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Jaén-Luchoro D, Karlsson R, Busquets A, Piñeiro-Iglesias B, Karami N, Marathe NP, Moore ERB. Knockout of Targeted Plasmid-Borne β-Lactamase Genes in an Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strain: Impact on Resistance and Proteomic Profile. Microbiol Spectr 2023; 11:e0386722. [PMID: 36622237 PMCID: PMC9927464 DOI: 10.1128/spectrum.03867-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Resistance to β-lactams is known to be multifactorial, although the underlying mechanisms are not well established. The aim of our study was to develop a system for assessing the phenotypic and proteomic responses of bacteria to antibiotic stress as a result of the loss of selected antimicrobial resistance genes. We applied homologous recombination to knock out plasmid-borne β-lactamase genes (blaOXA-1, blaTEM-1, and blaCTX-M15) in Escherichia coli CCUG 73778, generating knockout clone variants lacking the respective deleted β-lactamases. Quantitative proteomic analyses were performed on the knockout variants and the wild-type strain, using bottom-up liquid chromatography tandem mass spectrometry (LC-MS/MS), after exposure to different concentrations of cefadroxil. Loss of the blaCTX-M-15 gene had the greatest impact on the resulting protein expression dynamics, while losses of blaOXA-1 and blaTEM-1 affected fewer proteins' expression levels. Proteins involved in antibiotic resistance, cell membrane integrity, stress, and gene expression and unknown function proteins exhibited differential expression. The present study provides a framework for studying protein expression in response to antibiotic exposure and identifying the genomic, proteomic, and phenotypic impacts of resistance gene loss. IMPORTANCE The critical situation regarding antibiotic resistance requires a more in-depth effort for understanding underlying mechanisms involved in antibiotic resistance, beyond just detecting resistance genes. The methodology presented in this work provides a framework for knocking out selected resistance factors, to study the adjustments of the bacterium in response to a particular antibiotic stress, elucidating the genetic response and proteins that are mobilized. The protocol uses MS-based determination of the proteins that are expressed in response to an antibiotic, enabling the selection of strong candidates representing putative resistance factors or mechanisms and providing a basis for future studies to understand their implications in antibiotic resistance. This allows us to better understand how the cell responds to the presence of the antibiotic when a specific gene is lost and, consequently, identify alternative targets for possible future treatment development.
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Affiliation(s)
- Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg, Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Nanoxis Consulting AB, Gothenburg, Sweden
| | - Antonio Busquets
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Beatriz Piñeiro-Iglesias
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg, Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Nahid Karami
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | | | - Edward R. B. Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg, Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland and Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
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2
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Karlowsky JA, Hackel MA, Wise MG, Six DA, Uehara T, Daigle DM, Cusick SM, Pevear DC, Moeck G, Sahm DF. In Vitro Activity of Cefepime-Taniborbactam and Comparators against Clinical Isolates of Gram-Negative Bacilli from 2018 to 2020: Results from the Global Evaluation of Antimicrobial Resistance via Surveillance (GEARS) Program. Antimicrob Agents Chemother 2023; 67:e0128122. [PMID: 36541767 PMCID: PMC9872668 DOI: 10.1128/aac.01281-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Taniborbactam is a novel cyclic boronate β-lactamase inhibitor in clinical development in combination with cefepime. We assessed the in vitro activity of cefepime-taniborbactam and comparators against a 2018-2020 collection of Enterobacterales (n = 13,731) and Pseudomonas aeruginosa (n = 4,619) isolates cultured from infected patients attending hospitals in 56 countries. MICs were determined