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McGalliard R, Muhamadali H, AlMasoud N, Haldenby S, Romero-Soriano V, Allman E, Xu Y, Roberts AP, Paterson S, Carrol ED, Goodacre R. Bacterial discrimination by Fourier transform infrared spectroscopy, MALDI-mass spectrometry and whole-genome sequencing. Future Microbiol 2024. [PMID: 38652264 DOI: 10.2217/fmb-2024-0043] [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] [Indexed: 04/25/2024] Open
Abstract
Aim: Proof-of-concept study, highlighting the clinical diagnostic ability of FT-IR compared with MALDI-TOF MS, combined with WGS. Materials & methods: 104 pathogenic isolates of Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus were analyzed. Results: Overall prediction accuracy was 99.6% in FT-IR and 95.8% in MALDI-TOF-MS. Analysis of N. meningitidis serogroups was superior in FT-IR compared with MALDI-TOF-MS. Phylogenetic relationship of S. pyogenes was similar by FT-IR and WGS, but not S. aureus or S. pneumoniae. Clinical severity was associated with the zinc ABC transporter and DNA repair genes in S. pneumoniae and cell wall proteins (biofilm formation, antibiotic and complement permeability) in S. aureus via WGS. Conclusion: FT-IR warrants further clinical evaluation as a promising diagnostic tool.
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Affiliation(s)
- Rachel McGalliard
- Department of Clinical Infection, Microbiology & Immunology, University of Liverpool Institute of Infection, Veterinary & Ecological Sciences, Ronald Ross Building, 8 West Derby Street, Liverpool, UK
- Department of Infectious Diseases, Alder Hey Children's NHS Foundation Trust, Eaton Road, Liverpool, UK
| | - Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- center for Metabolomics Research, Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, UK
| | - Najla AlMasoud
- College of Science, Princess Nourah Bint Abdulrahman University, Department of Chemistry, Riyadh, 11671, Saudi Arabia
| | - Sam Haldenby
- center for Genomic Research, University of Liverpool, Mersey Bio Building, Crown Street, Liverpool, UK
| | - Valeria Romero-Soriano
- center for Genomic Research, University of Liverpool, Mersey Bio Building, Crown Street, Liverpool, UK
| | - Ellie Allman
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- center for Metabolomics Research, Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Steve Paterson
- center for Genomic Research, University of Liverpool, Mersey Bio Building, Crown Street, Liverpool, UK
| | - Enitan D Carrol
- Department of Clinical Infection, Microbiology & Immunology, University of Liverpool Institute of Infection, Veterinary & Ecological Sciences, Ronald Ross Building, 8 West Derby Street, Liverpool, UK
- Department of Infectious Diseases, Alder Hey Children's NHS Foundation Trust, Eaton Road, Liverpool, UK
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- center for Metabolomics Research, Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, UK
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Glover RE, Singer A, Roberts AP, Kirchhelle C. Why is the UK subscription model for antibiotics considered successful? Lancet Microbe 2023; 4:e852-e853. [PMID: 37625429 DOI: 10.1016/s2666-5247(23)00250-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Affiliation(s)
- Rebecca E Glover
- Department of Health Services Research and Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK.
| | | | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Claas Kirchhelle
- Department of History, University College Dublin, Dublin, Ireland
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Goodman RN, Tansirichaiya S, Roberts AP. Development of pBACpAK entrapment vector derivatives to detect intracellular transfer of mobile genetic elements within chloramphenicol resistant bacterial isolates. J Microbiol Methods 2023; 213:106813. [PMID: 37647945 DOI: 10.1016/j.mimet.2023.106813] [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: 05/18/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023]
Abstract
Antimicrobial resistance disseminates throughout bacterial populations via horizontal gene transfer, driven mainly by mobile genetic elements (MGEs). Entrapment vectors are key tools in determining MGE movement within a bacterial cell between different replicons or between sites within the same replicon. The pBACpAK entrapment vector has been previously used to study intracellular transfer in Gram-negative bacteria however since pBACpAK contains a chloramphenicol resistance gene, it cannot be used in bacterial isolates which are already resistant to chloramphenicol. Therefore, we developed new derivatives of the pBACpAK entrapment vector to determine intracellular transfer of MGEs in an Escherichia coli DH5α transconjugant containing the chloramphenicol resistance plasmid pD25466. The catA1 of pBACpAK was replaced by both mcr-1 in pBACpAK-COL and aph(3')-Ia in pBACpAK-KAN, allowing it to be used in chloramphenicol resistant strains. The plasmid constructs were verified and then used to transform the E. coli DH5α/pD25466 transconjugants in order to detect intracellular movement of the MGEs associated with the pD25466 plasmid. Here we report on the validation of the expanded suite of pBACpAK vectors which can be used to study the intracellular transfer of MGEs between, and within, replicons in bacteria with different antimicrobial resistance profiles.
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Affiliation(s)
- Richard N Goodman
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Supathep Tansirichaiya
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
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Hutton W, Allman E, McKeown C, Singer AC, Roberts AP. Complete genome sequence of mcr-9 containing Leclercia adecarboxylata. Microbiol Resour Announc 2023; 12:e0048123. [PMID: 37578246 PMCID: PMC10508152 DOI: 10.1128/mra.00481-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Here, we provide the genome sequence of a Leclercia adecarboxylata isolated from a screen of an environmental bacterial isolate library for resistance to the plant flavonoid berberine. We detected the colistin resistance gene mcr-9, located on an IncFII(pECLA) plasmid.
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Affiliation(s)
- William Hutton
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Ellie Allman
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Claudia McKeown
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Andrew C. Singer
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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Cocker D, Chidziwisano K, Mphasa M, Mwapasa T, Lewis JM, Rowlingson B, Sammarro M, Bakali W, Salifu C, Zuza A, Charles M, Mandula T, Maiden V, Amos S, Jacob ST, Kajumbula H, Mugisha L, Musoke D, Byrne R, Edwards T, Lester R, Elviss N, Roberts AP, Singer AC, Jewell C, Morse T, Feasey NA. Investigating One Health risks for human colonisation with extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Malawian households: a longitudinal cohort study. Lancet Microbe 2023; 4:e534-e543. [PMID: 37207684 PMCID: PMC10319635 DOI: 10.1016/s2666-5247(23)00062-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Low-income countries have high morbidity and mortality from drug-resistant infections, especially from enteric bacteria such as Escherichia coli. In these settings, sanitation infrastructure is of variable and often inadequate quality, creating risks of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales transmission. We aimed to describe the prevalence, distribution, and risks of ESBL-producing Enterobacterales colonisation in sub-Saharan Africa using a One Health approach. METHODS Between April 29, 2019, and Dec 3, 2020, we recruited 300 households in Malawi for this longitudinal cohort study: 100 each in urban, peri-urban, and rural settings. All households underwent a baseline visit and 195 were selected for longitudinal follow-up, comprising up to three additional visits over a 6 month period. Data on human health, antibiotic usage, health-seeking behaviours, structural and behavioural environmental health practices, and animal husbandry were captured alongside human, animal, and environmental samples. Microbiological processing determined the presence of ESBL-producing E coli and Klebsiella pneumoniae, and hierarchical logistic regression was performed to evaluate the risks of human ESBL-producing Enterobacterales colonisation. FINDINGS A paucity of environmental health infrastructure and materials for safe sanitation was identified across all sites. A total of 11 975 samples were cultured, and ESBL-producing Enterobacterales were isolated from 1190 (41·8%) of 2845 samples of human stool, 290 (29·8%) of 973 samples of animal stool, 339 (66·2%) of 512 samples of river water, and 138 (46·0%) of 300 samples of drain water. Multivariable models illustrated that human ESBL-producing E coli colonisation was associated with the wet season (adjusted odds ratio 1·66, 95% credible interval 1·38-2·00), living in urban areas (2·01, 1·26-3·24), advanced age (1·14, 1·05-1·25), and living in households where animals were observed interacting with food (1·62, 1·17-2·28) or kept inside (1·58, 1·00-2·43). Human ESBL-producing K pneumoniae colonisation was associated with the wet season (2·12, 1·63-2·76). INTERPRETATION There are extremely high levels of ESBL-producing Enterobacterales colonisation in humans and animals and extensive contamination of the wider environment in southern Malawi. Urbanisation and seasonality are key risks for ESBL-producing Enterobacterales colonisation, probably reflecting environmental drivers. Without adequate efforts to improve environmental health, ESBL-producing Enterobacterales transmission is likely to persist in this setting. FUNDING Medical Research Council, National Institute for Health and Care Research, and Wellcome Trust. TRANSLATION For the Chichewa translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Derek Cocker
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK.
| | - Kondwani Chidziwisano
- Centre for Water, Sanitation, Health and Appropriate Technology Development, Malawi University of Business and Applied Sciences, Blantyre, Malawi; Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, UK
| | - Madalitso Mphasa
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Taonga Mwapasa
- Centre for Water, Sanitation, Health and Appropriate Technology Development, Malawi University of Business and Applied Sciences, Blantyre, Malawi
| | - Joseph M Lewis
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
| | - Barry Rowlingson
- Centre for Health Informatics Computing and Statistics, Lancaster University, Lancaster, UK
| | - Melodie Sammarro
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Centre for Health Informatics Computing and Statistics, Lancaster University, Lancaster, UK
| | - Winnie Bakali
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Chifundo Salifu
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Allan Zuza
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Mary Charles
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Tamandani Mandula
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Victor Maiden
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Stevie Amos
- Centre for Water, Sanitation, Health and Appropriate Technology Development, Malawi University of Business and Applied Sciences, Blantyre, Malawi
| | - Shevin T Jacob
- Global Health Security Department, Infectious Disease Institute, Makerere University, Kampala, Uganda
| | - Henry Kajumbula
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Lawrence Mugisha
- College of Health Sciences, and College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda; Conservation and Ecosystem Health Alliance, Kampala, Uganda
| | - David Musoke
- Department of Disease Control and Environmental Health, Makerere University, Kampala, Uganda
| | - Rachel Byrne
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas Edwards
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Rebecca Lester
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Nicola Elviss
- Science Group, United Kingdom Health Security Agency, London, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Christopher Jewell
- Centre for Health Informatics Computing and Statistics, Lancaster University, Lancaster, UK
| | - Tracy Morse
- Centre for Water, Sanitation, Health and Appropriate Technology Development, Malawi University of Business and Applied Sciences, Blantyre, Malawi; Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, UK
| | - Nicholas A Feasey
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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6
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Lewis JM, Mphasa M, Banda R, Beale MA, Mallewa J, Anscome C, Zuza A, Roberts AP, Heinz E, Thomson NR, Feasey NA. Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity. Microb Genom 2023; 9:mgen001035. [PMID: 37314322 PMCID: PMC10327512 DOI: 10.1099/mgen.0.001035] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/15/2023] [Indexed: 06/15/2023] Open
Abstract
Escherichia coli is one of the most prevalent Gram-negative species associated with drug resistant infections. Strains that produce extended-spectrum beta-lactamases (ESBLs) or carbapenemases are both particularly problematic and disproportionately impact resource limited healthcare settings where last-line antimicrobials may not be available. A large number of E. coli genomes are now available and have allowed insights into pathogenesis and epidemiology of ESBL E. coli but genomes from sub-Saharan Africa (sSA) are significantly underrepresented. To reduce this gap, we investigated ESBL-producing E. coli colonising adults in Blantyre, Malawi to assess bacterial diversity and AMR determinants and to place these isolates in the context of the wider population structure. We performed short-read whole-genome sequencing of 473 colonising ESBL E. coli isolated from human stool and contextualised the genomes with a previously curated multi-country collection of 10 146 E. coli genomes and sequence type (ST)-specific collections for our three most commonly identified STs. These were the globally successful ST131, ST410 and ST167, and the dominant ESBL genes were bla CTX-M, mirroring global trends. However, 37 % of Malawian isolates did not cluster with any isolates in the curated multicountry collection and phylogenies were consistent with locally spreading monophyletic clades, including within the globally distributed, carbapenemase-associated B4/H24RxC ST410 lineage. A single ST2083 isolate in this collection harboured a carbapenemase gene. Long read sequencing demonstrated the presence of a globally distributed ST410-associated carbapenemase carrying plasmid in this isolate, which was absent from the ST410 strains in our collection. We conclude there is a risk that carbapenem resistance in E. coli could proliferate rapidly in Malawi under increasing selection pressure, and that both ongoing antimicrobial stewardship and genomic surveillance are critical as local carbapenem use increases.
