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Boralli CMDS, Paganini JA, Meneses RS, Mata CPSMD, Leite EMM, Schürch AC, Paganelli FL, Willems RJL, Camargo ILBC. Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone. Antibiotics (Basel) 2023; 12:antibiotics12050926. [PMID: 37237829 DOI: 10.3390/antibiotics12050926] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin America. In this study, we characterized four Klebsiella pneumoniae isolates harboring blaKPC and blaNDM from an outbreak during the COVID-19 pandemic in a Brazilian hospital. We assessed their plasmids' transference ability, fitness effects, and relative copy number in different hosts. The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. The WGS revealed that both isolates belong to ST11, and 20 resistance genes were identified in each isolate, including blaKPC-2 and blaNDM-1. The blaKPC gene was present on a ~56 Kbp IncN plasmid and the blaNDM-1 gene on a ~102 Kbp IncC plasmid, along with five other resistance genes. Although the blaNDM plasmid contained genes for conjugational transfer, only the blaKPC plasmid conjugated to E. coli J53, without apparent fitness effects. The minimum inhibitory concentrations (MICs) of meropenem/imipenem against BHKPC93 and BHKPC104 were 128/64 and 256/128 mg/L, respectively. Although the meropenem and imipenem MICs against E. coli J53 transconjugants carrying the blaKPC gene were 2 mg/L, this was a substantial increment in the MIC relative to the original J53 strain. The blaKPC plasmid copy number was higher in K. pneumoniae BHKPC93 and BHKPC104 than in E. coli and higher than that of the blaNDM plasmids. In conclusion, two ST11 K. pneumoniae isolates that were part of a hospital outbreak co-harbored blaKPC-2 and blaNDM-1. The blaKPC-harboring IncN plasmid has been circulating in this hospital since at least 2015, and its high copy number might have contributed to the conjugative transfer of this particular plasmid to an E. coli host. The observation that the blaKPC-containing plasmid had a lower copy number in this E. coli strain may explain why this plasmid did not confer phenotypic resistance against meropenem and imipenem.
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Affiliation(s)
- Camila Maria Dos Santos Boralli
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | | | - Rodrigo Silva Meneses
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | | | | | - Anita C Schürch
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Fernanda L Paganelli
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Rob J L Willems
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Ilana Lopes Baratella Cunha Camargo
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
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2
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Conzemius R, Bergman Y, Májek P, Beisken S, Lewis S, Jacobs EB, Tamma PD, Simner PJ. Automated antimicrobial susceptibility testing and antimicrobial resistance genotyping using Illumina and Oxford Nanopore Technologies sequencing data among Enterobacteriaceae. Front Microbiol 2022; 13:973605. [PMID: 36003946 PMCID: PMC9393496 DOI: 10.3389/fmicb.2022.973605] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Whole-genome sequencing (WGS) enables the molecular characterization of bacterial pathogens. We compared the accuracy of the Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for the determination of AMR classes and antimicrobial susceptibility testing (AST) among 181 clinical Enterobacteriaceae isolates. Sequencing reads for each isolate were uploaded to AREScloud (Ares Genetics) to determine the presence of AMR markers and the predicted WGS-AST profile. The profiles of both sequencing platforms were compared to broth microdilution (BMD) AST. Isolates were delineated by resistance to third-generation cephalosporins and carbapenems as well as the presence of AMR markers to determine clinically relevant AMR classes. The overall categorical agreement (CA) was 90% (Illumina) and 88% (ONT) across all antimicrobials, 96% for the prediction of resistance to third-generation cephalosporins for both platforms, and 94% (Illumina) and 91% (ONT) for the prediction of resistance to carbapenems. Carbapenem resistance was overestimated on ONT with a major error of 16%. Sensitivity for the detection of carbapenemases, extended-spectrum β-lactamases, and plasmid-mediated ampC genes was 98, 95, and 70% by ONT compared to the Illumina dataset as the reference. Our results highlight the potential of the ONT platform’s use in clinical microbiology laboratories. When combined with robust bioinformatics methods, WGS-AST predictions may be a future approach to guide effective antimicrobial decision-making.