by CLSI broth microdilution. Taniborbactam was tested at a fixed concentration of 4 μg/mL. Isolates with cefepime-taniborbactam MICs of ≥16 μg/mL underwent whole-genome sequencing. β-lactamase genes were identified in meropenem-resistant isolates by PCR/Sanger sequencing. Against Enterobacterales, taniborbactam reduced the cefepime MIC90 value by >64-fold (from >16 to 0.25 μg/mL). At ≤16 μg/mL, cefepime-taniborbactam inhibited 99.7% of all Enterobacterales isolates; >97% of isolates with multidrug-resistant (MDR) and ceftolozane-tazobactam-resistant phenotypes; ≥90% of isolates with meropenem-resistant, difficult-to-treat-resistant (DTR), meropenem-vaborbactam-resistant, and ceftazidime-avibactam-resistant phenotypes; 100% of VIM-positive, AmpC-positive, and KPC-positive isolates; 98.7% of extended-spectrum β-lactamase (ESBL)-positive; 98.8% of OXA-48-like-positive; and 84.6% of NDM-positive isolates. Against P. aeruginosa, taniborbactam reduced the cefepime MIC90 value by 4-fold (from 32 to 8 μg/mL). At ≤16 μg/mL, cefepime-taniborbactam inhibited 97.4% of all P. aeruginosa isolates; ≥85% of isolates with meropenem-resistant, MDR, and meropenem-vaborbactam-resistant phenotypes; >75% of isolates with DTR, ceftazidime-avibactam-resistant, and ceftolozane-tazobactam-resistant phenotypes; and 87.4% of VIM-positive isolates. Multiple potential mechanisms, including carriage of IMP, certain alterations in PBP3, permeability (porin) defects, and possibly, upregulation of efflux were present in most isolates with cefepime-taniborbactam MICs of ≥16 μg/mL. We conclude that cefepime-taniborbactam exhibited potent in vitro activity against Enterobacterales and P. aeruginosa and inhibited most carbapenem-resistant isolates, including those carrying serine carbapenemases or NDM/VIM metallo-β-lactamases (MBLs).
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Affiliation(s)
- James A. Karlowsky
- IHMA, Schaumburg, Illinois, USA
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | | | - David A. Six
- Venatorx Pharmaceuticals, Inc., Malvern, Pennsylvania, USA
| | | | | | | | | | - Greg Moeck
- Venatorx Pharmaceuticals, Inc., Malvern, Pennsylvania, USA
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3
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Collis RM, Biggs PJ, Burgess SA, Midwinter AC, Brightwell G, Cookson AL. Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments. Front Microbiol 2022; 13:960748. [PMID: 36033848 PMCID: PMC9403332 DOI: 10.3389/fmicb.2022.960748] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, the role antimicrobial usage on pasture-based dairy farms, such as those in NZ, plays in driving the spread of AMR within the dairy farm environment remains equivocal. Culture-based methods were used to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli from farm environmental samples collected over a 15-month period from two NZ dairy farms with contrasting management practices. Whole genome sequencing was utilised to understand the genomic epidemiology and antimicrobial resistance gene repertoire of a subset of third-generation cephalosporin resistant E. coli isolated in this study. There was a low sample level prevalence of ESBL-producing E. coli (faeces 1.7%; farm dairy effluent, 6.7% from Dairy 4 and none from Dairy 1) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3% and 8.3%; farm dairy effluent 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). ESBL- and AmpC-producing E. coli were isolated from faeces and farm dairy effluent in spring and summer, during months with varying levels of antimicrobial use, but no ESBL- or AmpC-producing E. coli were isolated from bulk tank milk or soil from recently grazed paddocks. Hybrid assemblies using short- and long-read sequence data from a subset of ESBL- and AmpC-producing E. coli enabled the assembly and annotation of nine plasmids from six E. coli, including one plasmid co-harbouring 12 antimicrobial resistance genes. ESBL-producing E. coli were infrequently identified from faeces and farm dairy effluent on the two NZ dairy farms, suggesting they are present at a low prevalence on these farms. Plasmids harbouring several antimicrobial resistance genes were identified, and bacteria carrying such plasmids are a concern for both animal and public health. AMR is a burden for human, animal and environmental health and requires a holistic “One Health” approach to address.