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Affiliation(s)
- Joseph M. Lewis
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Madalitso Mphasa
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Rachel Banda
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Jane Mallewa
- Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Catherine Anscome
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Allan Zuza
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Eva Heinz
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Hinxton, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas A. Feasey
- Malawi-Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- London School of Hygiene and Tropical Medicine, London, UK
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Kibwana UO, Manyahi J, Sandnes HH, Blomberg B, Mshana SE, Langeland N, Roberts AP, Moyo SJ. Fluoroquinolone resistance among fecal extended spectrum βeta lactamases positive Enterobacterales isolates from children in Dar es Salaam, Tanzania. BMC Infect Dis 2023; 23:135. [PMID: 36882712 PMCID: PMC9993647 DOI: 10.1186/s12879-023-08086-2] [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: 09/29/2022] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Fluoroquinolones have been, and continue to be, routinely used for treatment of many bacterial infections. In recent years, most parts of the world have reported an increasing trend of fluoroquinolone resistant (FQR) Gram-negative bacteria. METHODS A cross-sectional study was conducted between March 2017 and July 2018 among children admitted due to fever to referral hospitals in Dar es Salaam, Tanzania. Rectal swabs were used to screen for carriage of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE). ESBL-PE isolates were tested for quinolone resistance by disk diffusion method. Randomly selected fluroquinolone resistant isolates were characterized by using whole genome sequencing. RESULTS A total of 142 ESBL-PE archived isolates were tested for fluoroquinolone resistance. Overall phenotypic resistance to ciprofloxacin, levofloxacin and moxifloxacin was found in 68% (97/142). The highest resistance rate was seen among Citrobacter spp. (100%, 5/5), followed by Klebsiella. pneumoniae (76.1%; 35/46), Escherichia coli (65.6%; 42/64) and Enterobacter spp. (31.9%; 15/47). Whole genome sequencing (WGS) was performed on 42 fluoroquinolone resistant-ESBL producing isolates and revealed that 38/42; or 90.5%, of the isolates carried one or more plasmid mediated quinolone resistance (PMQR) genes. The most frequent PMQR genes were aac(6')-lb-cr (74%; 31/42), followed by qnrB1 (40%; 17/42), oqx, qnrB6 and qnS1. Chromosomal mutations in gyrA, parC and parE were detected among 19/42 isolates, and all were in E. coli. Most of the E. coli isolates (17/20) had high MIC values of > 32 µg/ml for fluoroquinolones. In these strains, multiple chromosomal mutations were detected, and all except three strains had additional PMQR genes. Sequence types, ST131 and ST617 predominated among E. coli isolates, while ST607 was more common out of 12 sequence types detected among the K. pneumoniae. Fluoroquinolone resistance genes were mostly associated with the IncF plasmids. CONCLUSION The ESBL-PE isolates showed high rates of phenotypic resistance towards fluoroquinolones likely mediated by both chromosomal mutations and PMQR genes. Chromosomal mutations with or without the presence of PMQR were associated with high MIC values in these bacteria strains. We also found a diversity of PMQR genes, sequence types, virulence genes, and plasmid located antimicrobial resistance (AMR) genes towards other antimicrobial agents.
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Affiliation(s)
- Upendo O Kibwana
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.
| | - Joel Manyahi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Bjørn Blomberg
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit On Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Stephen E Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit On Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sabrina J Moyo
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,Norwegian National Advisory Unit On Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway.,Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
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8
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Glover RE, Singer AC, Roberts AP, Kirchhelle C. The antibiotic subscription model: fostering innovation or repackaging old drugs? Lancet Microbe 2023; 4:e2-e3. [PMID: 36154717 DOI: 10.1016/s2666-5247(22)00235-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 01/04/2023]
Affiliation(s)
- Rebecca E Glover
- Department of Health Services Research and Policy, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
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9
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Tansirichaiya S, Hutton W, Roberts AP. Functional and Sequence-Specific Screening Protocols for the Detection of Novel Antimicrobial Resistance Genes in Metagenomic DNA. Methods Mol Biol 2023; 2555:51-72. [PMID: 36306078 DOI: 10.1007/978-1-0716-2795-2_4] [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] [Indexed: 03/23/2023]
Abstract
Antimicrobial resistance (AMR) is an increasingly important global challenge for healthcare systems as well as agricultural food production systems. Our ability to prepare for, and respond to, emerging AMR threats is dependent on our knowledge of genes able to confer AMR that are circulating within various environmental, animal, and human microbiomes. Targeted, sequence-specific, detection of AMR genes and functional resistance assays, described here, carried out on metagenomic DNA gives us unique insights into the presence of AMR genes and how these are associated with mobile genetic elements that may be responsible for their dissemination and can also provide important information about the mechanisms of resistance underpinning the phenotype.
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Affiliation(s)
- Supathep Tansirichaiya
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - William Hutton
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
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10
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Cantillon D, Roberts AP. Development and evaluation of TaqMan-based, one-step, real-time RT-PCR assays for pepper mild mottle virus detection for near source tracking and wastewater-based epidemiology validation. PLoS One 2022; 17:e0278784. [PMID: 36534927 PMCID: PMC9762892 DOI: 10.1371/journal.pone.0278784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Emergence of novel human pathogens pose significant challenges to human health as highlighted by the SARS-CoV-2 pandemic. Wastewater based epidemiology (WBE) has previously been employed to identify viral pathogens and outbreaks by testing samples from regional wastewater treatment plants. Near source tracking (NST) allows for more targeted WBE by analysing samples from individual buildings such as schools or even individual floors such as in multi-floor office buildings. Despite the public health advantages of WBE, few strategies exist for optimising NST sampling methodologies. Therefore, we developed a protocol to evaluate virus detection in NST sampling using Pepper Mild Mottle Virus (PMMoV) as a proxy for RNA viruses. PMMoV is the most abundant enteric human associated RNA virus and is present in peppers/pepper-containing foods. Two bespoke TaqMan RT-PCR assays were developed to detect a PMMoV genomic 5' region and a capsid associated gene. To evaluate the protocol against field samples, pepper homogenates were flushed down an in-use toilet (Liverpool School of Tropical Medicine, UK) to spike wastewater with PMMoV on multiple days, and samples collected from two sewage access points to validate NST samplers. These wastewater samples were assessed for PMMoV based on Ct values and results compared to pepper and Tabasco derived PMMoV positive controls. Positive detection of PMMoV was comparable and consistent in ten independent samples across two NST samplers regardless of pepper homogenate spiking. We have developed two novel one step TaqMan assays that amplify both PMMoV targets in viral RNA extractions from peppers, Tabasco, and wastewater samples with cDNA synthesis through to RT-PCR results taking approximately 30 minutes. Pepper homogenate flushing was not required to detect PMMoV in our wastewater samples, however this strategy of flushing PMMoV containing materials outlined here could be valuable in assessing and validating NST in buildings with no previous or current sewage flow.
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Affiliation(s)
- Daire Cantillon
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail:
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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11
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Kirchhelle C, Roberts AP. Embracing the monsters: moving from infection control to microbial management. Lancet Microbe 2022; 3:e806-e807. [PMID: 35964637 DOI: 10.1016/s2666-5247(22)00225-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 01/14/2023]
Affiliation(s)
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK.
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12
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Villacorta Linaza R, Genovezos C, Garner T, Panford-Quainoo E, Roberts AP. Global antimicrobial stewardship and the need for pharmaceutical system strengthening for antimicrobials within a One Health approach. Int J Pharm Pract 2022; 30:175-179. [PMID: 35325142 DOI: 10.1093/ijpp/riac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 05/03/2021] [Accepted: 02/07/2022] [Indexed: 11/14/2022]
Abstract
OBJECTIVES The COVID-19 pandemic has highlighted both the vulnerabilities and the critical role of global pharmaceutical systems in enabling equitable access to medicines. In this personal view, we position the pharmaceutical system as a missed research and investment opportunity that, if integrated properly, would benefit antimicrobial stewardship (AMS) programmes within a One Health approach. KEY FINDINGS The pharmaceutical supply management cycle (PSMC) illustrates the continuous interdependence between four key phases: selection, procurement, distribution and use. Furthermore, a PSMC is subject to external forces of market competition, policy and regulation - across human, animal and environmental health. We present examples of overlap in PSMCs across different One Health sectors and discuss the need for integration within human, animal and environmental health contexts. SUMMARY Despite pharmaceutical systems being fundamental to successful AMS programmes, they are currently neglected and undervalued. Research and investment into pharmaceutical system optimisation and integration into AMS programmes present an opportunity for both high-income countries and low- and middle-income countries to develop responsible, comparable and international AMS innovations and interventions.
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Affiliation(s)
- Rocio Villacorta Linaza
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | | | - Timothy Garner
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Edwin Panford-Quainoo
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
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13
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Edwards T, Heinz E, van Aartsen J, Howard A, Roberts P, Corless C, Fraser AJ, Williams CT, Bulgasim I, Cuevas LE, Parry CM, Roberts AP, Adams ER, Mason J, Hubbard ATM. Piperacillin/tazobactam-resistant, cephalosporin-susceptible Escherichia coli bloodstream infections are driven by multiple acquisition of resistance across diverse sequence types. Microb Genom 2022; 8. [PMID: 35404783 PMCID: PMC9453079 DOI: 10.1099/mgen.0.000789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Resistance to piperacillin/tazobactam (TZP) in Escherichia coli has predominantly been associated with mechanisms that confer resistance to third-generation cephalosporins. Recent reports have identified E. coli strains with phenotypic resistance to piperacillin/tazobactam but susceptibility to third-generation cephalosporins (TZP-R/3GC-S). In this study we sought to determine the genetic diversity of this phenotype in E. coli (n=58) isolated between 2014–2017 at a single tertiary hospital in Liverpool, UK, as well as the associated resistance mechanisms. We compare our findings to a UK-wide collection of invasive E. coli isolates (n=1509) with publicly available phenotypic and genotypic data. These data sets included the TZP-R/3GC-S phenotype (n=68), and piperacillin/tazobactam and third-generation cephalosporin-susceptible (TZP-S/3GC-S, n=1271) phenotypes. The TZP-R/3GC-S phenotype was displayed in a broad range of sequence types, which was mirrored in the same phenotype from the UK-wide collection, and the overall diversity of invasive E. coli isolates. The TZP-R/3GC-S isolates contained a diverse range of plasmids, indicating multiple acquisition events of TZP resistance mechanisms rather than clonal expansion of a particular plasmid or sequence type. The putative resistance mechanisms were equally diverse, including hyperproduction of TEM-1, either via strong promoters or gene amplification, carriage of inhibitor-resistant β-lactamases, and an S133G blaCTX-M-15 mutation detected for the first time in clinical isolates. Several of these mechanisms were present at a lower abundance in the TZP-S/3GC-S isolates from the UK-wide collection, but without the associated phenotypic resistance to TZP. Eleven (19%) of the isolates had no putative mechanism identified from the genomic data. Our findings highlight the complexity of this cryptic phenotype and the need for continued phenotypic monitoring, as well as further investigation to improve detection and prediction of the TZP-R/3GC-S phenotype from genomic data.
