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Ye L, Liu X, Ni Y, Xu Y, Zheng Z, Chen K, Hu Q, Tan L, Guo Z, Wai CK, Chan EWC, Li R, Chen S. Comprehensive genomic and plasmid characterization of multidrug-resistant bacterial strains by R10.4.1 nanopore sequencing. Microbiol Res 2024; 283:127666. [PMID: 38460283 DOI: 10.1016/j.micres.2024.127666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/17/2024] [Accepted: 02/25/2024] [Indexed: 03/11/2024]
Abstract
The escalating prevalence of multidrug-resistant (MDR) bacteria pose a significant public health threat. Understanding the genomic features and deciphering the antibiotic resistance profiles of these pathogens is crucial for development of effective surveillance and treatment strategies. In this study, we employed the R10.4.1 nanopore sequencing technology, specifically through the use of the MinION platform, to analyze eight MDR bacterial strains originating from clinical, ecological and food sources. A single 72-hour sequencing run could yield approximately 12 million reads which covered a total of 34 gigabases (Gbp). The nanopore R10.4.1 data was processed using the Flye assembler, successfully assembling the genomes of eight bacterial strains and their 18 plasmids. Notably, the assemblies generated solely from R10.4.1 nanopore data closely matched those from next-generation sequencing data. Diverse antibiotic resistance patterns and specific resistance genes in the test strains were identified. Hospital strains that exhibited multidrug resistance were found to harbor various resistance genes that encode efflux pumps and extended-spectrum β-lactamases. Environmental and food sources were found to display resistance profiles in a species-specific manner. The composition of structurally complex plasmids in the test strains could also be revealed by analysis of nanopore long reads, which also suggested evidence of horizontal transfer of plasmids between different bacterial species. These findings provide valuable insights into the genetic characteristics of MDR bacteria and demonstrating the practicality of nanopore sequencing technology for detecting of resistance elements in bacterial pathogens.
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Affiliation(s)
- Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR China; State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR China
| | - Xudong Liu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR China
| | - Ying Ni
- Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, Hong Kong, SAR China; Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, China
| | - Yating Xu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR China; State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR China
| | - Zhiwei Zheng
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR China; Shenzhen Key Lab for Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Kaichao Chen
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR China
| | - Qiao Hu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR China; State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR China
| | - Lu Tan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR China
| | - Zhihao Guo
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR China
| | - Chan Kwan Wai
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR China
| | - Edward Wai Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, SAR China; Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, China.
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR China; Shenzhen Key Lab for Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China; Animal Health Research Center, City University of Hong Kong Chengdu Research Institute, Chengdu, China.
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Kenyon C. Doxycycline post-exposure prophylaxis could theoretically select for resistance to various antimicrobials in 19 pathobionts: an in silico analysis. Int J Infect Dis 2024; 142:106974. [PMID: 38395219 DOI: 10.1016/j.ijid.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024] Open
Abstract
OBJECTIVES Doxycycline post exposure prophylaxis (PEP) has been shown to reduce the incidence of bacterial STIs. However, if there is genetic linkage between resistance to tetracycline and other antimicrobials, then it could also select for resistance to these other antimicrobials. We therefore undertook to evaluate if there is an association between the minimum inhibitory concentrations (MICs) of tetracycline and other antimicrobials in 19 clinically important bacterial species. METHODS Mixed-effects linear regression was used to assess if minocycline MICs were associated with the MICs of eight other antimicrobials (ceftriaxone, ampicillin, oxacillin, vancomycin, erythromycin, levofloxacin, amikacin, and trimethoprim-sulfamethoxazole) in 19 bacterial species in the Antimicrobial Testing Leadership and Surveillance (ATLAS) database. RESULTS With the notable exception of vancomycin, where no association was found, strong positive associations were typically found between the MICs of minocycline and each of the eight antimicrobials in each of the species assessed. For example, the minocycline MICs of all the Gram-positive species were positively associated with ampicillin, ceftriaxone, oxacillin and erythromycin MICs (all P-values < 0.001). The only exceptions were ampicillin for Streptococcus pyogenes and ceftriaxone for S. dysgalactiae, where no significant associations were found. Similarly in the Gram-negative species, the minocycline MICs of all the species except Haemophilus influenzae and Stenotrophomonas maltophilia were positively associated with the MICs of ceftriaxone, ampicillin, levofloxacin and amikacin (all P-values < 0.001). CONCLUSIONS There is a theoretical risk that doxycycline PEP could select for resistance not only to tetracyclines but to a range of other antimicrobials in each of the 19 pathobionts assessed.
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Affiliation(s)
- Chris Kenyon
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, South Africa.
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Robins K, O'Donnell G, Neumann A, Schmidt W, Hart A, Graham DW. Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments. Sci Total Environ 2024; 928:172348. [PMID: 38614353 DOI: 10.1016/j.scitotenv.2024.172348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.
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Affiliation(s)
- Katie Robins
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Greg O'Donnell
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Anke Neumann
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Wiebke Schmidt
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Alwyn Hart
- Chief Scientists Group, Environment Agency, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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Zamudio R, Boerlin P, Mulvey MR, Haenni M, Beyrouthy R, Madec JY, Schwarz S, Cormier A, Chalmers G, Bonnet R, Zhanel GG, Kaspar H, Mather AE. Global transmission of extended-spectrum cephalosporin resistance in Escherichia coli driven by epidemic plasmids. EBioMedicine 2024; 103:105097. [PMID: 38608515 PMCID: PMC11024496 DOI: 10.1016/j.ebiom.2024.105097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Extended-spectrum cephalosporins (ESCs) are third and fourth generation cephalosporin antimicrobials used in humans and animals to treat infections due to multidrug-resistant (MDR) bacteria. Resistance to ESCs (ESC-R) in Enterobacterales is predominantly due to the production of extended-spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC β-lactamases (AmpCs). The dynamics of ESBLs and AmpCs are changing across countries and host species, the result of global transmission of ESC-R genes. Plasmids are known to play a key role in this dissemination, but the relative importance of different types of plasmids is not fully understood. METHODS In this study, Escherichia coli with the major ESC-R genes blaCTX-M-1, blaCTX-M-15, blaCTX-M-14 (ESBLs) and blaCMY-2 (AmpC), were selected from diverse host species and other sources across Canada, France and Germany, collected between 2003 and 2017. To examine in detail the vehicles of transmission of the ESC-R genes, long- and short-read sequences were generated to obtain complete contiguous chromosome and plasmid sequences (n = 192 ESC-R E. coli). The types, gene composition and genetic relatedness of these plasmids were investigated, along with association with isolate year, source and geographical origin, and put in context with publicly available plasmid sequences. FINDINGS We identified five epidemic resistance plasmid subtypes with distinct genetic properties that are associated with the global dissemination of ESC-R genes across multiple E. coli lineages and host species. The IncI1 pST3 blaCTX-M-1 plasmid subtype was found in more diverse sources than the other main plasmid subtypes, whereas IncI1 pST12 blaCMY-2 was more frequent in Canadian and German human and chicken isolates. Clonal expansion also contributed to the dissemination of the IncI1 pST12 blaCMY-2 plasmid in ST131 and ST117 E. coli harbouring this plasmid. The IncI1 pST2 blaCMY-2 subtype was predominant in isolates from humans in France, while the IncF F31:A4:B1 blaCTX-M-15 and F2:A-:B- blaCTX-M-14 plasmid subtypes were frequent in human and cattle isolates across multiple countries. Beyond their epidemic nature with respect to ESC-R genes, in our collection almost all IncI1 pST3 blaCTX-M-1 and IncF F31:A4:B1 blaCTX-M-15 epidemic plasmids also carried multiple antimicrobial resistance (AMR) genes conferring resistance to other antimicrobial classes. Finally, we found genetic signatures in the regions surrounding specific ESC-R genes, identifying the predominant mechanisms of ESC-R gene movement, and using publicly available databases, we identified these epidemic plasmids from widespread bacterial species, host species, countries and continents. INTERPRETATION We provide evidence that epidemic resistance plasmid subtypes contribute to the global dissemination of ESC-R genes, and in addition, some of these epidemic plasmids confer resistance to multiple other antimicrobial classes. The success of these plasmids suggests that they may have a fitness advantage over other plasmid types and subtypes. Identification and understanding of the vehicles of AMR transmission are crucial to develop and target strategies and interventions to reduce the spread of AMR. FUNDING This project was supported by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR), through the Medical Research Council (MRC, MR/R000948/1), the Canadian Institutes of Health Research (CFC-150770), and the Genomics Research and Development Initiative (Government of Canada), the German Federal Ministry of Education and Research (BMBF) grant no. 01KI1709, the French Agency for food environmental and occupational health & safety (Anses), and the French National Reference Center (CNR) for antimicrobial resistance. Support was also provided by the Biotechnology and Biological Sciences Research Council (BBSRC) through the BBSRC Institute Strategic Programme Microbes in the Food ChainBB/R012504/1 and its constituent project BBS/E/F/000PR10348 (Theme 1, Epidemiology and Evolution of Pathogens in the Food Chain).
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Affiliation(s)
- Roxana Zamudio
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Patrick Boerlin
- Department of Pathobiology, University of Guelph, Guelph N1G 2W1, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba R3E 3R2, Canada
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Anses - Université de Lyon, Lyon 69007, France
| | - Racha Beyrouthy
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand 63001, France; Centre National de Référence de la Résistance Aux Antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Anses - Université de Lyon, Lyon 69007, France
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany; Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany
| | - Ashley Cormier
- Department of Pathobiology, University of Guelph, Guelph N1G 2W1, Canada
| | - Gabhan Chalmers
- Department of Pathobiology, University of Guelph, Guelph N1G 2W1, Canada
| | - Richard Bonnet
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand 63001, France; Centre National de Référence de la Résistance Aux Antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand 63000, France
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Heike Kaspar
- Department Method Standardisation, Resistance to Antibiotics Unit Monitoring of Resistance to Antibiotics, Federal Office of Consumer Protection and Food Safety, Berlin 12277, Germany
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom; University of East Anglia, Norwich NR4 7TJ, United Kingdom.
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Vanbaelen T, Manoharan-Basil SS, Kenyon C. Four recent insights suggest the need for more refined methods to assess the resistogenicity of doxycycline post exposure prophylaxis. Curr Res Microb Sci 2024; 6:100234. [PMID: 38646593 PMCID: PMC11033152 DOI: 10.1016/j.crmicr.2024.100234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024] Open
Abstract
Two recently published randomized trials of doxycycline post exposure prophylaxis (PEP) have concluded that this intervention is highly effective at reducing the incidence of bacterial sexually transmitted infections (STIs) and has little or no risk of promoting the spread of antimicrobial resistance (AMR). In this perspective piece, we review four types of evidence that suggest that the risk of promoting AMR has been inadequately assessed in these studies. 1) The studies have all used proportion resistant as the outcome measure. This is a less sensitive measure of resistogenicity than MIC distribution. 2) These RCTs have not considered population-level pathways of AMR selection. 3) In populations with very high antimicrobial consumption such as PrEP cohorts, the relationship between antimicrobial consumption and resistance may be saturated. 4) Genetic linkage of AMR means that increased tetracycline use may select for AMR to not only tetracyclines but also other antimicrobials in STIs and other bacterial species. We recommend novel study designs to more adequately assess the AMR-inducing risk of doxycycline PEP.
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Affiliation(s)
- Thibaut Vanbaelen
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, 2000, Belgium
| | | | - Chris Kenyon
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, 2000, Belgium
- Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, 7700, South Africa
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Vanbaelen T, Manoharan-Basil SS, Kenyon C. 45 years of tetracycline post exposure prophylaxis for STIs and the risk of tetracycline resistance: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:376. [PMID: 38575877 PMCID: PMC10996150 DOI: 10.1186/s12879-024-09275-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/31/2024] [Indexed: 04/06/2024] Open
Abstract
There is considerable interest in the use of doxycycline post exposure prophylaxis (PEP) to reduce the incidence of bacterial sexually transmitted infections (STIs). An important concern is that this could select for tetracycline resistance in these STIs and other species. We searched PubMed and Google Scholar, (1948-2023) for randomized controlled trials comparing tetracycline PEP with non-tetracycline controls. The primary outcome was antimicrobial resistance (AMR) to tetracyclines in all bacterial species with available data. Our search yielded 140 studies, of which three met the inclusion criteria. Tetracycline PEP was associated with an increasedprevalence of tetracycline resistance in Neisseria gonorrhoeae, but this effect was not statistically significant (Pooled OR 2.3, 95% CI 0.9-3.4). PEP had a marked effect on the N. gonorrhoeae tetracycline MIC distribution in the one study where this was assessed. Prophylactic efficacy was 100% at low MICs and 0% at high MICs. In the one study where this was assessed, PEP resulted in a significant increase in tetracycline resistance in commensal Neisseria species compared to the control group (OR 2.9, 95% CI 1.5-5.5) but no significant effect on the prevalence of tetracycline resistance in Staphylococcus aureus. The available evidence suggests that PEP with tetracyclines could be associated with selecting tetracycline resistance in N. gonorrhoeae and commensal Neisseria species.
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Affiliation(s)
- Thibaut Vanbaelen
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | | | - Chris Kenyon
- STI Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium.
- Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, 7700, South Africa.
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Straub C, Weaver L, Cornelius AJ, McGill E, Dyet K, Pattis I. Extended-spectrum beta-lactamase, AmpC, and carbapenemase-producing Gram-negative wastewater isolates from Aotearoa New Zealand. Microbiol Resour Announc 2024:e0013124. [PMID: 38564672 DOI: 10.1128/mra.00131-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
Extended-spectrum beta-lactamase, AmpC, and carbapenemase-producing bacteria were isolated from raw sewage, effluent, oxidation pond water, and sediment from a wastewater treatment plant in Aotearoa New Zealand. Here, we report the assemblies of 17 isolates belonging to the species Aeromonas veronii, Aeromonas hydrophila, Enterobacter cloacae, Enterobacter soli, Lelliottia amnigena, Aeromonas caviae, Escherichia coli, Pseudomonas moraviensis, Pseudomonas putida, and Kluyvera ascorbata.