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Affiliation(s)
| | - Yehudit Bergman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | | | - Shawna Lewis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Emily B. Jacobs
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Pranita D. Tamma
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Patricia J. Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Patricia J. Simner,
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3
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Sharma A, Yadav SP, Sarma D, Mukhopadhaya A. Modulation of host cellular responses by gram-negative bacterial porins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:35-77. [PMID: 35034723 DOI: 10.1016/bs.apcsb.2021.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The outer membrane of a gram-negative bacteria encapsulates the plasma membrane thereby protecting it from the harsh external environment. This membrane acts as a sieving barrier due to the presence of special membrane-spanning proteins called "porins." These porins are β-barrel channel proteins that allow the passive transport of hydrophilic molecules and are impermeable to large and charged molecules. Many porins form trimers in the outer membrane. They are abundantly present on the bacterial surface and therefore play various significant roles in the host-bacteria interactions. These include the roles of porins in the adhesion and virulence mechanisms necessary for the pathogenesis, along with providing resistance to the bacteria against the antimicrobial substances. They also act as the receptors for phage and complement proteins and are involved in modulating the host cellular responses. In addition, the potential use of porins as adjuvants, vaccine candidates, therapeutic targets, and biomarkers is now being exploited. In this review, we focus briefly on the structure of the porins along with their important functions and roles in the host-bacteria interactions.
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Affiliation(s)
- Arpita Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Shashi Prakash Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Dwipjyoti Sarma
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Arunika Mukhopadhaya
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
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Rapid Evolution of Reduced Susceptibility against a Balanced Dual-Targeting Antibiotic through Stepping-Stone Mutations. Antimicrob Agents Chemother 2019; 63:AAC.00207-19. [PMID: 31235632 DOI: 10.1128/aac.00207-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/14/2019] [Indexed: 11/20/2022] Open
Abstract
Multitargeting antibiotics, i.e., single compounds capable of inhibiting two or more bacterial targets, are generally considered to be a promising therapeutic strategy against resistance evolution. The rationale for this theory is that multitargeting antibiotics demand the simultaneous acquisition of multiple mutations at their respective target genes to achieve significant resistance. The theory presumes that individual mutations provide little or no benefit to the bacterial host. Here, we propose that such individual stepping-stone mutations can be prevalent in clinical bacterial isolates, as they provide significant resistance to other antimicrobial agents. To test this possibility, we focused on gepotidacin, an antibiotic candidate that selectively inhibits both bacterial DNA gyrase and topoisomerase IV. In a susceptible organism, Klebsiella pneumoniae, a combination of two specific mutations in these target proteins provide an >2,000-fold reduction in susceptibility, while individually, none of these mutations affect resistance significantly. Alarmingly, strains with decreased susceptibility against gepotidacin are found to be as virulent as the wild-type Klebsiella pneumoniae strain in a murine model. Moreover, numerous pathogenic isolates carry mutations which could promote the evolution of clinically significant reduction of susceptibility against gepotidacin in the future. As might be expected, prolonged exposure to ciprofloxacin, a clinically widely employed gyrase inhibitor, coselected for reduced susceptibility against gepotidacin. We conclude that extensive antibiotic usage could select for mutations that serve as stepping-stones toward resistance against antimicrobial compounds still under development. Our research indicates that even balanced multitargeting antibiotics are prone to resistance evolution.
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Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates. Antimicrob Agents Chemother 2018; 63:AAC.01923-18. [PMID: 30373801 DOI: 10.1128/aac.01923-18] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/22/2018] [Indexed: 01/19/2023] Open
Abstract
Standard antimicrobial susceptibility testing (AST) approaches lead to delays in the selection of optimal antimicrobial therapy. Here, we sought to determine the accuracy of antimicrobial resistance (AMR) determinants identified by Nanopore whole-genome sequencing in predicting AST results. Using a cohort of 40 clinical isolates (21 carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae, 10 non-carbapenemase-producing carbapenem-resistant K. pneumoniae, and 9 carbapenem-susceptible K. pneumoniae isolates), three separate sequencing and analysis pipelines were performed, as follows: (i) a real-time Nanopore analysis approach identifying acquired AMR genes, (ii) an assembly-based Nanopore approach identifying acquired AMR genes and chromosomal mutations, and (iii) an approach using short-read correction of Nanopore assemblies. The short-read correction of Nanopore assemblies served as the reference standard to determine the accuracy of Nanopore sequencing results. With the real-time analysis approach, full annotation of acquired AMR genes occurred within 8 h from subcultured isolates. Assemblies sufficient for full resistance gene and single-nucleotide polymorphism annotation were available within 14 h from subcultured isolates. The overall agreement of genotypic results and anticipated AST results for the 40 K. pneumoniae isolates was 77% (range, 30% to 100%) and 92% (range, 80% to 100%) for the real-time approach and the assembly approach, respectively. Evaluating the patients contributing the 40 isolates, the real-time approach and assembly approach could shorten the median time to effective antibiotic therapy by 20 h and 26 h, respectively, compared to standard AST. Nanopore sequencing offers a rapid approach to both accurately identify resistance mechanisms and to predict AST results for K. pneumoniae isolates. Bioinformatics improvements enabling real-time alignment, coupled with rapid extraction and library preparation, will further enhance the accuracy and workflow of the Nanopore real-time approach.
