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Ivanova M, Ovsepian A, Leekitcharoenphon P, Seyfarth AM, Mordhorst H, Otani S, Koeberl-Jelovcan S, Milanov M, Kompes G, Liapi M, Černý T, Vester CT, Perrin-Guyomard A, Hammerl JA, Grobbel M, Valkanou E, Jánosi S, Slowey R, Alba P, Carfora V, Avsejenko J, Pereckiene A, Claude D, Zerafa R, Veldman KT, Boland C, Garcia-Graells C, Wattiau P, Butaye P, Zając M, Amaro A, Clemente L, Vaduva AM, Romascu LM, Milita NM, Mojžišová A, Zdovc I, Escribano MJZ, De Frutos Escobar C, Overesch G, Teale C, Loneragan GH, Guerra B, Beloeil PA, Brown AMV, Hendriksen RS, Bortolaia V, Kjeldgaard JS. Azithromycin resistance in Escherichia coli and Salmonella from food-producing animals and meat in Europe. J Antimicrob Chemother 2024; 79:1657-1667. [PMID: 38775752 PMCID: PMC11215539 DOI: 10.1093/jac/dkae161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 04/30/2024] [Indexed: 07/02/2024] Open
Abstract
OBJECTIVES To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014-18 and the Danish AMR surveillance programme in 2016-19. METHODS WGS data of 1007 E. coli [165 azithromycin resistant (MIC > 16 mg/L)] and 269 Salmonella [29 azithromycin resistant (MIC > 16 mg/L)] were screened for acquired macrolide resistance genes and mutations in rplDV, 23S rRNA and acrB genes using ResFinder v4.0, AMRFinder Plus and custom scripts. Genotype-phenotype concordance was determined for all isolates. Transferability of mef(C)-mph(G)-carrying plasmids was assessed by conjugation experiments. RESULTS mph(A), mph(B), mef(B), erm(B) and mef(C)-mph(G) were detected in E. coli and Salmonella, whereas erm(C), erm(42), ere(A) and mph(E)-msr(E) were detected in E. coli only. The presence of macrolide resistance genes, alone or in combination, was concordant with the azithromycin-resistant phenotype in 69% of isolates. Distinct mph(A) operon structures were observed in azithromycin-susceptible (n = 50) and -resistant (n = 136) isolates. mef(C)-mph(G) were detected in porcine and bovine E. coli and in porcine Salmonella enterica serovar Derby and Salmonella enterica 1,4, [5],12:i:-, flanked downstream by ISCR2 or TnAs1 and associated with IncIγ and IncFII plasmids. CONCLUSIONS Diverse azithromycin resistance genes were detected in E. coli and Salmonella from food-producing animals and meat in Europe. Azithromycin resistance genes mef(C)-mph(G) and erm(42) appear to be emerging primarily in porcine E. coli isolates. The identification of distinct mph(A) operon structures in susceptible and resistant isolates increases the predictive power of WGS-based methods for in silico detection of azithromycin resistance in Enterobacterales.