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Affiliation(s)
- Christina Straub
- Institute of Environmental Science and Research Ltd., Health & Environment, Auckland, New Zealand
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Vienna, Austria
- Genomics Aotearoa, Dunedin, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., Health & Environment, Christchurch, New Zealand
| | - Angela J Cornelius
- Institute of Environmental Science and Research Ltd., Health & Environment, Christchurch, New Zealand
| | - Erin McGill
- Institute of Environmental Science and Research Ltd., Health & Environment, Christchurch, New Zealand
| | - Kristin Dyet
- Institute of Environmental Science and Research Ltd., Health & Environment, Wellington, New Zealand
| | - Isabelle Pattis
- Institute of Environmental Science and Research Ltd., Health & Environment, Christchurch, New Zealand
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Imran M, Singh S, Ahmad MN, Malik P, Mukhopadhyay A, Yadav KS, Gupta UD, Mugale MN, Mitra K, Srivastava KK, Chopra S, Mignani S, Apartsin E, Majoral JP, Dasgupta A. Polycationic phosphorous dendrimer potentiates multiple antibiotics against drug-resistant mycobacterial pathogens. Biomed Pharmacother 2024; 173:116289. [PMID: 38452653 DOI: 10.1016/j.biopha.2024.116289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/02/2024] [Accepted: 02/17/2024] [Indexed: 03/09/2024] Open
Abstract
Mycobacterium tuberculosis (Mtb), causative agent of tuberculosis (TB) and non-tubercular mycobacterial (NTM) pathogens such as Mycobacterium abscessus are one of the most critical concerns worldwide due to increased drug-resistance resulting in increased morbidity and mortality. Therefore, focusing on developing novel therapeutics to minimize the treatment period and reducing the burden of drug-resistant Mtb and NTM infections are an urgent and pressing need. In our previous study, we identified anti-mycobacterial activity of orally bioavailable, non-cytotoxic, polycationic phosphorus dendrimer 2G0 against Mtb. In this study, we report ability of 2G0 to potentiate activity of multiple classes of antibiotics against drug-resistant mycobacterial strains. The observed synergy was confirmed using time-kill kinetics and revealed significantly potent activity of the combinations as compared to individual drugs alone. More importantly, no re-growth was observed in any tested combination. The identified combinations were further confirmed in intra-cellular killing assay as well as murine model of NTM infection, where 2G0 potentiated the activity of all tested antibiotics significantly better than individual drugs. Taken together, this nanoparticle with intrinsic antimycobacterial properties has the potential to represents an alternate drug candidate and/or a novel delivery agent for antibiotics of choice for enhancing the treatment of drug-resistant mycobacterial pathogens.
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Affiliation(s)
- Mohmmad Imran
- Division of Molecular Microbiology & Immunology, CSIR-Central Drug Research Institute, Sitapur Road, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shriya Singh
- Division of Molecular Microbiology & Immunology, CSIR-Central Drug Research Institute, Sitapur Road, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India
| | - Mohammad Naiyaz Ahmad
- Division of Molecular Microbiology & Immunology, CSIR-Central Drug Research Institute, Sitapur Road, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pradip Malik
- Division of Molecular Microbiology & Immunology, CSIR-Central Drug Research Institute, Sitapur Road, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Atri Mukhopadhyay
- Division of Molecular Microbiology & Immunology, CSIR-Central Drug Research Institute, Sitapur Road, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Karan Singh Yadav
- Division of Toxicology & Experimental Medicine, CSIR-Central Drug Research Institute, Sitapur Road, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Umesh D Gupta
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Agra 282001, India
| | - Madhav N Mugale
- Division of Toxicology & Experimental Medicine, CSIR-Central Drug Research Institute, Sitapur Road, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kalyan Mitra
- Electron Microscopy Unit, CSIR-Central Drug Research Institute, Sitapur Road, Lucknow, 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kishore K Srivastava
- Division of Molecular Microbiology & Immunology, CSIR-Central Drug Research Institute, Sitapur Road, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sidharth Chopra
- Division of Molecular Microbiology & Immunology, CSIR-Central Drug Research Institute, Sitapur Road, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Serge Mignani
- Centre d'Etudes et de Recherche sur le Medicament de Normandie (CERMN), Université de Caen Normandie, Caen 14032, France; Centro de Quimica da Madeira, MMRG, Campus da Penteada, Universidade da Madeira, Funchal 9020-105 19, Portugal.
| | - Evgeny Apartsin
- Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Pessac F-33600, France
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination du CNRS, 205 Route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France; LCC-CNRS, Université de Toulouse, CNRS, Toulouse 31400, France.
| | - Arunava Dasgupta
- Division of Molecular Microbiology & Immunology, CSIR-Central Drug Research Institute, Sitapur Road, Jankipuram Extension, Lucknow, Uttar Pradesh 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Grunenberg O, Gerwing M, Oeckenpöhler S, Peez C, Briese T, Glasbrenner J, Hägerich LM, Raschke MJ, Kittl C, Herbst E. The anteromedial retinaculum in ACL-injured knees: An overlooked injury? Knee Surg Sports Traumatol Arthrosc 2024; 32:881-888. [PMID: 38469949 DOI: 10.1002/ksa.12137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 02/05/2024] [Accepted: 02/14/2024] [Indexed: 03/13/2024]
Abstract
PURPOSE The purpose of this study was to retrospectively analyse the pattern of injury to the medial knee structures in anterior cruciate ligament (ACL) injured patients. It was hypothesised that anteromedial injuries would be more common than posteromedial lesions. METHODS One hundred and twenty subjects aged 18-25 years with a primary ACL injury were included. Patients were excluded if the time between injury and magnetic resonance imaging (MRI) was more than 28 days or if a knee dislocation or fracture was present. The MRIs were analysed with particular emphasis on injuries to the medial knee structures, menisci and bone bruise patterns. Injuries to the ligaments and anteromedial retinaculum (AMR) were graded according to severity, ranging from periligamentous oedema (grade I), partial fibre disruption of less or more than 50% (grade IIa or IIb) to complete tears (grade III). RESULTS AMR injury was seen in 87 subjects (72.5%) on the coronal plane and in 88 (73.3%) on the axial plane, with grade III lesions observed in 27 (22.5%) and 29 knees (24.2%). Injuries to the superficial medial collateral ligament (sMCL), deep MCL (dMCL) and posterior oblique ligament (POL) were detected in 60 patients (50%), 93 patients (77.5%) and 38 patients (31.6%). However, grade III injuries to the POL were observed in only seven knees (5.8%). Medial meniscus injuries were associated with lesions of the sMCL and AMR (p < 0.05), while lateral meniscus injuries were significantly more common in patients with dMCL rupture (p < 0.05). CONCLUSION Data from this study suggest that injuries to the AMR are much more common than posteromedial lesions in subjects with ACL injuries. LEVEL OF EVIDENCE Level IV.
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Affiliation(s)
- Ole Grunenberg
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Mirjam Gerwing
- Clinic of Radiology, University of Muenster, Muenster, Germany
| | - Simon Oeckenpöhler
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Christian Peez
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Thorben Briese
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Johannes Glasbrenner
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Luise M Hägerich
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Michael J Raschke
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Christoph Kittl
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, University of Muenster, Muenster, Germany
| | - Elmar Herbst
- Department of Trauma, Hand and Reconstructive Surgery, University Hospital Muenster, University of Muenster, Muenster, Germany
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Sahoo R, Jadhav S, Nema V. Journey of technological advancements in the detection of antimicrobial resistance. J Formos Med Assoc 2024; 123:430-441. [PMID: 37598038 DOI: 10.1016/j.jfma.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/19/2023] [Accepted: 08/07/2023] [Indexed: 08/21/2023] Open
Abstract
Increased uses rather an extensive misuse of antibiotics due to easy availability and easy access have resulted in antibiotic resistance as a global crisis. The speed of discovery of new antibiotics has slowed down recently. Therefore, there is a need to reduce the rate of increase in resistance against the presently available antibiotics, or else many infections may be left untreatable or difficult to be treated due to the high prevalence of resistance. The judicious use of broad-spectrum antibiotics can control the increase in resistance profile. Various techniques are presently being used for the detection of antibiotic resistance. Conventional phenotypic methods are preferred that are highly reliable but are much more time-consuming. The patients cannot spare more time as the infection keeps increasing. The results with genotypic methods are obtained within 24 h as compared to phenotypic methods. Hence, recent molecular methods like qPCR can be used for detection. In this review, we present an overview of various methods useful for the detection of antibiotic resistance, with emphasis on their advantages and limitations. The review also emphasizes qPCR to be the most preferred method out of all because of various advantageous factors.
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Affiliation(s)
- Rituparna Sahoo
- ICMR-National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411 026, India
| | - Sushama Jadhav
- ICMR-National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411 026, India
| | - Vijay Nema
- ICMR-National AIDS Research Institute, 73 G MIDC Bhosari, Pune, 411 026, India.
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11
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Wyrsch ER, Hoye BJ, Sanderson-Smith M, Gorman J, Maute K, Cummins ML, Jarocki VM, Marenda MS, Dolejska M, Djordjevic SP. The faecal microbiome of the Australian silver gull contains phylogenetically diverse ExPEC, aEPEC and Escherichia coli carrying the transmissible locus of stress tolerance. Sci Total Environ 2024; 919:170815. [PMID: 38336047 DOI: 10.1016/j.scitotenv.2024.170815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/28/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Wildlife are implicated in the dissemination of antimicrobial resistance, but their roles as hosts for Escherichia coli that pose a threat to human and animal health is limited. Gulls (family Laridae) in particular, are known to carry diverse lineages of multiple-antibiotic resistant E. coli, including extra-intestinal pathogenic E. coli (ExPEC). Whole genome sequencing of 431 E. coli isolates from 69 healthy Australian silver gulls (Chroicocephalus novaehollandiae) sampled during the 2019 breeding season, and without antibiotic selection, was undertaken to assess carriage in an urban wildlife population. Phylogenetic analysis and genotyping resolved 123 sequence types (STs) representing most phylogroups, and identified diverse ExPEC, including an expansive phylogroup B2 cluster comprising 103 isolates (24 %; 31 STs). Analysis of the mobilome identified: i) widespread carriage of the Yersinia High Pathogenicity Island (HPI), a key ExPEC virulence determinant; ii) broad distribution of two novel phage elements, each carrying sitABCD and iii) carriage of the transmissible locus of stress tolerance (tLST), an element linked to sanitation resistance. Of the 169 HPI carrying isolates, 49 (48 %) represented diverse B2 isolates hosting FII-64 ColV-like plasmids that lacked iutABC and sitABC operons typical of ColV plasmids, but carried the serine protease autotransporter gene, sha. Diverse E. coli also carried archetypal ColV plasmids (52 isolates; 12 %). Clusters of closely related E. coli (<50 SNVs) from ST58, ST457 and ST746, sourced from healthy gulls, humans, and companion animals, were frequently identified. In summary, anthropogenically impacted gulls host an expansive E. coli population, including: i) putative ExPEC that carry ColV virulence gene cargo (101 isolates; 23.4 %) and HPI (169 isolates; 39 %); ii) atypical enteropathogenic E. coli (EPEC) (17 isolates; 3.9 %), and iii) E. coli that carry the tLST (20 isolates; 4.6 %). Gulls play an important role in the evolution and transmission of E. coli that impact human health.
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Affiliation(s)
- Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Martina Sanderson-Smith
- Molecular Horizons Research Institute, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jody Gorman
- Molecular Horizons Research Institute, School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Kimberly Maute
- School of Earth, Atmospheric and Life Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia
| | - Marc S Marenda
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC 3030, Australia
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Czech Republic; CEITEC VETUNI, University of Veterinary Sciences Brno, Czech Republic; Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Czech Republic; Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Pilsen, Czech Republic
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, Australia.
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Costa D, Picascia A, Grimaldi V, Amarelli C, Petraio A, Levi A, Di Donato M, Pirozzi AVA, Fiorito C, Moccia G, Gallo A, Strozziero M, Marra C, De Feo M, Cacciatore F, Maiello C, Napoli C. Role of HLA matching and donor specific antibody development in long-term survival, acute rejection and cardiac allograft vasculopathy. Transpl Immunol 2024; 83:102011. [PMID: 38403197 DOI: 10.1016/j.trim.2024.102011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Although there are different data supporting benefits of HLA matching in kidney transplantation, its role in heart transplantation is still unclear. HLA mismatch (MM) between donor and recipient can lead to the development of donor-specific antibodies (DSA) which produces negative events on the outcome of heart transplantation. Moreover, DSAs are involved in the development of antibody-mediated rejection (AMR) and are associated with an increase in cardiac allograft vasculopathy (CAV). In this study it is analyzed retrospectively the influence of HLA matching and anti-HLA antibodies on overall survival, AMR and CAV in heart transplantation. For this retrospective study are recruited heart transplanted patients at the Cardiac Transplantation Centre of Naples between 2000 and 2019. Among the 155 heart transplant patients, the mean number of HLA-A, B, -DR MM (0 to 6) between donor and recipient was 4.5 ± 1.1. The results show a negative association between MM HLA-DR and survival (p = 0.01). Comparison of patients with 0-1 MM at each locus to all others with 2 MM, for both HLA class I and class II, has not showed significant differences in the development of CAV. Our analysis detected DSA in 38.1% of patients. The production of de novo DSA reveals that there is not an influence on survival (p = 0.72) and/or AMR (p = 0.39). Instead, there is an association between the production of DSA class II and the probability of CAV development (p = 0.03). Mean fluorescence intensity (MFI) values were significantly higher in CAV-positive patients that CAV-negative patients (p = 0.02). Prospective studies are needed to evaluate HLA class II matching as an additional parameter for heart allocation, especially considering the increment of waiting list time.