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Tabassum R, Shafique M, Khawaja KA, Alvi IA, Rehman Y, Sheik CS, Abbas Z, Rehman SU. Complete genome analysis of a Siphoviridae phage TSK1 showing biofilm removal potential against Klebsiella pneumoniae. Sci Rep 2018; 8:17904. [PMID: 30559386 PMCID: PMC6297243 DOI: 10.1038/s41598-018-36229-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 10/07/2018] [Indexed: 01/21/2023] Open
Abstract
Multidrug-resistant Klebsiella pneumoniae is a nosocomial pathogen, produces septicemia, pneumonia and UTI. Excessive use of antibiotics contributes towards emergence of multidrug-resistance. Bacteriophage-therapy is a potential substitute of antibiotics with many advantages. In this investigation, microbiological and genome characterization of TSK1 bacteriophage and its biofilm elimination capability are presented. TSK1 showed narrow host range and highest stability at pH 7 and 37 °C. TSK1 reduced the growth of K. pneumoniae during the initial 14 hours of infection. Post-treatment with TSK1 against different age K. pneumoniae biofilms reduced 85-100% biomass. Pre-treatment of TSK1 bacteriophage against the biofilm of Klebsiella pneumoniae reduced > 99% biomass in initial 24 hr of incubation. The genome of TSK1 phage comprised 49,836 base pairs with GC composition of 50.44%. Total seventy-five open reading frames (ORFs) were predicted, 25 showed homology with known functional proteins, while 50 were called hypothetical, as no homologs with proved function exists in the genome databases. Blast and phylogenetic analysis put it in the Kp36 virus genus of family Siphoviridae. Proposed packaging strategy of TSK1 bacteriophage genome is headful packaging using the pac sites. The potential of TSK1 bacteriophage could be used to reduce the bacterial load and biofilm in clinical and non-clinical settings.
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Affiliation(s)
- Rabia Tabassum
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Muafia Shafique
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Komal Amer Khawaja
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Iqbal Ahmed Alvi
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Yasir Rehman
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Cody S Sheik
- Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, USA
| | - Zaigham Abbas
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Shafiq Ur Rehman
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan.
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7
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Mirzaii M, Jamshidi S, Zamanzadeh M, Marashifard M, Malek Hosseini SAA, Haeili M, Jahanbin F, Mansouri F, Darban-Sarokhalil D, Khoramrooz SS. Determination of gyrA and parC mutations and prevalence of plasmid-mediated quinolone resistance genes in Escherichia coli and Klebsiella pneumoniae isolated from patients with urinary tract infection in Iran. J Glob Antimicrob Resist 2018; 13:197-200. [PMID: 29747008 DOI: 10.1016/j.jgar.2018.04.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVES Fluoroquinolones (FQs) are recommended as the drugs of choice for the empirical treatment of urinary tract infections (UTIs). This study investigated the molecular determinants of FQ resistance in Escherichia coli and Klebsiella pneumoniae isolates in Iran. METHODS A total of 364 clinical isolates of E. coli (n=144) and K. pneumoniae (n=220) were collected from patients with UTI. Susceptibility of the isolates to ciprofloxacin, levofloxacin, gatifloxacin and nalidixic acid was evaluated by disk diffusion. The presence of qnrA, qnrB and qnrS genes was assessed by PCR. Nucleotide sequences of the gyrA and parC genes were determined. RESULTS Eighty-seven (60.4%) and 15 (6.8%) E. coli and K. pneumoniae isolates, respectively, were resistant to at least one of the tested FQs. Plasmid-mediated quinolone resistance (PMQR) genes were detected in 12.6% and 60.0% of FQ-resistant E. coli and K. pneumoniae, respectively. Whilst qnrB predominated in K. pneumoniae, qnrS was the most prevalent PMQR gene in E. coli. S83L (98.9%) and D87N (59.8%) were the most frequent mutations identified in GyrA of E. coli, and 55.2% (n=48) of FQ-resistant E. coli isolates had mutation in ParC harbouring S80I and E84V substitutions. The GyrAS83L substitution was found in only one FQ-resistant K. pneumoniae isolate. CONCLUSIONS FQ resistance was much more common in E. coli isolates than in K. pneumoniae. Whilst mutations in the drug target-encoding genes gyrA and parC were the major mechanisms involved in FQ resistance in E. coli, PMQR determinants commonly mediated FQ resistance in K. pneumoniae.
