification Approaches to Identify Patients with Clostridioides difficile Infection at Risk for Multidrug-Resistant Organism Gut Microbiota Colonization. Infect Dis Ther 2023; 12:2005-2015. [PMID: 37436677 PMCID: PMC10505131 DOI: 10.1007/s40121-023-00843-9] [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: 12/02/2022] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
INTRODUCTION Multidrug-resistant organisms (MDRO) commonly colonize the gut microbiota of patients with Clostridioides difficile infection (CDI). This increases the likelihood of systemic infections with these MDROs. To help guide MDRO screening and/or empiric antibiotic therapy, we derived and compared predictive indices for MDRO gut colonization in patients with CDI. METHODS This was a multicenter, retrospective cohort study of adult patients with CDI from July 2017 to April 2018. Stool samples were screened for MDRO via growth and speciation on selective antibiotic media and confirmed using resistance gene polymerase chain reaction. A regression-based risk score for MDRO colonization was constructed. Predictive performance via area under the receiver operating characteristic curve (aROC) of this index was compared with two other simplified risk stratification approaches: (1) prior healthcare exposure and/or high-CDI risk antibiotics; (2) number of prior high-CDI risk antibiotics. RESULTS 50 (20.8%) of 240 included patients had MDRO colonization; 35 (14.6%) VRE, 18 (7.5%) MRSA, 2 (0.8%) CRE. Prior fluoroquinolone (aOR 2.404, 95% CI 1.095-5.279) and prior vancomycin (1.996, 95% CI 1.014-3.932) were independently associated with MDRO colonization while prior clindamycin (aOR 3.257, 95% CI 0.842-12.597) and healthcare exposure (aOR 2.138, 95% CI 0.964-4.740) were retained as explanatory variables. The regression-based risk score significantly predicted MDRO colonization (aROC 0.679, 95% CI 0.595-0.763), but was not significantly more predictive than prior healthcare exposure + prior antibiotics (aROC 0.646, 95% CI 0.565-0.727) or number of prior antibiotic exposures (aROC 0.642, 95% CI 0.554-0.730); P > 0.05 for both comparisons. CONCLUSION A simplified approach using prior healthcare exposure and receipt of prior antibiotics known to increase CDI risk identified patients at risk for MDRO gut microbiome colonization as effectively as individual patient/antibiotic risk modeling.
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Affiliation(s)
- Evan J Zasowski
- Department of Clinical Sciences, Touro University California College of Pharmacy, Vallejo, CA, USA.
- Department of Clinical Pharmacy, UCSF School of Pharmacy, San Francisco, CA, USA.
| | - Maryam Ali
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Ada Anugo
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Nayle Ibragimova
- Department of Clinical Sciences, Touro University California College of Pharmacy, Vallejo, CA, USA
| | - Kierra M Dotson
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Bradley T Endres
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Khurshida Begum
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - M Jahangir Alam
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
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15
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Merrick B, Sergaki C, Edwards L, Moyes DL, Kertanegara M, Prossomariti D, Shawcross DL, Goldenberg SD. Modulation of the Gut Microbiota to Control Antimicrobial Resistance (AMR)-A Narrative Review with a Focus on Faecal Microbiota Transplantation (FMT). Infect Dis Rep 2023; 15:238-254. [PMID: 37218816 DOI: 10.3390/idr15030025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/19/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the greatest challenges facing humanity, causing a substantial burden to the global healthcare system. AMR in Gram-negative organisms is particularly concerning due to a dramatic rise in infections caused by extended-spectrum beta-lactamase and carbapenemase-producing Enterobacterales (ESBL and CPE). These pathogens have limited treatment options and are associated with poor clinical outcomes, including high mortality rates. The microbiota of the gastrointestinal tract acts as a major reservoir of antibiotic resistance genes (the resistome), and the environment facilitates intra and inter-species transfer of mobile genetic elements carrying these resistance genes. As colonisation often precedes infection, strategies to manipulate the resistome to limit endogenous infections with AMR organisms, as well as prevent transmission to others, is a worthwhile pursuit. This narrative review presents existing evidence on how manipulation of the gut microbiota can be exploited to therapeutically restore colonisation resistance using a number of methods, including diet, probiotics, bacteriophages and faecal microbiota transplantation (FMT).
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Affiliation(s)
- Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College, London SE1 7EH, UK
| | - Chrysi Sergaki
- Diagnostics R&D, Medicines and Healthcare Products Regulatory Agency (MHRA), Potters Bar EN6 3QG, UK
| | - Lindsey Edwards
- School of Immunology and Microbial Sciences, Institute of Liver Studies, Faculty of Life Sciences and Medicine, King's College, London SE1 1UL, UK
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, London SE5 9RS, UK
| | - David L Moyes
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College, London SE1 1UK, UK
| | - Michael Kertanegara
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College, London SE1 7EH, UK
| | - Désirée Prossomariti
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College, London SE1 7EH, UK
| | - Debbie L Shawcross
- School of Immunology and Microbial Sciences, Institute of Liver Studies, Faculty of Life Sciences and Medicine, King's College, London SE1 1UL, UK
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, London SE5 9RS, UK
| | - Simon D Goldenberg
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College, London SE1 7EH, UK
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16
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Rynkiewich K, Gole S, Won S, Schwartz DN. Cultures of antibiotic prescribing in medical intensive care. Soc Sci Med 2023; 324:115834. [PMID: 37003024 DOI: 10.1016/j.socscimed.2023.115834] [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: 06/20/2022] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023]
Abstract
Antimicrobial resistance (AMR) continues to present a challenge to international healthcare systems and structures of public health. The focus on optimizing antibiotic prescribing in human populations has challenged healthcare systems charged with making responsible their physician-prescribers. In the United States, physicians in almost every specialty and role use antibiotics as part of their therapeutic armamentariums. In United States hospitals, most patients are administered antibiotics during their stay. Therefore, antibiotic prescribing and utilization is a commonly accepted part of medical practice. In this paper, we utilize social science work on antibiotic prescribing to examine a critical space of care in United States hospital settings. From March to August 2018, we used ethnographic methods to study hospital-based medical intensive care unit physicians at the offices and hospital floors they frequent in two urban United States teaching hospitals. We focused on eliciting the interactions and discussions surrounding antibiotic decision-making that are uniquely influenced by the context of medical intensive care units. We argue that antibiotic use in the medical intensive care units under study was shaped by urgency, hierarchy, and uncertainty representative of the medical intensive care unit's role within the larger hospital system. We conclude that by studying the culture of antibiotic prescribing in medical intensive care units, we can see more clearly both the vulnerability of the looming antimicrobial resistance crisis and by contrast the perceived insignificance of stewarding antibiotic use when considered alongside the fragility of life amidst acute medical concerns regularly experienced in the unit.
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Affiliation(s)
| | - Sarin Gole
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, NB5, Cleveland, OH 44195, USA
| | - Sarah Won
- Department of Internal Medicine, Rush Medical College, USA
| | - David N Schwartz
- Department of Medicine, John H. Stroger Jr. Hospital of Cook County, USA
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Varada VV, Panneerselvam D, Pushpadass HA, Mallapa RH, Ram C, Kumar S. In vitro safety assessment of electrohydrodynamically encapsulated Lactiplantibacillus plantarum CRD7 and Lacticaseibacillus rhamnosus CRD11 for probiotics use. Curr Res Food Sci 2023; 6:100507. [PMID: 37215740 PMCID: PMC10196993 DOI: 10.1016/j.crfs.2023.100507] [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: 03/03/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
The current study aimed to validate the safety of electrohydrodynamically encapsulated Lactiplantibacillus plantarum CRD7 and Lacticaseibacillus rhamnosus CRD11 in accordance with guidelines of FAO/WHO and ICMR/DBT. In vitro assays such as mucin degradation, hemolysis of blood cells, antimicrobial susceptibility pattern, possession of virulence factors, biogenic amine, and ammonia production were assessed. In results, the cross-streak and co-culture techniques revealed that CRD7 and CRD11 were compatible in vitro. Upon visual inspection through scanning electron and fluorescence microscopy, the integrity of bacterial cell membrane was confirmed even after the encapsulation process. CRD7 and CRD11 were non-hemolytic and showed negative responses to gelatinase, urease, and DNase activities. Non-mucinolytic activity of CRD7 and CRD11 was verified by measuring cell growth rate (p < 0.05) in different modified media followed by SDS-PAGE. High-performance liquid chromatography analysis revealed that both the strains did not produce biogenic amines (putrescine, cadaverine, histamine, and tyramine). Neither of the Lactobacillus strains produced ammonia after growing in BHI broth for 5 days at 37 °C. L-lactate production was highest (p < 0.05) in CRD11 (8.83 g/L), followed by CRD7 (8.16 g/L), whereas the lowest (p < 0.05) D-lactate was registered for encapsulated CRD11 (0.33 g/L) and CRD7 (0.49 g/L). The antibiogram profile determined through minimum inhibitory concentration showed that CRD7 and CRD11 were sensitive to key antibiotics suggested by EFSA except for gentamycin and kanamycin. PCR data on virulence genes demonstrated that both strains were safe for probiotic use. Moreover, CRD7 and CRD11 strains caused insignificant (p > 0.05) changes in the cell viability of Caco-2 cells as estimated by MTT (98.94-99.50%) and NR uptake (95.42-97.03%) assays and showed sensitivity to human serum. According to the results of these evaluated attributes, it is concluded that L. plantarum CRD7 and L. rhamnosus CRD11 are safe, non-toxic to human epithelial cells, and thus may be potentially suitable for various food/feed applications.