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Affiliation(s)
- Thomas Edwards
- Centre for Drug and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Eva Heinz
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Jon van Aartsen
- Liverpool University Hospital Foundation Trust, Prescot street, Liverpool, L7 8XP, UK
| | - Alex Howard
- Liverpool University Hospital Foundation Trust, Prescot street, Liverpool, L7 8XP, UK
| | - Paul Roberts
- Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton WV1 1LY, UK
- Liverpool University Hospital Foundation Trust, Prescot street, Liverpool, L7 8XP, UK
| | - Caroline Corless
- Liverpool University Hospital Foundation Trust, Prescot street, Liverpool, L7 8XP, UK
| | - Alice J. Fraser
- Centre for Drug and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Christopher T. Williams
- Centre for Drug and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Issra Bulgasim
- Centre for Drug and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Luis E. Cuevas
- Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Christopher M. Parry
- Alder Hey Children’s NHS Foundation Trust, Liverpool, L12 2AP, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Emily R. Adams
- Centre for Drug and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Jenifer Mason
- Liverpool University Hospital Foundation Trust, Prescot street, Liverpool, L7 8XP, UK
| | - Alasdair T. M. Hubbard
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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14
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Manyahi J, Moyo SJ, Kibwana U, Goodman RN, Allman E, Hubbard ATM, Blomberg B, Langeland N, Roberts AP. First identification of bla
NDM-5 producing Escherichia coli from neonates and a HIV infected adult in Tanzania. J Med Microbiol 2022; 71. [PMID: 35225760 PMCID: PMC8941953 DOI: 10.1099/jmm.0.001513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Introduction. Carbapenem-resistant members of the family Enterobacteriaceae are emerging as a global public-health threat and cause substantial challenges in clinical practice. Gap Statement. There is a need for increased and continued genomic surveillance of antimicrobial resistance genes globally in order to detect outbreaks and dissemination of clinically important resistance genes and their associated mobile genetic elements in human pathogens. Aim. To describe the resistance mechanisms of carbapenem-resistant Escherichia coli. Methods. Rectal swabs from neonates and newly diagnosed human immunodeficiency virus (HIV) infected adults were collected between April 2017 and May 2018 and screened for faecal carriage of carbapenamases and OXA-48 producing members of the family Enterobacteriaceae. Bacterial isolates were identified using matrix assisted laser desorption ionization time of flight mass spectrometry. Antimicrobial susceptibility testing was performed by E-test. Whole genomes of carbapenem-resistant E. coli were investigated using a hybrid assembly of Illumina and Oxford Nanopore Technologies sequencing reads. Results. Three carbapenem-resistant E. coli were detected, two from neonates and one from an HIV infected adult. All three isolates carried blaNDM-5. Two E. coli from neonates belonged to ST167 and blaNDM-5 co-existed with blaCTX-M-15 and blaOXA-01, and all were carried on IncFIA type plasmids. The E. coli from the HIV infected adult belonged to ST2083, and carried blaNDM-5 on an IncX3 type plasmid and blaCMY-42 on an IncI type plasmid. All blaNDM-5 carrying plasmids contained conjugation related genes. In addition, E. coli from the HIV infected adult carried three more plasmid types; IncFIA, IncFIB and Col(BS512). One E. coli from a neonate also carried one extra plasmid Col(BS512). All three E. coli harboured resistance genes to fluoroquinolone, aminoglycosides, sulfamethoxazole, trimethoprim, macrolides and tetracycline, carried on the IncFIA type plasmid. Furthermore, E. coli from the neonates carried a chloramphenicol resistance gene (catB3), also on the IncFIA plasmid. All three isolates were susceptible to colistin. Conclusion. This is the first report, to our knowledge, from Tanzania detecting blaNDM-5 producing E. coli. The carbapenemase gene was carried on an IncFIA and IncX3 type plasmids. Our findings highlight the urgent need for a robust antimicrobial resistance (AMR) surveillance system to monitor and rapidly report on the incidence and spread of emerging resistant bacteria in Tanzania.
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Affiliation(s)
- Joel Manyahi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Norwegian National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Sabrina J. Moyo
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania
| | - Upendo Kibwana
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania
| | - Richard N. Goodman
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Ellie Allman
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Alasdair T. M. Hubbard
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Bjørn Blomberg
- Norwegian National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nina Langeland
- Norwegian National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
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15
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Affiliation(s)
- Rebecca E Glover
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Claas Kirchhelle
- University College Dublin, Dublin, Ireland
- Oxford Martin Schoool, Oxford, UK
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16
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Cocker D, Sammarro M, Chidziwisano K, Elviss N, Jacob ST, Kajumbula H, Mugisha L, Musoke D, Musicha P, Roberts AP, Rowlingson B, Singer AC, Byrne RL, Edwards T, Lester R, Wilson C, Hollihead B, Thomson N, Jewell CP, Morse T, Feasey N. Drivers of Resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs). Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17581.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In sub-Saharan Africa (sSA), there is high morbidity and mortality from severe bacterial infection and this is compounded by antimicrobial resistance, in particular, resistance to 3rd-generation cephalosporins. This resistance is typically mediated by extended-spectrum beta lactamases (ESBLs). To interrupt ESBL transmission it will be important to investigate how human behaviour, water, sanitation, and hygiene (WASH) practices, environmental contamination, and antibiotic usage in both urban and rural settings interact to contribute to transmission of ESBL E. coli and ESBL K. pneumoniae between humans, animals, and the environment. Here we present the protocol for the Drivers of Resistance in Uganda and Malawi (DRUM) Consortium, in which we will collect demographic, geospatial, clinical, animal husbandry and WASH data from a total of 400 households in Uganda and Malawi. Longitudinal human, animal and environmental sampling at each household will be used to isolate ESBL E. coli and ESBL K. pneumoniae. This will be complimented by a Risks, Attitudes, Norms, Abilities and Self-Regulation (RANAS) survey and structured observations to understand the contextual and psychosocial drivers of regional WASH practices. Bacterial isolates and plate sweeps will be further characterised using a mixture of short-,long-read and metagenomic whole-genome sequencing. These datasets will be integrated into agent-based models to describe the transmission of EBSL resistance in Uganda and Malawi and allow us to inform the design of interventions for interrupting transmission of ESBL-bacteria.
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17
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Glover RE, Singer AC, Roberts AP, Kirchhelle C. NIMble innovation—a networked model for public antibiotic trials. The Lancet Microbe 2021; 2:e637-e644. [DOI: 10.1016/s2666-5247(21)00182-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/12/2022] Open
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18
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Rodríguez-Baño J, Rossolini GM, Schultsz C, Tacconelli E, Murthy S, Ohmagari N, Holmes A, Bachmann T, Goossens H, Canton R, Roberts AP, Henriques-Normark B, Clancy CJ, Huttner B, Fagerstedt P, Lahiri S, Kaushic C, Hoffman SJ, Warren M, Zoubiane G, Essack S, Laxminarayan R, Plant L. Key considerations on the potential impacts of the COVID-19 pandemic on antimicrobial resistance research and surveillance. Trans R Soc Trop Med Hyg 2021; 115:1122-1129. [PMID: 33772597 PMCID: PMC8083707 DOI: 10.1093/trstmh/trab048] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/23/2021] [Accepted: 03/04/2021] [Indexed: 01/08/2023] Open
Abstract
Antibiotic use in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients during the COVID-19 pandemic has exceeded the incidence of bacterial coinfections and secondary infections, suggesting inappropriate and excessive prescribing. Even in settings with established antimicrobial stewardship (AMS) programmes, there were weaknesses exposed regarding appropriate antibiotic use in the context of the pandemic. Moreover, antimicrobial resistance (AMR) surveillance and AMS have been deprioritised with diversion of health system resources to the pandemic response. This experience highlights deficiencies in AMR containment and mitigation strategies that require urgent attention from clinical and scientific communities. These include the need to implement diagnostic stewardship to assess the global incidence of coinfections and secondary infections in COVID-19 patients, including those by multidrug-resistant pathogens, to identify patients most likely to benefit from antibiotic treatment and identify when antibiotics can be safely withheld, de-escalated or discontinued. Long-term global surveillance of clinical and societal antibiotic use and resistance trends is required to prepare for subsequent changes in AMR epidemiology, while ensuring uninterrupted supply chains and preventing drug shortages and stock outs. These interventions present implementation challenges in resource-constrained settings, making a case for implementation research on AMR. Knowledge and support for these practices will come from internationally coordinated, targeted research on AMR, supporting the preparation for future challenges from emerging AMR in the context of the current COVID-19 pandemic or future pandemics.
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Affiliation(s)
- Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Sevilla, Spain
- Departamento de Medicina, Universidad de Sevilla, Sevilla, Spain
- Instituto de Biomedicina de Sevilla (IBiS), Sevilla, Spain
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Constance Schultsz
- Department of Global Health - AIGHD Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Srinivas Murthy
- BC Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Alison Holmes
- Department of Medicine, Faculty of Medicine, Imperial College London, London, UK
| | - Till Bachmann
- The University of Edinburgh, Edinburgh Medical School, Division of Infection and Pathway Medicine, UK
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Rafael Canton
- Servicio de Microbiología. Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | - Benedikt Huttner
- Division of Infectious Diseases, Geneva, University Hospitals, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Shawon Lahiri
- JPIAMR Secretariat, Swedish Research Council, Stockholm, Sweden
| | - Charu Kaushic
- Institute of Infection and Immunity, Canadian Institutes of Health Research
- McMaster Immunology Research Center, Dept Pathology and Mol. Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Steven J Hoffman
- Global Strategy Lab, Dahdaleh Institute for Global Health Research, Faculty of Health and Osgoode Hall Law School, York University, Toronto, Canada
| | - Margo Warren
- Access to Medicine Foundation, Amsterdam, the Netherlands
| | - Ghada Zoubiane
- International Centre for Antimicrobial Resistance Solutions (ICARS), Copenhagen, Denmark
| | - Sabiha Essack
- International Centre for Antimicrobial Resistance Solutions (ICARS), Copenhagen, Denmark
- Antimicrobial Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | | | - Laura Plant
- Institute of Infection and Immunity, Canadian Institutes of Health Research
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19
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Yang Y, Yang Y, Chen G, Lin M, Chen Y, He R, Galvão KN, El-Gawad El-Sayed Ahmed MA, Roberts AP, Wu Y, Zhong LL, Liang X, Qin M, Ding X, Deng W, Huang S, Li HY, Dai M, Chen DQ, Zhang L, Liao K, Xia Y, Tian GB. Molecular characterization of carbapenem-resistant and virulent plasmids in Klebsiella pneumoniae from patients with bloodstream infections in China. Emerg Microbes Infect 2021; 10:700-709. [PMID: 33739229 PMCID: PMC8023600 DOI: 10.1080/22221751.2021.1906163] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 01/04/2023]
Abstract
Bloodstream infections (BSIs) caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) are potentially life-threatening and an urgent threat to public health. The present study aims to clarify the characteristics of carbapenemase-encoding and virulent plasmids, and their interactions with the host bacterium. A total of 425 Kp isolates were collected from the blood of BSI patients from nine Chinese hospitals, between 2005 and 2019. Integrated epidemiological and genomic data showed that ST11 and ST307 Kp isolates were associated with nosocomial outbreak and transmission. Comparative analysis of 147 Kp genomes and 39 completely assembled chromosomes revealed extensive interruption of acrR by ISKpn26 in all Kp carbapenemase-2 (KPC-2)-producing ST11 Kp isolates, leading to activation of the AcrAB-Tolc multidrug efflux pump and a subsequent reduction in susceptibility to the last-resort antibiotic tigecycline and six other antibiotics. We described 29 KPC-2 plasmids showing diverse structures, two virulence plasmids in two KPC-2-producing Kp, and two novel multidrug-resistant (MDR)-virulent plasmids. This study revealed a multifactorial impact of KPC-2 plasmid on Kp, which may be associated with nosocomial dissemination of MDR isolates.
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Affiliation(s)
- Yongqiang Yang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People's Republic of China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yanxian Yang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People's Republic of China
| | - Guanping Chen
- Sun Yat-sen University School of Medicine, Guangzhou, People's Republic of China
| | - Minmin Lin
- Department of Respiratory Medicine, the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, People's Republic of China
| | - Yuan Chen
- Sun Yat-sen University School of Medicine, Guangzhou, People's Republic of China
| | - Ruowen He
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People's Republic of China
| | - Klibs N Galvão
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Mohamed Abd El-Gawad El-Sayed Ahmed
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People's Republic of China.,Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Cairo, Egypt
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, UK.,Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, UK
| | - Yiping Wu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People's Republic of China
| | - Lan-Lan Zhong
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People's Republic of China
| | - Xiaoxue Liang
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, People's Republic of China
| | - Mingyang Qin
- Basic Medical College, Xinxiang Medical University, Xinxiang, People's Republic of China
| | - Xin Ding
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Wenbin Deng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Songyin Huang
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Hong-Yu Li
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Min Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, People's Republic of China
| | - Ding-Qiang Chen
- Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Liyan Zhang
- Department of Clinical Laboratory, Guangdong Provincial People's Hospital / Guangdong Academy of Medical Sciences, Guangzhou, People's Republic of China
| | - Kang Liao
- Department of Clinical Laboratory, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yong Xia
- Department of Clinical Laboratory Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People's Republic of China.,School of Medicine, Xizang Minzu University, Xianyang, People's Republic of China
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20
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Johansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP, Petersen TN. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother 2021; 76:101-109. [PMID: 33009809 PMCID: PMC7729385 DOI: 10.1093/jac/dkaa390] [Citation(s) in RCA: 224] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/19/2020] [Indexed: 11/17/2022] Open
Abstract
Objectives Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. Methods The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids. Results MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica. Conclusions MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/.