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Affiliation(s)
- Dario Costa
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology. Regional Reference Laboratory of Transplant Immunology (LIT). Department of Internal Medicine and Specialistics, University of Campania "L. Vanvitelli", Naples, Italy.
| | - Antonietta Picascia
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology. Regional Reference Laboratory of Transplant Immunology (LIT). Department of Internal Medicine and Specialistics, University of Campania "L. Vanvitelli", Naples, Italy
| | - Vincenzo Grimaldi
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology. Regional Reference Laboratory of Transplant Immunology (LIT). Department of Internal Medicine and Specialistics, University of Campania "L. Vanvitelli", Naples, Italy
| | - Cristiano Amarelli
- Cardiac Transplantation Unit, Department of Cardiac Surgery and Transplantation, Ospedali dei Colli, Naples, Italy
| | - Andrea Petraio
- Cardiac Transplantation Unit, Department of Cardiac Surgery and Transplantation, Ospedali dei Colli, Naples, Italy
| | - Anna Levi
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology. Regional Reference Laboratory of Transplant Immunology (LIT). Department of Internal Medicine and Specialistics, University of Campania "L. Vanvitelli", Naples, Italy
| | - Mario Di Donato
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology. Regional Reference Laboratory of Transplant Immunology (LIT). Department of Internal Medicine and Specialistics, University of Campania "L. Vanvitelli", Naples, Italy
| | - Anna Virginia Adriana Pirozzi
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology. Regional Reference Laboratory of Transplant Immunology (LIT). Department of Internal Medicine and Specialistics, University of Campania "L. Vanvitelli", Naples, Italy
| | - Carmela Fiorito
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology. Regional Reference Laboratory of Transplant Immunology (LIT). Department of Internal Medicine and Specialistics, University of Campania "L. Vanvitelli", Naples, Italy
| | - Giusi Moccia
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology. Regional Reference Laboratory of Transplant Immunology (LIT). Department of Internal Medicine and Specialistics, University of Campania "L. Vanvitelli", Naples, Italy
| | - Aurora Gallo
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology. Regional Reference Laboratory of Transplant Immunology (LIT). Department of Internal Medicine and Specialistics, University of Campania "L. Vanvitelli", Naples, Italy
| | | | - Claudio Marra
- Cardiac Transplantation Unit, Department of Cardiac Surgery and Transplantation, Ospedali dei Colli, Naples, Italy
| | - Marisa De Feo
- Cardiac Transplantation Unit, Department of Cardiac Surgery and Transplantation, Ospedali dei Colli, Naples, Italy
| | - Francesco Cacciatore
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | - Ciro Maiello
- Cardiac Transplantation Unit, Department of Cardiac Surgery and Transplantation, Ospedali dei Colli, Naples, Italy
| | - Claudio Napoli
- U.O.C. Division of Clinical Immunology, Immunohematology, Transfusion Medicine and Transplant Immunology. Regional Reference Laboratory of Transplant Immunology (LIT). Department of Internal Medicine and Specialistics, University of Campania "L. Vanvitelli", Naples, Italy
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13
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Kherabi Y, Thy M, Bouzid D, Antcliffe DB, Rawson TM, Peiffer-Smadja N. Machine learning to predict antimicrobial resistance: future applications in clinical practice? Infect Dis Now 2024; 54:104864. [PMID: 38355048 DOI: 10.1016/j.idnow.2024.104864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/16/2024]
Abstract
INTRODUCTION Machine learning (ML) is increasingly being used to predict antimicrobial resistance (AMR). This review aims to provide physicians with an overview of the literature on ML as a means of AMR prediction. METHODS References for this review were identified through searches of MEDLINE/PubMed, EMBASE, Google Scholar, ACM Digital Library, and IEEE Xplore Digital Library up to December 2023. RESULTS Thirty-six studies were included in this review. Thirty-two studies (32/36, 89 %) were based on hospital data and four (4/36, 11 %) on outpatient data. The vast majority of them were conducted in high-resource settings (33/36, 92 %). Twenty-four (24/36, 67 %) studies developed systems to predict drug resistance in infected patients, eight (8/36, 22 %) tested the performances of ML-assisted antibiotic prescription, two (2/36, 6 %) assessed ML performances in predicting colonization with carbapenem-resistant bacteria and, finally, two assessed national and international AMR trends. The most common inputs were demographic characteristics (25/36, 70 %), previous antibiotic susceptibility testing (19/36, 53 %) and prior antibiotic exposure (15/36, 42 %). Thirty-three (92 %) studies targeted prediction of Gram-negative bacteria (GNB) resistance as an output (92 %). The studies included showed moderate to high performances, with AUROC ranging from 0.56 to 0.93. CONCLUSION ML can potentially provide valuable assistance in AMR prediction. Although the literature on this topic is growing, future studies are needed to design, implement, and evaluate the use and impact of ML decision support systems.
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Affiliation(s)
- Yousra Kherabi
- Infectious and Tropical Disease Department, Bichat-Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France; Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris, France.
| | - Michaël Thy
- Medical and Infectious Diseases ICU (MI2) - Bichat-Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France; EA 7323 - Pharmacology and Therapeutic Evaluation in Children and Pregnant Women, Université Paris Cité, Paris, France
| | - Donia Bouzid
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris, France; Emergency Department, Bichat Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - David B Antcliffe
- Division of Anaesthetics, Pain Medicine and Intensive Care, Department of Surgery and Cancer, Imperial College London, London, UK; Department of Intensive Care Unit, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Timothy Miles Rawson
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK; Centre for Antimicrobial Optimisation Imperial College London, London, UK
| | - Nathan Peiffer-Smadja
- Infectious and Tropical Disease Department, Bichat-Claude Bernard Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France; Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME, Paris, France; National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
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14
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Kurono Y, Kudo F, Watanabe A, Yamatake T, Shimada S, Suzuki K. Efficacy, safety, and tissue penetration of solithromycin in Japanese patients with otorhinolaryngological infections. Auris Nasus Larynx 2024; 51:379-390. [PMID: 38065757 DOI: 10.1016/j.anl.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 01/18/2024]
Abstract
OBJECTIVE To assess the efficacy, safety, and tissue penetration of solithromycin for the treatment of otorhinolaryngological infections, we conducted three studies: a tissue penetration study with patients scheduled to undergo otorhinolaryngological tissue removal, an open-label study comprising patients with otitis media, pharyngitis, laryngitis, and tonsillitis, and a non-inferiority study compared with high-dose cefcapene-pivoxil (CFPN-PI). METHODS Tissue penetration study; 17 patients with chronic rhinosinusitis, chronic otitis media, chronic tonsillitis, or palatine tonsillar hypertrophy, who required resection or removal of their tissue, were enrolled. Solithromycin was administered orally, and otorhinolaryngological tissues were collected 3.5-6 h after drug administration; blood was collected within 15 min before and after drug administration. The collected tissues and blood concentrations were measured at a central laboratory. Open-label study; 55 patients who were diagnosed with acute otitis media, laryngopharyngitis, or tonsillitis were enrolled. Solithromycin was administered orally 800 mg on Day 1, while on days 2-7, 400 mg of the drug was administered once daily. The primary endpoint is the clinical response at Test-of-Cure (TOC: 5-10 days after completion) Non-inferiority study; 283 patients with acute rhinosinusitis or acute exacerbation of chronic rhinosinusitis were randomized into either the solithromycin group or CFPN-PI group. Solithromycin was administered 800 mg once daily on Day 1 and 400 mg once daily while on Days 2-7 in solithromycin group, and CFPN-PI was administered 150 mg three times a day while on Days 1-7 in CFPN-PI group. The primary endpoint is the clinical response at TOC. RESULTS In the tissue penetration study, the tissue concentration ratios (tissue concentration/plasma concentration) of solithromycin were 4.19 in the sinonasal mucosa, 1.33 in the middle ear mucosa, and 6.12 in the palatine tonsil tissue. In the open-label study, the efficacy rates at the TOC were 97.0 % for acute otitis media, 100 % for laryngopharyngitis, and 81.8 % for tonsillitis. In the non-inferiority study comprising patients with rhinosinusitis, the efficacy rate at the TOC was 87.7 % for solithromycin and 89.7 % for CFPN-PI. The difference in the efficacy rate (95 % confidence interval) was -2.0 % (-9.4 % to 5.4 %), verifying the non-inferiority of solithromycin to CFPN-PI. The most common adverse events in patients administered solithromycin were diarrhea (20.7 %), nausea and nasopharyngitis (3.6 %,), pharyngitis and elevated hepatic function test results (3.1 %), and abnormal hepatic function (2.1 %). CONCLUSION Based on the findings, it is suggested that solithromycin is useful for the treatment of otorhinolaryngological infections.
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Affiliation(s)
| | | | - Akira Watanabe
- Research Division for Development of Anti-Infective Agents, Tohoku Bunka Gakuen University, Japan
| | - Takahiro Yamatake
- Project Management Department, FUJIFILM Toyama chemical Co., Ltd., Chuo-ku, Tokyo 104-0031, Japan
| | - Satoshi Shimada
- Project Management Department, FUJIFILM Toyama chemical Co., Ltd., Chuo-ku, Tokyo 104-0031, Japan.
| | - Kenji Suzuki
- Department of Otorhinolaryngology, Yonaha Okanoue Hospital, Japan
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Bartlett HP, Dawson CC, Glickman CM, Osborn DW, Evans CR, Garcia BJ, Frost LC, Cummings JE, Whittel N, Slayden RA, Holder JW. Targeting intracellular nontuberculous mycobacteria and M. tuberculosis with a bactericidal enzymatic cocktail. Microbiol Spectr 2024:e0353423. [PMID: 38534149 DOI: 10.1128/spectrum.03534-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
To address intracellular mycobacterial infections, we developed a cocktail of four enzymes that catalytically attack three layers of the mycobacterial envelope. This cocktail is delivered to macrophages, through a targeted liposome presented here as ENTX_001. Endolytix Cocktail 1 (EC1) leverages mycobacteriophage lysin enzymes LysA and LysB, while also including α-amylase and isoamylase for degradation of the mycobacterial envelope from outside of the cell. The LysA family of proteins from mycobacteriophages has been shown to cleave the peptidoglycan layer, whereas LysB is an esterase that hydrolyzes the linkage between arabinogalactan and mycolic acids of the mycomembrane. The challenge of gaining access to the substrates of LysA and LysB provided exogenously was addressed by adding amylase enzymes that degrade the extracellular capsule shown to be present in Mycobacterium tuberculosis. This enzybiotic approach avoids antimicrobial resistance, specific receptor-mediated binding, and intracellular DNA surveillance pathways that limit many bacteriophage applications. We show this cocktail of enzymes is bactericidal in vitro against both rapid- and slow-growing nontuberculous mycobacteria (NTM) as well as M. tuberculosis strains. The EC1 cocktail shows superior killing activity when compared to previously characterized LysB alone. EC1 is also powerfully synergistic with standard-of-care antibiotics. In addition to in vitro killing of NTM, ENTX_001 demonstrates the rescue of infected macrophages from necrotic death by Mycobacteroides abscessus and Mycobacterium avium. Here, we demonstrate shredding of mycobacterial cells by EC1 into cellular debris as a mechanism of bactericide.IMPORTANCEThe world needs entirely new forms of antibiotics as resistance to chemical antibiotics is a critical problem facing society. We addressed this need by developing a targeted enzyme therapy for a broad range of species and strains within mycobacteria and highly related genera including nontuberculous mycobacteria such as Mycobacteroides abscessus, Mycobacterium avium, Mycobacterium intracellulare, as well as Mycobacterium tuberculosis. One advantage of this approach is the ability to drive our lytic enzymes through encapsulation into macrophage-targeted liposomes resulting in attack of mycobacteria in the cells that harbor them where they hide from the adaptive immune system and grow. Furthermore, this approach shreds mycobacteria independent of cell physiology as the drug targets the mycobacterial envelope while sidestepping the host range limitations observed with phage therapy and resistance to chemical antibiotics.
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Affiliation(s)
| | | | | | | | | | | | | | - Jason E Cummings
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Nicholas Whittel
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Richard A Slayden
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
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Dauda BJ, Offor MC, Adebusuyi O, Owolabi CP. Adopting telemedicine in the fight against antimicrobial resistance in West Africa. Int J Health Plann Manage 2024. [PMID: 38520202 DOI: 10.1002/hpm.3799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 02/02/2024] [Accepted: 03/07/2024] [Indexed: 03/25/2024] Open
Abstract
The detrimental effects of antimicrobial resistance (AMR) have called for several approaches in the fight against it in West Africa, where telemedicine is still in its infancy. In West Africa, self-medication is prevalent because the majority of these medications are easily accessible due to insufficient regulatory structures that control their production, distribution, and consumption. Also, access to healthcare facilities and professionals is limited. All of these and other inadequacies consequently result in the emergence of antimicrobial-resistant organisms. AMR, which is now a major global health crisis according to the WHO, may cause the deaths of about 10 million people before 2050, and Africa may make up 41% of these deaths, with the Western part of this continent affected the most. While several approaches have been adopted, unlike in other regions of the world, the use of telemedicine in West Africa to fight AMR has rarely been studied or considered and where it is now in partial use, its efficacy is constrained by several factors. This paper discusses the roles of telemedicine, the limitations to its application in the fight against AMR, and suggests remedies for these limitations.
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Affiliation(s)
- Babatunde Jamiu Dauda
- Department of Medicine and Surgery, Faculty of Clinical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Michael Chukwubuikem Offor
- Department of Medicine and Surgery, Faculty of Clinical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | - Caleb Promise Owolabi
- Department of Medicine and Surgery, Faculty of Clinical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
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Dhungana G, Nepal R, Houtak G, Bouras G, Vreugde S, Malla R. Preclinical characterization and in silico safety assessment of three virulent bacteriophages targeting carbapenem-resistant uropathogenic Escherichia coli. Int Microbiol 2024:10.1007/s10123-024-00508-8. [PMID: 38517580 DOI: 10.1007/s10123-024-00508-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/22/2024] [Accepted: 03/10/2024] [Indexed: 03/24/2024]
Abstract
Phage therapy has recently been revitalized in the West with many successful applications against multi-drug-resistant bacterial infections. However, the lack of geographically diverse bacteriophage (phage) genomes has constrained our understanding of phage diversity and its genetics underpinning host specificity, lytic capability, and phage-bacteria co-evolution. This study aims to locally isolate virulent phages against uropathogenic Escherichia coli (E. coli) and study its phenotypic and genomic features. Three obligately virulent Escherichia phages (øEc_Makalu_001, øEc_Makalu_002, and øEc_Makalu_003) that could infect uropathogenic E. coli were isolated and characterized. All three phages belonged to Krischvirus genus. One-step growth curve showed that the latent period of the phages ranged from 15 to 20 min, the outbreak period ~ 50 min, and the burst size ranged between 74 and 127 PFU/bacterium. Moreover, the phages could tolerate a pH range of 6 to 9 and a temperature range of 25-37 °C for up to 180 min without significant loss of phage viability. All phages showed a broad host spectrum and could lyse up to 30% of the 35 tested E. coli isolates. Genomes of all phages were approximately ~ 163 kb with a gene density of 1.73 gene/kbp and an average gene length of ~ 951 bp. The coding density in all phages was approximately 95%. Putative lysin, holin, endolysin, and spanin genes were found in the genomes of all three phages. All phages were strictly virulent with functional lysis modules and lacked any known virulence or toxin genes and antimicrobial resistance genes. Pre-clinical experimental and genomic analysis suggest these phages may be suitable candidates for therapeutic applications.
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Affiliation(s)
- Gunaraj Dhungana
- Central Department of Biotechnology, Institute of Science and Technology, Tribhuvan University, Kirtipur, Nepal.
- Government of Nepal, Nepal Health Research Council, Kathmandu, Nepal.
| | - Roshan Nepal
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.
- The Department of Surgery-Otolaryngology Head and Neck Surgery, The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia.