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Affiliation(s)
- Rose M. Collis
- The Hopkirk Research Institute, AgResearch Ltd., Massey University, Palmerston North, New Zealand
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- Rose M. Collis,
| | - Patrick J. Biggs
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Sara A. Burgess
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C. Midwinter
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Gale Brightwell
- The Hopkirk Research Institute, AgResearch Ltd., Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Adrian L. Cookson
- The Hopkirk Research Institute, AgResearch Ltd., Massey University, Palmerston North, New Zealand
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- *Correspondence: Adrian L. Cookson,
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Characterization of a Novel Carbapenem-Resistant Klebsiella michiganensis Strain Coharboring the bla SIM-1, bla OXA-1, bla CTX-M-14, qnrS, and aac(6')-Ib-cr Genes. Curr Microbiol 2022; 79:228. [PMID: 35751714 DOI: 10.1007/s00284-022-02920-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/30/2022] [Indexed: 12/31/2022]
Abstract
Carbapenem-resistant Klebsiella michiganensis (CRKM) and Klebsiella oxytoca (CRKO) strains have occasionally been reported to cause severe infections. However, SIM-producing K. michiganensis strains have never been described. In this study, we phenotypically and genetically characterized 6 CRKM and CRKO strains isolated over the past 10 years at a Chinese tertiary hospital. All six strains were positive for the mCIM test, and five were positive for the MBL test. Carbapenemase-encoding genes (blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-23, blaOXA-24, blaOXA-51, and blaOXA-58) and another 12 resistance genes were screened by PCR, and blaKPC, blaNDM, and blaIMP were identified in five strains. However, the CRKM strain KM41, which was resistant to IPM and MEM with minimum inhibitory concentrations (MICs) of 4 µg/ml and 16 µg/ml, respectively, had positive mCIM and MBL results but lacked the eight carbapenemase-encoding genes. Whole-genome sequencing of the KM41 strain revealed more than 20 drug resistance genes; in particular, blaSIM-1, blaOXA-1, blaCTX-M-14, qnrS, aac(6')-Ib-cr, aadA17, and aar-3 were found to be located in a single plasmid. To the best of our knowledge, this is the first description of a K. michiganensis strain coharboring blaSIM-1, blaOXA-1, blaCTX-M-14, qnrS, and aac(6')-Ib-cr in China.
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5
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Klebsiella pneumoniae Mutants Resistant to Ceftazidime-Avibactam Plus Aztreonam, Imipenem-Relebactam, Meropenem-Vaborbactam, and Cefepime-Taniborbactam. Antimicrob Agents Chemother 2022; 66:e0217921. [PMID: 35293781 DOI: 10.1128/aac.02179-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We show that a previously described Klebsiella pneumoniae variant that is resistant to ceftazidime-avibactam plus meropenem-vaborbactam, has a ramR plus ompK36 mutation, and produces the V239G variant KPC-3 (V240G per the standard numbering system) exhibits resistance to ceftazidime-avibactam plus aztreonam and imipenem-relebactam but not cefepime-taniborbactam. The V239G variant does not generate collateral β-lactam susceptibility like many KPC-3 variants associated with ceftazidime-avibactam resistance. Additional mutation of ompK35 and production of the OXA-48-like carbapenemase OXA-232 were required to confer cefepime-taniborbactam resistance.
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6
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Abstract
Class D β-lactamases are composed of 14 families and the majority of the member enzymes are included in the OXA family. The genes for class D β-lactamases are frequently identified in the chromosome as an intrinsic resistance determinant in environmental bacteria and a few of these are found in mobile genetic elements carried by clinically significant pathogens. The most dominant OXA family among class D β-lactamases is superheterogeneous and the family needs to have an updated scheme for grouping OXA subfamilies through phylogenetic analysis. The OXA enzymes, even the members within a subfamily, have a diverse spectrum of resistance. Such varied activity could be derived from their active sites, which are distinct from those of the other serine β-lactamases. Their substrate profile is determined according to the size and position of the P-, Ω- and β5-β6 loops, assembling the active-site channel, which is very hydrophobic. Also, amino acid substitutions occurring in critical structures may alter the range of hydrolysed substrates and one subfamily could include members belonging to several functional groups. This review aims to describe the current class D β-lactamases including the functional groups, occurrence types (intrinsic or acquired) and substrate spectra and, focusing on the major OXA family, a new model for subfamily grouping will be presented.