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Affiliation(s)
- Markus H K Johansson
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Supathep Tansirichaiya
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas N Petersen
- National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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21
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Klug DM, Idiris FIM, Blaskovich MAT, von Delft F, Dowson CG, Kirchhelle C, Roberts AP, Singer AC, Todd MH. There is no market for new antibiotics: this allows an open approach to research and development. Wellcome Open Res 2021; 6:146. [PMID: 34250265 PMCID: PMC8237369 DOI: 10.12688/wellcomeopenres.16847.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 11/20/2022] Open
Abstract
There is an increasingly urgent need for new antibiotics, yet there is a significant and persistent economic problem when it comes to developing such medicines. The problem stems from the perceived need for a “market” to drive commercial antibiotic development. In this article, we explore abandoning the market as a prerequisite for successful antibiotic research and development. Once one stops trying to fix a market model that has stopped functioning, one is free to carry out research and development (R&D) in ways that are more openly collaborative, a mechanism that has been demonstrably effective for the R&D underpinning the response to the COVID pandemic. New “open source” research models have great potential for the development of medicines for areas of public health where the traditional profit-driven model struggles to deliver. New financial initiatives, including major push/pull incentives, aimed at fixing the broken antibiotics market provide one possible means for funding an openly collaborative approach to drug development. We argue that now is therefore the time to evaluate, at scale, whether such methods can deliver new medicines through to patients, in a timely manner.
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Affiliation(s)
- Dana M Klug
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | | | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Lucia, Queensland, 4072, Australia
| | - Frank von Delft
- Centre for Medicines Discovery, The University of Oxford, Oxford, OX3 7DQ, UK.,Diamond Light Source Ltd, Didcot, OX11 0QX, UK.,Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | | | | | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Andrew C Singer
- UK Centre for Ecology & Hydrology, Wallingford, OX10 8BB, UK
| | - Matthew H Todd
- School of Pharmacy, University College London, London, WC1N 1AX, UK
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22
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Abd El-gawad El-sayed Ahmed M, Yang Y, Yang Y, Yan B, Chen G, Hassan RM, Zhong L, Chen Y, Roberts AP, Wu Y, He R, Liang X, Qin M, Dai M, Zhang L, Li H, Fan Y, Xu L, Tian G. Emergence of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Co-harbouring a blaNDM-1-carrying Virulent Plasmid and a blaKPC-2-carrying Plasmid in an Egyptian Hospital.. [DOI: 10.1101/2021.02.26.433140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
ABSTRACTThe emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in Egyptian hospitals has been reported. However, the genetic basis and the analysis of the plasmids associated with CR-hypervirulent-KP (CR-HvKP) in Egypt are not presented. Therefore, we attempt to decipher the plasmids sequences, which are responsible for transferring the determinants of carbapenem-resistance, particularly the blaNDM-1 and blaKPC-2. Out of 34 K. pneumoniae isolates collected from two tertiary hospitals in Egypt, 31 were CRKP. Whole-genome sequencing revealed that our isolates were related to 13 different sequence types (STs). The most prevalent ST was ST101, followed by ST383, and ST11. Among the CRKP isolates, one isolate named EBSI036 has been reassessed using Nanopore sequencing. Genetic environment analysis showed that EBSI036 carried 20 antibiotic resistance genes and was identified as CR-HvKP strain, it harboured four plasmids, namely; pEBSI036-1-NDM-VIR, pEBSI036-2-KPC, pEBSI036-3, and pEBSI036-4. The two carbapenemase genes, blaNDM-1 and blaKPC-2, were located on plasmids pEBSI036-1-NDM-VIR and pEBSI036-2-KPC, respectively. The IncFIB:IncHI1B hybrid plasmid pEBSI036-1-NDM-VIR also carried some virulence factors, including regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD, iutA). Thus, we set out this study to analyse in-depth the genetic basis of pEBSI036-1-NDM-VIR and pEBSI036-2-KPC plasmids. We reported for the first time a high-risk clone ST11 KL47 serotype of CR-HvKP strain isolated from the blood of a 60-year-old hospitalised female patient from the ICU in a tertiary-care hospital in Egypt, which showed the cohabitation of a novel hybrid plasmid coharbouring the blaNDM-1 and virulence genes, besides a blaKPC-2-carrying plasmid.IMPORTANCECRKP had been registered in the critical priority tier by the World Health Organization and became a significant menace to public health. Therefore, we set out this study to analyse in-depth the genetic basis of pEBSI036-1-NDM-VIR and pEBSI036-2-KPC plasmids. Herein, we reported for the first time (to the best of our knowledge) a high-risk clone ST11 KL47 serotype of CR-HvKP strain isolated from the blood of a 60-year-old hospitalised female patient in a tertiary-care hospital from the ICU in Egypt, which showed the cohabitation of a novel hybrid plasmid co-harbouring the blaNDM-1 and virulence genes, besides a blaKPC-2-carrying plasmid. Herein, the high rate of CRKP might be due to the continuous usage of carbapenems as empirical therapy, besides the failure to implement an antibiotic stewardship program in Egyptian hospitals. Thus, this study serves to alert the contagious disease clinicians to the presence of hypervirulence in CRKP isolates in Egyptian hospitals.
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23
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Rodríguez-Baño J, Rossolini GM, Schultsz C, Tacconelli E, Murthy S, Ohmagari N, Holmes A, Bachmann T, Goossens H, Canton R, Roberts AP, Henriques-Normark B, Clancy CJ, Huttner B, Fagerstedt P, Lahiri S, Kaushic C, Hoffman SJ, Warren M, Zoubiane G, Essack S, Laxminarayan R, Plant L. Antimicrobial resistance research in a post-pandemic world: Insights on antimicrobial resistance research in the COVID-19 pandemic. J Glob Antimicrob Resist 2021; 25:5-7. [PMID: 33662647 PMCID: PMC7919515 DOI: 10.1016/j.jgar.2021.02.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 01/15/2021] [Accepted: 02/16/2021] [Indexed: 12/23/2022] Open
Abstract
Antibiotics have been used excessively in hospitalised COVID-19 patients. COVID-19 has caused major disruptions to antimicrobial resistance surveillance and research. Global data on the use of antibiotics during the COVID-19 pandemic are needed. Antimicrobial resistance requires continued public and political engagement.
Antimicrobial resistance must be recognised as a global societal priority - even in the face of the worldwide challenge of the COVID-19 pandemic. COVID-19 has illustrated the vulnerability of our healthcare systems in co-managing multiple infectious disease threats as resources for monitoring and detecting, and conducting research on antimicrobial resistance have been compromised during the pandemic. The increased awareness of the importance of infectious diseases, clinical microbiology and infection control and lessons learnt during the COVID-19 pandemic should be exploited to ensure that emergence of future infectious disease threats, including those related to AMR, are minimised. Harnessing the public understanding of the relevance of infectious diseases towards the long-term pandemic of AMR could have major implications for promoting good practices about the control of AMR transmission.
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Affiliation(s)
- Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain; Departamento de Medicina, Universidad de Sevilla, Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III. Madrid, Spain
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Constance Schultsz
- Department of Global Health-AIGHD Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Srinivas Murthy
- BC Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Alison Holmes
- Department of Medicine, Faculty of Medicine, Imperial College London, London, UK
| | - Till Bachmann
- The University of Edinburgh, Edinburgh Medical School, Division of Infection and Pathway Medicine, The Chancellor's Building, Edinburgh, UK
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Rafael Canton
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Cornelius J Clancy
- University of Pittsburgh, 3550 Terrace St., Scaife Hall 867, Pittsburgh, PA, USA
| | - Benedikt Huttner
- Division of Infectious Diseases, Geneva University Hospitals, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Shawon Lahiri
- JPIAMR Secretariat, Swedish Research Council, Stockholm, Sweden
| | - Charu Kaushic
- Institute of Infection and Immunity, Canadian Institutes of Health Research, Canada; McMaster Immunology Research Center, Department Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Steven J Hoffman
- Global Strategy Lab, Dahdaleh Institute for Global Health Research, School of Global Health and Osgoode Hall Law School, York University, Toronto, Canada
| | - Margo Warren
- Access to Medicine Foundation, Naritaweg 227-A, 1043 CB, Amsterdam, The Netherlands
| | - Ghada Zoubiane
- International Centre for Antimicrobial Resistance Solutions (ICARS), Copenhagen, Denmark
| | - Sabiha Essack
- International Centre for Antimicrobial Resistance Solutions (ICARS), Copenhagen, Denmark; Antimicrobial Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | | | - Laura Plant
- Institute of Infection and Immunity, Canadian Institutes of Health Research, Canada.
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24
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Wu P, Tu B, Liang J, Guo S, Cao N, Chen S, Luo Z, Li J, Zheng W, Tang X, Li D, Xu X, Liu W, Zheng X, Sheng Z, Roberts AP, Zhang K, Hong WD. Synthesis and biological evaluation of pentacyclic triterpenoid derivatives as potential novel antibacterial agents. Bioorg Chem 2021; 109:104692. [PMID: 33626454 DOI: 10.1016/j.bioorg.2021.104692] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 01/11/2023]
Abstract
A series of ursolic acid (UA), oleanolic acid (OA) and 18β-glycyrrhetinic acid (GA) derivatives were synthesized by introducing a range of substituted aromatic side-chains at the C-2 position after the hydroxyl group at C-3 position was oxidized. Their antibacterial activities were evaluated in vitro against a panel of four Staphylococcus spp. The results revealed that the introduction of aromatic side-chains at the C-2 position of GA led to the discovery of potent triterpenoid derivatives for inhibition of both drug sensitive and resistant S. aureus, while the other two series derivatives of UA and OA showed no significant antibacterial activity even at high concentrations. In particular, GA derivative 33 showed good potency against all four Staphylococcus spp. (MIC = 1.25-5 μmol/L) with acceptable pharmacokinetics properties and low cytotoxicity in vitro. Molecular docking was also performed using S. aureus DNA gyrase to rationalize the observed antibacterial activity. This series of GA derivatives has strong potential for the development of a new type of triterpenoid antibacterial agent.
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Affiliation(s)
- Panpan Wu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; Department of Pharmaceutical Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Borong Tu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Jinfeng Liang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Shengzhu Guo
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Nana Cao
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Silin Chen
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Zhujun Luo
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Jiahao Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Wende Zheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Xiaowen Tang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Dongli Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Xuetao Xu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Wenfeng Liu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Xi Zheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China.
| | - Zhaojun Sheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Adam P Roberts
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom.
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; Department of Pharmaceutical Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, PR China.
| | - Weiqian David Hong
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom.
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25
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Moyo SJ, Manyahi J, Hubbard ATM, Byrne RL, Masoud NS, Aboud S, Manji K, Blomberg B, Langeland N, Roberts AP. Molecular characterisation of the first New Delhi metallo-β-lactamase 1-producing Acinetobacter baumannii from Tanzania. Trans R Soc Trop Med Hyg 2021; 115:1080-1085. [PMID: 33503660 PMCID: PMC8417080 DOI: 10.1093/trstmh/traa173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Received: 09/03/2020] [Revised: 12/01/2020] [Accepted: 12/22/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND We aimed to characterise the genetic determinants and context of two meropenem-resistant clinical isolates of Acinetobacter baumannii isolated from children hospitalised with bloodstream infections in Dar es Salaam, Tanzania. METHODS Antimicrobial susceptibility was determined by disc diffusion E-test and broth microdilution. Genomes were completed using a hybrid assembly of Illumina and Oxford Nanopore Technologies sequencing reads and characterisation of the genetic context of resistance genes, multi-locus sequence types (STs) and phylogenetic analysis was determined bioinformatically. RESULTS Twelve A. baumannii were isolated from 2226 blood cultures, two of which were meropenem-resistant. The two meropenem-resistant isolates, belonging to distinct STs, ST374 and ST239, were found to harbour blaNDM-1, which was chromosomally located in isolate DT0544 and plasmid-located in isolate DT01139. The genetic environment of blaNDM-1 shows the association of insertion sequence ISAba125 with blaNDM-1 in both isolates. Both isolates also harboured genes conferring resistance to other β-lactams, aminoglycosides and cotrimoxazole. CONCLUSIONS This is the first report of New Delhi metallo-β-lactamase-producing isolates of A. baumannii from Tanzania. The genetic context of blaNDM-1 provides further evidence of the importance of ISAba125 in the spread of blaNDM-1 in A. baumannii. Local surveillance should be strengthened to keep clinicians updated on the incidence of these and other multidrug-resistant and difficult-to-treat bacteria.