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Affiliation(s)
- Mehdi Mirzaii
- Faculty of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Sanaz Jamshidi
- Department of Basic Sciences, Islamic Azad University, Yasooj Branch, Yasooj, Iran
| | - Maryam Zamanzadeh
- Department of Basic Sciences, Islamic Azad University, Yasooj Branch, Yasooj, Iran
| | - Masoud Marashifard
- Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran
| | | | - Mehri Haeili
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Fariba Jahanbin
- Department of Basic Sciences, Islamic Azad University, Yasooj Branch, Yasooj, Iran
| | - Fariba Mansouri
- Department of Basic Sciences, Islamic Azad University, Yasooj Branch, Yasooj, Iran
| | - Davood Darban-Sarokhalil
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Sajjad Khoramrooz
- Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran; Department of Microbiology, School of Medicine, Yasuj University of Medical Sciences, Yasuj, Iran.
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8
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Wyres KL, Holt KE. Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones. Trends Microbiol 2016; 24:944-956. [PMID: 27742466 DOI: 10.1016/j.tim.2016.09.007] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/06/2016] [Accepted: 09/20/2016] [Indexed: 02/05/2023]
Abstract
Antimicrobial-resistant Klebsiella pneumoniae (Kp) has emerged as a major global public health problem. While resistance can occur across a broad range of Kp clones, a small number have become globally distributed and commonly cause outbreaks in hospital settings. Here we describe recent comparative genomics investigations that have shed light on Kp population structure and the evolution of antimicrobial-resistant clones. These studies provide the basic framework within which genomic epidemiology and evolution can be understood, but have merely scratched the surface of what can and should be explored. We assert that further large-scale comparative and functional genomics studies are urgently needed to better understand the biology of this clinically important bacterium.
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Affiliation(s)
- Kelly L Wyres
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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9
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Guo Y, Zhou H, Qin L, Pang Z, Qin T, Ren H, Pan Z, Zhou J. Frequency, Antimicrobial Resistance and Genetic Diversity of Klebsiella pneumoniae in Food Samples. PLoS One 2016; 11:e0153561. [PMID: 27078494 PMCID: PMC4831839 DOI: 10.1371/journal.pone.0153561] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/31/2016] [Indexed: 12/01/2022] Open
Abstract
This study aimed to assess the frequency of Klebsiella pneumoniae in food samples and to detect antibiotic resistance phenotypes, antimicrobial resistance genes and the molecular subtypes of the recovered isolates. A total of 998 food samples were collected, and 99 (9.9%) K. pneumoniae strains were isolated; the frequencies were 8.2% (4/49) in fresh raw seafood, 13.8% (26/188) in fresh raw chicken, 11.4% (34/297) in frozen raw food and 7.5% (35/464) in cooked food samples. Antimicrobial resistance was observed against 16 antimicrobials. The highest resistance rate was observed for ampicillin (92.3%), followed by tetracycline (31.3%), trimethoprim-sulfamethoxazole (18.2%), and chloramphenicol (10.1%). Two K. pneumoniae strains were identified as extended-spectrum β-lactamase (ESBL)–one strain had three beta-lactamases genes (blaSHV, blaCTX-M-1, and blaCTX-M-10) and one had only the blaSHV gene. Nineteen multidrug-resistant (MDR) strains were detected; the percentage of MDR strains in fresh raw chicken samples was significantly higher than in other sample types (P<0.05). Six of the 18 trimethoprim-sulfamethoxazole-resistant strains carried the folate pathway inhibitor gene (dhfr). Four isolates were screened by PCR for quinolone resistance genes; aac(6’)-Ib-cr, qnrB, qnrA and qnrS were detected. In addition, gyrA gene mutations such as T247A (Ser83Ile), C248T (Ser83Phe), and A260C (Asp87Ala) and a parC C240T (Ser80Ile) mutation were identified. Five isolates were screened for aminoglycosides resistance genes; aacA4, aacC2, and aadA1 were detected. Pulsed-field gel electrophoresis-based subtyping identified 91 different patterns. Our results indicate that food, especially fresh raw chicken, is a reservoir of antimicrobial-resistant K. pneumoniae, and the potential health risks posed by such strains should not be underestimated. Our results demonstrated high prevalence, antibiotic resistance rate and genetic diversity of K. pneumoniae in food in China. Improved control and prevention strategies are urgently needed.
