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Dulyayangkul P, Beavis T, Lee WWY, Ardagh R, Edwards F, Hamilton F, Head I, Heesom KJ, Mounsey O, Murarik M, Pinweha P, Reding C, Satapoomin N, Shaw JM, Takebayashi Y, Tooke CL, Spencer J, Williams PB, Avison MB. Harvesting and amplifying gene cassettes confers cross-resistance to critically important antibiotics. PLoS Pathog 2024; 20:e1012235. [PMID: 38843111 PMCID: PMC11156391 DOI: 10.1371/journal.ppat.1012235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/30/2024] [Indexed: 06/09/2024] Open
Abstract
Amikacin and piperacillin/tazobactam are frequent antibiotic choices to treat bloodstream infection, which is commonly fatal and most often caused by bacteria from the family Enterobacterales. Here we show that two gene cassettes located side-by-side in and ancestral integron similar to In37 have been "harvested" by insertion sequence IS26 as a transposon that is widely disseminated among the Enterobacterales. This transposon encodes the enzymes AAC(6')-Ib-cr and OXA-1, reported, respectively, as amikacin and piperacillin/tazobactam resistance mechanisms. However, by studying bloodstream infection isolates from 769 patients from three hospitals serving a population of 1.2 million people in South West England, we show that increased enzyme production due to mutation in an IS26/In37-derived hybrid promoter or, more commonly, increased transposon copy number is required to simultaneously remove these two key therapeutic options; in many cases leaving only the last-resort antibiotic, meropenem. These findings may help improve the accuracy of predicting piperacillin/tazobactam treatment failure, allowing stratification of patients to receive meropenem or piperacillin/tazobactam, which may improve outcome and slow the emergence of meropenem resistance.
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Affiliation(s)
- Punyawee Dulyayangkul
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | - Thomas Beavis
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Winnie W. Y. Lee
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Robbie Ardagh
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Frances Edwards
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
- North Bristol NHS Trust, Bristol, United Kingdom
| | | | - Ian Head
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Somerset NHS Foundation Trust, Taunton, United Kingdom
| | - Kate J. Heesom
- Bristol University Proteomics Facility, University of Bristol, Bristol, United Kingdom
| | - Oliver Mounsey
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Marek Murarik
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Peechanika Pinweha
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Carlos Reding
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Naphat Satapoomin
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - John M. Shaw
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Catherine L. Tooke
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - James Spencer
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Philip B. Williams
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Matthew B. Avison
- School of Cellular & Molecular Medicine, University of Bristol, Bristol, United Kingdom
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Struggle To Survive: the Choir of Target Alteration, Hydrolyzing Enzyme, and Plasmid Expression as a Novel Aztreonam-Avibactam Resistance Mechanism. mSystems 2020; 5:5/6/e00821-20. [PMID: 33144312 PMCID: PMC7646527 DOI: 10.1128/msystems.00821-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Aztreonam-avibactam is a promising antimicrobial combination against multidrug-resistant organisms, such as carbapenemase-producing Enterobacterales Resistance to aztreonam-avibactam has been found, but the resistance mechanism remains poorly studied. We recovered three Escherichia coli isolates of an almost identical genome but exhibiting varied aztreonam-avibactam resistance. The isolates carried a cephalosporinase gene, bla CMY-42, on IncIγ plasmids with a single-nucleotide variation in an antisense RNA-encoding gene, inc, of the replicon. The isolates also had four extra amino acids (YRIK) in penicillin-binding protein 3 (PBP3) due to a duplication of a 12-nucleotide (TATCGAATTAAC) stretch in pbp3 By cloning and plasmid-curing experiments, we found that elevated CMY-42 cephalosporinase production or amino acid insertions in PBP3 alone mediated slightly reduced susceptibility to aztreonam-avibactam, but their combination conferred aztreonam-avibactam resistance. We show that the elevated CMY-42 production results from increased plasmid copy numbers due to mutations in inc We also verified the findings using in vitro mutation assays, in which aztreonam-avibactam-resistant mutants also had mutations in inc and elevated CMY-42 production compared with the parental strain. This choir of target modification, hydrolyzing enzyme, and plasmid expression represents a novel, coordinated, complex antimicrobial resistance mechanism and also reflects the struggle of bacteria to survive under selection pressure imposed by antimicrobial agents.IMPORTANCE Carbapenemase-producing Enterobacterales (CPE) is a serious global challenge with limited therapeutic options. Aztreonam-avibactam is a promising antimicrobial combination with activity against CPE producing serine-based carbapenemases and metallo-β-lactamases and has the potential to be a major option for combatting CPE. Aztreonam-avibactam resistance has been found, but resistance mechanisms remain largely unknown. Understanding resistance mechanisms is essential for optimizing treatment and developing alternative therapies. Here, we found that either penicillin-binding protein 3 modification or the elevated expression of cephalosporinase CMY-42 due to increased plasmid copy numbers does not confer resistance to aztreonam-avibactam, but their combination does. We demonstrate that increased plasmid copy numbers result from mutations in antisense RNA-encoding inc of the IncIγ replicon. The findings reveal that antimicrobial resistance may be due to concerted combinatorial effects of target alteration, hydrolyzing enzyme, and plasmid expression and also highlight that resistance to any antimicrobial combination will inevitably emerge.
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Hong JS, Song W, Park HM, Oh JY, Chae JC, Jeong S, Jeong SH. Molecular Characterization of Fecal Extended-Spectrum β-Lactamase- and AmpC β-Lactamase-Producing Escherichia coli From Healthy Companion Animals and Cohabiting Humans in South Korea. Front Microbiol 2020; 11:674. [PMID: 32351490 PMCID: PMC7174606 DOI: 10.3389/fmicb.2020.00674] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/24/2020] [Indexed: 11/13/2022] Open
Abstract
This study aimed to describe the distribution and characterization of fecal extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli isolates from healthy companion animals and cohabiting humans. A total of 968 rectal swab samples from 340 participants, including healthy companion animals and cohabiting humans, were collected from 130 households in South Korea from 2018 to 2019. To determine the bacterial profiles of the participants, several experiments were performed as follows: antimicrobial susceptibility testing, PCR and direct sequencing for ESBL/AmpC production, PFGE, MLST, whole genome sequencing and qRT-PCR. A total of 24.9 and 21.5% of the E. coli isolates from healthy companion animals and cohabiting humans were ESBL/AmpC producers, respectively. The blaCTX–M–14 gene was the most prevalent ESC resistance gene in both pets (n = 25/95, 26.3%) and humans (n = 44/126, 34.9%). The blaCMY–2 gene was also largely detected in pets (n = 19, 20.0%). Overall, intrahousehold pet-human sharing of ESBL/AmpC E. coli isolates occurred in 4.8% of households, and the isolates were all CTX-M-14 producers. In particular, ten CMY-2-producing E. coli isolates from seven dogs and three humans in the different households belonged to the same pulsotype. The MIC values of cefoxitin and the transcription level in CMY-2-producing E. coli isolates were proportional to the blaCMY–2 copy number on the chromosome. Our results showed that the clonal spread of fecal ESBL/AmpC-producing E. coli households’ isolates between healthy companion animals and cohabiting humans was rare, but it could happen. In particular, E. coli ST405 isolates carrying multiple blaCMY–2 genes on the chromosome was sporadically spread between companion animals and humans in South Korea.