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Affiliation(s)
- Sabrina J Moyo
- Depart ment of Clinical Science, University of Bergen, Norway.,Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania.,Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Joel Manyahi
- Depart ment of Clinical Science, University of Bergen, Norway.,Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania
| | - Alasdair T M Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Rachel L Byrne
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Nahya Salim Masoud
- Department of Paediatrics and Child Health, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania
| | - Said Aboud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania
| | - Karim Manji
- Department of Paediatrics and Child Health, Muhimbili University of Health and Allied Sciences, MUHAS, Dar es Salaam, Tanzania
| | - Bjørn Blomberg
- Depart ment of Clinical Science, University of Bergen, Norway.,Norwegian National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Nina Langeland
- Depart ment of Clinical Science, University of Bergen, Norway.,Norwegian National Advisory Unit for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
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26
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Abstract
A large proportion of bacteria, from a multitude of environments, are not yet able to be grown in the laboratory, and therefore microbiological and molecular biological investigations of these bacteria are challenging. A way to circumvent this challenge is to analyze the metagenome, the entire collection of DNA molecules that can be isolated from a particular environment or sample. This collection of DNA molecules can be sequenced and assembled to determine what is present and infer functional potential, or used as a PCR template to detect known target DNA and potentially unknown regions of DNA nearby those targets; however assigning functions to new or conserved hypothetical, functionally cryptic, genes is difficult. Functional metagenomics allows researchers to determine which genes are responsible for selectable phenotypes, such as resistance to antimicrobials and metabolic capabilities, without the prerequisite needs to grow the bacteria containing those genes or to already know which genes are of interest. It is estimated that a third of the resident species of the human oral cavity is not yet cultivable and, together with the ease of sample acquisition, makes this metagenome particularly suited to functional metagenomic studies. Here we describe the methodology related to the collection of saliva samples, extraction of metagenomic DNA, construction of metagenomic libraries, as well as the description of functional assays that have previously led to the identification of new genes conferring antimicrobial resistance.
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Affiliation(s)
- Supathep Tansirichaiya
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway.
| | - Liam J Reynolds
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute and UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
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27
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Hubbard ATM, Mason J, Roberts P, Parry CM, Corless C, van Aartsen J, Howard A, Bulgasim I, Fraser AJ, Adams ER, Roberts AP, Edwards T. Piperacillin/tazobactam resistance in a clinical isolate of Escherichia coli due to IS26-mediated amplification of bla TEM-1B. Nat Commun 2020; 11:4915. [PMID: 33004811 PMCID: PMC7530762 DOI: 10.1038/s41467-020-18668-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
A phenotype of Escherichia coli and Klebsiella pneumoniae, resistant to piperacillin/tazobactam (TZP) but susceptible to carbapenems and 3rd generation cephalosporins, has emerged. The resistance mechanism associated with this phenotype has been identified as hyperproduction of the β-lactamase TEM. However, the mechanism of hyperproduction due to gene amplification is not well understood. Here, we report a mechanism of gene amplification due to a translocatable unit (TU) excising from an IS26-flanked pseudo-compound transposon, PTn6762, which harbours blaTEM-1B. The TU re-inserts into the chromosome adjacent to IS26 and forms a tandem array of TUs, which increases the copy number of blaTEM-1B, leading to TEM-1B hyperproduction and TZP resistance. Despite a significant increase in blaTEM-1B copy number, the TZP-resistant isolate does not incur a fitness cost compared to the TZP-susceptible ancestor. This mechanism of amplification of blaTEM-1B is an important consideration when using genomic data to predict susceptibility to TZP.
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MESH Headings
- Anti-Bacterial Agents/pharmacology
- Anti-Bacterial Agents/therapeutic use
- Chromosomes, Bacterial/genetics
- DNA Transposable Elements/genetics
- DNA, Bacterial/genetics
- Drug Resistance, Multiple, Bacterial/genetics
- Drug Therapy, Combination/methods
- Escherichia coli/drug effects
- Escherichia coli/genetics
- Escherichia coli/isolation & purification
- Escherichia coli Infections/drug therapy
- Escherichia coli Infections/microbiology
- Escherichia coli Proteins/genetics
- Gene Amplification
- Gene Expression Regulation, Bacterial
- Genome, Bacterial/genetics
- Humans
- Microbial Sensitivity Tests
- Piperacillin/pharmacology
- Piperacillin/therapeutic use
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/genetics
- Tazobactam/pharmacology
- Tazobactam/therapeutic use
- Whole Genome Sequencing
- beta-Lactamases/genetics
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Affiliation(s)
- Alasdair T M Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Jenifer Mason
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Paul Roberts
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
- Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Building MA, Wulfruna Street, Wolverhampton, WV1 1LY, UK
| | - Christopher M Parry
- Alder Hey Children's NHS Foundation Trust, Eaton Road, Liverpool, L12 2AP, UK
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, L69 7BE, UK
- Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- School of Tropical Medicine and Global Health, University of Nagasaki, Nagasaki, Japan
| | - Caroline Corless
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Jon van Aartsen
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Alex Howard
- Liverpool University Hospital Foundation Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Issra Bulgasim
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Alice J Fraser
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Emily R Adams
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Thomas Edwards
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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28
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Botelho J, Mourão J, Roberts AP, Peixe L. Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria. Microb Genom 2020; 6:mgen000424. [PMID: 32841111 PMCID: PMC7660259 DOI: 10.1099/mgen.0.000424] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/02/2020] [Indexed: 12/24/2022] Open
Abstract
Carbapenemases inactivate most β-lactam antibiotics, including carbapenems, and have frequently been reported among Enterobacteriaceae, Acinetobacter spp. and Pseudomonas spp. Traditionally, the horizontal gene transfer of carbapenemase-encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted an in silico analysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182 663). We detected 17 520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically relevant bacteria, such as Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFT and MPFF classes and often encode resistance to other antibiotics (e.g. aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.
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Affiliation(s)
- João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Present address: Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany; Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany
| | - Joana Mourão
- University of Coimbra, Center for Innovative Biomedicine and Biotechnology, Coimbra, Portugal
- University of Coimbra, Center for Neuroscience and Cell Biology, Coimbra, Portugal
- University of Coimbra, Institute for Interdisciplinary Research, Coimbra, Portugal
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Tansirichaiya S, Moyo SJ, Al-Haroni M, Roberts AP. Capture of a novel, antibiotic resistance encoding, mobile genetic element from Escherichia coli using a new entrapment vector. J Appl Microbiol 2020; 130:832-842. [PMID: 32881179 DOI: 10.1111/jam.14837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 07/21/2020] [Revised: 08/17/2020] [Accepted: 08/24/2020] [Indexed: 11/30/2022]
Abstract
AIMS Antimicrobial resistance genes (ARGs) are often associated with mobile genetic elements (MGEs), which facilitate their movement within and between bacterial populations. Detection of mobility is therefore important to understand the dynamics of MGE dissemination and their associated genes, especially in resistant clinical isolates that often have multiple ARGs associated with MGEs. Therefore, this study aimed to develop an entrapment vector to capture active MGEs and ARGs in clinical isolates of Escherichia coli. METHODS AND RESULTS We engineered an entrapment vector, called pBACpAK, to capture MGEs in clinical E. coli isolates. It contains a cI-tetA positive selection cartridge in which the cI gene encodes a repressor that inhibits the expression of tetA. Therefore, any disruption of cI, for example, by insertion of a MGE, will allow tetA to be expressed and result in a selectable tetracycline-resistant phenotype. The pBACpAK was introduced into clinical E. coli isolates and grown on tetracycline-containing agar to select for clones with the insertion of MGEs into the entrapment vector. Several insertion sequences were detected within pBACpAK, including IS26, IS903B and ISSbo1. A novel translocatable unit (TU), containing IS26 and dfrA8 was also captured, and dfrA8 was shown to confer trimethoprim resistance when it was cloned into E. coli DH5α. CONCLUSIONS The entrapment vector, pBACpAK was developed and shown to be able to capture MGEs and their associated ARGs from clinical E. coli isolates. We have captured, for the first time, a TU encoding antibiotic resistance. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first time that a TU and associated resistance gene has been captured from clinical E. coli isolates using an entrapment vector. The pBACpAK has the potential to be used not only as a tool to capture MGEs in clinical E. coli isolates, but also to study dynamics, frequency and potentiators of mobility for MGEs.
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Affiliation(s)
- S Tansirichaiya
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway.,Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway.,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - S J Moyo
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - M Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway.,Centre for New Antimicrobial Strategies, UiT the Arctic University of Norway, Tromsø, Norway
| | - A P Roberts
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
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Moyo SJ, Manyahi J, Blomberg B, Tellevik MG, Masoud NS, Aboud S, Manji K, Roberts AP, Hanevik K, Mørch K, Langeland N. Bacteraemia, Malaria, and Case Fatality Among Children Hospitalized With Fever in Dar es Salaam, Tanzania. Front Microbiol 2020; 11:2118. [PMID: 33013772 PMCID: PMC7511546 DOI: 10.3389/fmicb.2020.02118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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] [Received: 05/04/2020] [Accepted: 08/11/2020] [Indexed: 12/31/2022] Open
Abstract
Background Febrile illness is the commonest cause of hospitalization in children <5 years in sub-Saharan Africa, and bacterial bloodstream infections and malaria are major causes of death. Methods From March 2017 to July 2018, we enrolled 2,226 children aged 0–5 years hospitalized due to fever in four major public hospitals of Dar es Salaam, namely, Amana, Temeke, and Mwananyamala Regional Hospitals and Muhimbili National Hospital. We recorded social demographic and clinical data, and we performed blood-culture and HIV-antibody testing. We used qPCR to quantify Plasmodium falciparum parasitaemia and Matrix-Assisted Laser Desorption/Ionization-Time of Flight (MALDI-TOF) to identify bacterial isolates. Disk diffusion method was used for antimicrobial susceptibility testing. Results Nineteen percent of the children (426/2,226) had pathogens detected from blood. Eleven percent (236/2,226) of the children had bacteraemia/fungaemia and 10% (204/2,063) had P. falciparum malaria. Ten children had concomitant malaria and bacteraemia. Gram-negative bacteria (64%) were more frequent than Gram-positive (32%) and fungi (4%). Over 50% of Gram-negative bacteria were extended-spectrum beta-lactamase (ESBL) producers and multidrug resistant. Methicillin resistant Staphylococcus aureus (MRSA) was found in 11/42 (26.2%). The most severe form of clinical malaria was associated with high parasitaemia (>four million genomes/μL) of P. falciparum in plasma. Overall, in-hospital death was 4% (89/2,146), and it was higher in children with bacteraemia (8%, 18/227) than malaria (2%, 4/194, p = 0.007). Risk factors for death were bacteraemia (p = 0.03), unconsciousness at admission (p < 0.001), and admission at a tertiary hospital (p = 0.003). Conclusion Compared to previous studies in this region, our study showed a reduction in malaria prevalence, a decrease in in-hospital mortality, and an increase in antimicrobial resistance (AMR) including ESBLs and multidrug resistance. An increase of AMR highlights the importance of continued strengthening of diagnostic capability and antimicrobial stewardship programs. We also found malaria and bacteraemia contributed equally in causing febrile illness, but bacteraemia caused higher in-hospital death. The most severe form of clinical malaria was associated with P. falciparum parasitaemia.
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Affiliation(s)
- Sabrina J Moyo
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Joel Manyahi
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Bjørn Blomberg
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Marit Gjerde Tellevik
- Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Nahya Salim Masoud
- Department of Paediatrics, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Said Aboud
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Karim Manji
- Department of Paediatrics, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Kristine Mørch
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
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31
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Brouwer MSM, Goodman RN, Kant A, Mevius D, Newire E, Roberts AP, Veldman KT. Mobile colistin resistance gene mcr-1 detected on an IncI1 plasmid in Escherichia coli from meat. J Glob Antimicrob Resist 2020; 23:145-148. [PMID: 32889139 DOI: 10.1016/j.jgar.2020.08.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 07/14/2020] [Accepted: 08/20/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Mobile colistin resistance (mcr) genes encoded on conjugative plasmids, although described only relatively recently, have been reported globally both in humans and livestock. The genes are often associated with the insertion sequence ISApl1 that can transpose the genes to novel genetic locations. Since its first report, multiple variants of mcr have been discovered in a variety of genetic locations in Escherichia coli, in plasmids and integrated into the chromosome. METHODS Using hybrid assembly of short-read and long-read whole-genome sequencing data, the presence ofmcr-1 was confirmed on an IncI1 plasmid in E. coli. In vitro conjugation assays were performed to determine the potential to transfer between strains. Genetic comparison with previously reported IncI1 plasmids was performed. RESULTS The genomic sequence identified thatmcr-1 is present on a complete IncI1 plasmid. Comparison with previously reported extended-spectrum β-lactamase (ESBL)-encoding plasmids from E. coli in the Netherlands from the same time period indicated a distinct lineage for this plasmid. CONCLUSIONS The observation ofmcr-1 on an IncI1 plasmid confirms that the genetic region of this gene is actively transposed between genetic locations. This active transposition has consequences for the study of the epidemiology of mcr in populations.