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Affiliation(s)
- Eun-Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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7
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Alzayn M, Findlay J, Schubert H, Mounsey O, Gould VC, Heesom KJ, Turner KM, Barrett DC, Reyher KK, Avison MB. Characterization of AmpC-hyperproducing Escherichia coli from humans and dairy farms collected in parallel in the same geographical region. J Antimicrob Chemother 2021; 75:2471-2479. [PMID: 32542329 DOI: 10.1093/jac/dkaa207] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To characterize putative AmpC-hyperproducing third-generation cephalosporin-resistant E. coli from dairy farms and their phylogenetic relationships; to identify risk factors for their presence; and to assess evidence for their zoonotic transmission into the local human population. METHODS Proteomics was used to explain differences in antimicrobial susceptibility. WGS allowed phylogenetic analysis. Multilevel, multivariable logistic regression modelling was used to identify risk factors. RESULTS Increased use of amoxicillin/clavulanate was associated with an increased risk of finding AmpC hyperproducers on farms. Expansion of cephalosporin resistance in AmpC hyperproducers was seen in farm isolates with marR mutations (conferring cefoperazone resistance) or when AmpC was mutated (conferring fourth-generation cephalosporin and cefoperazone resistance). Phylogenetic analysis confirmed the dominance of ST88 amongst farm AmpC hyperproducers but there was no evidence for acquisition of farm isolates by members of the local human population. CONCLUSIONS Clear evidence was found for recent farm-to-farm transmission of AmpC-hyperproducing E. coli and of adaptive mutations to expand resistance. Whilst there was no evidence of isolates entering the local human population, efforts to reduce third-generation cephalosporin resistance on dairy farms must address the high prevalence of AmpC hyperproducers. The finding that amoxicillin/clavulanate use was associated with an increased risk of finding AmpC hyperproducers is important because this is not currently categorized as a highest-priority critically important antimicrobial and so is not currently targeted for specific usage restrictions in the UK.
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Affiliation(s)
- Maryam Alzayn
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK.,Biology Department, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Jacqueline Findlay
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Hannah Schubert
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Oliver Mounsey
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
| | - Virginia C Gould
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK.,Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Kate J Heesom
- University of Bristol Proteomics Facility, Bristol, UK
| | - Katy M Turner
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - David C Barrett
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | | | - Matthew B Avison
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, UK
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8
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Mushtaq S, Garello P, Vickers A, Woodford N, Livermore DM. Cefepime/tazobactam compared with other tazobactam combinations against problem Gram-negative bacteria. Int J Antimicrob Agents 2021; 57:106318. [PMID: 33716176 DOI: 10.1016/j.ijantimicag.2021.106318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/10/2021] [Accepted: 03/06/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES Piperacillin/tazobactam has long been a broad-spectrum 'workhorse' antibiotic; however, it is compromised by resistance. One response is to re-partner tazobactam with cefepime, which is easier to protect, being less β-lactamase labile, and to use a high-dose and prolonged infusion. On this basis, Wockhardt are developing cefepime/tazobactam (WCK 4282) as a 2+2 g q8h combination with a 90-min infusion. METHODS The activity of cc