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Affiliation(s)
- Jun Sung Hong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Hee-Myung Park
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Jae-Young Oh
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Jong-Chan Chae
- Division of Biotechnology, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan, South Korea
| | - Seri Jeong
- Department of Laboratory Medicine, College of Medicine, Hallym University, Chuncheon, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
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Heß S, Kneis D, Österlund T, Li B, Kristiansson E, Berendonk TU. Sewage from Airplanes Exhibits High Abundance and Diversity of Antibiotic Resistance Genes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:13898-13905. [PMID: 31713420 DOI: 10.1021/acs.est.9b03236] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Airplane sanitary facilities are shared by an international audience. We hypothesized the corresponding sewage to be an extraordinary source of antibiotic-resistant bacteria (ARB) and resistance genes (ARG) in terms of diversity and quantity. Accordingly, we analyzed ARG and ARB in airplane-borne sewage using complementary approaches: metagenomics, quantitative polymerase chain reaction (qPCR), and cultivation. For the purpose of comparison, we also quantified ARG and ARB in the inlets of municipal treatment plants with and without connection to airports. As expected, airplane sewage contained an extraordinarily rich set of mobile ARG, and the relative abundances of genes were mostly increased compared to typical raw sewage of municipal origin. Moreover, combined resistance against third-generation cephalosporins, fluorochinolones, and aminoglycosides was unusually common (28.9%) among Escherichia coli isolated from airplane sewage. This percentage exceeds the one reported for German clinical isolates by a factor of 8. Our findings suggest that airplane-borne sewage can effectively contribute to the fast and global spread of antibiotic resistance.
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Affiliation(s)
- Stefanie Heß
- Dept. of Microbiology , University of Helsinki , 00029 Helsinki , Finland
| | - David Kneis
- Institute of Hydrobiology , TU Dresden , 01217 Dresden , Germany
- Helmholtz-Centre for Environmental Research , 39114 Magdeburg , Germany
| | - Tobias Österlund
- Mathematical Sc. Dept. , Chalmers University of Technology , 41296 Gothenburg , Sweden
| | - Bing Li
- Division of Energy and Environment, Graduate School at Shenzhen , Tsinghua University , Shenzhen 518055 , China
| | - Erik Kristiansson
- Mathematical Sc. Dept. , Chalmers University of Technology , 41296 Gothenburg , Sweden
- Centre for Antibiotic Resistance Research (CARe) , University of Gothenburg , 41346 Gothenburg , Sweden
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Dissemination prevention of antibiotic resistant and facultative pathogenic bacteria by ultrafiltration and ozone treatment at an urban wastewater treatment plant. Sci Rep 2019; 9:12843. [PMID: 31492933 PMCID: PMC6731226 DOI: 10.1038/s41598-019-49263-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/22/2019] [Indexed: 11/10/2022] Open
Abstract
Conventional wastewater treatment is not sufficient for the removal of hygienically relevant bacteria and achieves only limited reductions. This study focuses on the reduction efficiencies of two semi-industrial ultrafiltration units operating at a large scale municipal wastewater treatment plant. In total, 7 clinically relevant antibiotic resistance genes, together with 3 taxonomic gene markers targeting specific facultative pathogenic bacteria were analysed via qPCR analyses before and after advanced treatment. In parallel with membrane technologies, an ozone treatment (1 g ozone/g DOC) was performed for comparison of the different reduction efficiencies. Both ultrafiltration units showed increased reduction efficiencies for facultative pathogenic bacteria and antibiotic resistance genes of up to 6 log units, resulting mostly in a strong reduction of the bacterial targets. In comparison, the ozone treatment showed some reduction efficiency, but was less effective compared with ultrafiltration due to low ozone dosages frequently used for micro-pollutant removal at municipal wastewater treatment plants. Additionally, metagenome analyses demonstrated the accumulation of facultative pathogenic bacteria, antibiotic resistance genes, virulence factor genes, and metabolic gene targets in the back flush retentate of the membranes, which opens further questions about retentate fluid material handling at urban wastewater treatment plants.