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Affiliation(s)
| | | | - Arie Kant
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Dik Mevius
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Enas Newire
- Institute of Systems, Molecular & Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | | | - Kees T Veldman
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
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Kirchhelle C, Atkinson P, Broom A, Chuengsatiansup K, Ferreira JP, Fortané N, Frost I, Gradmann C, Hinchliffe S, Hoffman SJ, Lezaun J, Nayiga S, Outterson K, Podolsky SH, Raymond S, Roberts AP, Singer AC, So AD, Sringernyuang L, Tayler E, Rogers Van Katwyk S, Chandler CIR. Setting the standard: multidisciplinary hallmarks for structural, equitable and tracked antibiotic policy. BMJ Glob Health 2020; 5:e003091. [PMID: 32967980 PMCID: PMC7513567 DOI: 10.1136/bmjgh-2020-003091] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 01/16/2023] Open
Abstract
There is increasing concern globally about the enormity of the threats posed by antimicrobial resistance (AMR) to human, animal, plant and environmental health. A proliferation of international, national and institutional reports on the problems posed by AMR and the need for antibiotic stewardship have galvanised attention on the global stage. However, the AMR community increasingly laments a lack of action, often identified as an 'implementation gap'. At a policy level, the design of internationally salient solutions that are able to address AMR's interconnected biological and social (historical, political, economic and cultural) dimensions is not straightforward. This multidisciplinary paper responds by asking two basic questions: (A) Is a universal approach to AMR policy and antibiotic stewardship possible? (B) If yes, what hallmarks characterise 'good' antibiotic policy? Our multistage analysis revealed four central challenges facing current international antibiotic policy: metrics, prioritisation, implementation and inequality. In response to this diagnosis, we propose three hallmarks that can support robust international antibiotic policy. Emerging hallmarks for good antibiotic policies are: Structural, Equitable and Tracked. We describe these hallmarks and propose their consideration should aid the design and evaluation of international antibiotic policies with maximal benefit at both local and international scales.
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Affiliation(s)
- Claas Kirchhelle
- School of History, University College Dublin, Dublin, Ireland
- Oxford Martin School, University of Oxford, Oxford, Oxfordshire, UK
| | - Paul Atkinson
- Department of Public Health and Policy/ Institute of Infection and Global Health, University of Liverpool, Liverpool, Merseyside, UK
| | - Alex Broom
- School of Social and Political Sciences, Faculty of Arts and Social Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Jorge Pinto Ferreira
- Antimicrobial Resistance and Veterinary Products Department, World Organisation for Animal Health, Paris, Île-de-France, France
| | - Nicolas Fortané
- Irisso, Paris-Dauphine University, PSL, INRAE, Paris, Île-de-France, France
| | - Isabel Frost
- Center for Disease Dynamics Economics and Policy, Washington, DC, USA
- Department of Infectious Disease, Imperial College London, London, UK
| | - Christoph Gradmann
- Institute for Health and Society, Dept. of Community Medicine and Global Health, University of Oslo, Oslo, Norway
| | - Stephen Hinchliffe
- Geography, College of Life and Environmental Sciences and Wellcome Centre for Cultures and Environments of Health, University of Exeter, Exeter, Devon, UK
| | - Steven J Hoffman
- Global Strategy Lab, Dahdaleh Institute for Global Health Research, Faculty of Health and Osgoode Hall Law School, York University, Toronto, Ontario, Canada
| | - Javier Lezaun
- Institute for Science, Innovation and Society, School of Anthropology and Museum Ethnography, University of Oxford, Oxford, Oxfordshire, UK
| | - Susan Nayiga
- Infectious Diseases Research Collaboration, Kampala, Central Region, Uganda
| | - Kevin Outterson
- School of Law, Social Innovation on Drug Program, Boston University, Boston, Massachusetts, USA
| | - Scott H Podolsky
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephanie Raymond
- School of Social and Political Sciences, Faculty of Arts and Social Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, Liverpool, UK
| | - Andrew C Singer
- Pollution, UK Centre for Ecology & Hydrology, Wallingford, UK
| | - Anthony D So
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- Innovation + Design Enabling Access (IDEA) Initiative, ReAct - Action on Antibiotic Resistance, Baltimore, Maryland, USA
| | | | - Elizabeth Tayler
- Global Coordination and Partnerships, AMR Division, World Health Organisation, Geneva, Switzerland
| | - Susan Rogers Van Katwyk
- Global Strategy Lab, Dahdaleh Institute for Global Health Research, Faculty of Health and Osgoode Hall Law School, York University, Toronto, Ontario, Canada
- Global Strategy Lab, York University, Toronto, Ontario, Canada
| | - Clare I R Chandler
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
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Newire E, Aydin A, Juma S, Enne VI, Roberts AP. Identification of a Type IV-A CRISPR-Cas System Located Exclusively on IncHI1B/IncFIB Plasmids in Enterobacteriaceae. Front Microbiol 2020; 11:1937. [PMID: 32903441 PMCID: PMC7434947 DOI: 10.3389/fmicb.2020.01937] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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] [Received: 05/04/2020] [Accepted: 07/22/2020] [Indexed: 12/15/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are diverse immune systems found in many prokaryotic genomes that target invading foreign DNA such as bacteriophages and plasmids. There are multiple types of CRISPR with arguably the most enigmatic being Type IV. During an investigation of CRISPR carriage in clinical, multi-drug resistant, Klebsiella pneumoniae, a Type IV-A3 CRISPR-Cas system was detected on plasmids from two K. pneumoniae isolates from Egypt (isolated in 2002-2003) and a single K. pneumoniae isolate from the United Kingdom (isolated in 2017). Sequence analysis of all other genomes available in GenBank revealed that this CRISPR-Cas system was present on 28 other plasmids from various Enterobacteriaceae hosts and was never found on a bacterial chromosome. This system is exclusively located on IncHI1B/IncFIB plasmids and is associated with multiple putative transposable elements. Expression of the cas loci was confirmed in the available clinical isolates by RT-PCR. In all cases, the CRISPR-Cas system has a single CRISPR array (CRISPR1) upstream of the cas loci which has several, conserved, spacers which, amongst things, match regions within conjugal transfer genes of IncFIIK/IncFIB(K) plasmids. Our results reveal a Type IV-A3 CRISPR-Cas system exclusively located on IncHI1B/IncFIB plasmids in Enterobacteriaceae that is likely to be able to target IncFIIK/IncFIB(K) plasmids presumably facilitating intracellular, inter-plasmid competition.
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Affiliation(s)
- Enas Newire
- UCL Eastman Dental Institute, University College London, London, United Kingdom
| | - Alp Aydin
- Centre for Clinical Microbiology, Royal Free Hospital, University College London, London, United Kingdom
| | - Samina Juma
- Centre for Clinical Microbiology, Royal Free Hospital, University College London, London, United Kingdom
| | - Virve I. Enne
- Centre for Clinical Microbiology, Royal Free Hospital, University College London, London, United Kingdom
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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Hubbard ATM, Bulgasim I, Roberts AP. A novel hemA mutation is responsible for a small-colony-variant phenotype in Escherichia coli. Microbiology (Reading) 2020; 167. [PMID: 32762803 DOI: 10.1099/mic.0.000962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We identified a small colony variant (SCV) of an amoxicillin/clavulanic acid-resistant derivative of a clinical isolate of Escherichia coli from Malawi, which was selected for in vitro in a subinhibitory concentration of gentamicin. The SCV was auxotrophic for hemin and had impaired biofilm formation compared to the ancestral isolates. A single novel nucleotide polymorphism (SNP) in hemA, which encodes a glutamyl-tRNA reductase that catalyses the initial step of porphyrin biosynthesis leading to the production of haem, was responsible for the SCV phenotype. We showed the SNP in hemA resulted in a significant fitness cost to the isolate, which persisted even in the presence of hemin. However, the phenotype quickly reverted during sequential sub-culturing in liquid growth media. As hemA is not found in mammalian cells, and disruption of the gene results in a significant fitness cost, it represents a potential target for novel drug development specifically for the treatment of catheter-associated urinary tract infections caused by E. coli.
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Affiliation(s)
- Alasdair T M Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Issra Bulgasim
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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35
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Yu P, Yang JN, Yan JW, Meng ZZ, Hong WD, Roberts AP, Ward SA, Zhang L, Li S. A novel fluorescent probe for the detection of AmpC beta-lactamase and the application in screening beta-lactamase inhibitors. Spectrochim Acta A Mol Biomol Spectrosc 2020; 234:118257. [PMID: 32208355 DOI: 10.1016/j.saa.2020.118257] [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] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/01/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
The rapid detection of β-lactamases (Blas) and effective screening of Bla inhibitors are critically important and urgent for solving antibiotic resistance and improving precision medicine. Here a novel fluorescent probe CDC-559 was designed and synthesized, which can be used for the selective and direct detection of AmpC Blas. More importantly, it can realize screening the Bla inhibitors with sulbactam sodium and tazobactam as model compounds, and the half-maximal inhibitory concentration are 0.279 μM and 0.053 μM, respectively. CDC-559 can be applied not only to examine the resistance of bacterial strains, but also to categorize its mode of action specifically, which is consistent with the essential result of the Blas. The research suggests that CDC-559 probe has tremendous potential in the rapid detection of AmpC Blas as well as the strains with AmpC-encoded gene, which is instructive in promoting better antibiotic stewardship practices and developments.
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Affiliation(s)
- Pan Yu
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jia-Ning Yang
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Jin-Wu Yan
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Zhi-Zhong Meng
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - W David Hong
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Adam P Roberts
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Stephen A Ward
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom
| | - Lei Zhang
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China; Guangdong Provincial Engineering and Technological Centre for Biopharmaceuticals, South China University of Technology, Guangzhou 510006, PR China.
| | - Shan Li
- MOE Joint International Research Laboratory of Synthesis Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, PR China.
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36
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Affiliation(s)
- Adam P Roberts
- Centre for Drugs and Diagnostics & Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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37
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Hughes-Games A, Roberts AP, Davis SA, Hill DJ. Identification of integrative and conjugative elements in pathogenic and commensal Neisseriaceae species via genomic distributions of DNA uptake sequence dialects. Microb Genom 2020; 6:e000372. [PMID: 32375974 PMCID: PMC7371117 DOI: 10.1099/mgen.0.000372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/13/2020] [Indexed: 02/02/2023] Open
Abstract
Mobile genetic elements (MGEs) are key factors responsible for dissemination of virulence determinants and antimicrobial-resistance genes amongst pathogenic bacteria. Conjugative MGEs are notable for their high gene loads donated per transfer event, broad host ranges and phylogenetic ubiquity amongst prokaryotes, with the subclass of chromosomally inserted integrative and conjugative elements (ICEs) being particularly abundant. The focus on a small number of model systems has biased the study of ICEs towards those conferring readily selectable phenotypes to host cells, whereas the identification and characterization of integrated cryptic elements remains challenging. Even though antimicrobial resistance and horizontally acquired virulence genes are major factors aggravating neisserial infection, conjugative MGEs of Neisseria gonorrhoeae and Neisseria meningitidis remain poorly characterized. Using a phenotype-independent approach based on atypical distributions of DNA uptake sequences (DUSs) in MGEs relative to the chromosomal background, we have identified two groups of chromosomally integrated conjugative elements in Neisseria: one found almost exclusively in pathogenic species possibly deriving from the genus Kingella, the other belonging to a group of Neisseria mucosa-like commensals. The former element appears to enable transfer of traditionally gonococcal-specific loci such as the virulence-associated toxin-antitoxin system fitAB to N. meningitidis chromosomes, whilst the circular form of the latter possesses a unique attachment site (attP) sequence seemingly adapted to exploit DUS motifs as chromosomal integration sites. In addition to validating the use of DUS distributions in Neisseriaceae MGE identification, the >170 identified ICE sequences provide a valuable resource for future studies of ICE evolution and host adaptation.