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Affiliation(s)
- Vinay Venkatesh Varada
- Rumen Biotechnology Lab., Animal Nutrition Division, ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Divya Panneerselvam
- Dairy Engineering Section, ICAR-National Dairy Research Institute, Southern Regional Station, Bengaluru, India
| | - Heartwin A. Pushpadass
- Dairy Engineering Section, ICAR-National Dairy Research Institute, Southern Regional Station, Bengaluru, India
| | | | - Chand Ram
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Sachin Kumar
- Rumen Biotechnology Lab., Animal Nutrition Division, ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
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Leinyuy JF, Ali IM, Ousenu K, Tume CB. Molecular characterization of antimicrobial resistance related genes in E. coli, Salmonella and Klebsiella isolates from broilers in the West Region of Cameroon. PLoS One 2023; 18:e0280150. [PMID: 36630464 PMCID: PMC9833522 DOI: 10.1371/journal.pone.0280150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Antibiotic resistance has become an enduring threat to human health. This has prompted extensive research to identify the determinants responsible in a bid to fight the spread of resistance and also develop new antibiotics. However, routine procedures focus on identifying genetic determinants of resistance only on phenotypically resistant isolates. We aimed to characterise plasmid mediated resistance determinants in key Enterobacteriaceae isolates with differential phenotypic susceptibility profiles and evaluated the contribution of resistance genes on phenotypic expression of susceptibility. METHODS The study was carried out on 200 Enterobacteriaceae isolates belonging to the genera E. coli, Salmonella, and Klebsiella; 100 resistant and 100 susceptible to quinolones, aminoglycosides, and ESBL-producing as determined by disk diffusion. Reduced susceptibility in susceptible isolates was determined as an increased MIC by broth microdilution. Plasmid-borne resistance genes were sought in all isolates by endpoint PCR. We performed correlations tests to determine the relationship between the occurrence of resistance genes and increased MIC in susceptible isolates. We then used the notion of penetrance to show adequacy between resistance gene carriage and phenotypic resistance as well as diagnostic odds ratio to evaluate how predictable phenotypic susceptibility profile could determine the presence of resistant genes in the isolates. RESULTS Reduced susceptibility was detected in 30% (9/30) ESBL negative, 50% (20/40) quinolone-susceptible and 53.33% (16/30) aminoglycoside-susceptible isolates. Plasmid-borne resistance genes were detected in 50% (15/30) of ESBL negative, 65% (26/40) quinolone susceptible and 66.67% (20/30) aminoglycoside susceptible isolates. Reduced susceptibility increased the risk of susceptible isolates carrying resistance genes (ORs 4.125, 8.36, and 8.89 respectively for ESBL, quinolone, and aminoglycoside resistance genes). Resistance gene carriage correlated significantly to reduced susceptibility for quinolone and aminoglycoside resistance genes (0.002 and 0.015 at CI95). Gene carriage correlated with phenotypic resistance at an estimated 64.28% for ESBL, 56.90% for quinolone, and 58.33% for aminoglycoside resistance genes. CONCLUSIONS A high carriage of plasmid-mediated genes for ESBL, quinolone, and aminoglycoside resistance was found among the Enterobacteriaceae tested. However, gene carriage was not always correlated with phenotypic expression. This allows us to suggest that assessing genetic determinants of resistance should not be based on AST profile only. Further studies, including assessing the role of chromosomal determinants will shed light on other factors that undermine antimicrobial susceptibility locally.
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Affiliation(s)
- Jude Fonbah Leinyuy
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
| | - Innocent Mbulli Ali
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
- The Biotechnology Centre, University of Yaoundé 1, Yaoundé, Cameroon
- * E-mail:
| | - Karimo Ousenu
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
| | - Christopher B. Tume
- Research Unit of Microbiology and Antimicrobial Substances, Department of Biochemistry, University of Dschang, Dschang, Cameroon
- Department of Biochemistry, Faculty of Science, University of Bamenda, Bamenda, Cameroon
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Hilaire SS, Chen C, Pan Z, Radolinski J, Stewart RD, Maguire RO, Xia K. Subsurface Manure Injection Reduces Surface Transport of Antibiotic Resistance Genes but May Create Antibiotic Resistance Hotspots in Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14972-14981. [PMID: 35839145 DOI: 10.1021/acs.est.2c00981] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Compared to surface application, manure subsurface injection reduces surface runoff of nutrients, antibiotic resistant microorganisms, and emerging contaminants. Less is known regarding the impact of both manure application methods on surface transport of antibiotic resistance genes (ARGs) in manure-amended fields. We applied liquid dairy manure to field plots by surface application and subsurface injection and simulated rainfall on the first or seventh day following application. The ARG richness, relative abundance (normalized to 16s rRNA), and ARG profiles in soil and surface runoff were monitored using shotgun metagenomic sequencing. Within 1 day of manure application, compared to unamended soils, soils treated with manure had 32.5-70.5% greater ARG richness and higher relative abundances of sulfonamide (6.5-129%) and tetracycline (752-3766%) resistance genes (p ≤ 0.05). On day 7, soil ARG profiles in the surface-applied plots were similar to, whereas subsurface injection profiles were different from, that of the unamended soils. Forty-six days after manure application, the soil ARG profiles in manure injection slits were 37% more diverse than that of the unamended plots. The abundance of manure-associated ARGs were lower in surface runoff from manure subsurface injected plots and carried a lower resistome risk score in comparison to surface-applied plots. This study demonstrated, for the first time, that although manure subsurface injection reduces ARGs in the runoff, it can create potential long-term hotspots for elevated ARGs within injection slits.
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Affiliation(s)
- Sheldon S Hilaire
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Chaoqi Chen
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
- School of Resource and Environmental Science, Wuhan University, Wuhan 430079, China
| | - Zhizhen Pan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jesse Radolinski
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department of Ecology, University of Innsbruck, Innsbruck 6020, Austria
| | - Ryan D Stewart
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rory O Maguire
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, United States
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20
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No Crystal Ball? Using Risk Factors and Scoring Systems to Predict Extended-Spectrum Beta-Lactamase Producing Enterobacterales (ESBL-E) and Carbapenem-Resistant Enterobacterales (CRE) Infections. Curr Infect Dis Rep 2022. [DOI: 10.1007/s11908-022-00785-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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21
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Speksnijder DC, Hopman NEM, Kusters NE, Timmerman A, Swinkels JM, Penterman PAA, Krömker V, Bradley AJ, Botteldoorn N, Gehring R, Zomer AL. Potential of ESBL-producing Escherichia coli selection in bovine feces after intramammary administration of first generation cephalosporins using in vitro experiments. Sci Rep 2022; 12:15083. [PMID: 36065056 PMCID: PMC9445091 DOI: 10.1038/s41598-022-15558-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
Selection and spread of Extended Spectrum Beta-Lactamase (ESBL) -producing Enterobacteriaceae within animal production systems and potential spillover to humans is a major concern. Intramammary treatment of dairy cows with first-generation cephalosporins is a common practice and potentially selects for ESBL-producing Enterobacteriaceae, although it is unknown whether this really occurs in the bovine fecal environment. We aimed to study the potential effects of intramammary application of cephapirin (CP) and cefalonium (CL) to select for ESBL-producing Escherichia coli in the intestinal content of treated dairy cows and in manure slurry, using in vitro competition experiments with ESBL and non-ESBL E. coli isolates. No selection of ESBL-producing E. coli was observed at or below concentrations of 0.8 µg/ml and 4.0 µg/ml in bovine feces for CP and CL, respectively, and at or below 8.0 µg/ml and 4.0 µg/ml, respectively, in manure slurry. We calculated that the maximum concentration of CP and CL after intramammary treatment with commercial products will not exceed 0.29 µg/ml in feces and 0.03 µg/ml in manure slurry. Therefore, the results of this study did not find evidence supporting the selection of ESBL-producing E. coli in bovine feces or in manure slurry after intramammary use of commercial CP or CL-containing products.
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Affiliation(s)
- David C Speksnijder
- Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands. .,University Farm Animal Clinic, Harmelen, The Netherlands.
| | - Nonke E M Hopman
- Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Nina E Kusters
- Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Arjen Timmerman
- Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jantijn M Swinkels
- Global Ruminant Business Unit, MSD Animal Health, Boxmeer, The Netherlands
| | | | - Volker Krömker
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrew J Bradley
- Quality Milk Management Services Ltd, Cedar Barn, Easton, Wells, UK.,School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | | | - Ronette Gehring
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Aldert L Zomer
- Division Infectious Diseases & Immunology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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22
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The Resistance Patterns in E. coli Isolates among Apparently Healthy Adults and Local Drivers of Antimicrobial Resistance: A Mixed-Methods Study in a Suburban Area of Nepal. Trop Med Infect Dis 2022; 7:tropicalmed7070133. [PMID: 35878145 PMCID: PMC9324341 DOI: 10.3390/tropicalmed7070133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/29/2022] [Accepted: 07/07/2022] [Indexed: 02/05/2023] Open
Abstract
Evidence-based decision-making to combat antimicrobial resistance (AMR) mandates a well-built community-based surveillance system for assessing resistance patterns among commensals and pathogenic organisms. As there is no such surveillance system in Nepal, we attempted to describe the antimicrobial resistance pattern in E. coli isolated from the fecal samples of apparently healthy individuals in Dhulikhel municipality and also explored the local drivers of AMR. We used a mixed-method design with a cross-sectional quantitative component and a descriptive qualitative component, with focus group discussion and key informant interviews as the data collection method. Fecal samples were collected from 424 individuals randomly selected for the study. E. coli was isolated from 85.9% of human fecal samples, of which 14% were resistant to ≥3 class of antimicrobials (multidrug resistant). Of the 368 isolates, resistance to ampicillin (40.0%), tetracycline (20.7%) and cefotaxime (15.5%) were most prevalent. The major drivers of AMR were: lack of awareness of AMR, weak regulations on sales of antimicrobials, poor adherence to prescribed medications, and incomplete dosage due to financial constraints. These findings indicate the need for strict implementation of a national drug act to limit the over-the-counter sales of antimicrobials. Additionally, awareness campaigns with a multimedia mix are essential for educating people on AMR.