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Donà V, Scheidegger M, Pires J, Furrer H, Atkinson A, Babouee Flury B. Gradual in vitro Evolution of Cefepime Resistance in an ST131 Escherichia coli Strain Expressing a Plasmid-Encoded CMY-2 β-Lactamase. Front Microbiol 2019; 10:1311. [PMID: 31244817 PMCID: PMC6581752 DOI: 10.3389/fmicb.2019.01311] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/27/2019] [Indexed: 11/13/2022] Open
Abstract
Background In a previous report, a clinical ST131 Escherichia coli isolate (Ec-1),producing a plasmid-encoded AmpC β-lactamase CMY-2, evolved in vivo under cefepime (FEP) treatment to the FEP-resistant Ec-2 strain expressing an extended-spectrum β-lactamase CMY-33. To compare factors responsible for in vitro and in vivo FEP resistance, we reproduced in vitro FEP resistance evolution in Ec-1. Methods FEP-resistant mutants were generated by subjecting Ec-1 (FEP MIC = 0.125 mg/L) to sub-inhibitory concentrations of FEP. MICs were obtained by broth microdilution or Etest. Strains were sequenced on an Illumina HiSeq platform. Transcriptional levels and plasmid copy numbers were determined by real-time PCR. Outer membrane proteins (OMPs) were extracted and separated by SDS-PAGE. Growth kinetics was evaluated by measuring OD450. Results The CMY-2 expressed by Ec-1 evolved to a CMY-69 (strain EC-4) by an Ala294Pro substitution after 24 passages. After 30 passages, the FEP MIC increased to 256 mg/L (strain EC-32). SDS PAGE did not reveal any lack of OMPs in the mutant strains. However, blaCMY transcription levels were up to 14-times higher than in Ec-1, which was partially explained by mutations in the upstream region of repA resulting in a higher copy number of the blaCMY-harboring IncI1 plasmid. All mutants showed a slight growth defect but no significant difference in relative growth rates compared to Ec-1. Conclusion In vitro sub-inhibitory concentrations of FEP resulted in the selection of resistance mutations altering the H-10 helix of the CMY-2 and increasing the plasmid copy number. Appropriate dosing strategies may help preventing resistance evolution during treatments.
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Affiliation(s)
- Valentina Donà
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - João Pires
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andrew Atkinson
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Baharak Babouee Flury
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.,Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1141] [Impact Index Per Article: 190.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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Roschanski N, Fischer J, Falgenhauer L, Pietsch M, Guenther S, Kreienbrock L, Chakraborty T, Pfeifer Y, Guerra B, Roesler UH. Retrospective Analysis of Bacterial Cultures Sampled in German Chicken-Fattening Farms During the Years 2011-2012 Revealed Additional VIM-1 Carbapenemase-Producing Escherichia coli and a Serologically Rough Salmonella enterica Serovar Infantis. Front Microbiol 2018; 9:538. [PMID: 29636734 PMCID: PMC5880886 DOI: 10.3389/fmicb.2018.00538] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/08/2018] [Indexed: 11/30/2022] Open
Abstract
Carbapenems are last-resort antibiotics used in human medicine. The increased detection of carbapenem-resistant Enterobacteriaceae (CRE) is therefore worrying. In 2011 we reported the first livestock-associated VIM-1-producing Salmonella (S.) enterica serovar Infantis (R3) isolate from dust, sampled in a German chicken fattening farm. Due to this observation we retrospectively investigated more than 536 stored bacterial cultures, isolated from 45 chicken fattening farms during the years 2011 and 2012. After a non-selective overnight incubation, the bacteria were transferred to selective media. Escherichia (E.) coli and Salmonella growing on these media were further investigated, including antibiotic susceptibility testing, carbapenemase gene screening and whole genome sequencing (WGS). In total, four CRE were found in three out of 45 investigated farms: Besides R3, one additional Salmonella (G-336-1a) as well as two E. coli isolates (G-336-2, G-268-2). All but G-268-2 harbored the blaVIM-1 gene. Salmonella isolates R3 and G-336-1 were closely related although derived from two different farms. All three blaVIM-1-encoding isolates possessed identical plasmids and the blaVIM-1- containing transposon showed mobility at least in vitro. In isolate G-268-2, the AmpC beta-lactamase gene blaCMY-2 but no known carbapenemase gene was identified. However, a transfer of the phenotypic resistance was possible. Furthermore, G-268-2 contained the mcr-1 gene, combining phenotypical carbapenem- as well as colistin resistance in one isolate. Carbapenem-resistant Enterobacteriaceae have been found in three out of 45 investigated chicken flocks. This finding is alarming and emphasizes the importance of intervention strategies to contain the environmental spread of resistant bacteria in animals and humans.