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- The Department of Surgery-Otolaryngology Head and Neck Surgery, The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- The Department of Surgery-Otolaryngology Head and Neck Surgery, The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- The Department of Surgery-Otolaryngology Head and Neck Surgery, The Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Rajani Malla
- Central Department of Biotechnology, Institute of Science and Technology, Tribhuvan University, Kirtipur, Nepal
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Sid Ahmed MA, Hamid JM, Hassan AMM, Abu Jarir S, Bashir Ibrahim E, Abdel Hadi H. Phenotypic and Genotypic Characterization of Pan-Drug-Resistant Klebsiella pneumoniae Isolated in Qatar. Antibiotics (Basel) 2024; 13:275. [PMID: 38534710 DOI: 10.3390/antibiotics13030275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/28/2024] Open
Abstract
In secondary healthcare, carbapenem-resistant Enterobacterales (CREs), such as those observed in Klebsiella pneumoniae, are a global public health priority with significant clinical outcomes. In this study, we described the clinical, phenotypic, and genotypic characteristics of three pan-drug-resistant (PDR) isolates that demonstrated extended resistance to conventional and novel antimicrobials. All patients had risk factors for the acquisition of multidrug-resistant organisms, while microbiological susceptibility testing showed resistance to all conventional antimicrobials. Advanced susceptibility testing demonstrated resistance to broad agents, such as ceftazidime-avibactam, ceftolozane-tazobactam, and meropenem-vaborbactam. Nevertheless, all isolates were susceptible to cefiderocol, suggested as one of the novel antimicrobials that demonstrated potent in vitro activity against resistant Gram-negative bacteria, including CREs, pointing toward its potential therapeutic role for PDR pathogens. Expanded genomic studies revealed multiple antimicrobial-resistant genes (ARGs), including blaNMD-5 and blaOXA derivative types, as well as a mutated outer membrane porin protein (OmpK37).
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Affiliation(s)
- Mazen A Sid Ahmed
- Laboratory Services, Department of Public Health, Philadelphia, PA 19146, USA
| | - Jemal M Hamid
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Ahmed M M Hassan
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Sulieman Abu Jarir
- Division of Infectious Diseases, Communicable Diseases Centre, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Emad Bashir Ibrahim
- Division of Microbiology, Department of Pathology and Laboratory Medicine, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
- Biomedical Research Centre, Qatar University, Doha P.O. Box 2713, Qatar
| | - Hamad Abdel Hadi
- Division of Infectious Diseases, Communicable Diseases Centre, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
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19
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Alessandrini A, Rosales IA. Down to the coronary arteries: When spatial multiomics open up a narrow path. Am J Transplant 2024:S1600-6135(24)00219-3. [PMID: 38508320 DOI: 10.1016/j.ajt.2024.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Affiliation(s)
- Alessandro Alessandrini
- Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ivy A Rosales
- Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Pathology, Immunopathology Research Laboratory, Massachusetts General Hospital, Boston, Massachusetts, USA.
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20
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Gensler CA, Hempstead SC, Keelara S, Fedorka-Cray PJ, Urie NJ, Wiedenheft AM, Stuart K, Marshall KL, Jacob ME. Antimicrobial Resistance Characteristics of Fecal Escherichia coli and Enterococcus Species in U.S. Goats: 2019 National Animal Health Monitoring System Enteric Study. Foodborne Pathog Dis 2024. [PMID: 38502797 DOI: 10.1089/fpd.2023.0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
Escherichia coli and Enterococcus species are normal bacteria of the gastrointestinal tract and serve as indicator organisms for the epidemiology and emergence of antimicrobial resistance in their hosts and the environment. Some E. coli serovars, including E. coli O157:H7, are important human pathogens, although reservoir species such as goats remain asymptomatic. We describe the prevalence and antimicrobial resistance of generic E. coli, E. coli O157:H7, and Enterococcus species collected from a national surveillance study of goat feces as part of the National Animal Health Monitoring System (NAHMS) Goat 2019 study. Fecal samples were collected from 4918 goats on 332 operations across the United States. Expectedly, a high prevalence of E. coli (98.7%, 4850/4915) and Enterococcus species (94.8%, 4662/4918) was found. E. coli O157:H7 prevalence was low (0.2%; 10/4918). E. coli isolates, up to three per operation, were evaluated for antimicrobial susceptibility and 84.7% (571/674) were pansusceptible. Multidrug resistance (MDR; ≥3 classes) was uncommon among E. coli, occurring in 8.2% of isolates (55/674). Resistance toward seven antimicrobial classes was observed in a single isolate. Resistance to tetracycline alone (13.6%, 92/674) or to tetracycline, streptomycin, and sulfisoxazole (7.0% 47/674) was the most common pattern. All E. coli O157:H7 isolates were pansusceptible. Enterococcus isolates, up to four per operation, were prioritized by public health importance, including Enterococcus faecium and Enterococcus faecalis and evaluated. Resistance to lincomycin (93.8%, 1232/1313) was most common, with MDR detected in 29.5% (388/1313) of isolates. The combination of ciprofloxacin, lincomycin, and quinupristin resistance (27.1%, 105/388) was the most common pattern detected. Distribution and characteristics of antimicrobial resistance in E. coli and Enterococcus in the U.S. goat population from this study can inform stewardship considerations and public health efforts surrounding goats and their products.
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Affiliation(s)
- Catherine A Gensler
- Department of Agricultural and Human Sciences, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Stephanie C Hempstead
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Natalie J Urie
- National Animal Health Monitoring System, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Alyson M Wiedenheft
- National Animal Health Monitoring System, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, USA
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Keira Stuart
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, Iowa, USA
| | - Katherine L Marshall
- National Animal Health Monitoring System, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, USA
| | - Megan E Jacob
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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21
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Bhatt A, Pujari S, Mantri S, Kirdat K, Thakkar L, Poojary R, Kuyare S, Patil K, Yadav A. A rare urinary tract infection of multidrug-resistant Chryseobacterium urinae sp. nov. isolated from a diabetic, non-catheterized patient. Arch Microbiol 2024; 206:150. [PMID: 38466448 DOI: 10.1007/s00203-024-03881-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 03/13/2024]
Abstract
Chryseobacterium demonstrates a diverse environmental presence and a significant pathogenic potential across various ecosystems. This clinical case showcases a rare instance of bacterial infection in a 75-year-old male with untreated diabetes and recurrent urinary tract infections (UTIs). The patient presented symptoms of abdominal pain, burning urination, fever, and an elevated eosinophil count. A subsequent urine culture identified a Chryseobacterium-related bacterium as the causative agent, exhibiting sensitivity to piperacillin/tazobactam, trimethoprim/sulfamethoxazole, and nitrofurantoin, which led to successful treatment using oral nitrofurantoin. Analysis of the 16S rRNA gene sequence of APV-1T revealed a close relationship of 98.2% similarity to Chryseobacterium gambrini strain 5-1St1aT (AM232810). Furthermore, comparative genome analysis, incorporating Average Nucleotide Identity (ANI), Digital DNA-DNA Hybridization (dDDH) values, and comprehensive phylogenetic assessments utilizing 16S rRNA gene sequences, core genes, and amino acid sequences of core proteins, highlighted the unique phylogenetic positioning of APV-1T within the Chryseobacterium genus. Distinct carbon utilization and assimilation patterns, along with major fatty acid content, set APV-1T apart from C. gambrini strain 5-1St1aT. These findings, encompassing phenotypic, genotypic, and chemotaxonomic characteristics, strongly support the proposal of a novel species named Chryseobacterium urinae sp. nov., with APV-1T designated as the type strain (= MCC 50690 = JCM 36476). Despite its successful treatment, the strain displayed resistance to multiple antibiotics. Genomic analysis further unveiled core-conserved genes, strain-specific clusters, and genes associated with antibiotic resistance and virulence. This report underscores the vital importance of elucidating susceptibility patterns of rare pathogens like Chryseobacterium, particularly in immunocompromised individuals. It advocates for further analyses to understand the functional significance of identified genes and their implications in treatment and pathogenesis.
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Affiliation(s)
- Agrima Bhatt
- Department of Biosciences and Technology, Vishwanath Karad MIT World Peace University, Kothrud, Pune, 411038, India
| | - Sujata Pujari
- Sujata Clinic, Mulund Colony, Mulund West, Mumbai, 400082, India
| | - Shailesh Mantri
- National Centre for Microbial Resource, National Centre for Cell Science, NCCS Complex, Ganeshkhind, 411007, Pune, India
| | - Kiran Kirdat
- National Centre for Microbial Resource, National Centre for Cell Science, NCCS Complex, Ganeshkhind, 411007, Pune, India
| | - Lucky Thakkar
- National Centre for Microbial Resource, National Centre for Cell Science, NCCS Complex, Ganeshkhind, 411007, Pune, India
| | - Reshma Poojary
- Apoorva Diagnostic and Healthcare, Kandivali (East), Mumbai, 400101, India
| | - Sunil Kuyare
- Apoorva Diagnostic and Healthcare, Kandivali (East), Mumbai, 400101, India
| | - Kritika Patil
- Vedantaa Institute of Medical Sciences, Saswand, Palghar, 401606, India
| | - Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, NCCS Complex, Ganeshkhind, 411007, Pune, India.
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22
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De R, Mukhopadhyay AK, Ghosh M, Basak S, Dutta S. Emerging resistome diversity in clinical Vibrio cholerae strains revealing their role as potential reservoirs of antimicrobial resistance. Mol Biol Rep 2024; 51:409. [PMID: 38461219 DOI: 10.1007/s11033-024-09313-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/01/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND This is a unique and novel study delineating the genotyping and subsequent prediction of AMR determinants of Vibrio cholerae revealing the potential of contemporary strains to serve as precursors of severe AMR crisis in cholera. METHODS AND RESULTS Genotyping of representative strains, VC1 and VC2 was undertaken to characterize antimicrobial resistance genes (ARGs) against chloramphenicol, SXT, nalidixic acid and streptomycin against which they were found to be resistant by antibiogram analysis in our previous investigation. strAB, sxt, sul2, qace∆1-sul1 were detected by PCR. Genome annotation and identification of ARGs with WGS helped to detect the presence of almG, varG, strA (APH(3'')-Ib), strB (APH(6)-Id), sul2, catB9, floR, CRP, dfrA1 genes. Signatures of resistance determinants and protein domains involved in antimicrobial resistance, primarily, efflux of antibiotics were identified on the basis of 30-100% homology to reference proteins. These domains were predicted to be involved in other metabolic functions on the basis of 100% identity with 100% coverage with reference protein and nucleotide sequences and were predicted to be of a diverse taxonomic origin accentuating the influence of the microbiota on AMR acquisition. Sequence analysis of QRDR (quinolone resistance-determining region) revealed SNPs. Cytoscape v3.8.2 was employed to analyse protein-protein interaction of MDR proteins, MdtA and EmrD-2, with nodes of vital AMR pathways. Vital nodes involved in efflux of different classes of antibiotics were found to be absent in VC1 and VC2 justifying the sensitivity of these strains to most antibiotics. CONCLUSIONS The study helped to examine the resistome of VC isolated from recent outbreaks to understand the underlying reason of sensitivity to most antibiotics and also to characterize the ARGs in their genome. It revealed that VC is a reservoir of signatures of resistance determinants and serving as precursors for severe AMR crisis in cholera. This is the first study, to our knowledge, which has scrutinized and presented systematically, information on prospective domains which bear the potential of serving as AMR determinants in VC with the help of bioinformatic tools. This pioneering approach may help in the prediction of AMR landfalls and benefit epidemiological surveillance and early warning systems.
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Affiliation(s)
- Rituparna De
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases (ICMR), Kolkata, India.
| | - Asish K Mukhopadhyay
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases (ICMR), Kolkata, India
| | - Manisha Ghosh
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Surajit Basak
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases (ICMR), Kolkata, India
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23
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Lorentzen ØM, Haukefer ASB, Johnsen PJ, Frøhlich C. The Biofilm Lifestyle Shapes the Evolution of β-Lactamases. Genome Biol Evol 2024; 16:evae030. [PMID: 38366392 PMCID: PMC10917518 DOI: 10.1093/gbe/evae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
The evolutionary relationship between the biofilm lifestyle and antibiotic resistance enzymes remains a subject of limited understanding. Here, we investigate how β-lactamases affect biofilm formation in Vibrio cholerae and how selection for a biofilm lifestyle impacts the evolution of these enzymes. Genetically diverse β-lactamases expressed in V. cholerae displayed a strong inhibitory effect on biofilm production. To understand how natural evolution affects this antagonistic pleiotropy, we randomly mutagenized a β-lactamase and selected for elevated biofilm formation. Our results revealed that biofilm evolution selects for β-lactamase variants able to hydrolyze β-lactams without inhibiting biofilms. Mutational analysis of evolved variants demonstrated that restoration of biofilm development was achieved either independently of enzymatic function or by actively leveraging enzymatic activity. Taken together, the biofilm lifestyle can impose a profound selective pressure on antimicrobial resistance enzymes. Shedding light on such evolutionary interplays is of importance to understand the factors driving antimicrobial resistance.
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Affiliation(s)
- Øyvind M Lorentzen
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Pål J Johnsen
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
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24
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Seyoum ET, Eguale T, Habib I, Oliveira CJB, Monte DFM, Yang B, Gebreyes WA, Alali WQ. Pre-Harvest Food Safety Challenges in Food-Animal Production in Low- and Middle-Income Countries. Animals (Basel) 2024; 14:786. [PMID: 38473171 DOI: 10.3390/ani14050786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Food safety remains a significant global public health concern, with the risk of unsafe food varying worldwide. The economies of several low- and middle-income countries (LMICs) heavily rely on livestock, posing a challenge to ensuring the production of safe food. This review discusses our understanding of pre-harvest critical issues related to food safety in LMICs, specifically focusing on animal-derived food. In LMICs, food safety regulations are weak and inadequately enforced, primarily concentrating on the formal market despite a substantial portion of the food sector being dominated by informal markets. Key critical issues at the farm level include animal health, a low level of good agriculture practices, and the misuse of antimicrobials. Effectively addressing foodborne diseases requires a comprehensive One Health framework. Unfortunately, the application of the One Health approach to tackle food safety issues is notably limited in LMICs. In conclusion, considering that most animal-source foods from LMICs are marketed through informal channels, food safety legislation and policies need to account for this context. Interventions aimed at reducing foodborne bacterial pathogens at the farm level should be scalable, and there should be strong advocacy for the proper implementation of pre-harvest interventions through a One Health approach.