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Affiliation(s)
- Mirena Ivanova
- European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR), Research Group for Global Capacity Building, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Armen Ovsepian
- European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR), Research Group for Global Capacity Building, Technical University of Denmark, Kongens Lyngby, Denmark
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | | | - Anne Mette Seyfarth
- European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR), Research Group for Global Capacity Building, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Hanne Mordhorst
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Saria Otani
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Mihail Milanov
- National Diagnostic and Research Veterinary Institute, Sofia, Bulgaria
| | | | - Maria Liapi
- Bacteriology Serology Laboratory, Veterinary Services, Cyprus
| | - Tomáš Černý
- State Veterinary Institute, Prague, Czech Republic
| | | | - Agnès Perrin-Guyomard
- French Agency for Food, Environmental and Occupational Health & Safety, Maisons-Alfort, France
| | - Jens A Hammerl
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - Mirjam Grobbel
- German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Szilárd Jánosi
- National Food Chain Safety Office, Veterinary Diagnostic Directorate, Budapest, Hungary
| | | | - Patricia Alba
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana ‘M. Aleandri’, Rome, Italy
| | - Virginia Carfora
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana ‘M. Aleandri’, Rome, Italy
| | - Jelena Avsejenko
- Institute of Food Safety, Animal Health and Environment BIOR, Riga, Latvia
| | - Asta Pereckiene
- National Food and Veterinary Risk Assessment Institute, Vilnius, Lithuania
| | - Dominique Claude
- Laboratoire de Médecine Vétérinaire de l’État, Dudelange, Luxembourg
| | | | - Kees T Veldman
- Wageningen Bioveterinary Research, Part of Wageningen University & Research, Lelystad, Netherlands
| | | | | | | | - Patrick Butaye
- Department of Pathobiology, Ghent University, Merelbeke, Belgium
- Jockey Club College of Veterinary Medicine and Life Sciences, Kowloon, Hong Kong
| | | | - Ana Amaro
- Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, Portugal
| | - Lurdes Clemente
- Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, Portugal
| | - Angela M Vaduva
- Institute for Hygiene and Veterinary Public Health, Bucharest, Romania
| | | | | | | | - Irena Zdovc
- Institute for Microbiology and Parasitology, Ljubljana, Slovenia
| | | | | | - Gudrun Overesch
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | - Guy H Loneragan
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, USA
| | | | | | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Rene S Hendriksen
- European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR), Research Group for Global Capacity Building, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valeria Bortolaia
- European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR), Research Group for Global Capacity Building, Technical University of Denmark, Kongens Lyngby, Denmark
- Statens Serum Institut, Copenhagen, Denmark
| | - Jette Sejer Kjeldgaard
- European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR), Research Group for Global Capacity Building, Technical University of Denmark, Kongens Lyngby, Denmark
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Ge B, Mukherjee S, Li C, Harrison LB, Hsu CH, Tran TT, Whichard JM, Dessai U, Singh R, Gilbert JM, Strain EA, McDermott PF, Zhao S. Genomic analysis of azithromycin-resistant Salmonella from food animals at slaughter and processing, and retail meats, 2011-2021, United States. Microbiol Spectr 2024; 12:e0348523. [PMID: 37991374 PMCID: PMC10783062 DOI: 10.1128/spectrum.03485-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE Macrolides of different ring sizes are critically important antimicrobials for human medicine and veterinary medicine, though the widely used 15-membered ring azithromycin in humans is not approved for use in veterinary medicine. We document here the emergence of azithromycin-resistant Salmonella among the NARMS culture collections between 2011 and 2021 in food animals and retail meats, some with co-resistance to ceftriaxone or decreased susceptibility to ciprofloxacin. We also provide insights into the underlying genetic mechanisms and genomic contexts, including the first report of a novel combination of azithromycin resistance determinants and the characterization of multidrug-resistant plasmids. Further, we highlight the emergence of a multidrug-resistant Salmonella Newport clone in food animals (mainly cattle) with both azithromycin resistance and decreased susceptibility to ciprofloxacin. These findings contribute to a better understating of azithromycin resistance mechanisms in Salmonella and warrant further investigations on the drivers behind the emergence of resistant clones.
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Affiliation(s)
- Beilei Ge
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Sampa Mukherjee
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Cong Li
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Lucas B. Harrison
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Chih-Hao Hsu
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Thu-Thuy Tran
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Jean M. Whichard
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Uday Dessai