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Affiliation(s)
- Nicole Roschanski
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Jennie Fischer
- Department for Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - Linda Falgenhauer
- German Center for Infection Research, Institute of Medical Microbiology, Justus Liebig University Giessen, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Michael Pietsch
- FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Sebastian Guenther
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Lothar Kreienbrock
- Epidemiology and Information Processing and WHO Collaborating Center for Research and Training for Health at the Human-Animal-Environment Interface, Institute for Biometry, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Trinad Chakraborty
- German Center for Infection Research, Institute of Medical Microbiology, Justus Liebig University Giessen, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Yvonne Pfeifer
- FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Beatriz Guerra
- Department for Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - Uwe H Roesler
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
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Occurrence of bla CMY-42 on an IncI1 plasmid in multidrug-resistant Escherichia coli from a tertiary referral hospital in India. J Glob Antimicrob Resist 2018; 14:78-82. [PMID: 29505913 DOI: 10.1016/j.jgar.2018.02.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES Plasmids of different replicon types are believed to be associated with the carriage and transmission of antimicrobial resistance genes. The present study was undertaken to examine the association of blaCIT with particular plasmid types and to identify Escherichia coli strains involve in the maintenance of this resistance determinant in the plasmid. METHODS Phenotypic screening of AmpC β-lactamases was performed by the modified three-dimensional extract method, followed by antimicrobial susceptibility testing and determination of minimum inhibitory concentrations (MICs). Genotyping screening of β-lactamase genes was performed by PCR assay, followed by sequencing. Transferability of the blaCMY gene was performed by transformation and conjugation experiments. Plasmid incompatibility typing and DNA fingerprinting by enterobacterial repetitive intergenic consensus (ERIC)-PCR were performed. RESULTS Among 203 E. coli obtained from different clinical specimens (pus, urine, stool and sputum), 37 were detected as harbouring the blaCIT gene and sequencing of this gene showed nucleotide sequence similarity with the blaCMY-42 variant. This study revealed IncI1-type plasmids as carriers of blaCMY-42 and its propagation within E. coli ST5377, ST361 and ST672. According to the stability results, the blaCMY-42-encoding plasmid can be maintained in E. coli strains for a longer duration without any antimicrobial pressure. CONCLUSIONS These finding document blaCMY-42 on IncI1-type plasmids, which are considered to be the main vehicles for the spread of blaCMY-42 in this hospital setting. Thus, a proper strategy should be developed to curb the expansion of IncI1-type plasmids in the hospital and community environment.
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Acquisition of Carbapenem Resistance by Plasmid-Encoded-AmpC-Expressing Escherichia coli. Antimicrob Agents Chemother 2016; 61:AAC.01413-16. [PMID: 27799202 DOI: 10.1128/aac.01413-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/22/2016] [Indexed: 01/06/2023] Open
Abstract
Although AmpC β-lactamases can barely degrade carbapenems, if at all, they can sequester them and prevent them from reaching their targets. Thus, carbapenem resistance in Escherichia coli and other Enterobacteriaceae can result from AmpC production and simultaneous reduction of antibiotic influx into the periplasm by mutations in the porin genes. Here we investigated the route and genetic mechanisms of acquisition of carbapenem resistance in a clinical E. coli isolate carrying blaCMY-2 on a plasmid by selecting for mutants that are resistant to increasing concentrations of meropenem. In the first step, the expression of OmpC, the only porin produced in the strain under laboratory conditions, was lost, leading to reduced susceptibility to meropenem. In the second step, the expression of the CMY-2 β-lactamase was upregulated, leading to resistance to meropenem. The loss of OmpC was due to the insertion of an IS1 element into the ompC gene or to frameshift mutations and premature stop codons in this gene. The blaCMY-2 gene was found to be located on an IncIγ plasmid, and overproduction of the CMY-2 enzyme resulted from an increased plasmid copy number due to a nucleotide substitution in the inc gene. The clinical relevance of these genetic mechanisms became evident from the analysis of previously isolated carbapenem-resistant clinical isolates, which appeared to carry similar mutations.