cefepime/tazobactam was assessed, with other tazobactam combinations as comparators, against 1632 Enterobacterales, 745 Pseudomonas aeruginosa and 450 other non-fermenters, as submitted to the UK National Reference Laboratory. These were categorised by carbapenemase-gene detection and interpretive reading of phenotypes, with MICs determined by British Society for Antimicrobial Chemotherapy agar dilution. RESULTS Although higher breakpoints may be justifiable, based on the pharmacodynamics, the results were reviewed against current cefepime criteria. On this basis, cefepime/tazobactam was broadly active against Enterobacterales with AmpC enzymes and extended-spectrum β-lactamases (ESBLs), even when they had ertapenem resistance, suggesting porin loss. At 8+8 mg/L, activity extended to > 90% of Enterobacterales with OXA-48 and KPC carbapenemases, although the MICs for KPC producers belonging to the international Klebsiella pneumoniae ST258 lineage were higher; metallo-β-lactamase producers remained resistant. Cefepime/tazobactam was less active than ceftolozane/tazobactam against Pseudomonas aeruginosa with AmpC de-repression or high-level efflux but achieved wider antipseudomonal coverage than piperacillin/tazobactam. Activity against other non-fermenters was species-specific. CONCLUSION Overall, cefepime/tazobactam had a spectrum exceeding those of piperacillin/tazobactam and ceftolozane/tazobactam and resembling or exceeding that of carbapenems. Used as a 'new-combination of old-agents' it has genuine potential to be 'carbapenem-sparing'.
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Affiliation(s)
- Shazad Mushtaq
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - Paolo Garello
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - Anna Vickers
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK
| | - David M Livermore
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, National Infection Service, Public Health England, London, UK; Norwich Medical School, University of East Anglia, Norwich, UK.
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9
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Thuy DB, Campbell J, Thuy CT, Hoang NVM, Voong Vinh P, Nguyen TNT, Nguyen Ngoc Minh C, Pham DT, Rabaa MA, Lan NPH, Hao NV, Thwaites GE, Thwaites CL, Baker S, Chau NVV, Chung The H. Colonization with Staphylococcus aureus and Klebsiella pneumoniae causes infections in a Vietnamese intensive care unit. Microb Genom 2021; 7:000514. [PMID: 33502303 PMCID: PMC8208697 DOI: 10.1099/mgen.0.000514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/21/2020] [Indexed: 12/26/2022] Open
Abstract
Pre-existing colonization with Staphylococcus aureus or Klebsiella pneumoniae has been found to increase the risk of infection in intensive care patients. We previously conducted a longitudinal study to characterize colonization of these two organisms in patients admitted to intensive care in a hospital in southern Vietnam. Here, using genomic and phylogenetic analyses, we aimed to assess the contribution these colonizing organisms made to infections. We found that in the majority of patients infected with S. aureus or K. pneumoniae, the sequence type of the disease-causing (infecting) isolate was identical to that of corresponding colonizing organisms in the respective patient. Further in-depth analysis revealed that in patients infected by S. aureus ST188 and by K. pneumoniae ST17, ST23, ST25 and ST86, the infecting isolate was closely related to and exhibited limited genetic variation relative to pre-infection colonizing isolates. Multidrug-resistant S. aureus ST188 was identified as the predominant agent of colonization and infection. Colonization and infection by K. pneumoniae were characterized by organisms with limited antimicrobial resistance profiles but extensive repertoires of virulence genes. Our findings augment the understanding of the link between bacterial colonization and infection in a low-resource setting, and could facilitate the development of novel evidence-based approaches to prevent and treat infections in high-risk patients in intensive care.