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Affiliation(s)
- Yumei Guo
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People’s Republic of China
- * E-mail: (HZ); (JZ)
| | - Liyun Qin
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
| | - Zhizhao Pang
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
| | - Tian Qin
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People’s Republic of China
| | - Hongyu Ren
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Zhuo Pan
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
| | - Jikun Zhou
- Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
- * E-mail: (HZ); (JZ)
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Searching for the Optimal Predictor of Ciprofloxacin Resistance in Klebsiella pneumoniae by Using In Vitro Dynamic Models. Antimicrob Agents Chemother 2015; 60:1208-15. [PMID: 26643328 DOI: 10.1128/aac.02334-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/23/2015] [Indexed: 12/20/2022] Open
Abstract
There is growing evidence of applicability of the hypothesis of the mutant selection window (MSW), i.e., the range between the MIC and the mutant prevention concentration (MPC), within which the enrichment of resistant mutants is most probable. However, it is not clear if MPC-based pharmacokinetic variables are preferable to the respective MIC-based variables as interstrain predictors of resistance. To examine the predictive power of the ratios of the area under the curve (AUC24) to the MPC and to the MIC, the selection of ciprofloxacin-resistant mutants of three Klebsiella pneumoniae strains with different MPC/MIC ratios was studied. Each organism was exposed to twice-daily ciprofloxacin for 3 days at AUC24/MIC ratios that provide peak antibiotic concentrations close to the MIC, between the MIC and the MPC, and above the MPC. Resistant K. pneumoniae mutants were intensively enriched at an AUC24/MIC ratio of 60 to 360 h (AUC24/MPC ratio from 2.5 to 15 h) but not at the lower or higher AUC24/MIC and AUC24/MPC ratios, in accordance with the MSW hypothesis. AUC24/MPC and AUC24/MIC relationships with areas under the time courses of ciprofloxacin-resistant K. pneumoniae (AUBCM) were bell shaped. These relationships predict highly variable "antimutant" AUC24/MPC ratios (20 to 290 h) compared to AUC24/MIC ratios (1,310 to 2,610 h). These findings suggest that the potential of the AUC24/MPC ratio as an interstrain predictor of K. pneumoniae resistance is lower than that of the AUC24/MIC ratio.
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Zowawi HM, Forde BM, Alfaresi M, Alzarouni A, Farahat Y, Chong TM, Yin WF, Chan KG, Li J, Schembri MA, Beatson SA, Paterson DL. Stepwise evolution of pandrug-resistance in Klebsiella pneumoniae. Sci Rep 2015; 5:15082. [PMID: 26478520 PMCID: PMC4609946 DOI: 10.1038/srep15082] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 09/01/2015] [Indexed: 01/21/2023] Open
Abstract
Carbapenem resistant Enterobacteriaceae (CRE) pose an urgent risk to global human health. CRE that are non-susceptible to all commercially available antibiotics threaten to return us to the pre-antibiotic era. Using Single Molecule Real Time (SMRT) sequencing we determined the complete genome of a pandrug-resistant Klebsiella pneumoniae isolate, representing the first complete genome sequence of CRE resistant to all commercially available antibiotics. The precise location of acquired antibiotic resistance elements, including mobile elements carrying genes for the OXA-181 carbapenemase, were defined. Intriguingly, we identified three chromosomal copies of an ISEcp1-bla(OXA-181) mobile element, one of which has disrupted the mgrB regulatory gene, accounting for resistance to colistin. Our findings provide the first description of pandrug-resistant CRE at the genomic level, and reveal the critical role of mobile resistance elements in accelerating the emergence of resistance to other last resort antibiotics.