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Patterns of Antibiotic Resistance in Enterobacteriaceae Isolates from Broiler Chicken in the West Region of Cameroon: A Cross-Sectional Study. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:4180336. [PMID: 35722039 PMCID: PMC9203226 DOI: 10.1155/2022/4180336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/12/2022] [Accepted: 05/21/2022] [Indexed: 11/18/2022]
Abstract
Background. The emergence of multidrug-resistant food-borne pathogens of animal origin including Enterobacteriaceae is a growing concern. Identifying and monitoring resistance in isolates from human-related environments are of clinical and epidemiological significance in containing antimicrobial resistance. This study aimed to contribute towards the fight against antibiotic resistance and ameliorate the management/treatment of Enterobacteriaceae-linked diseases in Cameroon. Methods. Cloacal swabs from healthy broilers were enriched in buffered-peptone-water and cultured on EMB agar. Antibiotic susceptibility was tested on Mueller-Hinton-Agar by disc diffusion. Plasmid-borne genes for extended-spectrum beta lactamase (ESBL) and resistance to Quinolones (PMQR) and Aminoglycosides were detected by standard endpoint polymerase chain reaction (PCR). Results. A total of 394 isolates were identified belonging to 12 Enterobacteriaceae genera, the most prevalent were Escherichia coli (81/394 = 20.56%), Salmonella spp (74/394 = 18.78%), and Klebsiella spp (39/394 = 9.90%) respectively. Overall, 84/394 (21.32%) were ESBL producers, 164/394 (41.62%) were resistant to quinolones, 66/394 (16.75%) resistant to aminoglycosides with 44.0% (173/394) expressing MDR phenotype. Poor hygiene practice (OR 2.55, 95% CI: 1.67, 3.89,
) and rearing for >45 days, (OR = 7.98, 95% CI: 5.05, 12.6,
) were associated with increased carriage of MDR. Plasmid-borne resistance genes were detected in 76/84 (90.48%) of ESBL-producing isolates, 151/164 (92.07%) quinolone resistant isolates and 59/66 (89.39%) aminoglycoside resistant isolates with co-occurrence of two or more genes per isolate in 58/84 (69.05%) of ESBLs, 132/164 (80.49%) of quinolone resistant isolates and 28/66 (42.42%) of aminoglycoside resistant isolates. Conclusion. This study found high carriage and widespread distribution of Enterobacteriaceae with ESBL and MDR in broiler chicken in the West Region of Cameroon. Most PMQR genes in bacteria were found at levels higher than is seen elsewhere, representing a risk in the wider human community.
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Intestinal Carriage of Extended-spectrum β-lactamase and Carbapenemase-producing Enterobacteriaceae in Hemodialysis Patients. Jundishapur J Microbiol 2022. [DOI: 10.5812/jjm-118946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Gastrointestinal colonization with resistant pathogens is significant because they could be easily transmitted to other hosts or spread to different microbiota through mobile genetic elements. Objectives: This study assessed the prevalence of fecal carriage of extended-spectrum β-lactamase-producing and carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE, respectively) among hemodialysis patients and the factors affecting its occurrence in a hospital in Tehran. Methods: From January 2018 to May 2019, 150 hemodialysis patients referred to a hospital in Tehran were sampled in this study. Stool samples of the patients were diluted in saline and cultured on MacConkey agar plates containing cefotaxime, ceftazidime, imipenem, and meropenem discs. The clinical data were analyzed to identify the risk factors using a logistic regression model. Results: The colonization rate of ESBL-E was 48.6%, while only 2% of patients were identified as the carriers of CPE (3 of 150). A higher prevalence rate was obtained for intestinal carriage of ESBL-E among hemodialysis patients aged 18 to 42 years using multivariate analysis. The prevalence rate of multidrug-resistant isolates was 73.8%. The blaCTX-M1 gene was identified as the most prevalent ESBL gene. Among carbapenemase-encoding genes, blaKPC and blaoxa-48 were found in 12 and two isolates, respectively. Conclusions: These results demonstrated a high prevalence rate of ESBLs among hemodialysis patients, although this rate was low for carbapenemases. Therefore, more control measures should be taken in hospitals to prevent the spread of antibiotic resistance genes in healthcare settings.
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Torres-Puig S, García V, Stærk K, Andersen TE, Møller-Jensen J, Olsen JE, Herrero-Fresno A. “Omics” Technologies - What Have They Told Us About Uropathogenic Escherichia coli Fitness and Virulence During Urinary Tract Infection? Front Cell Infect Microbiol 2022; 12:824039. [PMID: 35237532 PMCID: PMC8882828 DOI: 10.3389/fcimb.2022.824039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the main etiological agent of urinary tract infection (UTI), a widespread infectious disease of great impact on human health. This is further emphasized by the rapidly increase in antimicrobial resistance in UPEC, which compromises UTI treatment. UPEC biology is highly complex since uropathogens must adopt extracellular and intracellular lifestyles and adapt to different niches in the host. In this context, the implementation of forefront ‘omics’ technologies has provided substantial insight into the understanding of UPEC pathogenesis, which has opened the doors for new therapeutics and prophylactics discovery programs. Thus, ‘omics’ technologies applied to studies of UPEC during UTI, or in models of UTI, have revealed extensive lists of factors that are important for the ability of UPEC to cause disease. The multitude of large ‘omics’ datasets that have been generated calls for scrutinized analysis of specific factors that may be of interest for further development of novel treatment strategies. In this review, we describe main UPEC determinants involved in UTI as estimated by ‘omics’ studies, and we compare prediction of factors across the different ‘omics’ technologies, with a focus on those that have been confirmed to be relevant under UTI-related conditions. We also discuss current challenges and future perspectives regarding analysis of data to provide an overview and better understanding of UPEC mechanisms involved in pathogenesis which should assist in the selection of target sites for future prophylaxis and treatment.
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Affiliation(s)
- Sergi Torres-Puig
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Vanesa García
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Kristian Stærk
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Thomas E. Andersen
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- *Correspondence: Ana Herrero-Fresno,
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Antimicrobial Bacillus: Metabolites and Their Mode of Action. Antibiotics (Basel) 2022; 11:antibiotics11010088. [PMID: 35052965 PMCID: PMC8772736 DOI: 10.3390/antibiotics11010088] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 12/12/2022] Open
Abstract
The agricultural industry utilizes antibiotic growth promoters to promote livestock growth and health. However, the World Health Organization has raised concerns over the ongoing spread of antibiotic resistance transmission in the populace, leading to its subsequent ban in several countries, especially in the European Union. These restrictions have translated into an increase in pathogenic outbreaks in the agricultural industry, highlighting the need for an economically viable, non-toxic, and renewable alternative to antibiotics in livestock. Probiotics inhibit pathogen growth, promote a beneficial microbiota, regulate the immune response of its host, enhance feed conversion to nutrients, and form biofilms that block further infection. Commonly used lactic acid bacteria probiotics are vulnerable to the harsh conditions of the upper gastrointestinal system, leading to novel research using spore-forming bacteria from the genus Bacillus. However, the exact mechanisms behind Bacillus probiotics remain unexplored. This review tackles this issue, by reporting antimicrobial compounds produced from Bacillus strains, their proposed mechanisms of action, and any gaps in the mechanism studies of these compounds. Lastly, this paper explores omics approaches to clarify the mechanisms behind Bacillus probiotics.
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Interplay between Bacterial Clones and Plasmids in the Spread of Antibiotic Resistance Genes in the Gut: Lessons from a Temporal Study in Veal Calves. Appl Environ Microbiol 2021; 87:e0135821. [PMID: 34613750 DOI: 10.1128/aem.01358-21] [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] [Indexed: 11/20/2022] Open
Abstract
Intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is a frequent, increasing, and worrying phenomenon, but little is known about the molecular scenario and the evolutionary forces at play. We screened 45 veal calves, known to have high prevalence of carriage, for ESBL-producing E. coli on 514 rectal swabs (one randomly selected colony per sample) collected over 6 months. We characterized the bacterial clones and plasmids carrying blaESBL genes with a combination of genotyping methods, whole genome sequencing, and conjugation assays. One hundred and seventy-three ESBL-producing E. coli isolates [blaCTX-M-1 (64.7%), blaCTX-M-14 (33.5%), or blaCTX-M-15 (1.8%)] were detected, belonging to 32 bacterial clones, mostly of phylogroup A. Calves were colonized successively by different clones with a trend in decreasing carriage. The persistence of a clone in a farm was significantly associated with the number of calves colonized. Despite a high diversity of E. coli clones and blaCTX-M-carrying plasmids, few blaCTX-M gene/plasmid/chromosomal background combinations dominated, due to (i) efficient colonization of bacterial clones and/or (ii) successful plasmid spread in various bacterial clones. The scenario "clone versus plasmid spread" depended on the farm. Thus, epistatic interactions between resistance genes, plasmids, and bacterial clones contribute to optimize fitness in specific environments. IMPORTANCE The gut microbiota is the epicenter of the emergence of resistance. Considerable amount of knowledge on the molecular mechanisms of resistance has been accumulated, but the ecological and evolutionary forces at play in nature are less studied. In this context, we performed a field work on temporal intestinal carriage of extended spectrum β-lactamase (ESBL)-producing Escherichia coli in veal farms. Veal calves are animals with one of the highest levels of ESBL producing E. coli fecal carriage, due to early high antibiotic exposure. We were able to show that calves were colonized successively by different ESBL-producing E. coli clones, and that two main scenarios were at play in the spread of blaCTX-M genes among calves: efficient colonization of several calves by a few bacterial clones and successful plasmid spread in various bacterial clones. Such knowledge should help develop new strategies to fight the emergence of antibiotic-resistance.