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Affiliation(s)
- Duong Bich Thuy
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - James Campbell
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Cao Thu Thuy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Phat Voong Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Maia A. Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | | | - Nguyen Van Hao
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - C. Louise Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
| | | | - Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
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10
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Livermore DM, Day M, Cleary P, Hopkins KL, Toleman MA, Wareham DW, Wiuff C, Doumith M, Woodford N. OXA-1 β-lactamase and non-susceptibility to penicillin/β-lactamase inhibitor combinations among ESBL-producing Escherichia coli. J Antimicrob Chemother 2020; 74:326-333. [PMID: 30388219 DOI: 10.1093/jac/dky453] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/08/2018] [Indexed: 02/06/2023] Open
Abstract
Background ESBL-producing Escherichia coli have expanded globally since the turn of the century and present a major public health issue. Their in vitro susceptibility to penicillin/inhibitor combinations is variable, and clinical use of these combinations against ESBL producers remains controversial. We hypothesized that this variability related to co-production of OXA-1 penicillinase. Methods During a national study we collected 293 ESBL-producing E. coli from bacteraemias, determined MICs by BSAC agar dilution, and undertook genomic sequencing with Illumina methodology. Results The collection was dominated by ST131 (n = 188 isolates, 64.2%) and blaCTX-M-15 (present in 229 isolates, 78.2%); over half the isolates (159/293, 54.3%) were ST131 with blaCTX-M-15. blaOXA-1 was found in 149 ESBL producers (50.9%) and blaTEM-1/191 in 137 (46.8%). Irrespective of whether all isolates were considered, or ST131 alone, there were strong associations (P < 0.001) between co-carriage of blaOXA-1 and reduced susceptibility to penicillin/inhibitor combinations, whereas there was no significant association with co-carriage of blaTEM-1/191. For piperacillin/tazobactam the modal MIC rose from 2 mg/L in the absence of blaOXA-1 to 8 or 16 mg/L in its presence; for co-amoxiclav the shift was smaller, from 4 or 8 to 16 mg/L, but crossed the breakpoint. blaOXA-1 was strongly associated with co-carriage also of aac(6')-Ib-cr, which compromises amikacin and tobramycin. Conclusions Co-carriage of OXA-1, a penicillinase with weak affinity for inhibitors, is a major correlate of resistance to piperacillin/tazobactam and co-amoxiclav in E. coli and is commonly associated with co-carriage of aac(6')-Ib-cr, which narrows aminoglycoside options.
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Affiliation(s)
- David M Livermore
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, PHE National Infection Service, London, UK.,Norwich Medical School, University of East Anglia, Norwich, UK
| | - Michaela Day
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, PHE National Infection Service, London, UK
| | | | - Katie L Hopkins
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, PHE National Infection Service, London, UK
| | | | - David W Wareham
- Blizard Institute, Queen Mary University of London, London, UK
| | | | - Michel Doumith
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, PHE National Infection Service, London, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit, PHE National Infection Service, London, UK
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11
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Mlynarcik P, Chalachanova A, Vagnerovă I, Holy O, Zatloukalova S, Kolar M. PCR Detection of Oxacillinases in Bacteria. Microb Drug Resist 2020; 26:1023-1037. [PMID: 32212994 DOI: 10.1089/mdr.2019.0330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Oxacillinases (OXA) have been mostly described in Enterobacteriaceae, Acinetobacter, and Pseudomonas species. Recent years have witnessed an increased prevalence of intrinsic and/or acquired β-lactamase-producing Acinetobacter in food-producing animals. This study was conducted to assess the prevalence of OXA among selected bacterial species and to characterize these enzymes by in silico analysis. Screening of OXA was performed by PCR amplification using specific pairs of oligonucleotides. Overall, 40 pairs of primers were designed, of which 6 were experimentally tested in vitro. Among 49 bacterial isolates examined, the presence of blaOXA-1-like genes was confirmed in 20 cases (41%; 19 times in Klebsiella pneumoniae and once in Enterobacter cloacae). No OXA were found in animal isolates. The study results confirmed the specificity of the designed oligonucleotide pairs. Furthermore, the designed primers were found to possess the ability to specifically detect 90.2% of all OXA. These facts suggest that the in silico and in vitro tested primers could be used for single or multiplex PCR to screen for the presence of OXA in various bacteria, as well as to monitor their spread. At the same time, the presence of conserved characteristic amino acids and motifs was confirmed by in silico analysis of sequences of representative members of OXA.