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Affiliation(s)
- Alex Hughes-Games
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, University of Bristol, Bristol, UK
| | - Adam P. Roberts
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sean A. Davis
- School of Chemistry, University of Bristol, Bristol, UK
| | - Darryl J. Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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38
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Feng S, Liu Y, Liang W, El-Sayed Ahmed MAEG, Zhao Z, Shen C, Roberts AP, Liang L, Liao L, Zhong Z, Guo Z, Yang Y, Wen X, Chen H, Tian GB. Involvement of Transcription Elongation Factor GreA in Mycobacterium Viability, Antibiotic Susceptibility, and Intracellular Fitness. Front Microbiol 2020; 11:413. [PMID: 32265867 PMCID: PMC7104715 DOI: 10.3389/fmicb.2020.00413] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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] [Received: 01/02/2020] [Accepted: 02/27/2020] [Indexed: 11/13/2022] Open
Abstract
There is growing evidence that GreA aids adaptation to stressful environments in various bacteria. However, the functions of GreA among mycobacteria remain obscure. Here, we report on cellular consequences following deletion of greA gene in Mycobacterium spp. The greA mutant strain (ΔgreA) was generated in Mycobacterium smegmatis, Mycobacterium tuberculosis (MTB) H37Ra, and M. tuberculosis H37Rv. Deletion of greA results in growth retardation and poor survival in response to adverse stress, besides rendering M. tuberculosis more susceptible to vancomycin and rifampicin. By using RNA-seq, we observe that disrupting greA results in the differential regulation of 195 genes in M. smegmatis with 167 being negatively regulated. Among these, KEGG pathways significantly enriched for differentially regulated genes included tryptophan metabolism, starch and sucrose metabolism, and carotenoid biosynthesis, supporting a role of GreA in the metabolic regulation of mycobacteria. Moreover, like Escherichia coli GreA, M. smegmatis GreA exhibits a series of conservative features, and the anti-backtracking activity of C-terminal domain is indispensable for the expression of glgX, a gene was down-regulated in the RNA-seq data. Interestingly, the decrease in the expression of glgX by CRISPR interference, resulted in reduced growth. Finally, intracellular fitness significantly declines due to loss of greA. Our data indicates that GreA is an important factor for the survival and resistance establishment in Mycobacterium spp. This study provides new insight into GreA as a potential target in multi-drug resistant TB treatment.
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Affiliation(s)
- Siyuan Feng
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Yan Liu
- Clinical Laboratory, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Wanfei Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Mohamed Abd El-Gawad El-Sayed Ahmed
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Cairo, Egypt
| | - Zihan Zhao
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Cong Shen
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Lujie Liang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Liya Liao
- Clinical Laboratory, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Zhijuan Zhong
- Clinical Laboratory, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Zhaowang Guo
- Clinical Laboratory, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Yongqiang Yang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Xin Wen
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Hongtao Chen
- Clinical Laboratory, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Tropical Diseases Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
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Hubbard ATM, Newire E, Botelho J, Reiné J, Wright E, Murphy EA, Hutton W, Roberts AP. Isolation of an antimicrobial-resistant, biofilm-forming, Klebsiella grimontii isolate from a reusable water bottle. Microbiologyopen 2020; 9:1128-1134. [PMID: 32126585 PMCID: PMC7294305 DOI: 10.1002/mbo3.1023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Received: 11/01/2019] [Revised: 01/31/2020] [Accepted: 02/14/2020] [Indexed: 12/14/2022] Open
Abstract
A reusable water bottle was swabbed as part of the citizen science project "Swab and Send," and a Klebsiella grimontii isolate was recovered on chromogenic agar and designated SS141. Whole-genome sequencing of SS141 showed it has the potential to be a human pathogen as it contains the biosynthetic gene cluster for the potent cytotoxin, kleboxymycin, and genes for other virulence factors. The genome also contains the antibiotic-resistant genes, blaOXY-6-4 , and a variant of fosA, which is likely to explain the observed resistance to ampicillin, amoxicillin, and fosfomycin. We have also shown that SS141 forms biofilms on both polystyrene and polypropylene surfaces, providing a reasonable explanation for its ability to colonize a reusable water bottle. With the increasing use of reusable water bottles as an alternative to disposables and a strong forecast for growth in this industry over the next decade, this study highlights the need for cleanliness comparable to other reusable culinary items.
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Affiliation(s)
- Alasdair T M Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Enas Newire
- School of Pharmacy, College of Science, University of Lincoln, Lincoln, UK
| | - João Botelho
- Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, Plön, Germany.,Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Jesús Reiné
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Elli Wright
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Emma A Murphy
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - William Hutton
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
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Adler H, Nikolaou E, Gould K, Hinds J, Collins AM, Connor V, Hales C, Hill H, Hyder-Wright AD, Zaidi SR, German EL, Gritzfeld JF, Mitsi E, Pojar S, Gordon SB, Roberts AP, Rylance J, Ferreira DM. Pneumococcal Colonization in Healthy Adult Research Participants in the Conjugate Vaccine Era, United Kingdom, 2010-2017. J Infect Dis 2020; 219:1989-1993. [PMID: 30690468 PMCID: PMC6534187 DOI: 10.1093/infdis/jiz034] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/21/2019] [Indexed: 11/14/2022] Open
Abstract
Pneumococcal colonization is rarely studied in adults, except as part of family surveys. We report the outcomes of colonization screening in healthy adults (all were nonsmokers without major comorbidities or contact with children aged <5 years) who had volunteered to take part in clinical research. Using nasal wash culture, we detected colonization in 6.5% of volunteers (52 of 795). Serotype 3 was the commonest serotype (10 of 52 isolates). The majority of the remaining serotypes (35 of 52 isolates) were nonvaccine serotypes, but we also identified persistent circulation of serotypes 19A and 19F. Resistance to at least 1 of 6 antibiotics tested was found in 8 of 52 isolates.
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Affiliation(s)
- Hugh Adler
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Royal Liverpool University Hospital
- Correspondence: H. Adler, MRCPI, DTM&H, Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK ()
| | | | - Katherine Gould
- St George’s University of London
- BUGS Bioscience, London Bioscience Innovation Centre, London, United Kingdom
| | - Jason Hinds
- St George’s University of London
- BUGS Bioscience, London Bioscience Innovation Centre, London, United Kingdom
| | - Andrea M Collins
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Royal Liverpool University Hospital
- Aintree University Hospital
| | - Victoria Connor
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Royal Liverpool University Hospital
| | - Caz Hales
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Royal Liverpool University Hospital
| | - Helen Hill
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Royal Liverpool University Hospital
| | - Angela D Hyder-Wright
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Royal Liverpool University Hospital
- Clinical Research Network North West Coast, National Institute for Health Research, Liverpool
| | - Seher R Zaidi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Royal Liverpool University Hospital
| | - Esther L German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
| | - Jenna F Gritzfeld
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
| | - Elena Mitsi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
| | - Sherin Pojar
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
| | - Stephen B Gordon
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Adam P Roberts
- Department of Parasitology, Liverpool School of Tropical Medicine
| | - Jamie Rylance
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
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Almebairik N, Zamudio R, Ironside C, Joshi C, Ralph JD, Roberts AP, Gould IM, Morrissey JA, Hijazi K, Oggioni MR. Genomic Stability of Composite SCC mec ACME and COMER-Like Genetic Elements in Staphylococcus epidermidis Correlates With Rate of Excision. Front Microbiol 2020; 11:166. [PMID: 32117176 PMCID: PMC7029739 DOI: 10.3389/fmicb.2020.00166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Received: 12/13/2019] [Accepted: 01/23/2020] [Indexed: 01/08/2023] Open
Abstract
The epidemiological success of methicillin-resistant Staphylococcus aureus USA300 has been associated with the presence of two mobile elements, the arginine catabolic mobile element (ACME) and the copper and mercury resistance (COMER) element. These two mobile elements are associated with resistance to copper, which has been related to host fitness and survival within macrophages. Several studies found that ACME is more prevalent, and exhibits greater diversity, in Staphylococcus epidermidis while COMER has not been identified in S. epidermidis or any other staphylococcal species. We aimed in this study to evaluate the presence and diversity of ACME and COMER-like elements in our S. epidermidis clinical isolates. The genomes of 58 S. epidermidis clinical isolates, collected between 2009 and 2018 in a Scottish hospital, were sequenced. A core-genome phylogenetic tree and genome based MLST typing showed that more than half of the isolates belong to the clinically predominant sequence type2 (ST2) and these isolates have been found to split into two lineages within the phylogenetic tree. Analysis showed the presence of SCCmec in the majority of isolates. Comparative analysis identified a cluster of ACME-positive isolates with most of them belonging to ST48. ACME showed high variation even between isolates of the same ACME type and ST. COMER-like elements have been identified in one of the two major hospital adapted drug resistant ST2 lineages; and showed high stability. This difference in stability at the genomic level correlates well with the up to one hundred times higher excision frequency found for the SCCmec elements in ACME-containing isolates compared to COMER-like element containing isolates. ACME/COMER-like element positive isolates did not show a significant phenotype of decreased copper susceptibility, while resistance to mercury was over-represented in COMER-like element positive isolates. To the best of our knowledge, this is the first molecular characterization of COMER-like elements in S. epidermidis isolates. The presence of the COMER-like elements is the most prominent accessory genome feature of these successful lineages suggesting that this chromosomal island contributes to the success and wide clinical distribution of ST2 S. epidermidis.
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Affiliation(s)
- Nada Almebairik
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Roxana Zamudio
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Corinne Ironside
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Chaitanya Joshi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Joseph D Ralph
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Ian M Gould
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Julie A Morrissey
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Karolin Hijazi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Marco R Oggioni
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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42
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Singer AC, Kirchhelle C, Roberts AP. (Inter)nationalising the antibiotic research and development pipeline. Lancet Infect Dis 2019; 20:e54-e62. [PMID: 31753765 DOI: 10.1016/s1473-3099(19)30552-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/28/2019] [Accepted: 09/11/2019] [Indexed: 01/03/2023]
Abstract
In this Personal View, we critically examine the wider context of international efforts to stimulate commercial antibiotic research and development via public-private initiatives. Despite these efforts, antibiotics remain a global resource without an international support structure that is commensurate to the risks from antibiotic-resistant infections and the long-term nature of required solutions. To protect this resource, we propose a two-pronged antibiotic research and development strategy based on a short-term strengthening of incentives (such as market entry rewards) to maximise the delivery of existing opportunities in the pipeline, and on a concurrent medium-term to long-term establishment of a global, publicly funded antibiotic research and development institute. Designed sustainably to deliver novel and first-in-class antibiotics targeting key human health gaps, the institute and its staff would become a global resource that, unlike the private pharmaceutical sector, would be managed as an open science platform. Our model of internationalised public research and development would maximise scientific synergy and cross-fertilisation, minimise replication of effort, acquire and preserve existing know-how, and ensure equitable and sustainable access to novel and effective antibiotics. Its genuinely global focus would also help counteract tendencies to equate donor with global health priorities. Our proposal is not radical. Historical precedent and developments in other research areas show that sustained international funding of publicly owned research can hasten the delivery of critically needed drugs and lower barriers to access.
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Affiliation(s)
| | - Claas Kirchhelle
- Oxford Martin School and Wellcome Unit for the History of Medicine, University of Oxford, Oxford, UK
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43
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Abstract
Transposable elements in prokaryotes are found in many forms and therefore a robust nomenclature system is needed in order to allow researchers to describe and search for them in publications and databases. Here we provide an update on The Transposon Registry which allocates numbers to any prokaryotic transposable element. Additionally, we present the completion of registry records for all transposons assigned Tn numbers from Tn1 onwards where sequence data or publications exist.
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Affiliation(s)
- Supathep Tansirichaiya
- 1Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK.,2Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, 9037 Norway
| | - Md Ajijur Rahman
- 1Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK.,3Department of Pharmacy, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Adam P Roberts
- 1Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK
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44
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Hubbard ATM, Jafari NV, Feasey N, Rohn JL, Roberts AP. Effect of Environment on the Evolutionary Trajectories and Growth Characteristics of Antibiotic-Resistant Escherichia coli Mutants. Front Microbiol 2019; 10:2001. [PMID: 31555237 PMCID: PMC6722461 DOI: 10.3389/fmicb.2019.02001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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] [Received: 05/01/2019] [Accepted: 08/15/2019] [Indexed: 11/21/2022] Open
Abstract
The fitness cost to bacteria of acquisition of resistance determinants is critically under-investigated, and the identification and exploitation of these fitness costs may lead to novel therapeutic strategies that prevent the emergence of antimicrobial resistance. Here we used Escherichia coli and amoxicillin–clavulanic acid (AMC) resistance as a model to understand how the artificial environments utilized in studies of bacterial fitness could affect the emergence of resistance and associated fitness costs. Further, we explored the predictive value of this data when strains were grown in the more physiologically relevant environments of urine and urothelial organoids. Resistant E. coli isolates were selected for following 24-h exposure to sub-inhibitory concentrations of AMC in either M9, ISO, or LB, followed by growth on LB agar containing AMC. No resistant colonies emerged following growth in M9, whereas resistant isolates were detected from cultures grown in ISO and LB. We observed both within and between media-type variability in the levels of resistance and fitness of the resistant mutants grown in LB. MICs and fitness of these resistant strains in different media (M9, ISO, LB, human urine, and urothelial organoids) showed considerable variation. Media can therefore have a direct effect on the isolation of mutants that confer resistance to AMC and these mutants can exhibit unpredictable MIC and fitness profiles under different growth conditions. This preliminary study highlights the risks in relying on a single culture protocol as a model system to predict the behavior and treatment response of bacteria in vivo and highlights the importance of developing comprehensive experimental designs to ensure effective translation of diagnostic procedures to successful clinical outcomes.