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Affiliation(s)
- Eyasu T Seyoum
- Ohio State Global One Health, Addis Ababa 62347, Ethiopia
| | - Tadesse Eguale
- Ohio State Global One Health, Addis Ababa 62347, Ethiopia
| | - Ihab Habib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Department of Environmental Health, High Institute of Public Health, Alexandria University, Alexandria P.O. Box 21511, Egypt
- ASPIRE Research Institute for Food Security in the Drylands (ARIFSID), United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Celso J B Oliveira
- Ohio State Global One Health, Addis Ababa 62347, Ethiopia
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58397-000, PB, Brazil
| | - Daniel F M Monte
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58397-000, PB, Brazil
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Wondwossen A Gebreyes
- Ohio State Global One Health, Addis Ababa 62347, Ethiopia
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43214, USA
| | - Walid Q Alali
- Department of Biostatistics & Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN 37614, USA
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25
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Qurbani K. Antibiotic resistance in Kurdistan, Iraq: A growing concern. New Microbes New Infect 2024; 57:101221. [PMID: 38318281 PMCID: PMC10839436 DOI: 10.1016/j.nmni.2024.101221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/08/2024] [Accepted: 01/15/2024] [Indexed: 02/07/2024] Open
Affiliation(s)
- Karzan Qurbani
- Department of Biology, College of Science, University of Raparin, Rania, Sulaymaniyah, 46012, Iraq
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26
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Pantano D, Friedrich AW. Hub and Spoke: Next level in regional networks for infection prevention. Int J Med Microbiol 2024; 314:151605. [PMID: 38290401 DOI: 10.1016/j.ijmm.2024.151605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/14/2024] [Accepted: 01/18/2024] [Indexed: 02/01/2024] Open
Abstract
The threat of multidrug-resistant organisms (MDROs) and antimicrobial resistance (AMR) are real and increasing every day. They affect not only healthcare systems but also communities, causing economic and public health concerns. Governments must take action to tackle AMR and prevent the spread of MDROs and regional hubs have a critical role to play in achieving this outcome. Furthermore, bacteria have no borders, consequently, cooperation networks should be extended between countries as a crucial strategy for achieving the success of infection control. Euregions, which are a specific form of cooperation between local authorities of two or more bordering European countries, can help solve common problems and improve the lives of people living on both sides of the border. Regional collaboration strategies can enhance infection control and build resilience against antimicrobial resistance. This review identifies risk factors and the correct approaches to infection prevention and control, including education and awareness programs for healthcare professionals, appropriate prescribing practices, and infection prevention control measures. These measures can help reduce the incidence of antimicrobial resistance in the region and save lives. It is therefore essential to take concrete actions and foster the creation of more effective regional and cross-border centers to ensure the success of infection control policies and the management of healthcare-associated infections. This work sheds light on the issue of MDRO infections within healthcare settings, while also acknowledging the crucial role of the One Health concept in understanding the broader context of these infections. By recognizing the interdependence of human and animal health and the environment, we can take constructive steps toward mitigating the risks of these infections and promoting better health outcomes for all.
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Affiliation(s)
- Daniele Pantano
- University Hospital Münster, Institute of Hygiene, Münster, Germany.
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27
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Street TL, Sanderson ND, Barker L, Kavanagh J, Cole K, Llewelyn M, Eyre DW. Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with Nanopore sequencing. Microb Genom 2024; 10:001208. [PMID: 38529900 PMCID: PMC10995632 DOI: 10.1099/mgen.0.001208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/10/2024] [Indexed: 03/27/2024] Open
Abstract
Multi-drug-resistant Neisseria gonorrhoeae infection is a significant public health risk. Rapidly detecting N. gonorrhoeae and antimicrobial-resistant (AMR) determinants by metagenomic sequencing of urine is possible, although high levels of host DNA and overgrowth of contaminating species hamper sequencing and limit N. gonorrhoeae genome coverage. We performed Nanopore sequencing of nucleic acid amplification test-positive urine samples and culture-positive urethral swabs with and without probe-based target enrichment, using a custom SureSelect panel, to investigate whether selective enrichment of N. gonorrhoeae DNA improves detection of both species and AMR determinants. Probes were designed to cover the entire N. gonorrhoeae genome, with tenfold enrichment of probes covering selected AMR determinants. Multiplexing was tested in a subset of samples. The proportion of sequence bases classified as N. gonorrhoeae increased in all samples after enrichment, from a median (IQR) of 0.05 % (0.01-0.1 %) to 76 % (42-82 %), giving a corresponding median improvement in fold genome coverage of 365 times (112-720). Over 20-fold coverage, required for robust AMR determinant detection, was achieved in 13/15(87 %) samples, compared to 2/15(13 %) without enrichment. The four samples multiplexed together also achieved >20-fold genome coverage. Coverage of AMR determinants was sufficient to predict resistance conferred by changes in chromosomal genes, where present, and genome coverage also enabled phylogenetic relationships to be reconstructed. Probe-based target enrichment can improve N. gonorrhoeae genome coverage when sequencing DNA extracts directly from urine or urethral swabs, allowing for detection of AMR determinants. Additionally, multiplexing prior to enrichment provided enough genome coverage for AMR detection and reduces the costs associated with this method.
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Affiliation(s)
- Teresa L. Street
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Nicholas D. Sanderson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kevin Cole
- Department of Microbiology and Infection, University Hospitals Sussex NHS Trust, Brighton, UK
| | - The GonFast Investigators Group
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Department of Microbiology and Infection, University Hospitals Sussex NHS Trust, Brighton, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Martin Llewelyn
- Department of Microbiology and Infection, University Hospitals Sussex NHS Trust, Brighton, UK
| | - David W. Eyre
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
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Klemm EJ, Nisar MI, Bawn M, Nasrin D, Qamar FN, Page A, Qadri F, Shakoor S, Zaidi AKM, Levine MM, Dougan G, Kingsley RA. Genomic analysis of clinical Aeromonas isolates reveals genetic diversity but little evidence of genetic determinants for diarrhoeal disease. Microb Genom 2024; 10:001211. [PMID: 38451244 PMCID: PMC10999740 DOI: 10.1099/mgen.0.001211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/15/2024] [Indexed: 03/08/2024] Open
Abstract
Aeromonas spp. are associated with a number of infectious syndromes in humans including gastroenteritis and dysentery. Our understanding of the genetic diversity, population structure, virulence determinants and antimicrobial resistance of the genus has been limited by a lack of sequenced genomes linked to metadata. We performed a comprehensive analysis of the whole genome sequences of 447 Aeromonas isolates from children in Karachi, Pakistan, with moderate-to-severe diarrhoea (MSD) and from matched controls without diarrhoea that were collected as part of the Global Enteric Multicenter Study (GEMS). Human-associated Aeromonas isolates exhibited high species diversity and extensive antimicrobial and virulence gene content. Aeromonas caviae, A. dhankensis, A. veronii and A. enteropelogenes were all significantly associated with MSD in at least one cohort group. The maf2 and lafT genes that encode components of polar and lateral flagella, respectively, exhibited a weak association with isolates originating from cases of gastroenteritis.
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Affiliation(s)
| | - Muhammad Imran Nisar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich, UK
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Dilruba Nasrin
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Farah Naz Qamar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Farheen Qadri
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Sadia Shakoor
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Anita KM Zaidi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Myron M. Levine
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, England, UK
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Feizi H, Alizadeh M, Azimi H, Khodadadi E, Kamounah FS, Ganbarov K, Ghotaslou R, Rezaee MA, Kafil HS. Induction of proteome changes involved in the cloning of mcr-1 and mcr-2 genes in Escherichia coli DH5-α strain to evaluate colistin resistance. J Glob Antimicrob Resist 2024; 36:151-159. [PMID: 38154746 DOI: 10.1016/j.jgar.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023] Open
Abstract
OBJECTIVES Plasmid genes, termed mobile colistin resistance-1 (mcr-1) and mobile colistin resistance-2 (mcr-2), are associated with resistance to colistin in Escherichia coli (E. coli). These mcr genes result in a range of protein modifications contributing to colistin resistance. This study aims to discern the proteomic characteristics of E. coli-carrying mcr-1 and mcr-2 genes. Furthermore, it evaluates the expression levels of various proteins under different conditions (with and without colistin). METHODS Plasmid extraction was performed using an alkaline lysis-based plasmid extraction kit, whereas polymerase chain reaction was used to detect the presence of mcr-1 and mcr-2 plasmids. The E. coli DH5α strain served as the competent cell for accepting and transforming mcr-1 and mcr-2 plasmids. We assessed proteomic alterations in the E. coli DH5α strain both with and without colistin in the growth medium. Proteomic data were analysed using mass spectrometry. RESULTS The findings revealed significant protein changes in the E. coli DH5α strain following cloning of mcr-1 and mcr-2 plasmids. Of the 20 proteins in the DH5α strain, expression in 8 was suppressed following transformation. In the presence of colistin in the culture medium, 39 new proteins were expressed following transformation with mcr-1 and mcr-2 plasmids. The proteins with altered expression play various roles. CONCLUSION The results of this study highlight numerous protein alterations in E. coli resulting from mcr-1 and mcr-2-mediated resistance to colistin. This understanding can shed light on the resistance mechanism. Additionally, the proteomic variations observed in the presence and absence of colistin might indicate potential adverse effects of indiscriminate antibiotic exposure on treatment efficacy and heightened pathogenicity of microorganisms.
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Affiliation(s)
- Hadi Feizi
- Department of Medical Microbiology, Aalinasab Hospital, Social Security Organization, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Alizadeh
- Pharmaceutical Nanotechnology Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Azimi
- Department of Microbiology, Islamic Azad University of Zanjan, Zanjan, Iran
| | - Ehsaneh Khodadadi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Khudaverdi Ganbarov
- Research Laboratory of Microbiology and Virology, Baku State University, Baku, Azerbaijan
| | - Reza Ghotaslou
- Immunology Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Hossein Samadi Kafil
- Drug Applied Research Centre, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Janice J, Wagner TM, Olsen K, Hegstad J, Hegstad K. Emergence of vancomycin-resistant enterococci from vancomycin-susceptible enterococci in hospitalized patients under antimicrobial therapy. J Glob Antimicrob Resist 2024; 36:116-122. [PMID: 38128726 DOI: 10.1016/j.jgar.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
OBJECTIVES Enterococci are opportunistic pathogens with plastic genomes that evolve, acquire, and transmit antimicrobial-resistant determinants such as vancomycin resistance clusters. While vancomycin-resistant enterococci (VRE) have emerged as successful nosocomial pathogens, the mechanism by which vancomycin-susceptible enterococci (VSE) transform to VRE in hospitalized patients remains understudied. METHODS Genomes of Enterococcus faecium from two critically ill hospitalized patients subjected to multiple antibiotic therapies, including broad-spectrum antibiotics, were investigated. To identify mechanisms of resistance evolution, genomes of vancomycin-susceptible and -resistant isolates were compared. RESULTS While VSE isolates were initially identified, VRE strains emerged post-vancomycin therapy. Comparative genomics revealed horizontal transmission of mobile genetic elements containing the Tn1549 transposon, which harbours the vanB-type vancomycin resistance gene cluster. This suggests that broad-spectrum antibiotic stress promoted the transfer of resistance-conferring elements, presumably from another gut inhabitant. CONCLUSION This is one of the first studies investigating VSE and VRE isolates from the same patient. The mechanism of transmission and the within-patient evolution of vancomycin resistance via mobile genetic elements under antibiotic stress is illustrated. Our findings serve as a foundation for future studies building on this knowledge which can further elucidate the dynamics of antibiotic stress, resistance determinant transmission, and interactions within the gut microbiota.
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Affiliation(s)
- Jessin Janice
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Theresa Maria Wagner
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Karina Olsen
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Joachim Hegstad
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Kristin Hegstad
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway; Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.
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Batisti Biffignandi G, Chindelevitch L, Corbella M, Feil EJ, Sassera D, Lees JA. Optimising machine learning prediction of minimum inhibitory concentrations in Klebsiella pneumoniae. Microb Genom 2024; 10:001222. [PMID: 38529944 PMCID: PMC10995625 DOI: 10.1099/mgen.0.001222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024] Open
Abstract
Minimum Inhibitory Concentrations (MICs) are the gold standard for quantitatively measuring antibiotic resistance. However, lab-based MIC determination can be time-consuming and suffers from low reproducibility, and interpretation as sensitive or resistant relies on guidelines which change over time. Genome sequencing and machine learning promise to allow in silico MIC prediction as an alternative approach which overcomes some of these difficulties, albeit the interpretation of MIC is still needed. Nevertheless, precisely how we should handle MIC data when dealing with predictive models remains unclear, since they are measured semi-quantitatively, with varying resolution, and are typically also left- and right-censored within varying ranges. We therefore investigated genome-based prediction of MICs in the pathogen Klebsiella pneumoniae using 4367 genomes with both simulated semi-quantitative traits and real MICs. As we were focused on clinical interpretation, we used interpretable rather than black-box machine learning models, namely, Elastic Net, Random Forests, and linear mixed models. Simulated traits were generated accounting for oligogenic, polygenic, and homoplastic genetic effects with different levels of heritability. Then we assessed how model prediction accuracy was affected when MICs were framed as regression and classification. Our results showed that treating the MICs differently depending on the number of concentration levels of antibiotic available was the most promising learning strategy. Specifically, to optimise both prediction accuracy and inference of the correct causal variants, we recommend considering the MICs as continuous and framing the learning problem as a regression when the number of observed antibiotic concentration levels is large, whereas with a smaller number of concentration levels they should be treated as a categorical variable and the learning problem should be framed as a classification. Our findings also underline how predictive models can be improved when prior biological knowledge is taken into account, due to the varying genetic architecture of each antibiotic resistance trait. Finally, we emphasise that incrementing the population database is pivotal for the future clinical implementation of these models to support routine machine-learning based diagnostics.
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Affiliation(s)
- Gherard Batisti Biffignandi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, England, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Leonid Chindelevitch
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, England, UK
| | - Marta Corbella
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - John A. Lees
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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Zeden MS. mSphere of Influence: Targeting bacterial signaling and metabolism to overcome antimicrobial resistance. mSphere 2024; 9:e0063223. [PMID: 38305167 PMCID: PMC10900877 DOI: 10.1128/msphere.00632-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
Dr Merve Suzan Zeden works in the field of molecular bacteriology and antibiotic resistance. In this mSphere of Influence article, she reflects on how three papers, entitled "c-di-AMP modulates Listeria monocytogenes central metabolism to regulate growth, antibiotic resistance and osmoregulation," "Amino acid catabolism in Staphylococcus aureus and the function of carbon catabolite repression," and "Evolving MRSA: high-level β-lactam resistance in Staphylococcus aureus is associated with RNA polymerase alterations and fine tuning of gene expression," made an impact on her work on bacterial metabolism and antimicrobial resistance and how it shaped her research in understanding the link in between.