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Abstract
Horizontal gene transfer (HGT) is a driving force of microbial evolution. The gut of animals acts as a potent reservoir for the lateral transfer of virulence, fitness, and antimicrobial resistance genes through plasmids. Reduced-complexity models for the examination of host-microbe interactions involved in plasmid transfer are greatly desired. Thus, this study identifies the use of Drosophila melanogaster as a model organism for the conjugation of plasmids of various incompatibility groups in the gut. Enterobacteriaceae conjugation pairs were identified in vitro and used for oral inoculation of the Drosophila gut. Flies were enumerated for the donor, recipient, and transconjugant populations. Each donor-recipient pair was observed to persist in fly guts for the duration of the experiment. Gut concentrations of the donors and recipients were significantly different between male and female flies, with females generally demonstrating increased concentrations. Furthermore, host genetics significantly altered the concentrations of donors and recipients. However, transconjugant concentrations were not affected by host sex or genetics and were detected only in the IncPε and IncI1 plasmid groups. This study demonstrates Drosophila melanogaster as a model for gut-mediated plasmid transfer. IMPORTANCE Microbial evolution in the gut of animals due to horizontal gene transfer (HGT) is of significant interest for microbial evolution as well as within the context of human and animal health. Microbial populations evolve within the host, and factors from the bacteria and host interact to regulate this evolution. However, little is currently known about how host and bacterial factors regulate plasmid-mediated HGT in the gut. This study demonstrates the use of Drosophila and the roles of sexual dimorphism as well as plasmid incompatibility groups in HGT in the gut.
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Tian X, Han B, Liang J, Yang F, Zhang K. Tracking antibiotic resistance genes (ARGs) during earthworm conversion of cow dung in northern China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 222:112538. [PMID: 34325199 DOI: 10.1016/j.ecoenv.2021.112538] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 06/19/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Using cow dung to breed earthworms poses a risk of environmental transmission of antibiotic resistance genes (ARGs). The purpose of this study was to address the occurrence, persistence and environmental fate of ARGs during earthworm conversion of cow dung. The results showed that ARGs persisted through the whole process. Notably, earthworm conversion effectively reduced some ARGs in cow dung, but a definite concentration of ARGs still remained in earthworms and vermicompost (up to 10-1 and 10-2 copies/16S copies, respectively). We found that tet-ARGs were the most abundant in 15 earthworm farms (10-6~10-1 copies/16S copies) and some high-risk ARGs (i.e., blaampC, blaOXA-1 and blaTEM-1) were even prevalent in these farms. Interestingly, although ARGs differ widely in cow dung (10-10~10-1 copies/16S copies), the ARGs levels were comparable in vermicompost samples from different farms (10-8~10-2 copies/16S copies). Notably, earthworm conversion effectively reduced some ARGs in cow dung, but significant level of ARGs still remained in earthworms and vermicompost (up to 10-1 and 10-2 copies/16S copies, respectively). Nevertheless, the concentrations of some heavy metals (Cu, Zn and Ni), the abundance of mobile genetic elements (MGEs) and total nitrogen content were confirmed to be correlated to the enrichment of some ARGs. Overall, this study demonstrated the high prevalence of ARGs contamination in earthworm farms, and also highlighted the dissemination risk of ARGs during the earthworm conversion of cow dung.
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Affiliation(s)
- Xueli Tian
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Bingjun Han
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Junfeng Liang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
| | - Keqiang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
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Hotinger JA, Morris ST, May AE. The Case against Antibiotics and for Anti-Virulence Therapeutics. Microorganisms 2021; 9:2049. [PMID: 34683370 PMCID: PMC8537500 DOI: 10.3390/microorganisms9102049] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/14/2022] Open
Abstract
Although antibiotics have been indispensable in the advancement of modern medicine, there are downsides to their use. Growing resistance to broad-spectrum antibiotics is leading to an epidemic of infections untreatable by first-line therapies. Resistance is exacerbated by antibiotics used as growth factors in livestock, over-prescribing by doctors, and poor treatment adherence by patients. This generates populations of resistant bacteria that can then spread resistance genes horizontally to other bacterial species, including commensals. Furthermore, even when antibiotics are used appropriately, they harm commensal bacteria leading to increased secondary infection risk. Effective antibiotic treatment can induce bacterial survival tactics, such as toxin release and increasing resistance gene transfer. These problems highlight the need for new approaches to treating bacterial infection. Current solutions include combination therapies, narrow-spectrum therapeutics, and antibiotic stewardship programs. These mediate the issues but do not address their root cause. One emerging solution to these problems is anti-virulence treatment: preventing bacterial pathogenesis instead of using bactericidal agents. In this review, we discuss select examples of potential anti-virulence targets and strategies that could be developed into bacterial infection treatments: the bacterial type III secretion system, quorum sensing, and liposomes.
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Affiliation(s)
| | | | - Aaron E. May
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23219, USA; (J.A.H.); (S.T.M.)
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Stærk K, Grønnemose RB, Palarasah Y, Kolmos HJ, Lund L, Alm M, Thomsen P, Andersen TE. A Novel Device-Integrated Drug Delivery System for Local Inhibition of Urinary Tract Infection. Front Microbiol 2021; 12:685698. [PMID: 34248906 PMCID: PMC8267894 DOI: 10.3389/fmicb.2021.685698] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/26/2021] [Indexed: 11/29/2022] Open
Abstract
Background: Catheter-associated urinary tract infection (CAUTI) is a frequent community-acquired infection and the most common nosocomial infection. Here, we developed a novel antimicrobial catheter concept that utilizes a silicone-based interpenetrating polymer network (IPN) as balloon material to facilitate a topical slow-release prophylaxis of antibacterial agents across the balloon to the urinary bladder. Methods: The balloon material was achieved by modifying low shore hardness silicone tubes with a hydrogel interpenetrating polymer in supercritical CO2 using the sequential method. Release properties and antibacterial efficacy of the IPN balloon treatment concept was investigated in vitro and in a porcine CAUTI model developed for the study. In the latter, Bactiguard Infection Protection (BIP) Foley catheters were also assessed to enable benchmark with the traditional antimicrobial coating principle. Results: Uropathogenic Escherichia coli was undetectable in urinary bladders and on retrieved catheters in the IPN treatment group as compared to control that revealed significant bacteriuria (>105 colony forming units/ml) as well as catheter-associated biofilm. The BIP catheters failed to prevent E. coli colonization of the bladder but significantly reduced catheter biofilm formation compared to the control. Conclusion: The IPN-catheter concept provides a novel, promising delivery route for local treatment in the urinary tract.
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Affiliation(s)
- Kristian Stærk
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Rasmus Birkholm Grønnemose
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Yaseelan Palarasah
- Department of Cancer and Inflammation Research, University of Southern Denmark, Odense, Denmark
| | - Hans Jørn Kolmos
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Lars Lund
- Research Unit of Urology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | | | | | - Thomas Emil Andersen
- Research Unit of Clinical Microbiology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
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Bezabih YM, Sabiiti W, Alamneh E, Bezabih A, Peterson GM, Bezabhe WM, Roujeinikova A. The global prevalence and trend of human intestinal carriage of ESBL-producing Escherichia coli in the community. J Antimicrob Chemother 2021; 76:22-29. [PMID: 33305801 DOI: 10.1093/jac/dkaa399] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/28/2020] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Intestinal colonization by ESBL Escherichia coli and its association with community-acquired MDR infections is of great concern. This review determined the worldwide prevalence of human faecal ESBL E. coli carriage and its trend in the community over the past two decades. METHODS A systematic literature search was conducted using PubMed, EMBASE and Google Scholar to retrieve articles published between 1 January 2000 and 13 February 2020 that contained data on the prevalence of faecal carriage of ESBL E. coli among healthy individuals. A cumulative (for the whole period) meta-analysis was used to estimate the global and regional pooled prevalence rates. Articles were grouped into study periods of 3 years, and subgroup meta-analyses were undertaken to examine the global pooled prevalence over time. RESULTS Sixty-two articles covering 29 872 healthy persons were included in this meta-analysis. The cumulative (2003-18) global pooled prevalence of ESBL E. coli intestinal carriage in the community was 16.5% (95% CI 14.3%-18.7%; P < 0.001). The pooled prevalence showed an upward trend, increasing from 2.6% (95% CI 1.6%-4.0%) in 2003-05 to 21.1% (95% CI 15.8%-27.0%) in 2015-18. Over the whole period, the highest carriage rate was observed in South-East Asia (27%; 95% CI 2.9%-51.3%), while the lowest occurred in Europe (6.0%; 95% CI 4.6%-7.5%). CONCLUSIONS Globally, an 8-fold increase in the intestinal carriage rate of ESBL E. coli in the community has occurred over the past two decades. Prevention of its spread may require new therapeutic and public health strategies.
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Affiliation(s)
- Yihienew M Bezabih
- Arsi University College of Health Sciences, Arsi University, PO Box 0193, Asella, Ethiopia
| | - Wilber Sabiiti
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, UK
| | | | - Alamneh Bezabih
- École nationale vétérinaire, agroalimentaire et de l'alimentation, Nantes-Atlantique, BIOEPAR (UMR1300 INRA/ONIRIS), Nantes, France
| | | | | | - Anna Roujeinikova
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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Mukherjee S, Mitra S, Dutta S, Basu S. Neonatal Sepsis: The Impact of Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae. Front Med (Lausanne) 2021; 8:634349. [PMID: 34179032 PMCID: PMC8225938 DOI: 10.3389/fmed.2021.634349] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/26/2021] [Indexed: 01/12/2023] Open
Abstract
The convergence of a vulnerable population and a notorious pathogen is devastating, as seen in the case of sepsis occurring during the first 28 days of life (neonatal period). Sepsis leads to mortality, particularly in low-income countries (LICs) and lower-middle-income countries (LMICs). Klebsiella pneumoniae, an opportunistic pathogen is a leading cause of neonatal sepsis. The success of K. pneumoniae as a pathogen can be attributed to its multidrug-resistance and hypervirulent-pathotype. Though the WHO still recommends ampicillin and gentamicin for the treatment of neonatal sepsis, K. pneumoniae is rapidly becoming untreatable in this susceptible population. With escalating rates of cephalosporin use in health-care settings, the increasing dependency on carbapenems, a "last resort antibiotic," has led to the emergence of carbapenem-resistant K. pneumoniae (CRKP). CRKP is reported from around the world causing outbreaks of neonatal infections. Carbapenem resistance in CRKP is largely mediated by highly transmissible plasmid-encoded carbapenemase enzymes, including KPC, NDM, and OXA-48-like enzymes. Further, the emergence of a more invasive and highly pathogenic hypervirulent K. pneumoniae (hvKP) pathotype in the clinical context poses an additional challenge to the clinicians. The deadly package of resistance and virulence has already limited therapeutic options in neonates with a compromised defense system. Although there are reports of CRKP infections, a review on neonatal sepsis due to CRKP/ hvKP is scarce. Here, we discuss the current understanding of neonatal sepsis with a focus on the global impact of the CRKP, provide a perspective regarding the possible acquisition and transmission of the CRKP and/or hvKP in neonates, and present strategies to effectively identify and combat these organisms.