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Affiliation(s)
- Alasdair T M Hubbard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Nazila V Jafari
- Centre for Urological Biology, Department of Renal Medicine, University College London, London, United Kingdom
| | - Nicholas Feasey
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi, College of Medicine, Blantyre, Malawi
| | - Jennifer L Rohn
- Centre for Urological Biology, Department of Renal Medicine, University College London, London, United Kingdom
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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45
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Zhong LL, Zhou Q, Tan CY, Roberts AP, El-Sayed Ahmed MAEG, Chen G, Dai M, Yang F, Xia Y, Liao K, Liang Y, Yang Y, Feng S, Zheng X, Tian GB. Multiplex loop-mediated isothermal amplification (multi-LAMP) assay for rapid detection of mcr-1 to mcr-5 in colistin-resistant bacteria. Infect Drug Resist 2019; 12:1877-1887. [PMID: 31308708 PMCID: PMC6613457 DOI: 10.2147/idr.s210226] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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] [Received: 03/27/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Purpose: The discovery of the plasmid-mediated colistin resistance genes, mcr, revealed a mechanism of transmission of colistin resistance, which is a major, global public health concern especially among individuals infected with carbapenem-resistant Gram-negative bacteria. To monitor the spread and epidemiology of mcr genes, a convenient and reliable method to detect mcr genes in clinical isolates is needed, especially in the primary care institutions. This study aimed to establish a restriction endonuclease-based multiplex loop-mediated isothermal amplification (multi-LAMP) assay to detect mcr genes (mcr-1 to mcr-5) harbored by colistin-resistant bacteria. Methods: A triple-LAMP assay for mcr-1, mcr-3, and mcr-4 and a double-LAMP assay for mcr-2 and mcr-5 were established. The sensitivity and specificity of the LAMP reactions were determined via electrophoresis and visual detection. Results: The sensitivity of the LAMP assay was 10-fold greater than that of PCR, with high specificity among the screened primers. Specific mcr genes were distinguished in accordance with band numbers and the fragment length of the digested LAMP amplification products. Furthermore, the LAMP assay was confirmed as a rapid and reliable diagnostic technique upon application for clinical samples, and the results were consistent with those of conventional PCR assay. Conclusion: The multi-LAMP assay is a potentially promising method to detect mcr genes and will, if implemented, help prevent infections by drug-resistant bacteria in primary-care hospitals due to rapid and reliable surveillance. To our knowledge, this is the first study to report the application of LAMP to detect mcr-2 to mcr-5 genes and the first time that multi-LAMP has been applied to detect mcr genes.
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Affiliation(s)
- Lan-Lan Zhong
- Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong 519000, People's Republic of China.,Ministry of Education, Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Guangzhou 510080, People's Republic of China
| | - Qian Zhou
- Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, People's Republic of China
| | - Cui-Yan Tan
- Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, People's Republic of China
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK.,Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Mohamed Abd El-Gawad El-Sayed Ahmed
- Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong 519000, People's Republic of China.,Ministry of Education, Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology (MUST), Cairo, Egypt
| | - Guanping Chen
- Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong 519000, People's Republic of China.,Ministry of Education, Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Guangzhou 510080, People's Republic of China
| | - Min Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu 610500, People's Republic of China
| | - Fan Yang
- Department of Microbiology, School of Basic Medical Science, Xinxiang Medical University, Xinxiang 453003, People's Republic of China
| | - Yong Xia
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, People's Republic of China
| | - Kang Liao
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, People's Republic of China
| | - Yingjian Liang
- Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, People's Republic of China
| | - Yongqiang Yang
- Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong 519000, People's Republic of China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Siyuan Feng
- Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong 519000, People's Republic of China.,Ministry of Education, Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Guangzhou 510080, People's Republic of China
| | - Xiaobin Zheng
- Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, People's Republic of China
| | - Guo-Bao Tian
- Program in Pathobiology, The Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong 519000, People's Republic of China.,Ministry of Education, Key Laboratory of Tropical Diseases Control, Sun Yat-sen University, Guangzhou 510080, People's Republic of China
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Tansirichaiya S, Mullany P, Roberts AP. Promoter activity of ORF-less gene cassettes isolated from the oral metagenome. Sci Rep 2019; 9:8388. [PMID: 31182805 PMCID: PMC6557892 DOI: 10.1038/s41598-019-44640-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 05/17/2019] [Indexed: 01/09/2023] Open
Abstract
Integrons are genetic elements consisting of a functional platform for recombination and expression of gene cassettes (GCs). GCs usually carry promoter-less open reading frames (ORFs), encoding proteins with various functions including antibiotic resistance. The transcription of GCs relies mainly on a cassette promoter (PC), located upstream of an array of GCs. Some integron GCs, called ORF-less GCs, contain no identifiable ORF with a small number shown to be involved in antisense mRNA mediated gene regulation. In this study, the promoter activity of ORF-less GCs, previously recovered from the oral metagenome, was verified by cloning them upstream of a gusA reporter, proving they can function as a promoter, presumably allowing bacteria to adapt to multiple stresses within the complex physico-chemical environment of the human oral cavity. A bi-directional promoter detection system was also developed allowing direct identification of clones with promoter-containing GCs on agar plates. Novel promoter-containing GCs were identified from the human oral metagenomic DNA using this construct, called pBiDiPD. This is the first demonstration and detection of promoter activity of ORF-less GCs from Treponema bacteria and the development of an agar plate-based detection system will enable similar studies in other environments.
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Affiliation(s)
- Supathep Tansirichaiya
- Department of Microbial Diseases, University College London, Eastman Dental Institute, 256 Gray's Inn Road, London, WC1X 8LD, UK.,Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Peter Mullany
- Department of Microbial Diseases, University College London, Eastman Dental Institute, 256 Gray's Inn Road, London, WC1X 8LD, UK
| | - Adam P Roberts
- Department of Microbial Diseases, University College London, Eastman Dental Institute, 256 Gray's Inn Road, London, WC1X 8LD, UK. .,Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
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Abstract
The pipeline for new antibiotics is dry. Despite the creation of public/private initiatives like Combating Antibiotic Resistant Bacteria Biopharmaceutical Accelerator (Carb-X) and the Antimicrobial Resistance (AMR) Centre, the current focus on ‘push-pull’ incentives for the pharmaceutical industry still relies on economic return. We propose a joint, internationally-funded antimicrobial development institute that would fund permanent staff to take on roles previously assigned to pharmaceutical companies. This institute would receive ring-fenced, long-term, core funding from participating countries as well as charities, with the aim to focus on transforming the largely dormant antimicrobial pipeline. Resulting drugs would be sold globally and according to a principle of shared burdens. Our proposed model for antimicrobial development aims to maximise society’s investment, through open science, investment in people, and the sharing of intellectual property.
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Affiliation(s)
- Andrew C Singer
- NERC Centre for Ecology & Hydrology, Wallingford, OX10 8BB, UK
| | - Claas Kirchhelle
- Wellcome Unit for the History of Medicine, University of Oxford, Oxford, OX2 6PE, UK
| | - Adam P Roberts
- Antimicrobial Chemotherapy and Resistance, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
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48
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Abstract
Background The evolution and spread of antibiotic resistance is often mediated by mobile genetic elements. Integrative and conjugative elements (ICEs) are the most abundant conjugative elements among prokaryotes. However, the contribution of ICEs to horizontal gene transfer of antibiotic resistance has been largely unexplored. Results Here we report that ICEs belonging to mating-pair formation (MPF) classes G and T are highly prevalent among the opportunistic pathogen Pseudomonas aeruginosa, contributing to the spread of carbapenemase-encoding genes (CEGs). Most CEGs of the MPFG class were encoded within class I integrons, which co-harbour genes conferring resistance to other antibiotics. The majority of the integrons were located within Tn3-like and composite transposons. Conserved attachment site could be predicted for the MPFG class ICEs. MPFT class ICEs carried the CEGs within composite transposons which were not associated with integrons. Conclusions The data presented here provides a global snapshot of the different CEG-harbouring ICEs and sheds light on the underappreciated contribution of these elements to the evolution and dissemination of antibiotic resistance on P. aeruginosa. Electronic supplementary material The online version of this article (10.1186/s13100-018-0141-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- João Botelho
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Adam P Roberts
- 2Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK.,3Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ricardo León-Sampedro
- 4Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Filipa Grosso
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Luísa Peixe
- 1UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia da Universidade do Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
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49
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Lunde TM, Roberts AP, Al-Haroni M. Determination of copy number and circularization ratio of Tn 916-Tn 1545 family of conjugative transposons in oral streptococci by droplet digital PCR. J Oral Microbiol 2018; 11:1552060. [PMID: 30598735 PMCID: PMC6292373 DOI: 10.1080/20002297.2018.1552060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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] [Received: 03/22/2018] [Revised: 11/12/2018] [Accepted: 11/19/2018] [Indexed: 11/09/2022] Open
Abstract
Background: Tn916 and Tn1545 are paradigms of a large family of related, broad host range, conjugative transposons that are widely distributed in bacteria and contribute to the spread of antibiotic resistance genes (ARGs). Variation in the copy number (CN) of Tn916-Tn1545 elements and the circularization ratio (CR) may play an important role in propagation of ARGs carried by these elements. Objectives and Design: In this study, the CN and CR of Tn916-Tn1545 elements in oral streptococci were determined using droplet digital PCR (ddPCR). In addition, we investigated the influence of tetracycline on the CR of Tn916-Tn1545 elements. Results: The ddPCR assay designed in this study is a reliable way to rapidly determine CN and CR of Tn916-Tn1545 elements. Conclusions: Our data also suggest that Tn916-Tn1545 elements are generally stable without selective pressure in the clinical oral Streptococcus strains investigated in this study.
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Affiliation(s)
- Tracy Munthali Lunde
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Adam P Roberts
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK.,Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
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Podnecky NL, Fredheim EGA, Kloos J, Sørum V, Primicerio R, Roberts AP, Rozen DE, Samuelsen Ø, Johnsen PJ. Conserved collateral antibiotic susceptibility networks in diverse clinical strains of Escherichia coli. Nat Commun 2018; 9:3673. [PMID: 30202004 PMCID: PMC6131505 DOI: 10.1038/s41467-018-06143-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 08/16/2018] [Indexed: 01/09/2023] Open
Abstract
There is urgent need to develop novel treatment strategies to reduce antimicrobial resistance. Collateral sensitivity (CS), where resistance to one antimicrobial increases susceptibility to other drugs, might enable selection against resistance during treatment. However, the success of this approach would depend on the conservation of CS networks across genetically diverse bacterial strains. Here, we examine CS conservation across diverse Escherichia coli strains isolated from urinary tract infections. We determine collateral susceptibilities of mutants resistant to relevant antimicrobials against 16 antibiotics. Multivariate statistical analyses show that resistance mechanisms, in particular efflux-related mutations, as well as the relative fitness of resistant strains, are principal contributors to collateral responses. Moreover, collateral responses shift the mutant selection window, suggesting that CS-informed therapies may affect evolutionary trajectories of antimicrobial resistance. Our data allow optimism for CS-informed therapy and further suggest that rapid detection of resistance mechanisms is important to accurately predict collateral responses.
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Affiliation(s)
- Nicole L Podnecky
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway.
| | - Elizabeth G A Fredheim
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Julia Kloos
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Vidar Sørum
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Raul Primicerio
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | - Adam P Roberts
- Department of Parasitology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
- Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, PO Box 9505, 2300 RA, Leiden, The Netherlands
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9037, Tromsø, Norway
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037, Tromsø, Norway.
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