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Affiliation(s)
- Merve S Zeden
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway, Ireland
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Kim C, Riley A, Sriharan S, Nartea T, Ndegwa E, Dhakal R, Zheng G, Baffaut C. Examining Antimicrobial Resistance in Escherichia coli: A Case Study in Central Virginia's Environment. Antibiotics (Basel) 2024; 13:223. [PMID: 38534658 DOI: 10.3390/antibiotics13030223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/28/2024] Open
Abstract
While environmental factors may contribute to antimicrobial resistance (AMR) in bacteria, many aspects of environmental antibiotic pollution and resistance remain unknown. Furthermore, the level of AMR in Escherichia coli is considered a reliable indicator of the selection pressure exerted by antimicrobial use in the environment. This study aimed to assess AMR variance in E. coli isolated from diverse environmental samples, such as animal feces and water from wastewater treatment plants (WWTPs) and drainage areas of different land use systems in Central Virginia. In total, 450 E. coli isolates obtained between August 2020 and February 2021 were subjected to susceptibility testing against 12 antimicrobial agents approved for clinical use by the U.S. Food and Drug Administration. Approximately 87.8% of the tested isolates were resistant to at least one antimicrobial agent, with 3.1% showing multi-drug resistance. Streptomycin resistance was the most common (73.1%), while susceptibility to chloramphenicol was the highest (97.6%). One isolate obtained from WWTPs exhibited resistance to seven antimicrobials. AMR prevalence was the highest in WWTP isolates, followed by isolates from drainage areas, wild avians, and livestock. Among livestock, horses had the highest AMR prevalence, while cattle had the lowest. No significant AMR difference was found across land use systems. This study identifies potential AMR hotspots, emphasizing the environmental risk for antimicrobial resistant E. coli. The findings will aid policymakers and researchers, highlighting knowledge gaps in AMR-environment links. This nationally relevant research offers a scalable AMR model for understanding E. coli ecology. Further large-scale research is crucial to confirm the environmental impacts on AMR prevalence in bacteria.
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Affiliation(s)
- Chyer Kim
- Agricultural Research Station, Virginia State University, 1 Hayden Drive, Petersburg, VA 23806, USA
| | - Allissa Riley
- Department of Biology, Virginia State University, 1 Hayden Drive, Petersburg, VA 23806, USA
| | - Shobha Sriharan
- Department of Biology, Virginia State University, 1 Hayden Drive, Petersburg, VA 23806, USA
| | - Theresa Nartea
- Cooperative Extension, Virginia State University, 1 Hayden Drive, Petersburg, VA 23806, USA
| | - Eunice Ndegwa
- Agricultural Research Station, Virginia State University, 1 Hayden Drive, Petersburg, VA 23806, USA
| | - Ramesh Dhakal
- Agricultural Research Station, Virginia State University, 1 Hayden Drive, Petersburg, VA 23806, USA
| | - Guolu Zheng
- Department of Agriculture and Environmental Sciences, Cooperative Research Programs, Lincoln University, 820 Chestnut Street, Jefferson City, MO 65102, USA
| | - Claire Baffaut
- USDA ARS Cropping Systems and Water Quality Research Unit, 241 Agricultural Engineering Building, University of Missouri, Columbia, MO 65211, USA
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Sajjad U, Afzal N, Asif M, Rehman MB, Afridi AU, Kazmi T. Evaluation of antibiotic prescription patterns using WHO AWaRe classification. East Mediterr Health J 2024; 30:156-162. [PMID: 38491901 DOI: 10.26719/emhj.24.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/31/2023] [Indexed: 03/18/2024]
Abstract
Background Antimicrobial resistance is a rising problem worldwide and it poses a serious risk to public health. In Pakistan, about 70.0% of the Acinetobacter group of bacteria were resistant to all antibiotics and were responsible for high mortality among neonates within the first week of life. Aim To evaluate the pattern of antibiotic prescription in the Ear, Nose and Throat (ENT) Department of Shalamar Hospital, Lahore, Pakistan, using the WHO AWaRe 2021 classification. Methods We collected prescription data from the ENT outpatient department of Shalamar Hospital from October to December 2021. We compared the quantitative analysis of antibiotics with the WHO AWaRe classification. We analysed the data using SPSS version 26 and discussed the results with the ENT Department for possible improvements. Results Some 862 (12.1%) of the total 7126 entries were assessed. Others were excluded because they had some missing data or had no antibiotic prescription. Of all the antibiotics prescribed, around 54.9% belonged to the access category. The WHO 13th General Programme of Work 2019-2023 recommends a country-level target of at least 60% of the total antibiotic consumption in the access group antibiotics. Conclusion The outpatient department of the ENT did not prescribe any reserve or not recommended antibiotics. The use of watch antibiotics was higher than recommended by the WHO AWaRe classification. More efforts should be made to increase prescriptions from the AWaRe access group to achieve the 60% minimum target recommended by WHO for the country.
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Affiliation(s)
- Urooj Sajjad
- Shalamar Medical and Dental College, Lahore, Pakistan
| | - Nauman Afzal
- Shalamar Medical and Dental College, Lahore, Pakistan
| | - Manahil Asif
- Shalamar Medical and Dental College, Lahore, Pakistan
| | | | | | - Tahseen Kazmi
- Department of Community Medicine, Central Park Medical College, Lahore, Pakistan
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Amodio E, Pizzo S, Vella G, De Francisci V, Distefano SA, Giambelluca E, Graceffa D, Verso MG, Piro E, Giuffrè M, Giammanco GM, Calamusa G. Increase of multidrug-resistant bacteria after the COVID-19 pandemic in a major teaching Hospital in Sicily (2018-2021). Int J Antimicrob Agents 2024:107123. [PMID: 38408493 DOI: 10.1016/j.ijantimicag.2024.107123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
INTRODUCTION The COVID-19 pandemic has further highlighted the continuing threat of antimicrobial resistance (AMR) to global health and economic development. In the last two decades, AMR has raised increasing concern with an estimated 4.95 million deaths globally due to bacterial AMR in 2019 alone. This study aims to analyze the impact of the pandemic on the spread of multi-drug resistant organisms (MDROs) using data from the Hospital «P. Giaccone» in Palermo, comparing pre-pandemic and pandemic periods. METHODS This observational study involved adult patients discharged from the hospital between 01/01/2018-31/12/2021. Hospital Discharge Cards were linked with microbiological laboratory reports to assess MDRO isolations. SARS-CoV-2 positivity during hospitalization was evaluated using the National Institute of Health's surveillance system. RESULTS This study evaluated 58,427 hospitalizations, where half of the patients were over 65 years old (N=26,984) and most admissions were in the medical area (N=31,716). During the hospitalization period, the isolated MDRO were 2,681(5%), whereas there were 946 subjects (2%) positive for SARS-CoV-2. In the multivariable analyses, during 2020 and 2021 there was a significant increased risk of isolation of Staphylococcus aureus,Acinetobacter baumannii,and Klebsiella pneumoniae. Age, weight of the Diagnosis Related Group (DRG), wards with higher intensity of care, and length-of-stay were associated to a higher risk of MDRO isolation. CONCLUSION Our study provides new insights into the impact of the COVID-19 pandemic on MDRO isolation and has important implications for infection control and prevention efforts in healthcare facilities. Age, DRG-weight, and longer hospital stays further increase the risk of MDRO isolation. Thus, it is imperative to improve and follow hospital protocols to prevent healthcare-associated infections.
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Affiliation(s)
- Emanuele Amodio
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Stefano Pizzo
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Giuseppe Vella
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Valerio De Francisci
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Salvatore Antonino Distefano
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Eliana Giambelluca
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Domenico Graceffa
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Maria Gabriella Verso
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Ettore Piro
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Mario Giuffrè
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Giovanni Maurizio Giammanco
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy
| | - Giuseppe Calamusa
- University of Palermo, Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties «G. D'Alessandro», Via del Vespro 133, 90127, Palermo, Italy.
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Al Mana H, Abdel Hadi H, Wilson G, Almaslamani MA, Abu Jarir SH, Ibrahim E, Eltai NO. Antimicrobial Resistance in Qatar: Prevalence and Trends before and Amidst the COVID-19 Pandemic. Antibiotics (Basel) 2024; 13:203. [PMID: 38534638 DOI: 10.3390/antibiotics13030203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
Antimicrobial resistance (AMR) is a global healthcare challenge with substantial morbidity, mortality, and management costs. During the COVID-19 pandemic, there was a documented increase in antimicrobial consumption, particularly for severe and critical cases, as well as noticeable travel and social restriction measures that might influenced the spectrum of AMR. To evaluate the problem, retrospective data were collected on bacterial infections and antimicrobial susceptibility patterns in Qatar before and after the pandemic from 1 January 2019 to 31 December 2021, covering 53,183 pathogens isolated from reported infection episodes. The findings revealed a significant resistance pattern for extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-EBC), carbapenem-resistant Enterobacteriaceae (CR-EBC), and carbapenem-resistant Pseudomonas aeruginosa (CRPA), ciprofloxacin-resistant Salmonella and methicillin-resistant Staphylococcus aureus (MRSA). For correlation with social restrictions, ESBL-EBC and MRSA were positively correlated with changing patterns of international travel (ρ = 0.71 and 0.67, respectively; p < 0.05), while CRPA was moderately correlated with the number of COVID-19 hospitalized patients (ρ = 0.49; p < 0.05). CREBC and CRPA respiratory infections were associated with hospitalized patients (OR: 3.08 and 2.00, respectively; p < 0.05). The findings emphasize the challenges experienced during the COVID-19 pandemic and links to international travel, which probably will influence the local epidemiology of AMR that needs further surveillance and control strategies.
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Affiliation(s)
- Hassan Al Mana
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
| | - Hamad Abdel Hadi
- Communicable Diseases Centre, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Godwin Wilson
- Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Muna A Almaslamani
- Communicable Diseases Centre, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Sulieman H Abu Jarir
- Communicable Diseases Centre, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Emad Ibrahim
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
- Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Nahla O Eltai
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
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Soni J, Sinha S, Pandey R. Understanding bacterial pathogenicity: a closer look at the journey of harmful microbes. Front Microbiol 2024; 15:1370818. [PMID: 38444801 PMCID: PMC10912505 DOI: 10.3389/fmicb.2024.1370818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Bacteria are the most prevalent form of microorganisms and are classified into two categories based on their mode of existence: intracellular and extracellular. While most bacteria are beneficial to human health, others are pathogenic and can cause mild to severe infections. These bacteria use various mechanisms to evade host immunity and cause diseases in humans. The susceptibility of a host to bacterial infection depends on the effectiveness of the immune system, overall health, and genetic factors. Malnutrition, chronic illnesses, and age-related vulnerabilities are the additional confounders to disease severity phenotypes. The impact of bacterial pathogens on public health includes the transmission of these pathogens from healthcare facilities, which contributes to increased morbidity and mortality. To identify the most significant threats to public health, it is crucial to understand the global burden of common bacterial pathogens and their pathogenicity. This knowledge is required to improve immunization rates, improve the effectiveness of vaccines, and consider the impact of antimicrobial resistance when assessing the situation. Many bacteria have developed antimicrobial resistance, which has significant implications for infectious diseases and favors the survival of resilient microorganisms. This review emphasizes the significance of understanding the bacterial pathogens that cause this health threat on a global scale.
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Affiliation(s)
- Jyoti Soni
- Division of Immunology and Infectious Disease Biology, Integrative Genomics of Host Pathogen Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Sristi Sinha
- Division of Immunology and Infectious Disease Biology, Integrative Genomics of Host Pathogen Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
- School of Biosciences and Technology, Vellore Institute of Technology University, Vellore, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, Integrative Genomics of Host Pathogen Laboratory, Council of Scientific & Industrial Research-Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research, Ghaziabad, India
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Nimmo C, Ortiz AT, Tan CCS, Pang J, Acman M, Millard J, Padayatchi N, Grant AD, O'Donnell M, Pym A, Brynildsrud OB, Eldholm V, Grandjean L, Didelot X, Balloux F, van Dorp L. Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis. Genome Med 2024; 16:34. [PMID: 38374151 PMCID: PMC10877763 DOI: 10.1186/s13073-024-01289-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Drug resistance in tuberculosis (TB) poses a major ongoing challenge to public health. The recent inclusion of bedaquiline into TB drug regimens has improved treatment outcomes, but this advance is threatened by the emergence of strains of Mycobacterium tuberculosis (Mtb) resistant to bedaquiline. Clinical bedaquiline resistance is most frequently conferred by off-target resistance-associated variants (RAVs) in the mmpR5 gene (Rv0678), the regulator of an efflux pump, which can also confer cross-resistance to clofazimine, another TB drug. METHODS We compiled a dataset of 3682 Mtb genomes, including 180 carrying variants in mmpR5, and its immediate background (i.e. mmpR5 promoter and adjacent mmpL5 gene), that have been associated to borderline (henceforth intermediate) or confirmed resistance to bedaquiline. We characterised the occurrence of all nonsynonymous mutations in mmpR5 in this dataset and estimated, using time-resolved phylogenetic methods, the age of their emergence. RESULTS We identified eight cases where RAVs were present in the genomes of strains collected prior to the use of bedaquiline in TB treatment regimes. Phylogenetic reconstruction points to multiple emergence events and circulation of RAVs in mmpR5, some estimated to predate the introduction of bedaquiline. However, epistatic interactions can complicate bedaquiline drug-susceptibility prediction from genetic sequence data. Indeed, in one clade, Ile67fs (a RAV when considered in isolation) was estimated to have emerged prior to the antibiotic era, together with a resistance reverting mmpL5 mutation. CONCLUSIONS The presence of a pre-existing reservoir of Mtb strains carrying bedaquiline RAVs prior to its clinical use augments the need for rapid drug susceptibility testing and individualised regimen selection to safeguard the use of bedaquiline in TB care and control.
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Affiliation(s)
- Camus Nimmo
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
- Division of Infection and Immunity, University College London, London, UK.
- Africa Health Research Institute, Durban, South Africa.
| | - Arturo Torres Ortiz
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Department of Medicine, Imperial College, London, UK
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - Juanita Pang
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK
| | - James Millard
- Africa Health Research Institute, Durban, South Africa
- Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Nesri Padayatchi
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Max O'Donnell
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
- Department of Medicine & Epidemiology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alex Pym
- Africa Health Research Institute, Durban, South Africa
| | - Ola B Brynildsrud
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Louis Grandjean
- Division of Infection and Immunity, University College London, London, UK
- Laboratorio de Investigacion y Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - François Balloux
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Darwin Building, Gower Street, London, UK.
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Kurbatfinski N, Kramer CN, Goodman SD, Bakaletz LO. Corrigendum: ESKAPEE pathogens newly released from biofilm residence by a targeted monoclonal are sensitized to killing by traditional antibiotics. Front Microbiol 2024; 15:1382491. [PMID: 38426051 PMCID: PMC10903342 DOI: 10.3389/fmicb.2024.1382491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2023.1202215.].