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Affiliation(s)
- Subhankar Mukherjee
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shravani Mitra
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Sulagna Basu
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
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Hu Y, Rubin J, Mussio K, Riley LW. Risk factors for faecal carriage of multidrug-resistant Escherichia coli in a college community: a penalised regression model. J Glob Antimicrob Resist 2021; 26:166-173. [PMID: 34051401 DOI: 10.1016/j.jgar.2021.05.004] [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: 01/30/2021] [Revised: 04/02/2021] [Accepted: 05/16/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Bacterial antimicrobial resistance is a serious global public-health threat. Intestinal commensal drug-resistant bacteria have been suggested as an important reservoir of antimicrobial resistance genes (ARGs), which may be acquired via food. We aimed to identify risk factors associated with faecal carriage of drug-resistant commensal Escherichia coli among healthy adults focused on their dietary habits. METHODS We conducted a cross-sectional study targeting healthy adult volunteers in a college community. Faecal samples and questionnaires were obtained from 113 volunteers. We conducted backward elimination logistic regression and least absolute shrinkage and selection operator (LASSO) methods to identify risk factors. RESULTS We analysed responses from 81 of 113 volunteers who completed the questionnaire. The logistic regression and LASSO methods identified red meat consumption to be associated with an increased risk [OR = 6.13 (95% CI 1.83-24.2) and 1.82, respectively] and fish consumption with a reduced risk [OR = 0.27 (95% CI 0.08-0.85) and 0.81] for carriage of multidrug-resistant (MDR) E. coli, adjusted for biological sex, employment status, frequently used supermarket and previous travel. CONCLUSION Dietary habits are associated with risk of faecal carriage of MDR E. coli. This study supports the growing evidence that food may be an important source of ARGs present in human commensal E. coli.
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Affiliation(s)
- Yuan Hu
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Julia Rubin
- Division of Environmental Health Science, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Kaitlyn Mussio
- Division of Environmental Health Science, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Lee W Riley
- Division of Infectious Diseases and Immunology, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
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Gashaw M, Marame ZH, Abera M, Ali S. Assessment of Gut Bacteria Profile and Antibiotic Resistance Pattern Among Psychotropic Drug Users: Comparative Cross-Sectional Study. Infect Drug Resist 2021; 14:1875-1881. [PMID: 34079298 PMCID: PMC8164335 DOI: 10.2147/idr.s305992] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/06/2021] [Indexed: 01/08/2023] Open
Abstract
Introduction In the twenty-first century, antibiotic resistance is becoming one of the major global public health threats. Several complex factors are associated with the emergence and spread of antibiotic resistance. Emerging evidences are indicating that drugs used for chronic illness conditions might have a contribution for antibiotic resistance either through drug–drug interactions or metabolism of the drugs by gut microbiota. Objective The aim of this study was to compare the bacteria profile and resistance patterns of gut bacteria isolated from participants using psychotropic drugs and apparently healthy controls. Methods Socio-demographic data were collected from patients using psychotropic medications and apparently healthy persons. Clinical data were collected from patient records. Stool samples were collected from 107 patients using psychotropic medications and 107 apparently healthy controls. Gut bacterial flora were isolated and identified using oxidase, indole, and BD BBL crystal Enteric/Non-fermenter identification system. Antibiotic susceptibility test was done using the disk diffusion method, and Mast disks were used to identify extended-spectrum betalactamase (ESBL) and/or AmpC-producing isolates. Results A total of 245 bacterial isolates were isolated and identified. From these, 124 (50.6%) bacteria were isolated from patients using Psychotropic medications. There was no bacteria profile difference between the two groups. Escherichia coli was the prevalent [100 (80.6%) and 102 (84.3%)] bacteria isolated from patients using psychotropic medications and apparently healthy controls, respectively. Escherichia coli isolated from patients using psychotropic medications showed significantly higher resistance against amoxicillin-clavulanic acid, cephalosporin (2nd, 3rd, 4th generations), meropenem, ciprofloxacin and tetracycline. The odds of isolating ESBL-producing Enterobacteriaceae [(OR=2.3, 95% C.I: (1.4–4.0)] and MDR [OR=5.4, 95% C.I: (1.5–29.8)] were higher on patients using psychotropic medications. Conclusion The observed antibiotic resistance pattern of bacteria isolated from guts of patients using psychotropic medications was very high. The magnitude of antibiotic resistance is more pronounced among E. coli isolates.
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Affiliation(s)
- Mulatu Gashaw
- School of Medical Laboratory Science, Jimma University, Jimma, Ethiopia
| | - Zufan Hailu Marame
- Ambo University Referral Hospital Microbiology Laboratory, Ambo University Referral Hospital, Ambo, Ethiopia
| | - Mubarek Abera
- Department of Psychiatry, Jimma University, Jimma, Ethiopia
| | - Solomon Ali
- Department of Microbiology, Immunology and Parasitology, Saint Paul Hospital Millennium Medical College, Addis Ababa, Ethiopia
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Antibiotic Resistance Crisis: An Update on Antagonistic Interactions between Probiotics and Methicillin-Resistant Staphylococcus aureus (MRSA). Curr Microbiol 2021; 78:2194-2211. [PMID: 33881575 DOI: 10.1007/s00284-021-02442-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 03/01/2021] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance (AMR) havoc is a global multifaceted crisis endowing a significant challenge for the successful eradication of devastating pathogens. Methicillin-Resistant Staphylococcus aureus (MRSA) is an enduring superbug involved in causing devastating infections. Although MRSA is a frequent colonizer of human skin, wound, and anterior nares, the intestinal colonization of MRSA has greatly increased the risk of inducing MRSA-associated colitis besides creating a conducive environment for horizontal transfer of resistant genes to commensal microbes. On the other hand, staphylococcal resistance to last-resort antibiotics has urged the development of novel antimicrobial agents for the effective decolonization of MRSA. In response, probiotics and their metabolites (postbiotics) have been proposed as the adjunct therapeutic avenues. Probiotics exhibit a multitude of anti-MRSA actions (anti-bacterial, anti-biofilm, anti-virulence, anti-drug resistance, co-aggregation, and anti-quorum sensing) through the production of numerous antagonistic compounds such as organic acids, hydrogen peroxide, low molecular weight compounds, biosurfactants, bacteriocins, and bacteriocins like inhibitory substances. Besides, probiotics stabilize the epithelial barrier function and positively modulate the host immune system via regulating various signal transduction mechanisms. Preclinical and human intervention studies have suggested that probiotics outcompete with MRSA by exhibiting anti-colonization mechanisms via protective, competitive, and displacement mode. In this review, we aim to highlight the dynamics of MRSA associated virulence and drug resistance properties, and how probiotics antagonize MRSA through various mechanism of action.
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Intestinal Carriage of Extended-Spectrum β-Lactamase- (ESBL-) Possessing Escherichia coli and Klebsiella Species among Nepalese Health Science and Non-Health Science Students. ACTA ACUST UNITED AC 2021; 2021:4767429. [PMID: 33897921 PMCID: PMC8052163 DOI: 10.1155/2021/4767429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/03/2020] [Accepted: 03/27/2021] [Indexed: 11/18/2022]
Abstract
Infections due to extended-spectrum β-lactamase- (ESBL-) producing Gram-negative bacteria have led to increased mortality, morbidity, and economic burden worldwide. These bacteria can colonize the healthy intestine of human beings and can disseminate in communities and hospital. This study aimed to investigate the prevalence of fecal carriage of ESBL-producing Escherichia coli and Klebsiella species among health science (HS) and non-health science (NHS) students. This descriptive cross-sectional study was conducted on 104 HS and 104 NHS students in which one stool sample from each student was collected and processed for bacterial culture and sensitivity testing according to standard bacteriological procedures. Each morphotype was identified and characterized phenotypically. The antimicrobial sensitivity profile of bacterial isolates was determined by the Kirby–Bauer disk diffusion technique. ESBL production was tested by combination disk method as recommended by the Clinical and Laboratory Standards Institute. Out of 208 stool samples, E. coli and Klebsiella spp. were recovered from 203 (86.8%) and 31 (13.2%) stool samples, respectively. Among those 234 isolates, 69 were positive for ESBL which included E. coli (n = 66, 95.7%) and Klebsiella spp. (n = 3, 4.3%). Fifty (42.4%) out of 118 isolates from HS students and 19 (16.4%) out of 116 from NHS students were colonized by ESBL-producers. Compared to non-ESBL producers, a higher number of ESBL-producing isolates were resistant to ciprofloxacin (14.5% vs. 1.8%, p < 0.001), cotrimoxazole (59.4% vs. 16.4%, p < 0.001), and amikacin (10.1% vs 4.2%, p < 0.001). All E. coli and Klebsiella species isolates were susceptible to meropenem. The prevalence of fecal carriage of ESBL-producing bacteria was higher in HS students; however, there was a considerable number of these strains colonizing NHS students as well. This “iceberg phenomenon” of asymptomatic carriage of ESBL-producing pathogens might act as a source of infection in both the community and hospitals. Therefore, surveillance of carriage of drug-resistant bacteria should be performed regularly.