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Affiliation(s)
- Hosam M Zowawi
- The University of Queensland, Centre for Clinical Research (UQCCR), Herston QLD 4029, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,World Health Organization Collaborating Centre for Infection Prevention and Control, and the Gulf Cooperation Council Center for Infection Control, Riyadh, Saudi Arabia
| | - Brian M Forde
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Mubarak Alfaresi
- Pathology and Laboratory Medicine Department at Sheikh Khalifa General Hospital, Umm Al Quwain, United Arab Emirates
| | - Abdulqadir Alzarouni
- Urology Department, Sheikh Khalifa General Hospital, Umm Al Quwain, United Arab Emirates
| | - Yasser Farahat
- Urology Department, Sheikh Khalifa General Hospital, Umm Al Quwain, United Arab Emirates
| | - Teik-Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jian Li
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Mark A Schembri
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - David L Paterson
- The University of Queensland, Centre for Clinical Research (UQCCR), Herston QLD 4029, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
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Park DJ, Yu JK, Park KG, Park YJ. Genotypes of Ciprofloxacin-Resistant Klebsiella pneumoniae in Korea and Their Characteristics According to the Genetic Lineages. Microb Drug Resist 2015. [PMID: 26207318 DOI: 10.1089/mdr.2015.0001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated the molecular genotypes of ciprofloxacin-resistant Klebsiella pneumoniae and their characteristics according to the genetic lineages. For 160 K. pneumoniae collected in 2013, ciprofloxacin minimum inhibitory concentrations (MICs) were determined by agar dilution method. The genotypes of ciprofloxacin-resistant K. pneumoniae isolates were determined by multilocus sequence typing (MLST) and wzi gene typing. The presence of plasmid-mediated resistance determinants [qnrA, qnrB, qnrS, aac(6')-Ib-cr, blaCTX-M, and blaSHV] was investigated. The gyrA and parC genes were sequenced. Fifty-seven isolates showed ciprofloxacin resistance. By MLST, four major sequence types (STs) or clonal complexes (CCs), that is, ST307, CC11, CC147, and ST15, were found and the two most prevalent STs were ST307 (14/57, 24.6%) and ST11 (12/57, 21.1%). By wzi gene sequencing, 46 of the 57 isolates could be differentiated. All the ST307 isolates had an identical wzi sequence and harbored qnrB. The majority of them harbored aac(6')-Ib-cr (85.7%) and CTX-M-15 (92.9%). In contrast, 12 ST11 isolates were divided into five sublineages by wzi sequence and qnrB, qnrS, and aac(6')-Ib-cr were carried by nine, seven, and three isolates, respectively. They harbored SHV-type extended-spectrum β-lactamase more frequently than CTX-M-15 (nine and four isolates, respectively). The prevalence of CTX-M-15, qnrB1, and aac(6')-Ib-cr was significantly higher in ST307 than in ST11 (p=0.003, p=0.000, and p=0.002, respectively). Both clones had identical amino acid substitution in gyrA (S83I) and parC (S80I). K. pneumoniae ST307 and ST11 were the two most common clones, and the ST307 isolates were highly homogeneous, suggesting their recent emergence.
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Affiliation(s)
- Dong Jin Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea , Seoul, Korea
| | - Jin Kyung Yu
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea , Seoul, Korea
| | - Kang Gyun Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea , Seoul, Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea , Seoul, Korea
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13
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Adaptive and mutational resistance: role of porins and efflux pumps in drug resistance. Clin Microbiol Rev 2013; 25:661-81. [PMID: 23034325 DOI: 10.1128/cmr.00043-12] [Citation(s) in RCA: 525] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The substantial use of antibiotics in the clinic, combined with a dearth of new antibiotic classes, has led to a gradual increase in the resistance of bacterial pathogens to these compounds. Among the various mechanisms by which bacteria endure the action of antibiotics, those affecting influx and efflux are of particular importance, as they limit the interaction of the drug with its intracellular targets and, consequently, its deleterious effects on the cell. This review evaluates the impact of porins and efflux pumps on two major types of resistance, namely, mutational and adaptive types of resistance, both of which are regarded as key phenomena in the global rise of antibiotic resistance among pathogenic microorganisms. In particular, we explain how adaptive and mutational events can dramatically influence the outcome of antibiotic therapy by altering the mechanisms of influx and efflux of antibiotics. The identification of porins and pumps as major resistance markers has opened new possibilities for the development of novel therapeutic strategies directed specifically against these mechanisms.