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11
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Fan D, Liu C, Liu L, Zhu L, Peng F, Zhou Q. Large-scale gene expression profiling reveals physiological response to deletion of chaperone dnaKJ in Escherichia coli. Microbiol Res 2016; 186-187:27-36. [PMID: 27242140 DOI: 10.1016/j.micres.2016.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/28/2016] [Accepted: 03/03/2016] [Indexed: 11/18/2022]
Abstract
Chaperone DnaK and its co-chaperone DnaJ plays various essential roles such as in assisting in the folding of nascent peptides, preventing protein aggregation and maintaining cellular protein homeostasis. Global transcriptional changes in vivo associated with deletion of dnaKJ were monitored using DNA microarray to elucidate the role of DnaKJ at the transcriptional level. Microarray profiling and bioinformatics analysis revealed that a few chaperone and protease genes, stress-related genes and genes involved in the tricarboxylic acid cycle and oxidative phosphorylation were up-regulated, whereas various transporter genes, pentose phosphate pathway and transcriptional regulation related genes were down-regulated. This study is the first to systematically analyze the alterations at the transcriptional level in vivo in deletion of dnaKJ. Fatty acid methyl esters analysis indicated that the amount of unsaturated fatty acid sharply increased and subcellular location prediction analysis showed a marked decrease in transcription of inner-membrane protein genes, which might have triggered the development of aberrant cell shape and susceptibility for some antibiotics in the ΔdnaKJ strain.
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Affiliation(s)
- Dongjie Fan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Harbin 150080, China.
| | - Lushan Liu
- Department of Emergency, Beijing Bo'ai Hospital, 10 Jiaomen North Road, Fengtai District, Beijing, 100068, China; China Rehabilitation Research Center, Capital Medical University, Beijing 100068, China
| | - Lingxiang Zhu
- National Research Institute for Family Planning (NRIFP), Beijing 100081, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan430072, China; Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan 430072, China
| | - Qiming Zhou
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Street, Harbin 150080, China.
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Geyer CN, Fowler RC, Johnson JR, Johnston B, Weissman SJ, Hawkey P, Hanson ND. Evaluation of CTX-M steady-state mRNA, mRNA half-life and protein production in various STs of Escherichia coli. J Antimicrob Chemother 2015; 71:607-16. [PMID: 26612874 PMCID: PMC4743699 DOI: 10.1093/jac/dkv388] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/19/2015] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES High levels of β-lactamase production can impact treatment with a β-lactam/β-lactamase inhibitor combination. Goals of this study were to: (i) compare the mRNA and protein levels of CTX-M-15- and CTX-M-14-producing Escherichia coli from 18 different STs and 10 different phylotypes; (ii) evaluate the mRNA half-lives and establish a role for chromosomal- and/or plasmid-encoded factors; and (iii) evaluate the zones of inhibition for piperacillin/tazobactam and ceftolozane/tazobactam. METHODS Disc diffusion was used to establish zone size. RNA analysis was accomplished using real-time RT-PCR and CTX-M protein levels were evaluated by immunoblotting. Clinical isolates, transformants and transconjugants were used to evaluate mRNA half-lives. RESULTS mRNA levels of CTX-M-15 were up to 165-fold higher compared with CTX-M-14. CTX-M-15 protein levels were 2-48-fold less than their respective transcript levels, while CTX-M-14 protein production was comparable to the observed transcript levels. Nineteen of 25 E. coli (76%) had extended CTX-M-15 mRNA half-lives of 5-15 min and 16 (100%) CTX-M-14 isolates had mRNA half-lives of <2-3 min. Transformants had mRNA half-lives of <2 min for both CTX-M-type transcripts, while transconjugant mRNA half-lives corresponded to the half-life of the donor. Ceftolozane/tazobactam zone sizes were ≥19 mm, while piperacillin/tazobactam zone sizes were ≥17 mm. CONCLUSIONS CTX-M-15 mRNA and protein production did not correlate. Neither E. coli ST nor phylotype influenced the variability observed for CTX-M-15 mRNA or protein produced. mRNA half-life is controlled by a plasmid-encoded factor and may influence mRNA transcript levels, but not protein levels.