- Food Safety and Inspection Service, U.S. Department of Agriculture, Washington, DC, USA
| | - Ruby Singh
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, Maryland, USA
| | - Jeffrey M. Gilbert
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, Maryland, USA
| | - Errol A. Strain
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Patrick F. McDermott
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, Maryland, USA
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Elton L, Abdel Hamid MM, Tembo J, Elbadawi H, Maluzi K, Abdelraheem MH, Cullip T, Kabanda C, Roulston K, Honeyborne I, Thomason MJ, Elhag K, Mohammed A, Adam A, Mulonga K, Sikakena K, Matibula P, Kabaso M, Nakazwe R, Fwoloshi S, Zumla A, McHugh TD. A pandemic within a pandemic? Admission to COVID-19 wards in hospitals is associated with increased prevalence of antimicrobial resistance in two African settings. Ann Clin Microbiol Antimicrob 2023; 22:25. [PMID: 37055793 PMCID: PMC10101537 DOI: 10.1186/s12941-023-00575-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Patients who develop severe illness due to COVID-19 are more likely to be admitted to hospital and acquire bacterial co-infections, therefore the WHO recommends empiric treatment with antibiotics. Few reports have addressed the impact of COVID-19 management on emergence of nosocomial antimicrobial resistance (AMR) in resource constrained settings. This study aimed to ascertain whether being admitted to a COVID-19 ward (with COVID-19 infection) compared to a non-COVID-19 ward (as a COVID-19 negative patient) was associated with a change in the prevalence of bacterial hospital acquired infection (HAI) species or resistance patterns, and whether there were differences in antimicrobial stewardship (AMS) and infection prevention and control (IPC) guidelines between COVID-19 and non-COVID-19 wards. The study was conducted in Sudan and Zambia, two resource constrained settings with differing country-wide responses to COVID-19. METHODS Patients suspected of having hospital acquired infections were recruited from COVID-19 wards and non-COVID-19 wards. Bacteria were isolated from clinical samples using culture and molecular methods and species identified. Phenotypic and genotypic resistance patterns were determined by antibiotic disc diffusion and whole genome sequencing. Infection prevention and control guidelines were analysed for COVID-19 and non-COVID-19 wards to identify potential differences. RESULTS 109 and 66 isolates were collected from Sudan and Zambia respectively. Phenotypic testing revealed significantly more multi-drug resistant isolates on COVID-19 wards in both countries (Sudan p = 0.0087, Zambia p = 0.0154). The total number of patients with hospital acquired infections (both susceptible and resistant) increased significantly on COVID-19 wards in Sudan, but the opposite was observed in Zambia (both p = ≤ 0.0001). Genotypic analysis showed significantly more β-lactam genes per isolate on COVID-19 wards (Sudan p = 0.0192, Zambia p = ≤ 0.0001). CONCLUSIONS Changes in hospital acquired infections and AMR patterns were seen in COVID-19 patients on COVID-19 wards compared to COVID-19 negative patients on non-COVID-19 wards in Sudan and Zambia. These are likely due to a potentially complex combination of causes, including patient factors, but differing emphases on infection prevention and control, and antimicrobial stewardship policies on COVID-19 wards were highlighted.
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Affiliation(s)
- Linzy Elton
- Centre for Clinical Microbiology, University College London, London, UK.
| | | | - John Tembo
- HerpeZ, University Teaching Hospital, Lusaka, Zambia
| | - Hana Elbadawi
- Institute for Endemic Diseases, University of Khartoum, Khartoum, Sudan
- MRC Clinical Trials Unit, University College London, London, UK
| | | | - Mohammed H Abdelraheem
- Institute for Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Sudan Atomic Energy Commission, Nuclear Application in Biological Sciences, Khartoum, Sudan
| | - Teresa Cullip
- Institute for Global Health, University College London, London, UK
| | - Caren Kabanda
- HerpeZ, University Teaching Hospital, Lusaka, Zambia
| | - Kerry Roulston
- Centre for Clinical Microbiology, University College London, London, UK
| | | | - Margaret J Thomason
- Centre for Clinical Microbiology, University College London, London, UK
- MRC Clinical Trials Unit, University College London, London, UK
| | - Kamal Elhag
- Soba University Hospital, University of Khartoum, Khartoum, Sudan
| | | | - Abdelsalam Adam
- Soba University Hospital, University of Khartoum, Khartoum, Sudan
| | | | - Kapatiso Sikakena
- University Teaching Hospitals, Department of Internal Medicine, Infectious Diseases Unit, Lusaka, Zambia
| | - Peter Matibula
- University Teaching Hospitals, Department of Internal Medicine, Infectious Diseases Unit, Lusaka, Zambia
| | - Mwewa Kabaso
- University Teaching Hospitals, Department of Internal Medicine, Infectious Diseases Unit, Lusaka, Zambia
| | - Ruth Nakazwe
- University Teaching Hospitals, Department of Internal Medicine, Infectious Diseases Unit, Lusaka, Zambia
| | - Sombo Fwoloshi
- University Teaching Hospitals, Department of Internal Medicine, Infectious Diseases Unit, Lusaka, Zambia
| | - Alimuddin Zumla
- Centre for Clinical Microbiology, University College London, London, UK
- National Institute for Health and Care Research Biomedical Research Centre, University College London, London, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, University College London, London, UK
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