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Parmar N, Burrows K, Vornewald PM, Lindholm HT, Zwiggelaar RT, Díez-Sánchez A, Martín-Alonso M, Fosslie M, Vallance BA, Dahl JA, Zaph C, Oudhoff MJ. Intestinal-epithelial LSD1 controls goblet cell maturation and effector responses required for gut immunity to bacterial and helminth infection. PLoS Pathog 2021; 17:e1009476. [PMID: 33788902 PMCID: PMC8041206 DOI: 10.1371/journal.ppat.1009476] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/12/2021] [Accepted: 03/14/2021] [Indexed: 11/18/2022] Open
Abstract
Infectious and inflammatory diseases in the intestine remain a serious threat for patients world-wide. Reprogramming of the intestinal epithelium towards a protective effector state is important to manage inflammation and immunity and can be therapeutically targeted. The role of epigenetic regulatory enzymes within these processes is not yet defined. Here, we use a mouse model that has an intestinal-epithelial specific deletion of the histone demethylase Lsd1 (cKO mice), which maintains the epithelium in a fixed reparative state. Challenge of cKO mice with bacteria-induced colitis or a helminth infection model both resulted in increased pathogenesis. Mechanistically, we discovered that LSD1 is important for goblet cell maturation and goblet-cell effector molecules such as RELMß. We propose that this may be in part mediated by directly controlling genes that facilitate cytoskeletal organization, which is important in goblet cell biology. This study therefore identifies intestinal-epithelial epigenetic regulation by LSD1 as a critical element in host protection from infection. The epithelium that lines our intestine has the important task of taking up nutrients, while also providing a barrier against pathogens. The intestinal epithelium performs these different tasks by having specialized cell types; enterocytes take up nutrients whereas goblet cells are in charge of producing a mucus layer. In addition, goblet cells can be stimulated to make special antimicrobial proteins. This occurs in response to cues called cytokines that come from immune cells, which are able to detect and act on the presence of pathogens such as bacteria or parasitic worms. In this study, we found that LSD1, an enzyme that controls gene expression, was important for goblet cells. Mice that lacked LSD1 specifically in their intestinal epithelium were unable to respond to cytokines and could not defend themselves against bacterial and parasitic infections. In part, we also made use of a specific inhibitor against the enzyme activity of LSD1. This inhibitor also blocked goblet cell differentiation and goblet-cell specific antimicrobial responses to cytokines. We are thus able to manipulate epithelial responses, which may be an important tool in the future to treat patients with infectious diseases.
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Affiliation(s)
- Naveen Parmar
- CEMIR-Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kyle Burrows
- The Biomedical Research Centre, University of British Columbia, Vancouver, Canada.,Department of Immunology, University of Toronto, Toronto, Canada
| | - Pia M Vornewald
- CEMIR-Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Håvard T Lindholm
- CEMIR-Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rosalie T Zwiggelaar
- CEMIR-Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Alberto Díez-Sánchez
- CEMIR-Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Mara Martín-Alonso
- CEMIR-Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Madeleine Fosslie
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Bruce A Vallance
- Department of Pediatrics, Division of Gastroenterology, BC Children's Hospital Research Institute, Vancouver, British Columbia
| | - John Arne Dahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Colby Zaph
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Menno J Oudhoff
- CEMIR-Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
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Francius G, Cervulle M, Clément E, Bellanger X, Ekrami S, Gantzer C, Duval JFL. Impacts of Mechanical Stiffness of Bacteriophage-Loaded Hydrogels on Their Antibacterial Activity. ACS APPLIED BIO MATERIALS 2021; 4:2614-2627. [PMID: 35014378 DOI: 10.1021/acsabm.0c01595] [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] [Indexed: 02/07/2023]
Abstract
The elaboration of efficient hydrogel-based materials with antimicrobial properties requires a refined control of defining their physicochemical features, which includes mechanical stiffness, so as to properly mediate their antibacterial activity. In this work, we design hydrogels consisting of polyelectrolyte multilayer films for the loading of T4 and φX174 bacteria-killing viruses, also called bacteriophages. We investigate the antiadhesion and bactericidal performances of this biomaterial against Escherichia coli, with a specific focus on the effects of chemical cross-linking of the hydrogel matrix, which, in turn, mediates the hydrogel stiffness. Depending on the latter and on phage replication features, it is found that the hydrogels loaded with the bacteria-killing viruses make both contact killing (targeted bacteria are those adhered at the hydrogel surface) and release killing (planktonic bacteria are the targets) possible with ca. 20-80% efficiency after only 4 h of incubation at 25 °C as compared to cases where hydrogels are free of viruses. We further demonstrate the lack of dependence of virus diffusion within the hydrogel and of the maximal viral storage capacity on the hydrogel mechanical properties. In addition to the evidenced bacteriolytic activity of the phages loaded in the hydrogels, the antimicrobial property of the phage-loaded materials is shown to be partly controlled by the chemistry of the hydrogel skeleton and, more specifically, by the mobility of the peripheral free polycationic components, known for their ability to weaken and permeabilize membranes of bacteria, the latter then becoming "easier" targets for the viruses.
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Affiliation(s)
| | - Manon Cervulle
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | - Eloïse Clément
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
| | | | - Saeid Ekrami
- Université de Lorraine, CNRS, LCPME, F-54000 Nancy, France
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Andremont A, Cervesi J, Bandinelli PA, Vitry F, de Gunzburg J. Spare and repair the gut microbiota from antibiotic-induced dysbiosis: state-of-the-art. Drug Discov Today 2021; 26:2159-2163. [PMID: 33639249 DOI: 10.1016/j.drudis.2021.02.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/02/2021] [Accepted: 02/16/2021] [Indexed: 02/08/2023]
Abstract
Homeostasis of the intestinal microbiota is currently recognized as a major contributor to human health. Furthermore, intestinal dysbiosis is associated with a multitude of consequences, including intestinal colonization by antibiotic-resistant or pathogenic bacteria, such as Clostridioides difficile, and reduced efficacy of promising anticancer immunotherapies. By far, the most immediate and drastic exposure leading to dysbiosis is antibiotic treatment. Many attempts have been made to prevent or repair antibiotic-associated dysbiosis. Here, we review these innovations and the difficulties associated with their development.
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Affiliation(s)
- Antoine Andremont
- Da Volterra, Paris, France; Université de Paris, IAME, INSERM, Paris, France.
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Chen J, Chen S, Jiang Y, Zhang R, Cai J. Fecal Carriage and Genetic Characterization of CTX-M-1/9/1-Producing Escherichia coli From Healthy Humans in Hangzhou, China. Front Microbiol 2021; 12:616687. [PMID: 33664715 PMCID: PMC7921147 DOI: 10.3389/fmicb.2021.616687] [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: 10/13/2020] [Accepted: 01/15/2021] [Indexed: 11/16/2022] Open
Abstract
CTX-M-199, a novel chimeric β-lactamase which mediated resistance to sulbactam and tazobactam, was recently identified in Hangzhou, China. This study investigated the prevalence of fecal carriage of bacteria producing CTX-M-199 and other CTX-M-1/9/1-type enzymes among healthy individuals and characterized the genetic features of blaCTX–M–1/9/1-bearing mobile elements. A total of 74 Enterobacterales strains carrying various blaCTX–M–1/9/1 genes, including blaCTX–M–64 (n = 40, carriage rate of 0.74%), blaCTX–M–199 (n = 23, 0.40%), blaCTX–M–123 (n = 5, 0.10%), novel blaCTX–M–153 (n = 5, 0.10%), and blaCTX–M–132 (n = 2, 0.04%), were isolated from 68 out of 5,000 (1.36%) fecal samples of healthy adults in Hangzhou City. Phylogenetic analysis based on whole-genome sequencing data showed that 72 blaCTX–M–1/9/1-bearing Escherichia coli isolates were clustered into four major clades, three of which included CTX-M-199 producers. Sixty out of 75 blaCTX–M–1/9/1 genes were located on plasmids belonging to four Inc types: IncI2, IncI1, IncFIB, and IncHI2. The blaCTX–M–199 genes were harbored by three of the four types of plasmids except for IncHI2. All these blaCTX–M–1/9/1 genes were carried on an ISEcp1-mediated transposition unit. In conclusion, human fecal carriage of blaCTX–M–1/9/1 was low in healthy populations of China. The ISEcp1 was commonly associated with blaCTX–M–1/9/1 and may mediate its transmission on various mobile elements. Our findings provide insights into the dissemination and the development of further measures for the control of pathogens producing CTX-M-1/9/1-type enzymes.
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Affiliation(s)
- Jiawei Chen
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Yin Jiang
- Clinical Laboratory, The First People's Hospital of Fuyang Hangzhou, Hangzhou, China
| | - Rong Zhang
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiachang Cai
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
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Characteristics of ESBL-Producing Enterobacterales Colonizing the Gastrointestinal Tract in Patients Admitted to the Oncological Hospital. Curr Microbiol 2021; 78:642-648. [PMID: 33398444 DOI: 10.1007/s00284-020-02334-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022]
Abstract
We analyzed the prevalence and genetic characteristics of the extended-spectrum β-lactamases (ESBLs)-producing Enterobacterales isolated from adult patients hospitalized in the oncological center in 2019. Out of 9372 patients admitted to the hospital, 1373 had been in various medical facilities during the last year, which was an indication to perform a screening test for ESBL-producing Enterobacterales colonizing their gastrointestinal tract. In eighty-three patients (6.1%), 85 ESBL producers were detected. These isolates included the following: Escherichia coli (n = 67; 78.8%), Klebsiella pneumoniae (n = 14; 16.5%), Enterobacter cloacae cplx (n = 3; 3.5%), and Klebsiella oxytoca (n = 1; 1.2%). CTX-M-1-like enzymes were the most common ESBLs (n = 67; 78.8%). Two K. pneumoniae isolates (2/85; 2.4%) additionally produced New Delhi-metallo-β-lactamases (NDM). All isolates, except for K. oxytoca, were typed by pulsed-field gel electrophoresis (PFGE) and demonstrated high genetic diversity. The most prevalent phylogroups of E. coli were B2 group (n = 30; 44.8%), followed by A group (n = 25; 37.3%). These observations have motivated us to investigate the link between ESBL-E colonization and infection among patients with solid tumors.