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Affiliation(s)
- Chelsie N Geyer
- Department of Medical Microbiology and Immunology, Center for Research in Anti-Infectives and Biotechnology, Creighton University School of Medicine, 2500 California Plaza, Omaha, NE 68178, USA
| | - Randal C Fowler
- Department of Medical Microbiology and Immunology, Center for Research in Anti-Infectives and Biotechnology, Creighton University School of Medicine, 2500 California Plaza, Omaha, NE 68178, USA
| | - James R Johnson
- Veterans Affairs Medical Center, Minneapolis, MN, USA University of Minnesota, Minneapolis, MN, USA
| | - Brian Johnston
- Veterans Affairs Medical Center, Minneapolis, MN, USA University of Minnesota, Minneapolis, MN, USA
| | - Scott J Weissman
- Center for Global Infectious Diseases Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Peter Hawkey
- Public Health England (PHE), West Midlands Public Health Laboratory, Heart of England NHS Foundation Trust, Bordesley Green East, Birmingham B9 5SS, UK Institute of Microbiology and Infection, School of Biosciences, School of Immunity and Infection, University of Birmingham, Edgbaston Campus, Birmingham B15 2TT, UK
| | - Nancy D Hanson
- Department of Medical Microbiology and Immunology, Center for Research in Anti-Infectives and Biotechnology, Creighton University School of Medicine, 2500 California Plaza, Omaha, NE 68178, USA
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Fowler RC, Hanson ND. The OpdQ porin of Pseudomonas aeruginosa is regulated by environmental signals associated with cystic fibrosis including nitrate-induced regulation involving the NarXL two-component system. Microbiologyopen 2015; 4:967-82. [PMID: 26459101 PMCID: PMC4694141 DOI: 10.1002/mbo3.305] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is a versatile opportunistic pathogen that causes chronic infections in immunocompromised hosts. Multiple porins modulate outer membrane permeability under various environmental conditions. The lung environment of cystic fibrosis (CF) patients is unique with changes occurring in nutrient availability, osmolarity, and oxygen content. Although P. aeruginosa gene expression is modified under these conditions, little is known about how they influence porin regulation. In this study, we evaluated the regulation of the outer membrane porin OpdQ, a member of the OprD family of porins, with regard to oxygen, nitrate, and/or NaCl levels. We demonstrated using promoter::fusion clones of P. aeruginosa PAO1 and clinical strains collected from CF patients that OpdQ was transcriptionally repressed under low oxygen but increased in the presence of nitrate. The nitrate‐induced regulation of OpdQ was found to be dependent on the transcription factor NarL via the NarXL two‐component system. In addition, NaCl‐induced osmotic stress increased OpdQ production among most of the clinical strains evaluated. In conclusion, these data identify for the first time that specific environmental cues associated with the CF microenvironment influence porin regulation, and that the nitrate‐induced regulation of OpdQ is associated with nitrate metabolism via the NarXL two‐component system of P. aeruginosa.