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Affiliation(s)
- Nikola Kurbatfinski
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Cameron N. Kramer
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Steven D. Goodman
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Lauren O. Bakaletz
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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Zarske M, Luu HQ, Deneke C, Knüver MT, Thieck M, Hoang HTT, Bretschneider N, Pham NT, Huber I, Stingl K. Identification of knowledge gaps in whole-genome sequence analysis of multi-resistant thermotolerant Campylobacter spp. BMC Genomics 2024; 25:156. [PMID: 38331708 PMCID: PMC10851486 DOI: 10.1186/s12864-024-10014-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Campylobacter spp. is the most frequent cause of bacterial food-borne gastroenteritis and a high priority antibiotic resistant bacterium according to the World Health Organization (WHO). European monitoring of thermotolerant Campylobacter spp. does not reflect the global burden of resistances already circulating within the bacterial population worldwide. METHODS We systematically compared whole genome sequencing with comprehensive phenotypic antimicrobial susceptibility, analyzing 494 thermotolerant Campylobacter poultry isolates from Vietnam and Germany. Any discrepancy was checked by repeating the wet lab and improving the dry lab part. Selected isolates were additionally analyzed via long-read Oxford Nanopore technology, leading to closed chromosomes and plasmids. RESULTS Overall, 22 different resistance genes and gene variants (e. g. erm(B), aph(3')-IIIa, aph(2'')-If, catA, lnu(C), blaOXA, sat4) and point mutations in three distinct genes (gyrA, 23S rRNA, rpsL) associated with AMR were present in the Campylobacter isolates. Two AMR genes were missing in the database and one falsely associated with resistance. Bioinformatic analysis based on short-read data partly failed to identify tet(O) and aadE, when the genes were present as duplicate or homologous gene variants. Intriguingly, isolates also contained different determinants, redundantly conferring resistance to chloramphenicol, gentamicin, kanamycin, lincomycin and streptomycin. We found a novel tet(W) in tetracycline sensitive strains, harboring point mutations. Furthermore, analysis based on assemblies from short-read data was impaired to identify full length phase variable aad9, due to variations of the poly-C tract within the gene. The genetic determinant responsible for gentamicin resistance of one isolate from Germany could not be identified. GyrT86I, presenting the main determinant for (fluoro-)quinolone resistance led to a rare atypical phenotype of ciprofloxacin resistance but nalidixic acid sensitivity. Long-read sequencing predicted AMR genes were mainly located on the chromosome, and rarely on plasmids. Predictions from long- and short-read sequencing, respectively, often differed. AMR genes were often organized in multidrug resistance islands (MDRI) and partially located in proximity to transposase genes, suggesting main mobilization of resistance determinants is via natural transformation and transposition in Campylobacter. CONCLUSIONS The results of this study suggest that there is frequent resistance gene duplication, mosaicism, and mutation leading to gene variation and truncation in Campylobacter strains that have not been reported in previous studies and are missing from databases. Furthermore, there is a need for deciphering yet unknown resistance mechanisms and resistance spread in thermotolerant Campylobacter spp. that may pose a challenge to global food safety.
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Affiliation(s)
- Michael Zarske
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Huong Quynh Luu
- National Institute of Veterinary Research (NIVR), 86 Truong Chinh Street, Hanoi, Dong Da District, Vietnam
| | - Carlus Deneke
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Marie-Theres Knüver
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Maja Thieck
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Ha Thi Thu Hoang
- Department of Bacteriology, National Institute of Hygiene and Epidemiology (NIHE), 1 Yersin Street, Hanoi, Trung District, Vietnam
| | - Nancy Bretschneider
- Department of Molecular Biology and Gene Technology, Bavarian Health and Food Safety Authority, Oberschleissheim, D-85764, Germany
| | - Ngoc Thi Pham
- National Institute of Veterinary Research (NIVR), 86 Truong Chinh Street, Hanoi, Dong Da District, Vietnam
| | - Ingrid Huber
- Department of Molecular Biology and Gene Technology, Bavarian Health and Food Safety Authority, Oberschleissheim, D-85764, Germany
| | - Kerstin Stingl
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany.
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Gilham EL, Pearce-Smith N, Carter V, Ashiru-Oredope D. Assessment of global antimicrobial resistance campaigns conducted to improve public awareness and antimicrobial use behaviours: a rapid systematic review. BMC Public Health 2024; 24:396. [PMID: 38321479 PMCID: PMC10848528 DOI: 10.1186/s12889-024-17766-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/13/2024] [Indexed: 02/08/2024] Open
Abstract
INTRODUCTION Public health campaigns with a well-defined outcome behaviour have been shown to successfully alter behaviour. However, the complex nature of antimicrobial resistance (AMR) creates challenges when evaluating campaigns aimed at raising awareness and changing behaviour. AIMS To determine what campaigns have been conducted and which reported being effective at improving awareness of antimicrobial resistance and changing behaviour around antimicrobial use in members of the public. It also sought to determine the outcome measures studies have used to assess campaign effectiveness. METHODS A systematic search of Ovid MEDLINE and Embase, was conducted in October 2022 using a predefined search strategy. Studies which were published between 2010 and September 2022 that outlined a campaign or invention aimed at the public and focusing on AMR or antibiotic usage were eligible for inclusion and studies which solely targeted healthcare professionals (HCP) were excluded. RESULTS Literature searches retrieved 6961 results. De-duplication and screening removed 6925 articles, five articles from grey literature and reference screening were included, giving a total of 41 studies and 30 unique interventions. There was a distribution of campaigns globally with the majority run in Europe (n = 15) with most campaigns were conducted nationally (n = 14). Campaigns tended to focus on adult members of the public (n = 14) or targeted resources towards both the public and HCPs (n = 13) and predominately assessed changes in knowledge of and/or attitudes towards AMR (n = 16). Campaigns where an improvement was seen in their primary outcome measure tended to use mass media to disseminate information, targeted messaging towards a specific infection, and including the use of HCP-patient interactions. DISCUSSION This review provides some evidence that campaigns can significantly improve outcome measures relating to AMR and antibiotic usage. Despite a lack of homogeneity between studies some common themes emerged between campaigns reported as being effective. However, the frequent use of observational study designs makes it difficult to establish causation between the campaign and changes seen in the studies outcome measures. It is important that clear evaluation processes are embedded as part of the design process for future campaigns; a campaign evaluation framework for use by campaign developers may facilitate this.
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Affiliation(s)
- Ellie L Gilham
- HCAI and AMR Division, Health Security Agency, London, UK
| | | | | | - Diane Ashiru-Oredope
- HCAI and AMR Division, Health Security Agency, London, UK.
- School of Pharmacy, University of Nottingham, Nottingham, UK.
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Reinicke M, Braun SD, Diezel C, Lemuth O, Engelmann I, Liebe T, Ehricht R. From Shadows to Spotlight: Enhancing Bacterial DNA Detection in Blood Samples through Cutting-Edge Molecular Pre-Amplification. Antibiotics (Basel) 2024; 13:161. [PMID: 38391548 PMCID: PMC10886392 DOI: 10.3390/antibiotics13020161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
One of the greatest challenges to the use of molecular methods for diagnostic purposes is the detection of target DNA that is present only in low concentrations. One major factor that negatively impacts accuracy, diagnostic sensitivity, and specificity is the sample matrix, which hinders the attainment of the required detection limit due to the presence of residual background DNA. To address this issue, various methods have been developed to enhance sensitivity through targeted pre-amplification of marker sequences. Diagnostic sensitivity to the single molecular level is critical, particularly when identifying bloodstream infections. In cases of clinically manifest sepsis, the concentration of bacteria in the blood may reach as low as one bacterial cell/CFU per mL of blood. Therefore, it is crucial to achieve the highest level of sensitivity for accurate detection. In the present study, we have established a method that fills the analytical gap between low concentrations of molecular markers and the minimum requirements for molecular testing. For this purpose, a sample preparation of whole blood samples with a directly downstream pre-amplification was developed, which amplifies specific species and resistance markers in a multiplex procedure. When applying pre-amplification techniques, the sensitivity of the pathogen detection in whole blood samples was up to 100 times higher than in non-pre-amplified samples. The method was tested with blood samples that were spiked with several Gram-positive and Gram-negative bacterial pathogens. By applying this method to artificial spiked blood samples, it was possible to demonstrate a sensitivity of 1 colony-forming unit (CFU) per millilitre of blood for S. aureus and E. faecium. A detection limit of 28 and 383 CFU per ml of blood was achieved for E. coli and K. pneumoniae, respectively. If the sensitivity is also confirmed for real clinical blood samples from septic patients, the novel technique can be used for pathogen detection without cultivation, which might help to accelerate diagnostics and, thus, to decrease sepsis mortality rates.
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Affiliation(s)
- Martin Reinicke
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Sascha Daniel Braun
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Oliver Lemuth
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Ines Engelmann
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Theresa Liebe
- InfectoGnostics Research Campus, 07743 Jena, Germany
- BLINK AG, 07747 Jena, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), Leibniz Centre for Photonics in Infection Research (LPI), 07745 Jena, Germany
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich-Schiller University, 07743 Jena, Germany
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Kubasakova I, Kubanova J, Benco D, Kadlecová D. Implementation of Automated Guided Vehicles for the Automation of Selected Processes and Elimination of Collisions between Handling Equipment and Humans in the Warehouse. Sensors (Basel) 2024; 24:1029. [PMID: 38339744 PMCID: PMC10857765 DOI: 10.3390/s24031029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/24/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
This article deals with the implementation of automated guided vehicles (AGVs) in a selected company. The aim is to analyse the use of AGVs in our country and abroad and to provide information about the use of AGVs in other countries and operations other than ours. The result of the analysis was a literature review, which points out the individual advantages and disadvantages of the use of AGVs in companies. Within the review we also address the issue of AMR vehicles, due to the modernization of existing AGVs in the company, or the replacement of AMRs with AGVs in general. Our aim is to show why AGVs can replace human work. This is mainly because of the continuous increase in the wages of employees, because of safety, but also because of the modernization of the selected company. The company has positive experience of AGVs in other sites. We wanted to point out a higher form of automation, and how it would be possible to use AMR vehicles for the same work as AGVs. In the company, we have identified jobs where we would like to introduce AGVs or AMR vehicles. Consequently, we chose the AGV from CEIT operated by magnetic tape and the AMR from SEER as an example. Based on studies, the demand for AGVs is expected to increase by up to 17% in 2019-2024. Therefore, the company is looking into the issue of the implementation of AGVs at multiple sites. The question which remains is the economic return and the possibility of investing in the automation of processes in the company, which we discuss in more detail in the conclusion of the article and in the research. The article describes the exact processes for AGVs, their workload, and also the routes for AGVs, such as loading/unloading points, stopping points, checkpoints, junctions with other AGVs, charging stations, and field elements, as well as their speed, frequency and the possibility of collision with other AGVs. Our research shows that by applying the new technology, the company will save a large amount of money on employee wages. The purchase of two AGVs will cost the company EUR 49,000, while the original technology used in the company cost EUR 79,200 annually. The payback period for such an investment is 8 months. The benefits of implementing AGVs are evaluated in the last section of this paper, where both the economic and time requirements of the different proposals are included. This section also includes recommendations for improving specific parts of the enterprise.
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Affiliation(s)
| | - Jaroslava Kubanova
- Department of Road and Urban Transport, Faculty of Operation and Economics of Transport and Communication, University of Zilina, Univerzitna 8215/1, 01026 Zilina, Slovakia; (I.K.); (D.B.); (D.K.)
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Pattnaik M, Nayak AK, Karna S, Rehman T, Sahoo SK, Palo SK, Kanungo S, Kshatri JS, Parai D, Walia K, Pati S, Bhattacharya D. Social and biological evaluation of antimicrobial resistance (SOBEAR) in rural India: a study protocol. Front Public Health 2024; 12:1296382. [PMID: 38362213 PMCID: PMC10867149 DOI: 10.3389/fpubh.2024.1296382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
Background Antimicrobial resistance (AMR) has been one of the biggest global health threats in recent years, mostly in low- and middle-income countries, which requires urgent research using a multidisciplinary research approach. The use of large quantities of antimicrobial drugs inappropriately for humans, poultry and agriculture has been recognized as a leading cause of antibiotic resistance and the predominance of drug-resistance pathogens in the environment. This protocol aims to describe the use/misuse of antibiotics (ABs) in the community and evaluate clinical samples from healthcare settings to detect genes associated with antimicrobial resistance. Methods We will conduct a community-level survey in different villages of the Tigiria block to assess knowledge and awareness on ABs and AMR. We will conduct in-depth interviews (IDIs) with doctors, pharmacists, nurses and drug sellers, as well as focus group discussions (FGDs) with ASHA and ANM workers who are involved in antibiotic supplies to the community. Quantitative data from the community survey and qualitative data of IDIs and FGDs will be linked and analyzed using statistical modeling and iterative thematic content analysis. Specimens (stool, urine, blood and wound/pus) will be collected from clinically diagnosed patients of different healthcare centers of Tigiria block. The samples will be cultured for bacterial isolation and antibiotic sensitivity testing. Genomic DNA will be isolated from positive bacterial cultures and sequenced using PCR to evaluate high-threat multi-drug resistance organisms (MDROs), screening of plasmid-mediated quinolone resistance (PMQR) genes, antimicrobial genes responsible for MDR and quinolone resistance-determining regions (QRDRs). Conclusion This is the community-based protocol to evaluate the knowledge, attitudes, awareness and practices regarding ABs and AMR. The study protocol establishes a foundation for evaluating population-based prevalence and risk factors for AMR and MDROs in rural areas of the Odisha state, India.
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Affiliation(s)
- Matrujyoti Pattnaik
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
| | - Ashish Kumar Nayak
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
| | - Sonam Karna
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
| | - Tanveer Rehman
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
| | - Subrat Kumar Sahoo
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
| | - Subrata Kumar Palo
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
| | - Srikanta Kanungo
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
| | - Jaya Singh Kshatri
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
| | - Debaprasad Parai
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
| | - Kamini Walia
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Sanghamitra Pati
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
| | - Debdutta Bhattacharya
- Model Rural Health Research Unit, ICMR-Regional Medical Research Centre, Cuttack, India
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Byrne AW, Garvan C, Bolton J, Naranjo-Lucena A, Madigan G, McElroy M, Slowey R. Antimicrobial resistance in Escherichia coli isolated from pigs and associations with aggregated antimicrobial usage in Ireland: A herd-level exploration. Zoonoses Public Health 2024; 71:71-83. [PMID: 37899534 DOI: 10.1111/zph.13086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/05/2023] [Accepted: 10/14/2023] [Indexed: 10/31/2023]
Abstract
AIMS Antimicrobial resistance (AMR) is of significant global concern and is a major One Health issue. There is evidence to suggest that increased antimicrobial usage (AMU) can be associated with AMR patterns, and therefore, there have been efforts to reduce AMU in anticipation of reducing AMR emergence risk. The aim of this study was to investigate whether there were any associations between AMU and AMR patterns of commensal Escherichia coli isolated from pig herds in Ireland. METHODS AND RESULTS Data on AMR from a panel of antimicrobials (AMDs) were gathered as part of national surveillance activities. These data were associated with reported usage of AMDs, on a year-quarter basis, measured in mg/kg at a herd-level using generalized estimating equation regression analysis. Associations were tested with AMR presence or multi-drug resistance (MDR; ≥3 classes) profiles and total AMU during the contemporaneous quarter and previous quarter, respectively. Furthermore, individual and AMD class-based associations were tested. The final dataset contained 218 observations (herd-quarter usage and AMR resistance profile) from 122 herds during 2019-2021. Apparent resistance prevalence varied according to AMD type, with the highest mean prevalence found with tetracycline at 51.57% (95% CI: 45.06%-58.09%). There were significant associations between a herd obtaining a positive AMR result for any AMDs and the overall levels of AMU during the year-quarter. Furthermore, there were significant positive associations between MDR and total AMU. At the compound level, chloramphenicol resistance was significantly associated with increased usage of trimethoprim/sulfadiazine and chlortetracycline, respectively (p < 0.010). Tetracycline resistance was associated with increased use of chlortetracycline (p = 0.008). At the antimicrobial class level, there was a significant positive relationship between the usage of phenicol and the probability of a resistance for chloramphenicol (p = 0.026) and between the usage of tetracycline and tetracycline resistance probability (p = 0.018). CONCLUSIONS Our data provide evidence of associations between overall AMU and AMR or MDR risk at the herd-quarter level. There was also evidence of associations between specific AMDs and patterns of resistance. Associations varied depending on whether time lags in usage were modelled or how usage was modelled (e.g. dichotomized or continuous). Associations with rarely used AMDs (e.g. critically important AMDs) were precluded due to a lack of statistical power. Continued monitoring of both AMU and AMR is crucial to assess the impacts of policy changes aimed at reducing AMU.