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Nawaz M, Khan SA, Tran Q, Sung K, Khan AA, Adamu I, Steele RS. Isolation and characterization of multidrug-resistant Klebsiella spp. isolated from shrimp imported from Thailand. Int J Food Microbiol 2012; 155:179-84. [PMID: 22405354 DOI: 10.1016/j.ijfoodmicro.2012.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 01/30/2012] [Accepted: 02/02/2012] [Indexed: 11/26/2022]
Abstract
A study was undertaken to isolate and characterize tetracycline and nalidixic acid-resistant Klebsiella spp. in farm-raised, imported shrimp sold in the United States. Sixty-seven multiple antibiotic-resistant Klebsiella spp. strains were isolated from imported shrimp samples. Using morphological and biochemical methods, fifty-three strains were tentatively identified as Klebsiella pneumoniae and fourteen as K. oxytoca. Although all isolates were resistant to tetracycline, only 8 were resistant to nalidixic acid. These 8 isolates were further screened by PCR for quinolone resistance genes (qnrA, B, S, gyrA, B and parC). PCR protocols failed to amplify any qnr genes. The purified PCR amplicons of gyrA, gyrB and parC were sequenced and analyzed for point mutations that confer resistance to fluoroquinolone antibiotics. Analysis of the sequences of the gyrA amplicons from nalidixic acid-resistant Klebsiella spp. indicated two point mutations in gyrA at positions 83 (Ser→Phe) and 87 (Asp→Ala). Sequence analysis of the parC amplicons indicated an amino acid change at position 80 (Ser→Ile). No mutations were detected in gyrB. Template DNA from all isolates was screened for tetracycline resistance genes (tetA-E). Oligonucleotide primers specifically targeting a 305-bp region of tetB and a 477-bp region of tetD successfully amplified sequences from 91.0 and 44.0% of the isolates, respectively. None of the isolates contained tetA, tetC or tetE genes. Plasmids (2.0-16.0kb) were found in 23 of the 67 isolates. XbaI-PFGE identified 32 distinct macro restriction patterns (mrps) among the 61 multiple drug-resistant Klebsiella spp. that were typable. Our results indicate that imported shrimp is a reservoir for multidrug resistant Klebsiella spp. and potential health risks posed by such strains should not be underestimated.
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Affiliation(s)
- Mohamed Nawaz
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
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Plasmid-mediated quinolone resistance in pseudomonas putida isolates from imported shrimp. Appl Environ Microbiol 2010; 77:1885-7. [PMID: 21193671 DOI: 10.1128/aem.01176-10] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fourteen quinolone-resistant Pseudomonas putida isolates were recovered from imported frozen shrimp sold in the United States. Two isolates harbored plasmids with qnrA and qnrB genes. PCR and DNA sequencing of quinolone resistance-determining regions identified novel substitutions in GyrA (His139→Glu and Thr128→Ala) and GyrB (Thr442→Asn, Gly470→Ala, and Ile487→Pro) and previously reported substitutions in GyrB (Asp489→Glu) and ParC (Thr105→Pro).
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Ogawa W, Li DW, Yu P, Begum A, Mizushima T, Kuroda T, Tsuchiya T. Multidrug resistance in Klebsiella pneumoniae MGH78578 and cloning of genes responsible for the resistance. Biol Pharm Bull 2005; 28:1505-8. [PMID: 16079502 DOI: 10.1248/bpb.28.1505] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Klebsiella pneumoniae MGH78578, a clinical isolate, showed high level of resistance to many antimicrobial agents. We cloned genes responsible for drug resistance from chromosomal DNA of K. pneumoniae MGH78578 by shotgun method using Escherichia coli KAM32, a drug hypersensitive strain, as host. We obtained 43 hybrid plasmids that made host cells resistant to several antimicrobial agents. We classified them into 17 groups based on growth properties in the presence of each one of 9 antimicrobial agents and on restriction patterns of each hybrid plasmid. Analysis of the cloned genes must be very useful for investigation of major parts of multidrug resistance systems including multidrug efflux pumps in K. pneumoniae MGH78578 in which genome sequence is available.
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Affiliation(s)
- Wakano Ogawa
- Department of Molecular Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Tsushima-Naka, Okayama 700-8530, Japan
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