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Eltai NO, Yassine HM, El-Obeid T, Al-Hadidi SH, Al Thani AA, Alali WQ. Prevalence of Antibiotic-Resistant Escherichia coli Isolates from Local and Imported Retail Chicken Carcasses. J Food Prot 2020; 83:2200-2208. [PMID: 32730573 DOI: 10.4315/jfp-20-113] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022]
Abstract
ABSTRACT The spread of antibiotic resistance among bacterial strains has been associated with consumption of food contaminated with both pathogenic and nonpathogenic bacteria. The objective of this study was to determine the prevalence of antibiotic resistant Escherichia coli isolates in local and imported retail raw chicken meat in Qatar. A total of 270 locally produced (chilled) and imported (chilled or frozen) whole chicken carcasses were obtained from three Hypermarket stores in Qatar. The 216 E. coli isolates recovered from the chicken samples were subjected to antibiotic susceptibility testing with the disk diffusion method. Extended-spectrum β-lactamase (ESBL) production was evaluated with the double disk synergy test. Isolates harboring colistin resistance were identified with a multiplex PCR assay and DNA sequencing. Nearly 89% (192) of the 216 isolates were resistant to at least one of the 18 antibiotics tested. Isolates from local and imported chicken carcasses had relatively higher resistance to sulfamethoxazole (62% of isolates), tetracycline (59.7%), ampicillin and trimethoprim (52.3% each), ciprofloxacin (47.7%), cephalothin (45.4%), and colistin (31.9%). Less resistance was found to amoxicillin-clavulanic acid (6%), ceftriaxone (5.1%), nitrofurantoin (4.2%), piperacillin-tazobactam (4.2%), cefepime (2.3%), meropenem (1.4%), ertapenem (0.9%), and amikacin (0.9%). Nine isolates (4.2%) were ESBL producers, and 137 (63.4%) were multidrug resistant. The percentages of multidrug-resistant, ESBL-producing, and colistin resistant isolates were significantly higher among isolates from local chilled than from imported chilled and frozen chicken samples. Our findings indicate the high prevalence of antibiotic-resistant E. coli in chicken meat sold at retail in Qatar. HIGHLIGHTS
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Affiliation(s)
| | | | - Tahra El-Obeid
- Department of Health Nutrition, College of Health Sciences, Qatar University, Doha, Qatar
| | | | | | - Walid Q Alali
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Kuwait University, Safat, Kuwait
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Sharma S, Tandlich R, Docrat M, Srinivas S. Antibiotic procurement and ABC analysis for a comprehensive primary health care clinic in the Eastern Cape province, South Africa. S Afr J Infect Dis 2020; 35:134. [PMID: 34604377 PMCID: PMC8477259 DOI: 10.4102/sajid.v35i1.134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/27/2020] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR), a major threat to global public health, can be addressed using a managed care approach. This includes timely analysis of antibiotic consumption and procurement data to drive evidence-based policies and practices in healthcare facilities. 'ABC analysis' presents an opportunity for this. METHODS ABC analysis data for a comprehensive Primary Health Care (PHC) clinic in the Eastern Cape province of South Africa was obtained from the Provincial Department of Health for 01 April 2015 to 31 March 2018. Procured antibiotics were analysed on the quantities purchased, total cost, route of administration and spectrum of activity. Antibiotic categorization was also carried out according to the World Health Organization Model List of Essential Medicines (WHO EML) 2017. RESULTS Antibiotics made up approximately 7% of the total annual pharmaceutical expenditure. A total of 31, 35 and 34 antibiotics were procured in the first, second and third years, respectively. The most procured antibiotics were: (1) isoniazid, (2) flucloxacillin, (3) azithromycin, (4) a combination of rifampicin, isoniazid, pyrazinamide, and ethambutol and (5) amoxicillin. Overall, 55%, 2% and 15% of antibiotics accounted for the 'Access', 'Watch' and 'Access and Watch' categories, respectively, of the WHO EML. No 'Reserve' antibiotics were procured. The remaining 28% were antituberculosis medicines. Altogether, 89%, 8% and 3% of the antibiotics were respectively administered orally, systemically, and topically. A total of 58% were broad-spectrum and 42% were narrow-spectrum antibiotics. CONCLUSION Oral antibiotics in the 'Access' category presented favourable usage of antibiotics. Decreasing the use of broad-spectrum antibiotics requires consideration.
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Affiliation(s)
- Samridhi Sharma
- Division of Pharmacy Practice, Faculty of Pharmacy, Rhodes University, Grahamstown, South Africa
| | - Roman Tandlich
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Rhodes University, Grahamstown, South Africa
| | - Mohamed Docrat
- Eastern Cape Department of Health, Grahamstown, South Africa
| | - Sunitha Srinivas
- Division of Pharmacy Practice, Faculty of Pharmacy, Rhodes University, Grahamstown, South Africa
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Doan T, Worden L, Hinterwirth A, Arzika AM, Maliki R, Abdou A, Zhong L, Chen C, Cook C, Lebas E, O’Brien KS, Oldenburg CE, Chow ED, Porco TC, Lipsitch M, Keenan JD, Lietman TM. Macrolide and Nonmacrolide Resistance with Mass Azithromycin Distribution. N Engl J Med 2020; 383:1941-1950. [PMID: 33176084 PMCID: PMC7492079 DOI: 10.1056/nejmoa2002606] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Mass distribution of azithromycin to preschool children twice yearly for 2 years has been shown to reduce childhood mortality in sub-Saharan Africa but at the cost of amplifying macrolide resistance. The effects on the gut resistome, a reservoir of antimicrobial resistance genes in the body, of twice-yearly administration of azithromycin for a longer period are unclear. METHODS We investigated the gut resistome of children after they received twice-yearly distributions of azithromycin for 4 years. In the Niger site of the MORDOR trial, we enrolled 30 villages in a concurrent trial in which they were randomly assigned to receive mass distribution of either azithromycin or placebo, offered to all children 1 to 59 months of age every 6 months for 4 years. Rectal swabs were collected at baseline, 36 months, and 48 months for analysis of the participants' gut resistome. The primary outcome was the ratio of macrolide-resistance determinants in the azithromycin group to those in the placebo group at 48 months. RESULTS Over the entire 48-month period, the mean (±SD) coverage was 86.6±12% in the villages that received placebo and 83.2±16.4% in the villages that received azithromycin. A total of 3232 samples were collected during the entire trial period; of the samples obtained at the 48-month monitoring visit, 546 samples from 15 villages that received placebo and 504 from 14 villages that received azithromycin were analyzed. Determinants of macrolide resistance were higher in the azithromycin group than in the placebo group: 7.4 times as high (95% confidence interval [CI], 4.0 to 16.7) at 36 months and 7.5 times as high (95% CI, 3.8 to 23.1) at 48 months. Continued mass azithromycin distributions also selected for determinants of nonmacrolide resistance, including resistance to beta-lactam antibiotics, an antibiotic class prescribed frequently in this region of Africa. CONCLUSIONS Among villages assigned to receive mass distributions of azithromycin or placebo twice yearly for 4 years, antibiotic resistance was more common in the villages that received azithromycin than in those that received placebo. This trial showed that mass azithromycin distributions may propagate antibiotic resistance. (Funded by the Bill and Melinda Gates Foundation and others; ClinicalTrials.gov number, NCT02047981.).
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Affiliation(s)
- Thuy Doan
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
| | - Lee Worden
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Armin Hinterwirth
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | | | | | - Amza Abdou
- Ministry of Health, Niger
- Programme National de Santé Oculaire, Niger
| | - Lina Zhong
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Cindi Chen
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Catherine Cook
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Elodie Lebas
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Kieran S. O’Brien
- Francis I Proctor Foundation, University of California San
Francisco, USA
| | - Catherine E. Oldenburg
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
- Department of Epidemiology and Biostatistics, University
of California San Francisco, USA
| | - Eric D. Chow
- Department of Biochemistry and Biophysics, University of
California San Francisco, USA
| | - Travis C. Porco
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
- Department of Epidemiology and Biostatistics, University
of California San Francisco, USA
| | - Marc Lipsitch
- Department of Epidemiology, Harvard T.H. Chan School of
Public Health, Harvard University, MA, USA
| | - Jeremy D. Keenan
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
| | - Thomas M. Lietman
- Francis I Proctor Foundation, University of California San
Francisco, USA
- Department of Ophthalmology, University of California San
Francisco, USA
- Department of Epidemiology and Biostatistics, University
of California San Francisco, USA
- Institute for Global Health Sciences, University of
California San Francisco, USA
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Limited Genetic Diversity of blaCMY-2-Containing IncI1-pST12 Plasmids from Enterobacteriaceae of Human and Broiler Chicken Origin in The Netherlands. Microorganisms 2020; 8:microorganisms8111755. [PMID: 33171694 PMCID: PMC7695270 DOI: 10.3390/microorganisms8111755] [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: 10/27/2020] [Revised: 11/06/2020] [Accepted: 11/07/2020] [Indexed: 11/17/2022] Open
Abstract
Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1–pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1–pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNPs) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences, and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1–pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1–pST12 plasmids revealed a low number of SNP differences (range of 0–9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. Next generation sequencing analysis of blaCMY-2-containing IncI1–pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.