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Affiliation(s)
- Andrew W Byrne
- Department of Agriculture, Food and The Marine, One Health Scientific Support Unit, National Diseases Control Centre (NDCC), Dublin 2, Ireland
| | - Caroline Garvan
- AMR Section, Department of Agriculture, Food and The Marine, Dublin 2, Ireland
| | - Julie Bolton
- AMR Section, Department of Agriculture, Food and The Marine, Dublin 2, Ireland
| | - Amalia Naranjo-Lucena
- Department of Agriculture, Food and the Marine, Backweston Laboratory Campus, National Reference Laboratory for Antimicrobial Resistance, Celbridge, Ireland
- UCD School of Veterinary Medicine, Dublin 4, Ireland
| | - Gillian Madigan
- Department of Agriculture, Food and the Marine, Backweston Laboratory Campus, National Reference Laboratory for Antimicrobial Resistance, Celbridge, Ireland
| | - Máire McElroy
- Department of Agriculture, Food and the Marine, Backweston Laboratory Campus, National Reference Laboratory for Antimicrobial Resistance, Celbridge, Ireland
| | - Rosemarie Slowey
- Department of Agriculture, Food and the Marine, Backweston Laboratory Campus, National Reference Laboratory for Antimicrobial Resistance, Celbridge, Ireland
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Sumon SA, Anwar MMU, Akther FM, Priyanka AS, Tamanna T, Rahman A, Islam MS, Harun MGD. Perceptions of antibiotic stewardship programmes and determinants of antibiotic prescribing patterns among physicians in tertiary hospitals in Bangladesh: implications for future policy and practice. J Hosp Infect 2024; 144:56-65. [PMID: 38070709 DOI: 10.1016/j.jhin.2023.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024]
Abstract
BACKGROUND The concerning growth of antimicrobial resistance (AMR) renders common infections life-threatening due to irrational antibiotic use and a lack of effective antimicrobial stewardship programmes (ASPs). AIM To investigate the awareness, perceptions and practices of physicians regarding ASPs, AMR and antibiotic prescribing in tertiary care hospitals in Bangladesh. METHODS This hospital-based cross-sectional survey was conducted in 11 tertiary care hospitals across Bangladesh between September 2020 and January 2021. A semi-structured questionnaire was administered through face-to-face interviews for data collection. Descriptive and multi-variate analyses were performed using STATA Version 13. RESULTS In total, 559 physicians were enrolled in this survey. Overall, 40.6% [95% confidence interval (CI) 36.5-44.8] of physicians reported being aware of ASPs, and this figure was higher in public hospitals compared with private hospitals (43.8% vs 27.1%). None of the study hospitals had any ASP initiatives. More than half (55.1%) of the participants were willing to receive feedback from an ASP on their antibiotic selection. Only 30.9% of respondents stated that they wait for the findings of microbiological tests before prescribing antibiotics, although challenges included empiric use of broad-spectrum antibiotics, delayed laboratory results and the existence of drug-resistant patients. In contrast, physicians aware of ASPs were 33% (adjusted odds ratio 0.67, 95% CI 0.45-0.98; P=0.033) less likely to wait for laboratory results before prescribing antibiotics. However, 42.5% of physicians considered patient affordability of purchasing antibiotics when prescribing. CONCLUSIONS Physicians' fundamental knowledge of ASPs and rational antibiotic prescription were found to fall short of the standard. Context-specific and integrated ASP activities, availability and use of guidelines, and improved laboratory facilities are required to battle AMR in Bangladesh.
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Affiliation(s)
- S A Sumon
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh.
| | - M M U Anwar
- Department of Population Sciences, University of Dhaka, Dhaka, Bangladesh
| | - F M Akther
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - A S Priyanka
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - T Tamanna
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
| | - A Rahman
- Communicable Disease Control, Directorate General of Health Services, Dhaka, Bangladesh
| | - M S Islam
- School of Population Health, University of New South Wales, Sydney, Australia
| | - M G D Harun
- Infectious Diseases Division, icddr,b, Dhaka, Bangladesh
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Monte DFM, Gonzalez-Escalona N, Cao G, Pedrosa GTDS, Saraiva MMS, Balkey M, Jin Q, Brown E, Allard M, Macarisin D, Magnani M. Genomic analysis of a cAmpC (CMY-41)-producing Citrobacter freundii ST64 isolated from patient. Lett Appl Microbiol 2024; 77:ovae010. [PMID: 38327245 DOI: 10.1093/lambio/ovae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024]
Abstract
Antibiotic resistance in Citrobacter freundii is a public health concern. This study evaluated the closed genome of a C. freundii isolated from the stool of a hospitalized patient initially related to a Salmonella outbreak. Confirmation of the isolate was determined by whole-genome sequencing. Nanopore sequencing was performed using a MinION with a Flongle flow cell. Assembly using SPAdes and Unicycler yielded a closed genome annotated by National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline. Genomic analyses employed MLST 2.0, ResFinder4.1, PlasmidFinder2.1, and VFanalyzer. Phylogenetic comparison utilized the Center for Food Safety and Applied Nutrition (CFSAN)-single nucleotide polymorphism pipeline and Genetic Algorithm for Rapid Likelihood Inference. Antimicrobial susceptibility was tested by broth microdilution following Clinical and Laboratory Standards Institute criteria. Multi-locus sequence type in silico analysis assigned the C. freundii as sequence type 64 and the blaCMY-41 gene was detected in resistome investigation. The susceptibility to antibiotics, determined using Sensititre® plates, revealed resistance to aztreonam, colistin, cefoxitin, amoxicillin/clavulanic acid, sulfisoxazole, ampicillin, and streptomycin. The genetic relatedness of the C. freundii CFSAN077772 with publicly available C. freundii genomes revealed a close relationship to a C. freundii SRR1186659, isolated in 2009 from human stool in Tanzania. In addition, C. freundii CFSAN077772 is nested in the same cluster with C. freundii clinical strains isolated in Denmark, Mexico, Myanmar, and Canada, suggesting a successful intercontinental spread.
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Affiliation(s)
- Daniel F M Monte
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397000, Brazil
| | - Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Guojie Cao
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Geany Targino de Souza Pedrosa
- Laboratory of Microbial Processes in Foods, Department of Food Engineering, Federal University of Paraíba, João Pessoa, PB 58059900, Brazil
| | - Mauro M S Saraiva
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP 14884-900, Brazil
| | - Maria Balkey
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Qing Jin
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Eric Brown
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Marc Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Dumitru Macarisin
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Marciane Magnani
- Laboratory of Microbial Processes in Foods, Department of Food Engineering, Federal University of Paraíba, João Pessoa, PB 58059900, Brazil
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Gunathilaka GADKK, Dewasmika WAPM, Sandaruwan UM, Neelawala NGDAK, Madhumali GED, Dissanayake BN, Priyantha MAR, Prasada DVP, Dissanayake DRA. Biofilm-forming ability, antibiotic resistance and phylogeny of Escherichia coli isolated from extra intestinal infections of humans, dogs, and chickens. Comp Immunol Microbiol Infect Dis 2024; 105:102123. [PMID: 38217950 DOI: 10.1016/j.cimid.2023.102123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/15/2024]
Abstract
Escherichia coli (E. coli) causes various infections in humans and animals. The biofilm-forming ability of E. coli has increased antimicrobial resistance and capacity to cause recurrent and chronic infections. This study determined the biofilm-forming ability of E. coli isolated from extraintestinal infections of humans, chickens, and dogs in relation to the phylogroup, type of infection, and antibiotic resistance. Isolates from chickens showed significantly higher biofilm-forming ability compared to those causing urinary tract infections in humans (p = 0.0001). Further, isolates belonging to phylogroup B1 displayed a higher likelihood to form biofilms. Resistance to ciprofloxacin and trimethoprim-sulfamethoxazole was positively correlated with biofilm-forming ability. Harbouring plasmid-mediated quinolone resistance gene, qnrS was also positively correlated with biofilm formation. This study provides insight into factors such as phylogroup and the type of infections that could enhance biofilm formation, as well as genotypic and phenotypic antibiotic resistance that could correlate with the ability to form biofilms.
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Affiliation(s)
- G A D K K Gunathilaka
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - W A P M Dewasmika
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - U M Sandaruwan
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - N G D A K Neelawala
- Department of Basic Sciences, Faculty of Allied Health Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - G E D Madhumali
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - B N Dissanayake
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - D V P Prasada
- Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - D R A Dissanayake
- Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka.
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van der Sande M, Ingelbeen B, Meudec M, van Kleef E, Campbell L, Wouters E, Marien J, van Vredendaal R, Leirs H, Valia D, Yougbare S, Kouanda Juste S, Welgo A, Tinto H, Mpanzu D, Mbangi B, Khoso Muaka CA, Kiabanza O, Melanda A, Makuaya R, Ndomba D, Diagne PM, Heyerdahl L, Giles-Vernick T, Van Puyvelde S, Cooper B. Evaluating the effect of a behavioural intervention bundle on antibiotic use, quality of care, and household transmission of resistant Enterobacteriaceae in intervention versus control clusters in rural Burkina Faso and DR Congo (CABU-EICO). Trials 2024; 25:91. [PMID: 38281023 PMCID: PMC10821568 DOI: 10.1186/s13063-023-07856-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/06/2023] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a rising threat in low-resource settings, largely driven by transmission in the community, outside health facilities. Inappropriate antibiotic use is one of the main modifiable drivers of AMR. Its risk is especially high in poor resource settings, with limited diagnostic and surveillance capacities, and many informal medicine vendors determining community use. We hypothesise that to optimise community antibiotic use, especially Watch antibiotics (recommended only as first-choice for more severe clinical presentations or for causative pathogens likely to be resistant to Access antibiotics), both the supply side (medicine vendors) and the demand side (communities) should be pro-actively involved in any intervention. METHODS In two existing demographic health surveillance sites (HDSS) in Burkina Faso and in the Democratic Republic of Congo, behavioural intervention bundles were co-created in a participatory approach, aiming to rationalise (Watch) antibiotic use and improve hygiene and sanitation practices. Bundles consisted of interactive interventions, including theatre, posters, discussions, etc. To evaluate impact, 11 of 22 clusters (a HDSS community with at least one (in)formal medicine vendor) were randomly assigned to this intervention, which will run over a year. The effect of the intervention will be evaluated by comparing outcomes before and after in intervention and control villages from a) exit interviews of clients from vendors, b) mystery patients presenting to vendors with a set of predefined symptoms, c) household interviews to assess behavioural changes related to antibiotic use, health literacy and water-sanitation-hygiene indicators. Long-term impact on AMR will be estimated by modelling changes in resistant Enterobacteriaceae carriage from repeated household surveys before, during and after the intervention in both arms. DISCUSSION Most existing interventions aimed at improving antibiotic use focus on health care use, but in resource-limited settings, community use is highly prevalent. Previous studies targeting only providers failed to show an effect on antibiotic use. Evaluation will be done with before-after epidemiological measurements of actual prescriptions and use. If effective in reducing (Watch) antibiotic use, this would be an empowering methodology for communities, which has significant promise for long-term impact. TRIAL REGISTRATION ClinicalTrials.gov NCT05378880 . 13 May 2022.
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50
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Qu C, Rozsa J, Running M, McNamara S, Walsh K. I-GLAD: a new strategy for fabricating antibacterial surfaces. Discov Nano 2024; 19:17. [PMID: 38270785 PMCID: PMC10810768 DOI: 10.1186/s11671-024-03959-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024]
Abstract
The paper uses inverted glancing angle deposition (I-GLAD) for creating antibacterial surfaces. Antibacterial surfaces are found in nature, such as on insect wings, eyes, and plant leaves. Since the bactericidal mechanism is purely physical for these surfaces, the antimicrobial resistance of bacteria to traditional chemical antibiotics can be overcome. The technical problem is how to mimic, synthesize, and scale up the naturally occurring antibacterial surfaces for practical applications, given the fact that most of those surfaces are composed of three-dimensional hierarchical micro-nano structures. This paper proposes to use I-GLAD as a novel bottom-up nanofabrication technique to scale up bio-inspired nano-structured antibacterial surfaces. Our innovative I-GLAD nanofabrication technique includes traditional GLAD deposition processes alongside the crucial inverting process. Following fabrication, we explore the antibacterial efficacy of I-GLAD surfaces using two types of bacteria: Escherichia coli (E. coli), a gram-negative bacterium, and Staphylococcus aureus (S. aureus), a gram-positive bacterium. Scanning electron microscopy (SEM) shows the small tips and flexible D/P (feature size over period) ratio of I-GLAD nanoneedles, which is required to achieve the desired bactericidal mechanism. Antibacterial properties of the I-GLAD samples are validated by achieving flat growth curves of E. coli and S. aureus, and direct observation under SEM. The paper bridges the knowledge gaps of seeding techniques for GLAD, and the control/optimization of the I-GLAD process to tune the morphologies of the nano-protrusions. I-GLAD surfaces are effective against both gram-negative and gram-positive bacteria, and they have tremendous potentials in hospital settings and daily surfaces.
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Affiliation(s)
- Chuang Qu
- Department of Electrical and Computer Engineering, University of Louisville, Louisville, KY, 40292, USA.
| | - Jesse Rozsa
- Department of Biology, University of Louisville, Louisville, KY, 40292, USA
| | - Mark Running
- Department of Biology, University of Louisville, Louisville, KY, 40292, USA
| | - Shamus McNamara
- Department of Electrical and Computer Engineering, University of Louisville, Louisville, KY, 40292, USA
| | - Kevin Walsh
- Department of Electrical and Computer Engineering, University of Louisville, Louisville, KY, 40292, USA
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