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Affiliation(s)
- Randal C Fowler
- Department of Medical Microbiology and Immunology, Center for Research in Anti-Infectives and Biotechnology, Creighton University School of Medicine, 2500 California Plaza, Omaha, Nebraska, 68178
| | - Nancy D Hanson
- Department of Medical Microbiology and Immunology, Center for Research in Anti-Infectives and Biotechnology, Creighton University School of Medicine, 2500 California Plaza, Omaha, Nebraska, 68178
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Xu W, Chen H, He CL, Wang Q. Deep sequencing-based identification of small regulatory RNAs in Synechocystis sp. PCC 6803. PLoS One 2014; 9:e92711. [PMID: 24647397 PMCID: PMC3960264 DOI: 10.1371/journal.pone.0092711] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 02/24/2014] [Indexed: 11/30/2022] Open
Abstract
Synechocystis sp. PCC 6803 is a genetically tractable model organism for photosynthesis research. The genome of Synechocystis sp. PCC 6803 consists of a circular chromosome and seven plasmids. The importance of small regulatory RNAs (sRNAs) as mediators of a number of cellular processes in bacteria has begun to be recognized. However, little is known regarding sRNAs in Synechocystis sp. PCC 6803. To provide a comprehensive overview of sRNAs in this model organism, the sRNAs of Synechocystis sp. PCC 6803 were analyzed using deep sequencing, and 7,951,189 reads were obtained. High quality mapping reads (6,127,890) were mapped onto the genome and assembled into 16,192 transcribed regions (clusters) based on read overlap. A total number of 5211 putative sRNAs were revealed from the genome and the 4 megaplasmids, and 27 of these molecules, including four from plasmids, were confirmed by RT-PCR. In addition, possible target genes regulated by all of the putative sRNAs identified in this study were predicted by IntaRNA and analyzed for functional categorization and biological pathways, which provided evidence that sRNAs are indeed involved in many different metabolic pathways, including basic metabolic pathways, such as glycolysis/gluconeogenesis, the citrate cycle, fatty acid metabolism and adaptations to environmentally stress-induced changes. The information from this study provides a valuable reservoir for understanding the sRNA-mediated regulation of the complex physiology and metabolic processes of cyanobacteria.
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Affiliation(s)
- Wen Xu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Chen-Liu He
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Qiang Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
- * E-mail:
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Multiplex high-resolution melting analysis as a diagnostic tool for detection of plasmid-mediated AmpC β-lactamase genes. J Clin Microbiol 2014; 52:1262-5. [PMID: 24478414 DOI: 10.1128/jcm.00214-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-resolution melting (HRM) analysis can be a diagnostic tool to evaluate the presence of resistance genes with the added bonus of discriminating sequence modifications. A real-time, multiplex PCR assay using HRM was designed for the detection of plasmid-mediated ampC genes. The specificity and sensitivity of this assay were 96% and 100%, respectively.
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Roth AL, Lister PD, Hanson ND. Effect of drug treatment options on the mobility and expression of blaKPC. J Antimicrob Chemother 2013; 68:2779-85. [PMID: 23861308 DOI: 10.1093/jac/dkt280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES Both transposition and increases in gene expression have been implicated in the success of KPC-producing pathogens, but the stimulus required for these phenomena are unknown. It is possible that exposure to antimicrobials during patient treatment increases bla(KPC) expression or induces Tn4401 transposition. The purpose of this study was to determine if exposure to carbapenems or other antimicrobial drug classes could stimulate expression of bla(KPC) or the in vitro transposition of Tn4401. METHODS Five KPC-producing clinical isolates were evaluated in this study. Gene expression of RNA from each isolate exposed to subinhibitory, MIC or suprainhibitory levels of antibiotics was evaluated using real-time RT-PCR. Southern blots were performed on plasmids from isolates exposed to subinhibitory levels of antibiotics. RESULTS There were subtle changes in bla(KPC) RNA expression following antibiotic exposure that were both strain and drug dependent. Multiple plasmids ranging from ~8 to >200 kb were observed for the Enterobacteriaceae isolates, whereas the Pseudomonas aeruginosa isolate had one ~55 kb plasmid. No changes in hybridization patterns or binding intensity for the bla(KPC) probe were observed after antibiotic exposure. CONCLUSIONS While the changes in bla(KPC) RNA expression are subtle, the different responses observed suggest both strain- and genera-specific variations in response to different antibiotic treatments.
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Affiliation(s)
- Amanda L Roth
- Center for Research in Anti-Infectives and Biotechnology, Department of Medical Microbiology and Immunology, Creighton University School of Medicine, 2500 California Plaza, Omaha, NE 68178, USA
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