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Ferreira RDS, Mendonça LABM, Ribeiro CFA, Calças NC, Guimarães RDCA, Nascimento VAD, Gielow KDCF, Carvalho CME, Castro APD, Franco OL. Relationship between intestinal microbiota, diet and biological systems: an integrated view. Crit Rev Food Sci Nutr 2020; 62:1166-1186. [PMID: 33115284 DOI: 10.1080/10408398.2020.1836605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The health-disease process can be influenced by the intestinal microbiota. As this plays a fundamental role in protecting the organism, the importance of studying the composition and diversity of this community becomes increasingly evident. Changes in the composition of the intestinal bacterial community may result in dysbiosis, and this process may contribute to triggering various diseases in all biological systems. This imbalance of intestinal microbiota homeostasis may alter commensal bacteria and the host metabolism, as well as immune function. Dysbiosis also causes an increase in intestinal permeability due to exposure to molecular patterns associated with the pathogen and lipopolysaccharides, leading to a chronic inflammatory process that can result in diseases for all biological systems. In this context, dietary intervention through the use of probiotics, prebiotics and antioxidant foods can be considered a contribution to the modulation of intestinal microbiota. Probiotics have been used to provide up to 10 billion colony forming units, and probiotic foods, Kefir and fermented natural yogurt are also used. Prebiotics, in turn, are found in supplemental formulations of processed foods and in functional foods that are also sources of phenolic compounds, such as flavonoids, antioxidant and anti-inflammatory substances, polyunsaturated fatty acids, vitamins, and minerals. In this review, we will discuss the relationship between an imbalance in the intestinal microbiota with the development of diseases, besides indicating the need for future studies that can establish bacterial parameters for the gastrointestinal tract by modulating the intestinal microbiota, associated with the adoption of healthy habits during all life cycles.
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Affiliation(s)
- Rosângela Dos Santos Ferreira
- S-Inova Biotech, Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Camila Fontoura Acosta Ribeiro
- S-Inova Biotech, Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Natali Camposano Calças
- S-Inova Biotech, Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Rita de Cássia Avellaneda Guimarães
- Post Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Valter Aragão do Nascimento
- Post Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Karine de Cássia Freitas Gielow
- Post Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Alinne Pereira de Castro
- S-Inova Biotech, Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil
| | - Octávio Luiz Franco
- S-Inova Biotech, Post Graduate Program in Biotechnology, Catholic University Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil.,Center of Proteomic and Biochemical Analysis, Post Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasilia, Brasilia, Distrito Federal, Brazil
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Vanegas JM, Salazar-Ospina L, Montoya-Urrego D, Builes J, Roncancio GE, Jiménez JN. High frequency of colonization by diverse clones of beta-lactam-resistant Gram-negative bacilli in haemodialysis: different sources of transmission outside the renal unit? J Med Microbiol 2020; 69:1132-1144. [PMID: 32812863 DOI: 10.1099/jmm.0.001244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. While colonization by Staphylococcus aureus in haemodialysis patients has been assessed, knowledge about colonization by beta-lactam-resistant Gram-negative bacilli is still limited.Aim. To describe clinical and molecular characteristics in haemodialysis patients colonized by S. aureus (MSSA-MRSA) and beta-lactam-resistant Gram-negative bacilli in an ambulatory renal unit.Methodology. The study included patients with central venous catheters in an outpatient haemodialysis facility in Medellín, Colombia (October 2017-October 2018). Swab specimens were collected from the nostrils and skin around vascular access to assess colonization by S. aureus (MSSA-MRSA). Stool samples were collected from each patient to evaluate beta-lactam-resistant Gram-negative bacilli colonization. Molecular typing included PFGE, multilocus sequence typing (MLST), spa typing and enterobacterial repetitive intergenic consensus-PCR (ERIC). Clinical information was obtained from medical records and personal interview.Results. A total of 210 patients were included in the study. S. aureus colonization was observed in 33.8 % (n=71) of the patients, 4.8 % (n=10) of which were colonized by methicillin-resistant S. aureus. Stool samples were collected from 165 patients and of these 41.2 % (n=68) and 11.5 % (n=19) were colonized by extended-spectrum-beta-lactamase-producing (ESBL) and carbapenem-resistant bacilli, respectively. Typing methods revealed high genetic diversity among S. aureus and ESBL-producing Gram-negative bacilli (ESBL-GNB). Antibiotic use and hospitalization in the previous 6 months were observed in more than half of the studied population.Conclusion. The high colonization by ESBL-GNB in haemodialysis patients shows evidence for the need for stronger surveillance, not only for S. aureus but also for multidrug-resistant bacilli in order to avoid their spread. Additionally, the high genetic diversity suggests other sources of transmission outside the renal unit instead of horizontal transmission between patients.
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Affiliation(s)
- Johanna M Vanegas
- Línea de Epidemiología Molecular Bacteriana, Grupo de Investigación en Microbiología Básica y Aplicada, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Lorena Salazar-Ospina
- Línea de Epidemiología Molecular Bacteriana, Grupo de Investigación en Microbiología Básica y Aplicada, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Daniela Montoya-Urrego
- Línea de Epidemiología Molecular Bacteriana, Grupo de Investigación en Microbiología Básica y Aplicada, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Julián Builes
- Departamento de Nefrología, Hospital San Vicente Fundación, Medellín, Colombia
| | - Gustavo E Roncancio
- Departamento de Enfermedades Infecciosas, Clínica CardioVID, Medellín, Colombia
- Línea de Epidemiología Molecular Bacteriana, Grupo de Investigación en Microbiología Básica y Aplicada, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - J Natalia Jiménez
- Línea de Epidemiología Molecular Bacteriana, Grupo de Investigación en Microbiología Básica y Aplicada, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
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Guk J, Guedj J, Burdet C, Andremont A, de Gunzburg J, Ducher A, Mentré F. Modeling the Effect of DAV132, a Novel Colon-Targeted Adsorbent, on Fecal Concentrations of Moxifloxacin and Gut Microbiota Diversity in Healthy Volunteers. Clin Pharmacol Ther 2020; 109:1045-1054. [PMID: 32617960 DOI: 10.1002/cpt.1977] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/12/2020] [Indexed: 11/06/2022]
Abstract
To prevent antibiotic-induced perturbations on gut microbiota, DAV132, a novel colon-targeted adsorbent, which sequesters antibiotic residues in the lower gastrointestinal tract, was developed. We built an integrated pharmacological model of how DAV132 reduces fecal free moxifloxacin and preserves gut microbiota. We used plasma and fecal free moxifloxacin concentrations, and Shannon diversity index from 16S ribosomal RNA gene metagenomics analysis of fecal microbiota, of 143 healthy volunteers assigned randomly to receive moxifloxacin only, or with 10 DAV132 dose regimens, or to a control group. We modeled reduced fecal moxifloxacin concentrations using a transit model for DAV132 kinetics and a Michaelis-Menten model with an effect of the amount of activated charcoal on adsorption efficacy. Changes in moxifloxacin-induced perturbations on gut microbiota diversity were then quantified through a turnover model with the Emax model. With the developed model, the efficiency of pharmacokinetic antagonism and its consequences on gut microbiota diversity were quantified.
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Affiliation(s)
- Jinju Guk
- Université de Paris, IAME, INSERM, Paris, France
| | | | | | - Antoine Andremont
- Université de Paris, IAME, INSERM, Paris, France.,Da Volterra, Paris, France
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50
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Le Bastard Q, Chapelet G, Birgand G, Hillmann BM, Javaudin F, Hayatgheib N, Bourigault C, Bemer P, De Decker L, Batard E, Lepelletier D, Montassier E. Gut microbiome signatures of nursing home residents carrying Enterobacteria producing extended-spectrum β-lactamases. Antimicrob Resist Infect Control 2020; 9:107. [PMID: 32665016 PMCID: PMC7359458 DOI: 10.1186/s13756-020-00773-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/03/2020] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The prevalence of extended beta-lactamase producing Enterobacteriaceae (ESBL-E) has been constantly increasing over the last few decades. These microorganisms that have acquired broad antibiotic resistance are now common human pathogens. Changes in the gut microbiome, induced by antibiotics or other drugs, enable expansion of these microorganisms, but the mechanisms are not yet fully understood. OBJECTIVES The main objective was to identify specific bacteria and functional pathways and genes characterizing the gut microbiome of nursing home residents carrying ESBL-E, using metagenomics. SUBJECTS AND METHODS We included 144 residents living in two different nursing homes. All fecal samples were screened for ESBL-E and gut microbiome was characterized using shallow shotgun metagenomic DNA sequencing. RESULTS Ten nursing home residents were colonized by ESBL-E, namely Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae species, and were compared to non-carriers. We found that ESBL-E carriers had an alteration in within-sample diversity. Using a bootstrap algorithm, we found that the gut microbiome of ESBL-E carriers was depleted in butyrate-producing species, enriched in succinate-producing species and enriched in pathways involved in intracellular pH homeostasis compared to non-carriers individuals. Several energy metabolism pathways were overrepresented in ESBL-E carriers suggesting a greater ability to metabolize multiple microbiota and mucus layer-derived nutrients. CONCLUSIONS The gut microbiome of ESBL-E carriers in nursing homes harbors specific taxonomic and functional characteristics, conferring an environment that enables Enterobacteriaceae expansion. Here we describe new functional features associated with ESBL-E carriage that could help us to elucidate the complex interactions leading to colonization persistence in the human gut microbiota.
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Affiliation(s)
- Quentin Le Bastard
- MiHAR lab, Université de Nantes, 44000, Nantes, France.
- Department of Emergency Medicine, CHU Nantes, Nantes University Hospital, 44000, Nantes, France.
| | - Guillaume Chapelet
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Pole de gérontologie clinique, Nantes University Hospital, 44000, Nantes, France
| | - Gabriel Birgand
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Regional Infection Control Centre, Pays de la Loire, Nantes, France
| | - Benjamin M Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - François Javaudin
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Department of Emergency Medicine, CHU Nantes, Nantes University Hospital, 44000, Nantes, France
| | | | - Céline Bourigault
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Bacteriology and Infection Control Department, Nantes University Hospital, Nantes, France
| | - Pascale Bemer
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Bacteriology and Infection Control Department, Nantes University Hospital, Nantes, France
| | - Laure De Decker
- Pole de gérontologie clinique, Nantes University Hospital, 44000, Nantes, France
| | - Eric Batard
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Department of Emergency Medicine, CHU Nantes, Nantes University Hospital, 44000, Nantes, France
| | - Didier Lepelletier
- MiHAR lab, Université de Nantes, 44000, Nantes, France
- Bacteriology and Infection Control Department, Nantes University Hospital, Nantes, France
| | - Emmanuel Montassier
- MiHAR lab, Université de Nantes, 44000, Nantes, France.
- Department of Emergency Medicine, CHU Nantes, Nantes University Hospital, 44000, Nantes, France.
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