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Affiliation(s)
- Patrik Mlynarcik
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Andrea Chalachanova
- Department of Cell Biology and Genetics, Faculty of Science, Palacky University Olomouc, Olomouc, Czech Republic
| | - Iva Vagnerovă
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Ondrej Holy
- Department of Public Health, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Simona Zatloukalova
- Department of Public Health, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Milan Kolar
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic.,Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
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12
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Luque-González P, López-Cerero L, Díaz-de-Alba P, Rodríguez-Martínez JM. Association of bla OXA-1, and aac(6')-Ib-cr with ST405 K. pneumoniae clone. Enferm Infecc Microbiol Clin 2019; 37:417-418. [PMID: 31155040 DOI: 10.1016/j.eimc.2018.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/28/2018] [Accepted: 06/01/2018] [Indexed: 10/28/2022]
Affiliation(s)
- P Luque-González
- Departamento de Microbiologia, Facultad de Medicina, Seville, Spain
| | - L López-Cerero
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla/Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain.
| | - P Díaz-de-Alba
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla/Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain
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13
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Pereira JL, Volcão LM, Klafke GB, Vieira RS, Gonçalves CV, Ramis IB, da Silva PEA, von Groll A. Antimicrobial Resistance and Molecular Characterization of Extended-Spectrum β-Lactamases of Escherichia coli and Klebsiella spp. Isolates from Urinary Tract Infections in Southern Brazil. Microb Drug Resist 2018; 25:173-181. [PMID: 30133334 DOI: 10.1089/mdr.2018.0046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The objective of this study was to evaluate the frequency of different extended-spectrum β-lactamases (ESBL) as well as to associate these ESBL with antimicrobial (ATM) resistance in Escherichia coli and Klebsiella spp. isolates from outpatients and inpatients with urinary tract infections. The study included 435 consecutive nonduplicate clinical isolates, including 362 E. coli isolates, 62 Klebsiella pneumoniae isolates, and 11 K. oxytoca isolates. Isolates were obtained from patients who were treated in a University Hospital between August 2012 and July 2013. Three multiplex PCR were performed to identify the ESBL groups. A total of 48 (11%) ESBL-producing isolates were found. The risk for the ESBL presence was significantly higher in males (26.4%) than females (8%), from hospital-acquired infections (29.1%) than community-acquired infections (7.0%) and in Klebsiella spp. (27.4%) than in E. coli (7.7%). ESBL-producing isolates presented a significantly higher percentage of resistance in 21 of the 23 ATMs analyzed. The CTX-M-1 group was the most predominant ESBL identified. The blaCTX-M-1-group gene was found in 56% of the total ESBL producers from community and in 42.4% from hospital origins; it was followed in frequency by the blaCTX-M-8/25-group, also found in both environments. Klebsiella spp. presented the largest variety of β-lactamase enzyme combinations and a higher level of resistance to cefotaxime. These findings contribute to better knowledge of the epidemiology of ESBL enzymes and are alarming for the reduced therapeutic options available for the risk groups identified in the studied populations.
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Affiliation(s)
- Juliano Lacava Pereira
- 1 Faculdade de Medicina, Medical Microbiology Research Center (NUPEMM), Universidade Federal do Rio Grande-FURG , Rio Grande, Brazil
| | - Lisiane Martins Volcão
- 1 Faculdade de Medicina, Medical Microbiology Research Center (NUPEMM), Universidade Federal do Rio Grande-FURG , Rio Grande, Brazil
| | - Gabriel Baracy Klafke
- 2 Faculdade de Medicina, Universidade Federal do Rio Grande-FURG , Rio Grande, Brazil
| | - Roseli Stone Vieira
- 3 Hospital Universitário Dr. Miguel Riet Correa , Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
| | | | - Ivy Bastos Ramis
- 1 Faculdade de Medicina, Medical Microbiology Research Center (NUPEMM), Universidade Federal do Rio Grande-FURG , Rio Grande, Brazil
| | - Pedro Eduardo Almeida da Silva
- 1 Faculdade de Medicina, Medical Microbiology Research Center (NUPEMM), Universidade Federal do Rio Grande-FURG , Rio Grande, Brazil
| | - Andrea von Groll
- 1 Faculdade de Medicina, Medical Microbiology Research Center (NUPEMM), Universidade Federal do Rio Grande-FURG , Rio Grande, Brazil
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14
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Li P, Wang M, Li X, Hu F, Yang M, Xie Y, Cao W, Xia X, Zheng R, Tian J, Zhang K, Chen F, Tang A. ST37 Klebsiella pneumoniae: development of carbapenem resistance in vivo during antimicrobial therapy in neonates. Future Microbiol 2017; 12:891-904. [PMID: 28699768 DOI: 10.2217/fmb-2016-0165] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To investigate the mechanism leading to in vivo carbapenem resistance development in Klebsiella pneumoniae. Methods: Carbapenemase was detected using the modified carbapenem inactivation method. β-lactamases resistant genes were identified by PCR and sequencing. Clonal relatedness was evaluated by random amplified polymorphic DNA and multiple locus sequence typing. The relationship between sequence typing and resistant genes was analyzed by using the chi-squared test. Results: All ST37 carbapenem-resistant isolates were blaOXA-1 positive and all ST37 carbapenem-sensitive isolates were blaOXA-1 negative at Stage I. A significant relationship between carbapenem resistance and blaOXA-1 was observed. The blaOXA-1 -positive rate was significantly higher in ST37 K. pneumoniae than others. Conclusion: This is the first study about the development of carbapenem resistance in vivo potentially mediated by blaOXA-1 in ST37 K. pneumoniae among neonates.
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Affiliation(s)
- Pengling Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Min Wang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xianping Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Feihu Hu
- Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Min Yang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yixin Xie
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Wei Cao
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xiaomeng Xia
- Department of Obstetrics & Gynecology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Rong Zheng
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Jingjing Tian
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Kan Zhang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Fang Chen
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Aiguo Tang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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15
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Dsouza R, Pinto NA, Hwang I, Cho Y, Yong D, Choi J, Lee K, Chong Y. Panel strain of Klebsiella pneumoniae for beta-lactam antibiotic evaluation: their phenotypic and genotypic characterization. PeerJ 2017; 5:e2896. [PMID: 28133574 PMCID: PMC5251932 DOI: 10.7717/peerj.2896] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/10/2016] [Indexed: 01/21/2023] Open
Abstract
Klebsiella pneumoniae is responsible for numerous infections caused in hospitals, leading to mortality and morbidity. It has been evolving as a multi-drug resistant pathogen, acquiring multiple resistances such as such as horizontal gene transfer, transposon-mediated insertions or change in outer membrane permeability. Therefore, constant efforts are being carried out to control the infections using various antibiotic therapies. Considering the severity of the acquired resistance, we developed a panel of strains of K. pneumoniae expressing different resistance profiles such as high-level penicillinase and AmpC production, extended spectrum beta-lactamases and carbapenemases. Bacterial strains expressing different resistance phenotypes were collected and examined for resistance genes, mutations and porin alterations contributing to the detected phenotypes. Using the Massive parallel sequencing (MPS) technology we have constructed and genotypically characterized the panel strains to elucidate the multidrug resistance. These panel strains can be used in the clinical laboratory as standard reference strains. In addition, these strains could be significant in the field of pharmaceuticals for the antibiotic drug testing to verify its efficiency on pathogens expressing various resistances.
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Affiliation(s)
- Roshan Dsouza
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine , Seoul , South Korea
| | - Naina Adren Pinto
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | - InSik Hwang
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | | | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine , Seoul , South Korea
| | - Jongrak Choi
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine , Seoul , South Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine , Seoul , South Korea
| | - Yunsop Chong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine , Seoul , South Korea
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